From 422af937dc7686e182da0223789fc09e4fe79d4a Mon Sep 17 00:00:00 2001 From: Adrian Edwards Date: Wed, 25 Jun 2025 15:56:43 -0400 Subject: [PATCH 01/66] update container build automation for new branching model Signed-off-by: Adrian Edwards --- .github/workflows/build_docker.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build_docker.yml b/.github/workflows/build_docker.yml index f99831da32..17264f072d 100644 --- a/.github/workflows/build_docker.yml +++ b/.github/workflows/build_docker.yml @@ -178,7 +178,7 @@ jobs: # Releases update the *:latest tag and the *: tag # Main does not update any tags tags: | - type=raw,value=devel-latest,enable=${{ github.ref == 'refs/heads/dev' }} + type=raw,value=devel-latest,enable=${{ github.ref == 'refs/heads/main' }} type=raw,value=latest,enable=${{ github.event_name == 'release' }} type=raw,value=${{ github.event.release.tag_name }},enable=${{ github.event_name == 'release' }} From ccfc86163440c1c1e9411635e3bdbf529e937e6f Mon Sep 17 00:00:00 2001 From: Adrian Edwards Date: Wed, 25 Jun 2025 15:57:32 -0400 Subject: [PATCH 02/66] remove dev, add release as branches to run jobs on push Signed-off-by: Adrian Edwards --- .github/workflows/build_docker.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build_docker.yml b/.github/workflows/build_docker.yml index 17264f072d..7b43e2adc2 100644 --- a/.github/workflows/build_docker.yml +++ b/.github/workflows/build_docker.yml @@ -3,7 +3,7 @@ on: push: branches: - main - - dev + - release pull_request: release: types: From fe56e69f45528d9565a74b704e3253d1557ce743 Mon Sep 17 00:00:00 2001 From: Adrian Edwards Date: Wed, 25 Jun 2025 16:21:59 -0400 Subject: [PATCH 03/66] remove automerge workflow Signed-off-by: Adrian Edwards --- .github/workflows/auto_merge.yml | 27 --------------------------- 1 file changed, 27 deletions(-) delete mode 100644 .github/workflows/auto_merge.yml diff --git a/.github/workflows/auto_merge.yml b/.github/workflows/auto_merge.yml deleted file mode 100644 index d3e0e6f59f..0000000000 --- a/.github/workflows/auto_merge.yml +++ /dev/null @@ -1,27 +0,0 @@ -name: Merge main into dev - -on: - push: - branches: - - main - -jobs: - update-dev: - permissions: write-all - name: update-dev - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v4 - with: - fetch-depth: 0 - - run: | - git config user.name 'GitHub Actions' - git config user.email 'actions@users.noreply.github.com' - git checkout dev - git merge main - echo "Done with merge" - - name: Push to dev - uses: CasperWA/push-protected@v2 - with: - token: ${{ secrets.GITHUB_TOKEN }} - branch: dev \ No newline at end of file From bb57a7a5ce9c5ca174add26abc044e3aa26f39a2 Mon Sep 17 00:00:00 2001 From: Adrian Edwards Date: Wed, 25 Jun 2025 16:23:45 -0400 Subject: [PATCH 04/66] update branch name in checks.yml Signed-off-by: Adrian Edwards --- .github/workflows/checks.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/checks.yml b/.github/workflows/checks.yml index c23bfd7bb3..40607add57 100644 --- a/.github/workflows/checks.yml +++ b/.github/workflows/checks.yml @@ -1,7 +1,7 @@ name: "run-linting-checks" on: pull_request: - branches: [main, dev] + branches: [main, release] jobs: run-pylint: From 5e5f70f3781b80b317ca80602d6bc9cf3a60b131 Mon Sep 17 00:00:00 2001 From: Adrian Edwards Date: Wed, 25 Jun 2025 16:29:12 -0400 Subject: [PATCH 05/66] update comments in build_docker workflow Signed-off-by: Adrian Edwards --- .github/workflows/build_docker.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.github/workflows/build_docker.yml b/.github/workflows/build_docker.yml index 7b43e2adc2..be81010d54 100644 --- a/.github/workflows/build_docker.yml +++ b/.github/workflows/build_docker.yml @@ -174,9 +174,8 @@ jobs: labels: | org.opencontainers.image.title=augur_${{ matrix.image}} images: ghcr.io/${{ github.repository_owner }}/augur_${{ matrix.image }} - # Pushes to the dev branch update the *:devel-latest tag + # Pushes to the main branch update the *:devel-latest tag # Releases update the *:latest tag and the *: tag - # Main does not update any tags tags: | type=raw,value=devel-latest,enable=${{ github.ref == 'refs/heads/main' }} type=raw,value=latest,enable=${{ github.event_name == 'release' }} From 641db32b8536203e6c2d30177cfe773176fb3dc8 Mon Sep 17 00:00:00 2001 From: John Strunk Date: Tue, 29 Apr 2025 14:53:12 -0400 Subject: [PATCH 06/66] Initial conversion of main augur package to uv - Replaces setup.py with pyproject.toml - Creates .python-version file that will control the python version that uv uses in the virtualenv Signed-off-by: John Strunk --- .gitignore | 4 - .python-version | 1 + pyproject.toml | 114 ++ setup.py | 111 -- uv.lock | 2991 +++++++++++++++++++++++++++++++++++++++++++++++ 5 files changed, 3106 insertions(+), 115 deletions(-) create mode 100644 .python-version create mode 100644 pyproject.toml delete mode 100644 setup.py create mode 100644 uv.lock diff --git a/.gitignore b/.gitignore index 2c29307851..93be721ef1 100644 --- a/.gitignore +++ b/.gitignore @@ -106,10 +106,6 @@ target/ profile_default/ ipython_config.py -# pyenv -.python-version -.python-version-hash - # pipenv # According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. # However, in case of collaboration, if having platform-specific dependencies or dependencies diff --git a/.python-version b/.python-version new file mode 100644 index 0000000000..2c0733315e --- /dev/null +++ b/.python-version @@ -0,0 +1 @@ +3.11 diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000000..c0dbe7842b --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,114 @@ +[build-system] +requires = ["setuptools>=61", "wheel"] +build-backend = "setuptools.build_meta" + +[project] +name = "augur" +requires-python = ">=3.9" +dynamic = ["version"] +description = "Python 3 package for free/libre and open-source software community metrics, models & data collection" +readme = "README.md" +authors = [ + { name = "Derek Howard", email = "derek@howderek.com" } +] +license = "MIT" +license-files = ["LICENSE"] +classifiers = [ + "Intended Audience :: Developers", + "Topic :: Software Development :: Version Control", + "Programming Language :: Python :: 3.9" +] +dependencies = [ + "graphene", + "graphene_sqlalchemy", + "flask_graphql", + "wheel", + "sendgrid", + "textual>=0.73.0", + "alembic==1.8.1", + "coloredlogs==15.0", + "Beaker==1.11.0", + "SQLAlchemy==2.0.22", + "itsdangerous==2.0.1", + "Jinja2~=3.0.3", + "Flask==2.0.2", + "Flask-Cors==4.0.1", + "Flask-Login==0.5.0", + "Flask-WTF==1.0.0", + "pandas==1.5.3", + "numpy==1.26.0", + "requests==2.32.0", + "psycopg2-binary==2.9.9", + "click==8.0.3", + "psutil==5.8.0", + "gunicorn==22.0.0", + "six==1.15.0", + "bokeh==2.0.2", + "selenium==3.141.0", + "dask>=2021.6.2", + "cloudpickle >= 0.2.2", + "fsspec >= 0.6.0", + "toolz >= 0.8.2", + "partd >= 0.3.10", + "distributed >= 2021.03.0", + "nltk==3.6.6", + "h5py==3.10.0", + "scipy>=1.10.0, <1.13.0", + "blinker==1.4", + "protobuf<3.22", + "slack==0.0.2", + "boto3==1.17.57", + "toml", + "mistune", + "pyYaml", + "redis==4.3.3", + "XlsxWriter==1.3.7", + "celery==5.2.7", + "httpx==0.23.0", + "eventlet==0.35.2", + "flower==2.0.1", + "tornado==6.4.1", + "pylint==2.15.5", + "dnspython==2.6.1", + "Werkzeug~=2.0.0", + "mdpdf==0.0.18", + "typing-extensions==4.7.1", + "tenacity==8.3.0", +] + +[dependency-groups] +dev = [ + "tox==3.24.4", + "pytest==6.2.5", + "toml>=0.10.2", + "ipdb==0.13.9", + "sphinx==7.2.6", + "sphinx_rtd_theme==2.0.0", + "sphinxcontrib-openapi==0.8.3", + "sphinxcontrib-redoc==1.6.0", + "docutils==0.20.1" +] + +[project.scripts] +augur = "augur.application.cli._multicommand:run" + +[project.urls] +Homepage = "https://github.com/chaoss/augur" +Documentation = "https://oss-augur.readthedocs.io/en/main/" + + +############################################################ +## setuptools options +# https://setuptools.pypa.io/en/latest/userguide/pyproject_config.html +[tool.setuptools] +include-package-data = true + +[tool.setuptools.dynamic] +version = { attr = "metadata.__version__" } + +[tool.setuptools.packages.find] +# Note: While this should just be where = ["augur"], that doesn't allow the +# dynamic version lookup to work. `uv lock` will fail with: +# ModuleNotFoundError: metadata +where = ["."] +include = ["augur*"] diff --git a/setup.py b/setup.py deleted file mode 100644 index a356fef858..0000000000 --- a/setup.py +++ /dev/null @@ -1,111 +0,0 @@ -#SPDX-License-Identifier: MIT -""" -SPDX-License-Identifier: MIT - -Install augur package with pip. -""" -from setuptools import setup, find_packages -from os import path - -here = path.abspath(path.dirname(__file__)) - -# Get the long description from the README file -with open(path.join(here, "README.md"), encoding="utf-8") as f: - long_description = f.read() - -exec(open("metadata.py").read()) - -setup( - name=__slug__, - version=__version__, - include_package_data=True, - description=__short_description__, - long_description=long_description, - url=__url__, - author="Derek Howard", - author_email="derek@howderek.com", - packages=find_packages(), - license=__license__, - classifiers=[ - "Intended Audience :: Developers", - "Topic :: Software Development :: Version Control", - "License :: OSI Approved :: MIT License", - "Programming Language :: Python :: 3.8", - ], - install_requires=[ - "graphene", - "graphene_sqlalchemy", - "flask_graphql", - "wheel", - "sendgrid", - "textual>=0.73.0", - "alembic==1.8.1", # 1.8.1 - "coloredlogs==15.0", # 15.0.1 - "Beaker==1.11.0", # 1.11.0 - "SQLAlchemy==2.0.22", # 1.4.40 - "itsdangerous==2.0.1", # 2.1.2 - 'Jinja2~=3.0.3', - "Flask==2.0.2", # 2.2.2 - "Flask-Cors==4.0.1", - "Flask-Login==0.5.0", - "Flask-WTF==1.0.0", - "pandas==1.5.3", # 1.4.3 - "numpy==1.26.0", # 1.23.2 - "requests==2.32.0", # 2.28.1 - "psycopg2-binary==2.9.9", #2.9.3 what is pscopg-binary 3.0.16 - "click==8.0.3", # 8.1.3 - "psutil==5.8.0", # 5.9.1 - "gunicorn==22.0.0", # 20.1.0 - "six==1.15.0", # 1.16.0 - "bokeh==2.0.2", # 2.4.3 - "selenium==3.141.0",# 4.4.3 - "dask>=2021.6.2", # 2022.8.1 - "cloudpickle >= 0.2.2", # 2.1.0 - "fsspec >= 0.6.0", # 2022.7.1 - "toolz >= 0.8.2", # 0.12.0 - "partd >= 0.3.10", # 1.3.0 - "distributed >= 2021.03.0", # 2022.8.1 - "nltk==3.6.6", # 3.7 - "h5py==3.10.0", # 3.7 - "scipy>=1.10.0, <1.13.0", # 1.9.0 - "blinker==1.4", # 1.5 - "protobuf<3.22", # 4.21.5 - "slack==0.0.2", # 0.0.2 - "boto3==1.17.57", # 1.24.56 - "toml", # 0.10.2 - "mistune", # 2.0.4 - "pyYaml", # 6.0 - "redis==4.3.3", # 4.3.4 - "XlsxWriter==1.3.7", # 3.0.3 - "celery==5.2.7", # 5.2.7 - "httpx==0.23.0", # 0.23.0 - "eventlet==0.35.2", - "flower==2.0.1", - "tornado==6.4.1", # added because it sometimes errors when tornado is not 6.1 even though nothing we install depends on it - 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Add dependencies for sub-packages into main pyproject.toml Signed-off-by: John Strunk --- .../data_analysis/clustering_worker/setup.py | 45 - .../contributor_breadth_worker/setup.py | 44 - .../data_analysis/discourse_analysis/setup.py | 52 - .../data_analysis/insight_worker/setup.py | 48 - .../data_analysis/message_insights/setup.py | 57 - .../pull_request_analysis_worker/setup.py | 47 - augur/tasks/git/util/facade_worker/setup.py | 47 - pyproject.toml | 106 +- uv.lock | 1236 ++++++++++++++++- 9 files changed, 1224 insertions(+), 458 deletions(-) delete mode 100644 augur/tasks/data_analysis/clustering_worker/setup.py delete mode 100644 augur/tasks/data_analysis/contributor_breadth_worker/setup.py delete mode 100644 augur/tasks/data_analysis/discourse_analysis/setup.py delete mode 100644 augur/tasks/data_analysis/insight_worker/setup.py delete mode 100644 augur/tasks/data_analysis/message_insights/setup.py delete mode 100644 augur/tasks/data_analysis/pull_request_analysis_worker/setup.py delete mode 100644 augur/tasks/git/util/facade_worker/setup.py diff --git a/augur/tasks/data_analysis/clustering_worker/setup.py b/augur/tasks/data_analysis/clustering_worker/setup.py deleted file mode 100644 index bd591554c3..0000000000 --- a/augur/tasks/data_analysis/clustering_worker/setup.py +++ /dev/null @@ -1,45 +0,0 @@ -import io -import os -import re - -from setuptools import find_packages -from setuptools import setup - -def read(filename): - filename = os.path.join(os.path.dirname(__file__), filename) - text_type = type(u"") - with io.open(filename, mode="r", encoding='utf-8') as fd: - return re.sub(text_type(r':[a-z]+:`~?(.*?)`'), text_type(r'``\1``'), fd.read()) - -setup( - name="clustering_worker", - version="0.0.2", - url="https://github.com/chaoss/augur", - license='MIT', - author="Sarit Adhikari", - author_email="sarit.adhikari@gmail.com", - description="worker to cluster repository based on messages on issues and pull requests ", - packages=find_packages(), - install_requires=[ - 'Flask==2.0.2', - 'Flask-Cors==4.0.1', - 'Flask-Login==0.5.0', - 'Flask-WTF==1.0.0', - 'requests==2.32.0', - 'psycopg2-binary==2.9.9', - #'sklearn==0.0.0', - 'scikit-learn==1.5.0', - 'numpy==1.26.0', - 'nltk==3.6.6', - 'seaborn==0.11.1', - 'pandas==1.5.3', - 'matplotlib>=3.5.1' - ], - classifiers=[ - 'Development Status :: 2 - Pre-Alpha', - 'License :: OSI Approved :: MIT License', - 'Programming Language :: Python', - 'Programming Language :: Python :: 3', - 'Programming Language :: Python :: 3.7', - ] -) diff --git a/augur/tasks/data_analysis/contributor_breadth_worker/setup.py b/augur/tasks/data_analysis/contributor_breadth_worker/setup.py deleted file mode 100644 index 70a4cd6312..0000000000 --- a/augur/tasks/data_analysis/contributor_breadth_worker/setup.py +++ /dev/null @@ -1,44 +0,0 @@ -#SPDX-License-Identifier: MIT -import io -import os -import re - -from setuptools import find_packages -from setuptools import setup - -def read(filename): - filename = os.path.join(os.path.dirname(__file__), filename) - text_type = type(u"") - with io.open(filename, mode="r", encoding='utf-8') as fd: - return re.sub(text_type(r':[a-z]+:`~?(.*?)`'), text_type(r'``\1``'), fd.read()) - -setup( - name="contributor_breadth_worker", - version="0.0.0", - url="https://github.com/chaoss/augur", - license='MIT', - author="AugurLabs", - author_email="gabe@gabehe.im", - description="Augur worker that collects the repos people have contirbuted to", - packages=find_packages(), - install_requires=[ - 'Flask==2.0.2', - 'Flask-Cors==4.0.1', - 'Flask-Login==0.5.0', - 'Flask-WTF==1.0.0', - 'requests==2.32.0', - 'psycopg2-binary==2.9.9' - ], - entry_points={ - 'console_scripts': [ - 'contributor_breadth_worker_start=workers.contributor_breadth_worker.runtime:main', - ], - }, - classifiers=[ - 'Development Status :: 2 - Pre-Alpha', - 'License :: OSI Approved :: MIT License', - 'Programming Language :: Python', - 'Programming Language :: Python :: 3', - 'Programming Language :: Python :: 3.7', - ] -) diff --git a/augur/tasks/data_analysis/discourse_analysis/setup.py b/augur/tasks/data_analysis/discourse_analysis/setup.py deleted file mode 100644 index 67cb4dd7e7..0000000000 --- a/augur/tasks/data_analysis/discourse_analysis/setup.py +++ /dev/null @@ -1,52 +0,0 @@ -import io -import os -import re - -from setuptools import find_packages -from setuptools import setup - -def read(filename): - filename = os.path.join(os.path.dirname(__file__), filename) - text_type = type(u"") - with io.open(filename, mode="r", encoding='utf-8') as fd: - return re.sub(text_type(r':[a-z]+:`~?(.*?)`'), text_type(r'``\1``'), fd.read()) - -setup( - name="discourse_analysis_worker", - version="0.1.0", - url="https://github.com/chaoss/augur", - license='MIT', - author="Augur Team", - author_email="s@goggins.com", - description="Worker to classify messages into discourse acts", - packages=find_packages(), - install_requires=[ - 'Flask==2.0.2', - 'Flask-Cors==4.0.1', - 'Flask-Login==0.5.0', - 'Flask-WTF==1.0.0', - 'requests==2.32.0', - 'psycopg2-binary==2.9.9', - 'click==8.0.3', - 'scipy>=1.10.0', - 'nltk==3.6.6', - 'pandas==1.5.3', - 'scikit-learn==1.5.0', - 'textblob==0.15.3', - 'python-crfsuite>=0.9.8', - 'sklearn-crfsuite>=0.3.6', - 'tabulate==0.8.9' - ], # python-crfsuite-0.9.8 sklearn-crfsuite-0.3.6 tabulate-0.8.9 - entry_points={ - 'console_scripts': [ - 'discourse_analysis_worker_start=workers.discourse_analysis_worker.runtime:main', - ], - }, - classifiers=[ - 'Development Status :: 2 - Pre-Alpha', - 'License :: OSI Approved :: MIT License', - 'Programming Language :: Python', - 'Programming Language :: Python :: 3', - 'Programming Language :: Python :: 3.7', - ] -) diff --git a/augur/tasks/data_analysis/insight_worker/setup.py b/augur/tasks/data_analysis/insight_worker/setup.py deleted file mode 100644 index b28b4bf5ab..0000000000 --- a/augur/tasks/data_analysis/insight_worker/setup.py +++ /dev/null @@ -1,48 +0,0 @@ -#SPDX-License-Identifier: MIT -import io -import os -import re - -from setuptools import find_packages -from setuptools import setup - -def read(filename): - filename = os.path.join(os.path.dirname(__file__), filename) - text_type = type(u"") - with io.open(filename, mode="r", encoding='utf-8') as fd: - return re.sub(text_type(r':[a-z]+:`~?(.*?)`'), text_type(r'``\1``'), fd.read()) - -setup( - name="insight_worker", - version="1.0.0", - url="https://github.com/chaoss/augur", - license='MIT', - author="Augurlabs", - author_email="s@goggins.com", - description="Augur Worker that discovers and stores data anomalies", - packages=find_packages(exclude=('tests',)), - install_requires=[ - 'Flask==2.0.2', - 'Flask-Cors==4.0.1', - 'Flask-Login==0.5.0', - 'Flask-WTF==1.0.0', - 'requests==2.32.0', - 'psycopg2-binary==2.9.9', - 'click==8.0.3', - 'scipy>=1.10.0', - 'sklearn==0.0', - 'numpy==1.26.0', - ], - entry_points={ - 'console_scripts': [ - 'insight_worker_start=workers.insight_worker.runtime:main', - ], - }, - classifiers=[ - 'Development Status :: 2 - Pre-Alpha', - 'License :: OSI Approved :: MIT License', - 'Programming Language :: Python', - 'Programming Language :: Python :: 3', - 'Programming Language :: Python :: 3.7', - ] -) diff --git a/augur/tasks/data_analysis/message_insights/setup.py b/augur/tasks/data_analysis/message_insights/setup.py deleted file mode 100644 index bd136fdfec..0000000000 --- a/augur/tasks/data_analysis/message_insights/setup.py +++ /dev/null @@ -1,57 +0,0 @@ -#SPDX-License-Identifier: MIT - -import io -import os -import re - -from setuptools import find_packages -from setuptools import setup - -def read(filename): - filename = os.path.join(os.path.dirname(__file__), filename) - text_type = type(u"") - with io.open(filename, mode="r", encoding='utf-8') as fd: - return re.sub(text_type(r':[a-z]+:`~?(.*?)`'), text_type(r'``\1``'), fd.read()) - -setup( - name="message_insights", - version="0.3.1", - url="https://github.com/chaoss/augur", - license='MIT', - author="Augur Team", - author_email="akshblr555@gmail.com", - description="Message Insights worker that detects novel messages & analyzes sentiment from issue, PR messages", - packages=find_packages(), - install_requires=[ - 'Flask==2.0.2', - 'Flask-Cors==4.0.1', - 'Flask-Login==0.5.0', - 'Flask-WTF==1.0.0', - 'requests==2.32.0', - 'psycopg2-binary==2.9.9', - 'click==8.0.3', - 'scipy>=1.10.0', - 'scikit-learn==1.5.0', #0.24.2', - 'numpy==1.26.0', - 'nltk==3.6.6', - 'pandas==1.5.3', - 'emoji==1.2.0', - 'keras>=2.15.0', - 'Keras-Preprocessing', - 'tensorflow==2.15.0', - 'h5py==3.10.0', - 'scikit-image==0.19.1', - 'joblib==1.2.0', - 'xgboost', - 'bs4==0.0.1', - 'xlrd==2.0.1', - 'gensim>=4.2.0' - ], - classifiers=[ - 'Development Status :: 3 - Alpha', - 'License :: OSI Approved :: MIT License', - 'Programming Language :: Python', - 'Programming Language :: Python :: 3', - 'Programming Language :: Python :: 3.7', - ] -) diff --git a/augur/tasks/data_analysis/pull_request_analysis_worker/setup.py b/augur/tasks/data_analysis/pull_request_analysis_worker/setup.py deleted file mode 100644 index 391b368f32..0000000000 --- a/augur/tasks/data_analysis/pull_request_analysis_worker/setup.py +++ /dev/null @@ -1,47 +0,0 @@ -import io -import os -import re - -from setuptools import find_packages -from setuptools import setup - -def read(filename): - filename = os.path.join(os.path.dirname(__file__), filename) - text_type = type(u"") - with io.open(filename, mode="r", encoding='utf-8') as fd: - return re.sub(text_type(r':[a-z]+:`~?(.*?)`'), text_type(r'``\1``'), fd.read()) - -setup( - name="pull_request_analysis_worker", - version="0.0.0", - url="https://github.com/chaoss/augur", - license='MIT', - author="Augur Team", - author_email="akshblr555@gmail.com", - description="Pull Request Analysis worker that predicts acceptance of a PR", - packages=find_packages(), - install_requires=[ - 'Flask==2.0.2', - 'Flask-Cors==4.0.1', - 'Flask-Login==0.5.0', - 'Flask-WTF==1.0.0', - 'requests==2.32.0', - 'psycopg2-binary==2.9.9', - 'sklearn==0.0', - 'nltk==3.6.6', - 'numpy==1.26.0', - 'pandas==1.5.3', - 'emoji==1.2.0', - 'joblib==1.2.0', - 'xgboost==1.4.2', - 'scipy>=1.10.0' - ], - classifiers=[ - 'Development Status :: 2 - Pre-Alpha', - 'License :: OSI Approved :: MIT License', - 'Programming Language :: Python', - 'Programming Language :: Python :: 3', - 'Programming Language :: Python :: 3.7', - ] - -) diff --git a/augur/tasks/git/util/facade_worker/setup.py b/augur/tasks/git/util/facade_worker/setup.py deleted file mode 100644 index ef65f223a2..0000000000 --- a/augur/tasks/git/util/facade_worker/setup.py +++ /dev/null @@ -1,47 +0,0 @@ -#SPDX-License-Identifier: MIT -import io -import os -import re - -from setuptools import find_packages -from setuptools import setup - -def read(filename): - filename = os.path.join(os.path.dirname(__file__), filename) - text_type = type(u"") - with io.open(filename, mode="r", encoding='utf-8') as fd: - return re.sub(text_type(r':[a-z]+:`~?(.*?)`'), text_type(r'``\1``'), fd.read()) - -setup( - name="facade_worker", - version="1.3.0", - url="https://github.com/chaoss/augur", - license='MIT', - author="Augurlabs", - author_email="s@goggins.com", - description="Augur Worker that parses and collects git log data", - packages=find_packages(exclude=('tests',)), - install_requires=[ - 'Flask==2.0.2', - 'Flask-Cors==4.0.1', - 'Flask-Login==0.5.0', - 'Flask-WTF==1.0.0', - 'requests==2.32.0', - 'psycopg2-binary==2.9.9', - 'click==8.0.3', - 'XlsxWriter==1.3.7' - ], - entry_points={ - #TODO: change to celery - 'console_scripts': [ - 'facade_worker_start=facade_worker.runtime:main', - ], - }, - classifiers=[ - 'Development Status :: 2 - Pre-Alpha', - 'License :: OSI Approved :: MIT License', - 'Programming Language :: Python', - 'Programming Language :: Python :: 3', - 'Programming Language :: Python :: 3.7', - ] -) diff --git a/pyproject.toml b/pyproject.toml index c0dbe7842b..34a7c15ba6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -19,61 +19,79 @@ classifiers = [ "Programming Language :: Python :: 3.9" ] dependencies = [ - "graphene", - "graphene_sqlalchemy", - "flask_graphql", - "wheel", - "sendgrid", - "textual>=0.73.0", "alembic==1.8.1", - "coloredlogs==15.0", "Beaker==1.11.0", - "SQLAlchemy==2.0.22", + "blinker==1.4", + "bokeh==2.0.2", + "boto3==1.17.57", + "bs4==0.0.1", + "celery==5.2.7", + "click==8.0.3", + "cloudpickle>=0.2.2", + "coloredlogs==15.0", + "dask>=2021.6.2", + "distributed>=2021.03.0", + "dnspython==2.6.1", + "emoji==1.2.0", + "eventlet==0.35.2", + "flask==2.0.2", + "flask-cors==4.0.1", + "flask-login==0.5.0", + "flask-wtf==1.0.0", + "flask_graphql", + "flower==2.0.1", + "fsspec>=0.6.0", + "gensim>=4.2.0", + "graphene", + "graphene_sqlalchemy", + "gunicorn==22.0.0", + "h5py==3.10.0", + "httpx==0.23.0", "itsdangerous==2.0.1", "Jinja2~=3.0.3", - "Flask==2.0.2", - 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= { url = "https://files.pythonhosted.org/packages/f3/af/4182184d3c338792894f34a62672919db7ca008c89abee9b564dd34d8029/astunparse-1.6.3.tar.gz", hash = "sha256:5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872", size = 18290 } +wheels = [ + { url = "https://files.pythonhosted.org/packages/2b/03/13dde6512ad7b4557eb792fbcf0c653af6076b81e5941d36ec61f7ce6028/astunparse-1.6.3-py2.py3-none-any.whl", hash = "sha256:c2652417f2c8b5bb325c885ae329bdf3f86424075c4fd1a128674bc6fba4b8e8", size = 12732 }, +] + [[package]] name = "async-timeout" version = "5.0.1" @@ -120,6 +142,7 @@ dependencies = [ { name = "blinker" }, { name = "bokeh" }, { name = "boto3" }, + { name = "bs4" }, { name = "celery" }, { name = "click" }, { name = "cloudpickle" }, @@ -127,6 +150,7 @@ dependencies = [ { name = "dask" }, { name = "distributed" }, { name = "dnspython" }, + { name = "emoji" }, { name = "eventlet" }, { name = "flask" }, { name = "flask-cors" }, @@ -135,6 +159,7 @@ dependencies = [ { name = "flask-wtf" }, { name = "flower" }, { name = "fsspec" }, + { name = "gensim" }, { name = "graphene" }, { name = "graphene-sqlalchemy" }, { name = "gunicorn" }, @@ -142,6 +167,10 @@ dependencies = [ { name = "httpx" }, { name = "itsdangerous" }, { name = "jinja2" }, + { name = "joblib" }, + { name = "keras" }, + { name = "keras-preprocessing" }, + { name = "matplotlib" }, { name = "mdpdf" }, { name = "mistune" }, { name = "nltk" }, @@ -152,16 +181,25 @@ dependencies = [ { name = "psutil" }, { name = "psycopg2-binary" }, { name = "pylint" }, + { name = "python-crfsuite" }, { name = "pyyaml" }, { name = "redis" }, { name = "requests" }, + { name = "scikit-image" }, + { name = "scikit-learn" }, { name = "scipy" }, + { name = "seaborn" }, { name = "selenium" }, { name = "sendgrid" }, { name = "six" }, + { name = "sklearn" }, + { name = "sklearn-crfsuite" }, { name = "slack" }, { name = "sqlalchemy" }, + { name = "tabulate" }, { name = "tenacity" }, + { name = "tensorflow" }, + { name = 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Date: Mon, 5 May 2025 15:01:34 -0400 Subject: [PATCH 08/66] Update docker build for uv Signed-off-by: John Strunk --- docker/backend/Dockerfile | 89 +- docker/backend/entrypoint.sh | 5 +- docker/backend/init.sh | 4 +- pyproject.toml | 5 +- uv.lock | 3487 +++++++++++++++++----------------- 5 files changed, 1800 insertions(+), 1790 deletions(-) diff --git a/docker/backend/Dockerfile b/docker/backend/Dockerfile index 34ef8ed788..7ffeae30ed 100644 --- a/docker/backend/Dockerfile +++ b/docker/backend/Dockerfile @@ -6,6 +6,9 @@ FROM golang:1.23-bullseye AS golang-builder # Write final binaries to / so it's easy to copy them out ENV GOBIN=/ +# Disable CGO to ensure the binaries are statically linked +# Discussion: https://github.com/chaoss/augur/pull/3142 +ENV CGO_ENABLED=0 RUN go install github.com/boyter/scc/v3@v3.4.0 \ && /scc --version @@ -24,7 +27,7 @@ ENV PATH="/usr/bin/:/usr/local/bin:/usr/lib:${PATH}" RUN set -x \ && apt-get update \ - && apt-get -y install \ + && apt-get -y install --no-install-recommends \ git \ bash \ curl \ @@ -32,24 +35,17 @@ RUN set -x \ software-properties-common \ postgresql-contrib \ musl-dev \ - python3-dev \ - python3-distutils \ - python3-venv \ wget \ postgresql-client \ libpq-dev \ build-essential \ chromium \ tar \ - jq \ + jq \ chromium-driver \ - && apt-get clean \ - && rm -rf /var/lib/apt/lists/* - -# Install Firefox from Debian repositories for ARM64 architecture -RUN set -x \ - && apt-get update \ - && apt-get install -y firefox-esr + firefox-esr \ + && apt-get clean \ + && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* # Install Geckodriver RUN GECKODRIVER_VERSION=$(curl -s https://api.github.com/repos/mozilla/geckodriver/releases/latest | jq -r '.tag_name' | sed 's/v//') \ @@ -71,46 +67,61 @@ RUN firefox --version RUN geckodriver --version - - - EXPOSE 5000 -WORKDIR /augur -COPY --chmod=u=rw,u+X,go=r,go+X ./README.md . -COPY --chmod=u=rw,u+X,go=r,go+X ./alembic.ini . -COPY --chmod=u=rw,u+X,go=r,go+X ./augur/ augur/ -COPY --chmod=u=rw,u+X,go=r,go+X ./metadata.py . -COPY --chmod=u=rw,u+X,go=r,go+X ./setup.py . -COPY --chmod=u=rw,u+X,go=r,go+X ./scripts/ scripts/ -COPY --chmod=u=rw,u+X,go=r,go+X ./keyman/ keyman/ - -RUN python3 -m venv /opt/venv +# Install uv (https://docs.astral.sh/uv/guides/integration/docker/#installing-uv) +COPY --from=ghcr.io/astral-sh/uv:latest /uv /uvx /bin/ +ENV UV_COMPILE_BYTECODE=1 +# The uv package cache will be on a cache volume, so can't be linked +ENV UV_LINK_MODE=copy +# Assert that the lockfile (uv.lock) is up-to-date. Use `uv lock` to update it +# manually if this fails the container build. +ENV UV_LOCKED=1 -RUN set -x \ - && /opt/venv/bin/pip install --upgrade pip - -RUN set -x \ - && /opt/venv/bin/pip install wheel - -RUN set -x \ - && /opt/venv/bin/pip install . - -RUN set -x \ - && /opt/venv/bin/pip install --upgrade pip \ - && /opt/venv/bin/pip install wheel \ - && /opt/venv/bin/pip install . +WORKDIR /augur -RUN ./scripts/docker/install-workers-deps.sh +# Install augur's dependencies +RUN --mount=type=cache,target=/root/.cache/uv \ + --mount=type=bind,source=uv.lock,target=uv.lock \ + --mount=type=bind,source=pyproject.toml,target=pyproject.toml \ + --mount=type=bind,source=.python-version,target=.python-version \ + uv sync --no-install-project --no-dev + +# Copy in the actual code +# The --chmod flags ensure that permissions are set correctly: +# - u=rw,u+X: user can read and write all files/dirs and execute directories +# - go=r,go+X: group and others can read all files/dirs and execute directories +COPY --chmod=u=rw,u+X,go=r,go+X pyproject.toml . +COPY --chmod=u=rw,u+X,go=r,go+X uv.lock . +COPY --chmod=u=rw,u+X,go=r,go+X .python-version . +COPY --chmod=u=rw,u+X,go=r,go+X README.md . +COPY --chmod=u=rw,u+X,go=r,go+X LICENSE . +COPY --chmod=u=rw,u+X,go=r,go+X alembic.ini . +COPY --chmod=u=rw,u+X,go=r,go+X augur/ augur/ +COPY --chmod=u=rw,u+X,go=r,go+X metadata.py . +COPY --chmod=u=rw,u+X,go=r,go+X scripts/ scripts/ +COPY --chmod=u=rw,u+X,go=r,go+X keyman/ keyman/ + +# Install the main project +RUN --mount=type=cache,target=/root/.cache/uv \ + uv sync --no-dev + +# We aren't going to activate the virtualenv (manually or via uv run), so we +# need adjust the PATH +ENV PATH="/augur/.venv/bin:${PATH}" ENV SCC_DIR=/scc COPY --from=golang-builder --chmod=u=rw,u+X,go=r,go+X "/scc" "/scc/scc" ENV SCORECARD_DIR=/scorecard COPY --from=golang-builder --chmod=u=rw,u+X,go=r,go+X "/scorecard" "/scorecard/scorecard" +# Verify installations +RUN ${SCC_DIR}/scc --version +RUN ${SCORECARD_DIR}/scorecard version RUN mkdir -p repos/ logs/ /augur/facade/ RUN ln -s /cache /augur/augur/static/cache +# Copy in the entrypoint and init scripts, ensuring they are executable COPY --chmod=u=rwx,go=rx ./docker/backend/entrypoint.sh / COPY --chmod=u=rwx,go=rx ./docker/backend/init.sh / RUN chmod +x /entrypoint.sh /init.sh diff --git a/docker/backend/entrypoint.sh b/docker/backend/entrypoint.sh index a8c0e6971f..3f7ae68387 100644 --- a/docker/backend/entrypoint.sh +++ b/docker/backend/entrypoint.sh @@ -2,9 +2,6 @@ #SPDX-License-Identifier: MIT set -e -source /opt/venv/bin/activate - - if [[ "$AUGUR_DB" == *"localhost"* ]]; then echo "localhost db connection" export AUGUR_DB="${AUGUR_DB/localhost/host.docker.internal}" @@ -24,4 +21,4 @@ else export redis_conn_string=$REDIS_CONN_STRING fi -exec $* +exec "$@" diff --git a/docker/backend/init.sh b/docker/backend/init.sh index e77342e359..4aa2b4ebca 100644 --- a/docker/backend/init.sh +++ b/docker/backend/init.sh @@ -19,6 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workflow to include a new job that checks the uv lockfile, ensuring it is up to date by installing uv and running the lock check command. Signed-off-by: John Strunk --- .github/workflows/checks.yml | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) diff --git a/.github/workflows/checks.yml b/.github/workflows/checks.yml index c23bfd7bb3..69b2fe7e22 100644 --- a/.github/workflows/checks.yml +++ b/.github/workflows/checks.yml @@ -28,4 +28,15 @@ jobs: uses: reviewdog/action-misspell@v1 with: github_token: ${{ secrets.GITHUB_TOKEN }} - locale: "US" \ No newline at end of file + locale: "US" + + uv-lock: + name: runner / uv-lock + runs-on: ubuntu-latest + steps: + - name: Check out repository + uses: actions/checkout@v4 + - name: Install uv + uses: astral-sh/setup-uv@v6 + - name: Ensure uv lockfile is up to date + run: uv lock --check From fbb61abe85397ec60a72f5704214d0c37c5c039b Mon Sep 17 00:00:00 2001 From: John Strunk Date: Mon, 5 May 2025 16:59:34 -0400 Subject: [PATCH 10/66] Fix documention build on RTD Added post_create_environment job to generate requirements.txt using uv, and updated python install method to use the generated requirements file. Signed-off-by: John Strunk --- .readthedocs.yml | 15 ++++++++------- Makefile | 14 +++++++++++--- pyproject.toml | 9 +++++++-- uv.lock | 20 ++++++++++++++++++-- 4 files changed, 44 insertions(+), 14 deletions(-) diff --git a/.readthedocs.yml b/.readthedocs.yml index 3b0e387327..120fd08332 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -5,10 +5,15 @@ # Required version: 2 -build: +build: os: ubuntu-22.04 # <- add this line tools: python: "3.10" + jobs: + post_create_environment: + # Use uv to create a requirements file that RTD can install + - pip install uv + - uv export --format requirements.txt --only-group docs -o requirements.txt # Build documentation in the docs/ directory with Sphinx sphinx: @@ -24,12 +29,8 @@ formats: all # Optionally set the version of Python and requirements required to build your docs python: install: - - method: pip - path: . - extra_requirements: - - dev - - method: setuptools - path: . + # Install the requirements file created during the post_create_environment job + - requirements: requirements.txt # build: # os: ubuntu-22.04 diff --git a/Makefile b/Makefile index d9f199a867..0015c8efc4 100644 --- a/Makefile +++ b/Makefile @@ -124,12 +124,20 @@ test-api: # @ bash -c 'tox -e ALL' +# +# UV installation +# +.PHONY: uv +uv: + @ command -v uv >/dev/null 2>&1 || { echo "Installing uv..."; pip install --user uv; } + # # Documentation # .PHONY: docs docs-view -docs: - @ bash -c 'cd docs/ && rm -rf build/ && make html;' +docs: uv + -rm -rf docs/build + uv run --only-group docs make -C docs html docs-view: docs @ bash -c 'open docs/build/html/index.html' @@ -184,4 +192,4 @@ docker-run-database: docker-run-rabbitmq: @ - docker stop augur_rabbitmq @ - docker rm augur_rabbitmq - docker run -p 5434:5432 --name augur_rabbitmq augurlabs/augur:rabbitmq \ No newline at end of file + docker run -p 5434:5432 --name augur_rabbitmq augurlabs/augur:rabbitmq diff --git a/pyproject.toml b/pyproject.toml index cb0b7477e0..1f4d148b35 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -88,7 +88,6 @@ dependencies = [ "tornado==6.4.1", "typing-extensions==4.7.1", "Werkzeug~=2.0.0", - "wheel", "xgboost==1.4.2", "xlrd==2.0.1", "xlsxwriter==1.3.7", @@ -100,11 +99,17 @@ dev = [ "pytest==6.2.5", "toml>=0.10.2", "ipdb==0.13.9", + {include-group = "docs"}, +] +docs = [ + "docutils==0.20.1", + # setuptools is needed for pkg_resources due to sphinxcontrib-redoc + # See: https://github.com/sphinx-contrib/redoc/issues/47 + "setuptools", "sphinx==7.2.6", "sphinx_rtd_theme==2.0.0", "sphinxcontrib-openapi==0.8.3", "sphinxcontrib-redoc==1.6.0", - "docutils==0.20.1" ] [project.scripts] diff --git a/uv.lock b/uv.lock index a708745740..c31c358996 100644 --- a/uv.lock +++ b/uv.lock @@ -206,7 +206,6 @@ dependencies = [ { name = "tornado" }, { name = "typing-extensions" }, { name = "werkzeug" }, - { name = "wheel" }, { name = "xgboost" }, { name = "xlrd" }, { name = "xlsxwriter" }, @@ -217,6 +216,7 @@ dev = [ { name = "docutils" }, { name = "ipdb" }, { name = "pytest" }, + { name = "setuptools" }, { name = "sphinx" }, { name = "sphinx-rtd-theme" }, { name = "sphinxcontrib-openapi" }, @@ -224,6 +224,14 @@ dev = [ { name = "toml" }, { name = "tox" }, ] +docs = [ + { name = "docutils" }, + { name = "setuptools" }, + { name = "sphinx" }, + { name = "sphinx-rtd-theme" }, + { name = "sphinxcontrib-openapi" }, + { name = "sphinxcontrib-redoc" }, +] [package.metadata] requires-dist = [ @@ -296,7 +304,6 @@ requires-dist = [ { name = "tornado", specifier = "==6.4.1" }, { name = "typing-extensions", specifier = "==4.7.1" }, { name = "werkzeug", specifier = "~=2.0.0" }, - { name = "wheel" }, { name = "xgboost", specifier = "==1.4.2" }, { name = "xlrd", specifier = "==2.0.1" }, { name = "xlsxwriter", specifier = "==1.3.7" }, @@ -307,6 +314,7 @@ dev = [ { name = "docutils", specifier = "==0.20.1" }, { name = "ipdb", specifier = "==0.13.9" }, { name = "pytest", specifier = "==6.2.5" }, + { name = "setuptools" }, { name = "sphinx", specifier = "==7.2.6" }, { name = "sphinx-rtd-theme", specifier = "==2.0.0" }, { name = "sphinxcontrib-openapi", specifier = "==0.8.3" }, @@ -314,6 +322,14 @@ dev = [ { name = "toml", specifier = ">=0.10.2" }, { name = "tox", specifier = "==3.24.4" }, ] +docs = [ + { name = "docutils", specifier = "==0.20.1" }, + { name = "setuptools" }, + { name = "sphinx", specifier = "==7.2.6" }, + { name = "sphinx-rtd-theme", specifier = "==2.0.0" }, + { name = "sphinxcontrib-openapi", specifier = "==0.8.3" }, + { name = "sphinxcontrib-redoc", specifier = "==1.6.0" }, +] [[package]] name = "babel" From 9c3087f4331e5bad1de763c370ae91d7ede44e9f Mon Sep 17 00:00:00 2001 From: John Strunk Date: Wed, 28 May 2025 16:32:48 -0400 Subject: [PATCH 11/66] Update documentation for using uv Signed-off-by: John Strunk --- Makefile | 8 ++-- .../source/deployment/nginx-configuration.rst | 4 +- docs/source/deployment/server-deployment.rst | 23 +++++------ .../development-guide/documentation.rst | 16 ++++---- .../getting-started/collecting-data.rst | 10 ++--- .../command-line-interface/backend.rst | 33 ++++++++------- .../command-line-interface/configure.rst | 10 ++--- .../command-line-interface/db.rst | 14 +++---- .../command-line-interface/logging.rst | 10 ++--- .../command-line-interface/toc.rst | 4 +- .../getting-started/dev-osx-install.rst | 25 +++++++----- docs/source/getting-started/frontend.rst | 2 +- docs/source/getting-started/installation.rst | 30 +++++++------- docs/source/getting-started/new-install.rst | 26 +++++++----- scripts/control/rebuild-backend.sh | 1 - scripts/control/rebuild.sh | 1 - scripts/install/backend.sh | 14 ------- scripts/install/install.sh | 5 --- scripts/install/workers.sh | 40 ++----------------- 19 files changed, 110 insertions(+), 166 deletions(-) delete mode 100755 scripts/install/backend.sh diff --git a/Makefile b/Makefile index 0015c8efc4..4fe926edc4 100644 --- a/Makefile +++ b/Makefile @@ -32,8 +32,8 @@ default: .PHONY: install .PHONY: install-spdx install-spdx-sudo install-augur-sbom .PHONY: clean rebuild -install: - @ ./scripts/install/install.sh dev +install: uv + @ uv run ./scripts/install/install.sh dev wizard: @ ./scripts/install/install.sh graphical @@ -50,8 +50,8 @@ install-augur-sbom: clean: @ scripts/control/clean.sh -rebuild: - @ scripts/control/rebuild.sh dev +rebuild: uv + @ uv run scripts/control/rebuild.sh dev # # Development diff --git a/docs/source/deployment/nginx-configuration.rst b/docs/source/deployment/nginx-configuration.rst index 5142420db2..7718a171b7 100644 --- a/docs/source/deployment/nginx-configuration.rst +++ b/docs/source/deployment/nginx-configuration.rst @@ -31,7 +31,7 @@ Server Compilation } 2. Compile Augur (this wires the host and port into the frontend so people pulling the web pages of Augur, in the `frontend/` subdirectory are referring to the right endpoints for this instance.): ``make rebuild`` -3. Run Augur: ``nohup augur backend start >augur.log 2>augur.err &`` +3. Run Augur: ``nohup uv run augur backend start >augur.log 2>augur.err &`` ------------------ @@ -210,5 +210,3 @@ First, we will start with lines 29, 33, & 207 of ``augur/frontend/src/AugurAPI.t 'certfile': '/home/ubuntu/augur/fullchain.pem', 'keyfile': '/home/ubuntu/augur/privkey.pem' } - - diff --git a/docs/source/deployment/server-deployment.rst b/docs/source/deployment/server-deployment.rst index b1488d3c3f..c510dfe5e3 100644 --- a/docs/source/deployment/server-deployment.rst +++ b/docs/source/deployment/server-deployment.rst @@ -16,17 +16,16 @@ Detailed Steps --------------------------- 1. Login to your server. -2. Create or activate the Python3 virtual environment for the Augur instance you want to deploy as a public server. -3. If you have not already done so, clone Augur. -4. Change into that directory. -5. ``git checkout dev``, if you want to deploy the latest features, otherwise remain in the main branch. -6. You need a database owned by an Augur user. -7. ``make install`` ... now is a good time to go get some tea. -8. When you return with your tea, follow the prompts: +2. If you have not already done so, clone Augur. +3. Change into that directory. +4. ``git checkout dev``, if you want to deploy the latest features, otherwise remain in the main branch. +5. You need a database owned by an Augur user. +6. ``make install`` ... now is a good time to go get some tea. +7. When you return with your tea, follow the prompts: - respond to the SERVER prompt with localhost. - the current standard is to put the repos in a repos/ directory in the root augur directory (these will never get checked in to VC). -9. Load repos, following instructions in docs. -10. If you have more than one instance of Augur or another service on port 5000, you need to edit the ``augur.config.json`` to update the server port: +8. Load repos, following instructions in docs. +9. If you have more than one instance of Augur or another service on port 5000, you need to edit the ``augur.config.json`` to update the server port: - ``sudo lsof -i -P -n | grep LISTEN`` shows you ports in use if you are not sure. - ``sudo ufw status`` lets you know if the port you are looking for is available as open through your firewall. - ``sudo ufw status | grep 5005`` checks to see if port 5005 is open, for example: @@ -45,7 +44,7 @@ Detailed Steps | 5005/udp (v6) | ALLOW | Anywhere (v6) | +---------------+--------+---------------------------------------------+ -11. In the Frontend block of ``augur.config.json``, set the host value to be the domain you want the front end compiled for. +10. In the Frontend block of ``augur.config.json``, set the host value to be the domain you want the front end compiled for. For example, we set ours to ``test.augurlabs.io``. .. code-block:: json @@ -57,8 +56,6 @@ For example, we set ours to ``test.augurlabs.io``. } } -12. Then do a ``make rebuild-dev``. +11. Then do a ``make rebuild-dev``. Next up: configure ``nginx``! - - diff --git a/docs/source/development-guide/documentation.rst b/docs/source/development-guide/documentation.rst index 5c510152a7..59f17427c0 100644 --- a/docs/source/development-guide/documentation.rst +++ b/docs/source/development-guide/documentation.rst @@ -11,9 +11,9 @@ we update with each release. The following sections briefly outline how to contr Library and Usage Documentation -------------------------------- -The library documentation is written using `reStructuredText `_ for the raw markdown and then built into web pages using `Sphinx `_. +The library documentation is written using `reStructuredText `_ for the raw markdown and then built into web pages using `Sphinx `_. -We'll avoid going over reStructuredText in detail here, +We'll avoid going over reStructuredText in detail here, but `here `__ is a good reference document. Similarly, we'll avoid going over Sphinx in great detail as well; `here `__ is a good reference document for the @@ -23,13 +23,11 @@ Building ~~~~~~~~ To see your changes and make sure everything rendered correctly, First activate the python virtual enivroment and run ``make docs`` in the root -``augur/`` directory, and then open ``docs/build/html/index.html`` in your web browser to view it. +``augur/`` directory, and then open ``docs/build/html/index.html`` in your web browser to view it. .. code-block:: bash - - $ cd augur - $ python3 -m venv $HOME/.virtualenvs/augur_env - $ source $HOME/.virtualenvs/augur_env/bin/activate + + $ cd augur $ make docs Or, you can use the shortcut which does exactly this: @@ -51,6 +49,6 @@ Hosting ~~~~~~~ Our documentation is graciously hosted by `Read the Docs `_. -Enabled branches of the main ``chaoss/augur`` repository will each have their own documentation, with the -default ``main`` corresponding to ``main`` on the readthedocs. The documentation will automatically be +Enabled branches of the main ``chaoss/augur`` repository will each have their own documentation, with the +default ``main`` corresponding to ``main`` on the readthedocs. The documentation will automatically be built and deployed on a push to one of these branches or on any incoming PR, but please don't forget to check before you push! diff --git a/docs/source/getting-started/collecting-data.rst b/docs/source/getting-started/collecting-data.rst index 3996999737..38e824870f 100644 --- a/docs/source/getting-started/collecting-data.rst +++ b/docs/source/getting-started/collecting-data.rst @@ -16,11 +16,11 @@ Now that you’ve installed Augur’s application server, it’s time to configu # Terminal Window 3 # To Start Augur: - (nohup augur backend start) + (nohup uv run augur backend start) # To Stop Augur: - augur backend stop - augur backend kill + uv run augur backend stop + uv run augur backend kill Now, here's a ton of brain-splitting detail about celery collection. There are 2 pieces to data collection with Augur: the celery worker processes, and the job messages passed through rabbitmq. The jobs to collect are determined by a monitor process started through the cli that starts the rest of augur. The monitor process generates the jobs messages to send to rabbitmq through the collection_status table that informs the status of jobs that have yet to be run. The celery collection workers can then accept these jobs, after which they will use the information provided in the job to find the repositories in question and collect the requested data. @@ -53,7 +53,7 @@ Next up are the configuration options specific to some collection tasks (but som - ``limited_run``, toggle between 0 and 1 to determine whether to run all facade tasks or not. Runs all tasks if set to 0 - ``pull_repos``, toggle whether to pull updates from repos after cloning them. If turned off updates to repos will not be collected. - ``run_analysis``, toggle whether to process commit data at all. If turned off will only clone repos and run tertiary tasks such as resolving contributors from any existing commits or collecting dependency relationships. Mainly used for testing. -- ``run_facade_contributors``, toggle whether to run contributor resolution tasks. This will process and parse through commit data to link emails to contributors as well as aliases, etc. +- ``run_facade_contributors``, toggle whether to run contributor resolution tasks. This will process and parse through commit data to link emails to contributors as well as aliases, etc. - ``force_invalidate_caches``, set every repo to reset the status of commit email affillation, which is the organization that an email is associated with. - ``rebuild_caches``, toggle whether to enable parsing through commit data to determine affillation and web cache @@ -79,7 +79,7 @@ This section is for toggling sets of jobs on or off. - ``prelim_phase``, toggles whether to run preliminary tasks that check to see whether repos are valid or not. - ``primary_repo_collect_phase``, toggle the standard collection jobs, mainly pull requests and issues -- ``secondary_repo_collect_phase``, toggle the secondary collection jobs, mainly jobs that take a while +- ``secondary_repo_collect_phase``, toggle the secondary collection jobs, mainly jobs that take a while - ``facade_phase``, toggle all facade jobs - ``machine_learning_phase``, toggle all ml related jobs diff --git a/docs/source/getting-started/command-line-interface/backend.rst b/docs/source/getting-started/command-line-interface/backend.rst index 7c614a8b37..c587ee241c 100644 --- a/docs/source/getting-started/command-line-interface/backend.rst +++ b/docs/source/getting-started/command-line-interface/backend.rst @@ -20,7 +20,7 @@ This command is for starting Augur's API server & (optionally) data collection w .. code-block:: - augur backend start + uv run augur backend start # successful output looks like: >[43389] augur [INFO] Augur application initialized @@ -56,7 +56,7 @@ To start the backend as a background process: .. code-block:: bash - nohup augur backend start >logs/base.log 2>logs/base.err & + nohup uv run augur backend start >logs/base.log 2>logs/base.err & Successful output looks like the generation of standard Augur logfiles in the logs/ directory. @@ -64,7 +64,7 @@ To start the backend server without the housekeeper: .. code-block:: bash - augur backend start --disable-housekeeper + uv run augur backend start --disable-housekeeper Successful output looks like: @@ -85,11 +85,11 @@ Example usage: .. code-block:: bash - augur backend stop + uv run augur backend stop Successful output looks like: -.. code-block:: bash +.. code-block:: bash > CLI: [backend.stop] [INFO] Stopping process 33607 > CLI: [backend.stop] [INFO] Stopping process 33775 @@ -99,13 +99,13 @@ Successful output looks like: ``kill`` --------- **Forcefully** terminates (using ``SIGKILL``) all currently running backend Augur processes, including any workers. Will only work in a virtual environment. -Should only be used when ``augur backend stop`` is not working. +Should only be used when ``uv run augur backend stop`` is not working. Example usage: .. code-block:: bash - augur backend kill + uv run augur backend kill # successful output looks like: > CLI: [backend.kill] [INFO] Killing process 87340 @@ -121,13 +121,13 @@ Outputs the process ID (PID) of all currently running backend Augur processes, i Example usage: -.. code-block:: bash +.. code-block:: bash - augur backend processes + uv run augur backend processes Successful output looks like: -.. code-block:: bash +.. code-block:: bash > CLI: [backend.processes] [INFO] Found process 14467 > CLI: [backend.processes] [INFO] Found process 14725 @@ -160,11 +160,11 @@ Start the http server with:: Then start Augur with ``logstash`` flag:: - $ augur backend start --logstash + $ uv run augur backend start --logstash If you'd like to clean all previously collected errors, run:: - - $ augur backend start --logstash-with-cleanup + + $ uv run augur backend start --logstash-with-cleanup Open http://localhost:8003 and select workers to check for errors. @@ -175,10 +175,10 @@ Exports your GitHub key and database credentials to 2 files. The first is ``augu Example usage: -.. code-block:: bash +.. code-block:: bash # to export your environment - $ augur util export-env + $ uv run augur util export-env Successful output looks like: @@ -218,8 +218,7 @@ Example usage: .. code-block:: bash # to reset the repo collection status to "New" - $ augur util repo-reset + $ uv run augur util repo-reset # successful output looks like: > CLI: [util.repo_reset] [INFO] Repos successfully reset - diff --git a/docs/source/getting-started/command-line-interface/configure.rst b/docs/source/getting-started/command-line-interface/configure.rst index d0d21fe7ba..6018771509 100644 --- a/docs/source/getting-started/command-line-interface/configure.rst +++ b/docs/source/getting-started/command-line-interface/configure.rst @@ -35,17 +35,13 @@ Example usage\: .. code-block:: bash # to generate an augur.config.json file with all the defaults - $ augur config init + $ uv run augur config init # to generate an augur.config.json given all credentials as literals - $ augur config init --db_name "db_name" --db_host "host" --db_port "port" --db_user "db_user" --db_password "password" --github_api_key "github_api_key" --facade_repo_directory "facade_repo_directory" + $ uv run augur config init --db_name "db_name" --db_host "host" --db_port "port" --db_user "db_user" --db_password "password" --github_api_key "github_api_key" --facade_repo_directory "facade_repo_directory" # to generate an augur.config.json given all credentials and environment variables - $ augur config init --db_name $AUGUR_DB_NAME --db_host $AUGUR_DB_HOST --db_port $AUGUR_DB_PORT --db_user $AUGUR_DB_DB_USER --db_password $AUGUR_DB_PASSWORD --github_api_key $AUGUR_GITHUB_API_KEY --facade_repo_directory $AUGUR_FACADE_REPO_DIRECTORY + $ uv run augur config init --db_name $AUGUR_DB_NAME --db_host $AUGUR_DB_HOST --db_port $AUGUR_DB_PORT --db_user $AUGUR_DB_DB_USER --db_password $AUGUR_DB_PASSWORD --github_api_key $AUGUR_GITHUB_API_KEY --facade_repo_directory $AUGUR_FACADE_REPO_DIRECTORY # successful output looks like: > CLI: [config.init] [INFO] Config written to /Users/carter/.augur/augur.config.json - - - - diff --git a/docs/source/getting-started/command-line-interface/db.rst b/docs/source/getting-started/command-line-interface/db.rst index 1fec827e6f..b544ba7860 100644 --- a/docs/source/getting-started/command-line-interface/db.rst +++ b/docs/source/getting-started/command-line-interface/db.rst @@ -25,7 +25,7 @@ Example usage\: .. code-block:: bash # to add new repos to the database - $ augur db add-repo-groups repo_groups.csv + $ uv run augur db add-repo-groups repo_groups.csv # contents of repo_groups.csv 10,Repo Group 1 @@ -45,7 +45,7 @@ Example usage\: .. code-block:: bash # to retrieve the repo groups - $ augur db get-repo-groups + $ uv run augur db get-repo-groups # successful output looks like: > repo_group_id rg_name rg_description @@ -110,7 +110,7 @@ Example usage\: .. code-block:: bash # to generate a key - $ augur db generate-api-key + $ uv run augur db generate-api-key # successful output looks like (this will be an actual key): > CLI: [db.update_api_key] [INFO] Updated Augur API key to: new_key_abc_123 @@ -126,7 +126,7 @@ Example usage\: .. code-block:: bash # to retrieve the key - $ augur db get-api-key + $ uv run augur db get-api-key # successful output looks like (this will be an actual key): > existing_key_def_456 @@ -141,7 +141,7 @@ Example usage\: .. code-block:: bash # to return the current database version - $ augur db print-db-version + $ uv run augur db print-db-version # successful output looks like: > 1 @@ -156,7 +156,7 @@ Example usage\: .. code-block:: bash # to upgrade the user's database to the current version - $ augur db upgrade-db-version + $ uv run augur db upgrade-db-version # successful output if your DB is already up to date > CLI: [db.check_pgpass_credentials] [INFO] Credentials found in $HOME/.pgpass @@ -190,7 +190,7 @@ Example usage\: .. code-block:: bash # to create the schema - $ augur db create-schema + $ uv run augur db create-schema .. note:: If this runs successfully, you should see a bunch of schema creation commands fly by pretty fast. If everything worked you should see: ``update "augur_operations"."augur_settings" set value = xx where setting = 'augur_data_version';`` at the end. diff --git a/docs/source/getting-started/command-line-interface/logging.rst b/docs/source/getting-started/command-line-interface/logging.rst index fb98f7b299..eef16cc340 100644 --- a/docs/source/getting-started/command-line-interface/logging.rst +++ b/docs/source/getting-started/command-line-interface/logging.rst @@ -13,8 +13,8 @@ Prints the location of the directory to which Augur is configured to write its l Example usage:: - # to stop the server and workers - $ augur logging directory + # to print the logs directory + $ uv run augur logging directory # successful output looks like: > /Users/carter/projects/work/augur/logs/ @@ -26,8 +26,8 @@ Prints the last ``n`` lines of each ``.log`` and ``.err`` file in the logs direc Example usage:: - # to stop the server and workers - $ augur logging tail + # to print the last 20 lines of each log file + $ uv run augur logging tail # successful output looks like: > ********** Logfile: augur.log @@ -35,5 +35,3 @@ Example usage:: > ********** Logfile: augur.err - - diff --git a/docs/source/getting-started/command-line-interface/toc.rst b/docs/source/getting-started/command-line-interface/toc.rst index 238015a85e..38080a0269 100644 --- a/docs/source/getting-started/command-line-interface/toc.rst +++ b/docs/source/getting-started/command-line-interface/toc.rst @@ -4,7 +4,7 @@ Command Line Interface Augur provides a command line interface (CLI) for interacting with your Augur installation. It's broken up into a few categories: ``db``, ``backend``, ``util``, ``config``, and ``logging``. -Each command is invoked by first specifying the category, then the command name, and then the parameters/options; e.g. the ``list`` command under ``augur util`` would be invoked as ``augur backend start --option1 ...``. +Each command is invoked by first specifying the category, then the command name, and then the parameters/options; e.g. the ``list`` command under ``augur util`` would be invoked as ``uv run augur utli list --option1 ...``. .. note:: @@ -16,4 +16,4 @@ Each command is invoked by first specifying the category, then the command name, db backend configure - logging \ No newline at end of file + logging diff --git a/docs/source/getting-started/dev-osx-install.rst b/docs/source/getting-started/dev-osx-install.rst index 05c652ca09..40f6e4e824 100644 --- a/docs/source/getting-started/dev-osx-install.rst +++ b/docs/source/getting-started/dev-osx-install.rst @@ -278,11 +278,16 @@ only exist if you have already installed the rabbitmq_management plugin. Installing and Configuring Augur! --------------------------------- -Create a Python Virtual Environment -``python3 -m venv ~/virtual-env-directory`` +We use `uv `_ to manage Augur’s virtual +environment and dependencies. Any time you run an Augur command, you should +prefix it with ``uv run`` to ensure you are using the correct virtual +environment. -Activate your Python Virtual Environment -``source ~/virtual-env-directory/bin/activate`` +``uv`` can be installed with pip: + +.. code:: shell + + pip install --user uv From the root of the Augur Directory, type ``make install``. You will be prompted to provide: @@ -551,16 +556,16 @@ utility may change these characteristics. Augur Commands -------------- -To access command line options, use ``augur --help``. To load repos from +To access command line options, use ``uv run augur --help``. To load repos from GitHub organizations prior to collection, or in other ways, the direct -route is ``augur db --help``. +route is ``uv run augur db --help``. Start a Flower Dashboard, which you can use to monitor progress, and report any failed processes as issues on the Augur GitHub site. The error rate for tasks is currently 0.04%, and most errors involve unhandled platform API timeouts. We continue to identify and add fixes to handle these errors through additional retries. Starting Flower: -``(nohup celery -A augur.tasks.init.celery_app.celery_app flower --port=8400 --max-tasks=1000000 &)`` +``(nohup uv run celery -A augur.tasks.init.celery_app.celery_app flower --port=8400 --max-tasks=1000000 &)`` NOTE: You can use any open port on your server, and access the dashboard in a browser with http://servername-or-ip:8400 in the example above (assuming you have access to that port, and its open on your network.) @@ -574,7 +579,7 @@ disable Hyper-V, and afterward AVX should pass to the VM. Starting your Augur Instance ---------------------------- -Start Augur: ``(nohup augur backend start &)`` +Start Augur: ``(nohup uv run augur backend start &)`` When data collection is complete you will see only a single task running in your flower Dashboard. @@ -593,8 +598,8 @@ change that in augur_operations.config for OSX) Stopping your Augur Instance ---------------------------- -You can stop augur with ``augur backend stop``, followed by -``augur backend kill``. We recommend waiting 5 minutes between commands +You can stop augur with ``uv run augur backend stop``, followed by +``uv run augur backend kill``. We recommend waiting 5 minutes between commands so Augur can shutdown more gently. There is no issue with data integrity if you issue them seconds apart, its just that stopping is nicer than killing. diff --git a/docs/source/getting-started/frontend.rst b/docs/source/getting-started/frontend.rst index 0a4fd7ebab..7d0c9cace6 100644 --- a/docs/source/getting-started/frontend.rst +++ b/docs/source/getting-started/frontend.rst @@ -2,7 +2,7 @@ Augur's Frontend ================= To compile Augur's frontend for deployment in a production environment (i.e., behind an nginx server), you must go through the folowing steps - 1. Run ``augur config init-frontend`` from within your python virtual environment. + 1. Run ``uv run augur config init-frontend``. 2. Enter Augur's home directory 3. Run ``npm install``, and then ``npm run build`` in the frontend directory. 4. After that, follow the instructions for configuring Augur behind Nginx. diff --git a/docs/source/getting-started/installation.rst b/docs/source/getting-started/installation.rst index 4e367958c1..25837e2b34 100644 --- a/docs/source/getting-started/installation.rst +++ b/docs/source/getting-started/installation.rst @@ -2,15 +2,16 @@ Installation Guide =================== This section shows how to install Augur's Python library from the source. If you don't have a required dependency, please follow the provided links to install and configure it. + .. note:: - There are three main issues new developers encounter when first installing Augur: + There are three main issues new developers encounter when first installing Augur: 1. The absence of a `GCC` or `Fortran` compiler; which are required by NumPy and NLTK Python libraries. Look up how to install these compilers for your local operating system. Many times they need to be updated to a more current version. - + 2. Conflicting versions of Python: The fix is platform-specific. On Mac OS X, multiple versions of Python often have been installed by the OS, brew, Anaconda, or both. The result is some python commands draw from different paths because of how they link in `/usr/local/bin` - 3. Multiple, or conflicting versions of PostgreSQL, sometimes due to the absence of a functional `psql` function at the command line. + 3. Multiple, or conflicting versions of PostgreSQL, sometimes due to the absence of a functional `psql` function at the command line. General Requirements ~~~~~~~~~~~~~~~~~~~~ @@ -19,7 +20,12 @@ Backend --------- Required: -- `GitHub Access Token `__ (``repo`` and all ``read`` scopes except ``enterprise``) +- `GitHub Access Token `_ (This token + only needs to have sufficient privileges to read the repos you want to + collect. Assuming those are all "public" repositories, this token can be a + `"no scope" token + `_, + i.e., leave all scopes UNchecked.) - `GitLab Access Token `__ - `Python 3.6 - 3.8 `__ @@ -181,16 +187,12 @@ General Augur Installation Steps (Irrespective of Operating System) $ git clone 'https://github.com/chaoss/augur.git' $ cd augur/ -2. Create a virtual environment in a directory of your choosing. Be sure to use the correct ``python`` command for -your installation of Python 3: on most systems, this is ``python3``, but yours may differ (you can use ``python -V`` or ``python3 -V`` to check). +2. Install ``uv`` via pip: -.. code-block:: bash +.. code:: shell - # to create the environment - $ python3 -m venv $HOME/.virtualenvs/augur_env + pip install --user uv - # to activate the environment - $ source $HOME/.virtualenvs/augur_env/bin/activate 3. Set AUGUR_DB environment variable with a postgres database connection string (if you have not setup a database yet, refer to :ref:`database setup`) Note: Three terminals will be needed to collect data for augur, and AUGUR_DB needs to be set for 2 out of the 3. If you don't want to add it to both terminals you can add it permanently in your .bashrc file if running bash, or .zshrc file if in running zsh. @@ -218,12 +220,12 @@ your installation of Python 3: on most systems, this is ``python3``, but yours m If you think something went wrong, check the log files in ``logs/``. If you want to try again, you can use ``make clean`` to delete any build files before running ``make install`` again. -MacOS users: +MacOS users: ------------ If your build fails and in gunicorn.log you see this error: ``Connection in use: ('0.0.0.0', 5000)``, that means port 5000 is being used by another process. To solve this issue, go to System Preferences -> Sharing -> Disable Airplay Receiver. -If you want to test new code you have written, you can rebuild Augur using: +If you want to test new code you have written, you can rebuild Augur using: .. code-block:: bash @@ -238,7 +240,7 @@ To enable log parsing for errors, you need to install `Elasticsearch `_ . diff --git a/docs/source/getting-started/new-install.rst b/docs/source/getting-started/new-install.rst index b10aa0b41e..2fe380993b 100644 --- a/docs/source/getting-started/new-install.rst +++ b/docs/source/getting-started/new-install.rst @@ -308,11 +308,17 @@ look like this: Installing and Configuring Augur! --------------------------------- -Create a Python Virtual Environment -``python3 -m venv ~/virtual-env-directory`` +We use `uv `_ to manage Augur’s virtual +environment and dependencies. Any time you run an Augur command, you should +prefix it with ``uv run`` to ensure you are using the correct virtual +environment. + +``uv`` can be installed with pip: + +.. code:: shell + + pip install --user uv -Activate your Python Virtual Environment -``source ~/virtual-env-directory/bin/activate`` From the root of the Augur Directory, type ``make install``. You will be prompted to provide: @@ -451,16 +457,16 @@ utility may change these characteristics. Augur Commands -------------- -To access command line options, use ``augur --help``. To load repos from +To access command line options, use ``uv run augur --help``. To load repos from GitHub organizations prior to collection, or in other ways, the direct -route is ``augur db --help``. +route is ``uv run augur db --help``. Start a Flower Dashboard, which you can use to monitor progress, and report any failed processes as issues on the Augur GitHub site. The error rate for tasks is currently 0.04%, and most errors involve unhandled platform API timeouts. We continue to identify and add fixes to handle these errors through additional retries. Starting Flower: -``(nohup celery -A augur.tasks.init.celery_app.celery_app flower --port=8400 --max-tasks=1000000 &)`` +``(nohup uv run celery -A augur.tasks.init.celery_app.celery_app flower --port=8400 --max-tasks=1000000 &)`` NOTE: You can use any open port on your server, and access the dashboard in a browser with http://servername-or-ip:8400 in the example above (assuming you have access to that port, and its open on your network.) @@ -474,7 +480,7 @@ disable Hyper-V, and afterward AVX should pass to the VM. Starting your Augur Instance ---------------------------- -Start Augur: ``(nohup augur backend start &)`` +Start Augur: ``(nohup uv run augur backend start &)`` When data collection is complete you will see only a single task running in your flower Dashboard. @@ -493,8 +499,8 @@ change that in augur_operations.config for OSX) Stopping your Augur Instance ---------------------------- -You can stop augur with ``augur backend stop``, followed by -``augur backend kill``. We recommend waiting 5 minutes between commands +You can stop augur with ``uv run augur backend stop``, followed by +``uv run augur backend kill``. We recommend waiting 5 minutes between commands so Augur can shutdown more gently. There is no issue with data integrity if you issue them seconds apart, its just that stopping is nicer than killing. diff --git a/scripts/control/rebuild-backend.sh b/scripts/control/rebuild-backend.sh index b537f3b9e9..956073fd33 100755 --- a/scripts/control/rebuild-backend.sh +++ b/scripts/control/rebuild-backend.sh @@ -10,7 +10,6 @@ fi target=${1-prod} -scripts/install/backend.sh $target scripts/install/workers.sh $target echo diff --git a/scripts/control/rebuild.sh b/scripts/control/rebuild.sh index 417a899883..acdb6d70a1 100755 --- a/scripts/control/rebuild.sh +++ b/scripts/control/rebuild.sh @@ -9,7 +9,6 @@ if [[ $? -ne 0 ]]; then fi -scripts/install/backend.sh scripts/install/workers.sh echo diff --git a/scripts/install/backend.sh b/scripts/install/backend.sh deleted file mode 100755 index 4d0e12a235..0000000000 --- a/scripts/install/backend.sh +++ /dev/null @@ -1,14 +0,0 @@ -#!/bin/bash -set -eo pipefail - -echo "Installing backend dependencies..." -echo "**********************************" -echo - -target=$1 - -if [[ $target == *"prod"* ]]; then - pip install . -else - pip install -e .[dev] -fi diff --git a/scripts/install/install.sh b/scripts/install/install.sh index 62e7f25067..9084ade044 100755 --- a/scripts/install/install.sh +++ b/scripts/install/install.sh @@ -23,9 +23,6 @@ else echo fi -scripts/install/backend.sh $target 2>&1 | tee logs/backend-install.log -echo "Done!" - scripts/install/workers.sh $target 2>&1 | tee logs/workers-install.log echo "Done!" @@ -168,5 +165,3 @@ echo "**********************************" # echo # fi # fi - - diff --git a/scripts/install/workers.sh b/scripts/install/workers.sh index e31fb07d32..d145888a2c 100755 --- a/scripts/install/workers.sh +++ b/scripts/install/workers.sh @@ -1,45 +1,11 @@ #!/bin/bash set -eo pipefail -echo "Installing workers and their dependencies..." +echo "Installing worker dependencies..." echo "**********************************" echo -target=$1 - -for WORKER in $(ls -d augur/tasks/data_analysis/*/) -do - if [[ \ - $WORKER != *"spdx_worker"* \ - && $WORKER != *"template_worker"* \ - && $WORKER != *"metric_status_worker"* \ - && $WORKER != *"__pycache__"* \ - && $WORKER != *"contributor_breadth_worker"* \ - ]]; then - - # make it pretty for formatting - FORMATTED_WORKER=$(basename $WORKER) - - echo - echo "**********************************" - echo "Installing $FORMATTED_WORKER..." - echo "**********************************" - echo - - cd $WORKER - rm -rf build/*; - rm -rf dist/*; - if [[ $target == *"prod"* ]]; then - pip install . - else - pip install -e .[dev] - fi - cd ../../../../ - fi - -done - -if [[ ! -z "$(which go)" ]]; then +if [[ -n "$(which go)" ]]; then echo "found go!" else echo "Installing go!" @@ -73,7 +39,7 @@ if [ -d "$SCORECARD_DIR" ]; then echo "ERROR: $PWD is not an existing scorecard directory" exit 127 fi - + git pull go mod tidy go build; From a45dff9195a235182f7543d23d1ff4e514e62435 Mon Sep 17 00:00:00 2001 From: John Strunk Date: Mon, 16 Jun 2025 16:42:30 -0400 Subject: [PATCH 12/66] Push the keyman container image Add keyman image and remove conditional login to GitHub Container Registry Signed-off-by: John Strunk --- .github/workflows/build_docker.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build_docker.yml b/.github/workflows/build_docker.yml index f99831da32..bb69ab9402 100644 --- a/.github/workflows/build_docker.yml +++ b/.github/workflows/build_docker.yml @@ -145,6 +145,7 @@ jobs: image: - backend - database + - keyman - rabbitmq runs-on: ubuntu-latest steps: @@ -157,7 +158,6 @@ jobs: - name: Login to GitHub Container Registry uses: docker/login-action@v3 - if: github.event_name != 'pull_request' with: registry: ghcr.io username: ${{ github.repository_owner }} From bc5bb745c5696cd1aa2eef859614af4217595226 Mon Sep 17 00:00:00 2001 From: John Strunk Date: Mon, 30 Jun 2025 14:01:53 -0400 Subject: [PATCH 13/66] Add macOS test job This adds a new test job to run on macOS. It installs the package dependencies and runs the worker setup script. Due to the interactive nature of `make install`, we can't use that directly. Signed-off-by: John Strunk --- .github/workflows/build_docker.yml | 38 ++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) diff --git a/.github/workflows/build_docker.yml b/.github/workflows/build_docker.yml index f99831da32..cdf54a35ab 100644 --- a/.github/workflows/build_docker.yml +++ b/.github/workflows/build_docker.yml @@ -13,6 +13,44 @@ on: permissions: {} jobs: + test-macos: + name: Test on macOS + runs-on: macos-latest + env: + UV_LOCKED: true # Assert that uv.lock is up-to-date + steps: + - name: Checkout repository + uses: actions/checkout@v4 + + - name: Install uv + uses: astral-sh/setup-uv@v6 + + - name: Set up Python + uses: actions/setup-python@v5 + with: + python-version-file: ".python-version" + + - name: Install Go + uses: actions/setup-go@v5 + with: + go-version: "stable" + + # We don't use `make install` because it requires user input + # Instead, we manually sync and run a subset of commands + - name: Install dependencies + run: uv sync --all-groups + + - name: Install workers + run: uv run scripts/install/workers.sh dev + + - name: Install nltk + run: | + uv run python -m nltk.downloader stopwords + uv run python -m nltk.downloader punkt + uv run python -m nltk.downloader popular + uv run python -m nltk.downloader universal_tagset + + test-e2e: name: End-to-end test runs-on: ubuntu-latest From 68431f1e3adb22cc756d1e7bf014b355edb41fd5 Mon Sep 17 00:00:00 2001 From: John Strunk Date: Mon, 30 Jun 2025 14:16:14 -0400 Subject: [PATCH 14/66] Upgrade xgboost to 3.0.2 This updates ugboost to fix the build on macos Signed-off-by: John Strunk --- pyproject.toml | 6 +- uv.lock | 1734 +++++++++++++++++++++--------------------------- 2 files changed, 767 insertions(+), 973 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 1f4d148b35..55b0593db7 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta" [project] name = "augur" -requires-python = ">=3.9" +requires-python = ">=3.10" 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Goggins" Date: Tue, 1 Jul 2025 19:01:30 -0500 Subject: [PATCH 16/66] Update nginx-configuration.rst We fixed some documentation around how `uv run` gets executed in sequence with `nohup` Signed-off-by: Sean P. Goggins --- docs/source/deployment/nginx-configuration.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/deployment/nginx-configuration.rst b/docs/source/deployment/nginx-configuration.rst index 7718a171b7..c4aa07c92d 100644 --- a/docs/source/deployment/nginx-configuration.rst +++ b/docs/source/deployment/nginx-configuration.rst @@ -31,7 +31,7 @@ Server Compilation } 2. Compile Augur (this wires the host and port into the frontend so people pulling the web pages of Augur, in the `frontend/` subdirectory are referring to the right endpoints for this instance.): ``make rebuild`` -3. Run Augur: ``nohup uv run augur backend start >augur.log 2>augur.err &`` +3. Run Augur: ``uv run nohup augur backend start >augur.log 2>augur.err &`` ------------------ From bc51a811024c02456af24ecdbc4cd2b8d1573f74 Mon Sep 17 00:00:00 2001 From: "Sean P. Goggins" Date: Tue, 1 Jul 2025 19:02:39 -0500 Subject: [PATCH 17/66] Update server-deployment.rst Changed `git checkout dev` to `git checkout main` in docs file. Signed-off-by: Sean P. Goggins --- docs/source/deployment/server-deployment.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/source/deployment/server-deployment.rst b/docs/source/deployment/server-deployment.rst index c510dfe5e3..c966594905 100644 --- a/docs/source/deployment/server-deployment.rst +++ b/docs/source/deployment/server-deployment.rst @@ -18,7 +18,7 @@ Detailed Steps 1. Login to your server. 2. If you have not already done so, clone Augur. 3. Change into that directory. -4. ``git checkout dev``, if you want to deploy the latest features, otherwise remain in the main branch. +4. ``git checkout main``, if you want to deploy the latest features, otherwise remain in the main branch. 5. You need a database owned by an Augur user. 6. ``make install`` ... now is a good time to go get some tea. 7. When you return with your tea, follow the prompts: @@ -56,6 +56,6 @@ For example, we set ours to ``test.augurlabs.io``. } } -11. Then do a ``make rebuild-dev``. +11. Then do a ``make rebuild``. Next up: configure ``nginx``! From 9aa9b43599a6cbce23556cf0ae4248ca93a98c83 Mon Sep 17 00:00:00 2001 From: "Sean P. Goggins" Date: Tue, 1 Jul 2025 19:03:33 -0500 Subject: [PATCH 18/66] Update collecting-data.rst Fixing `nohup` and `uv` order in docs. Signed-off-by: Sean P. Goggins --- docs/source/getting-started/collecting-data.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/getting-started/collecting-data.rst b/docs/source/getting-started/collecting-data.rst index 38e824870f..1ca39d6981 100644 --- a/docs/source/getting-started/collecting-data.rst +++ b/docs/source/getting-started/collecting-data.rst @@ -16,7 +16,7 @@ Now that you’ve installed Augur’s application server, it’s time to configu # Terminal Window 3 # To Start Augur: - (nohup uv run augur backend start) + (uv run nohup augur backend start) # To Stop Augur: uv run augur backend stop From f8adc95c141cc951ba5e7bf7aefdd44d46c84303 Mon Sep 17 00:00:00 2001 From: "Sean P. Goggins" Date: Tue, 1 Jul 2025 19:04:32 -0500 Subject: [PATCH 19/66] Update backend.rst Fixing `nohup` sequencing using `uv run` as tested. Signed-off-by: Sean P. Goggins --- docs/source/getting-started/command-line-interface/backend.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/getting-started/command-line-interface/backend.rst b/docs/source/getting-started/command-line-interface/backend.rst index c587ee241c..6f0f5826e0 100644 --- a/docs/source/getting-started/command-line-interface/backend.rst +++ b/docs/source/getting-started/command-line-interface/backend.rst @@ -56,7 +56,7 @@ To start the backend as a background process: .. code-block:: bash - nohup uv run augur backend start >logs/base.log 2>logs/base.err & + uv run nohup augur backend start >logs/base.log 2>logs/base.err & Successful output looks like the generation of standard Augur logfiles in the logs/ directory. From 195a7c07b38102ce3a7ed5a866e48581745ff869 Mon Sep 17 00:00:00 2001 From: "Sean P. Goggins" Date: Tue, 1 Jul 2025 19:06:02 -0500 Subject: [PATCH 20/66] Update backend.rst Fixed references to the `housekeeper` Signed-off-by: Sean P. Goggins --- .../source/getting-started/command-line-interface/backend.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/source/getting-started/command-line-interface/backend.rst b/docs/source/getting-started/command-line-interface/backend.rst index 6f0f5826e0..a6b3d84c2a 100644 --- a/docs/source/getting-started/command-line-interface/backend.rst +++ b/docs/source/getting-started/command-line-interface/backend.rst @@ -10,9 +10,9 @@ The ``augur backend`` CLI group is for controlling Augur's API server & data col ``start`` ============ -This command is for starting Augur's API server & (optionally) data collection workers. Example usages are shown below the parameters. After starting up, it will run indefinitely (but might not show any output, unless it's being queried or the housekeeper is working). +This command is for starting Augur's API server & (optionally) data collection workers. Example usages are shown below the parameters. After starting up, it will run indefinitely (but might not show any output, unless it's being queried or the data collection is working). ---disable-housekeeper Flag that turns off the housekeeper. Useful for testing the REST API or if you want to pause data collection without editing your config. +--disable-collection Flag that turns off the data collection. Useful for testing the REST API or if you want to pause data collection without editing your config. --skip-cleanup Flag that disables the old process cleanup that runs before Augur starts. Useful for Python scripts where Augur needs to be run in the background: see the `test/api/runner.py` file for an example. From 4a128161b7faecdfe8ff6ba1cf547302cb3f99f8 Mon Sep 17 00:00:00 2001 From: "Sean P. Goggins" Date: Tue, 1 Jul 2025 19:07:11 -0500 Subject: [PATCH 21/66] Update dev-osx-install.rst `nohup` ordering with `uv run` Signed-off-by: Sean P. Goggins --- docs/source/getting-started/dev-osx-install.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/source/getting-started/dev-osx-install.rst b/docs/source/getting-started/dev-osx-install.rst index 40f6e4e824..b899ac92ec 100644 --- a/docs/source/getting-started/dev-osx-install.rst +++ b/docs/source/getting-started/dev-osx-install.rst @@ -565,7 +565,7 @@ report any failed processes as issues on the Augur GitHub site. The error rate for tasks is currently 0.04%, and most errors involve unhandled platform API timeouts. We continue to identify and add fixes to handle these errors through additional retries. Starting Flower: -``(nohup uv run celery -A augur.tasks.init.celery_app.celery_app flower --port=8400 --max-tasks=1000000 &)`` +``(uv run nohup celery -A augur.tasks.init.celery_app.celery_app flower --port=8400 --max-tasks=1000000 &)`` NOTE: You can use any open port on your server, and access the dashboard in a browser with http://servername-or-ip:8400 in the example above (assuming you have access to that port, and its open on your network.) @@ -579,7 +579,7 @@ disable Hyper-V, and afterward AVX should pass to the VM. Starting your Augur Instance ---------------------------- -Start Augur: ``(nohup uv run augur backend start &)`` +Start Augur: ``(uv run nohup augur backend start &)`` When data collection is complete you will see only a single task running in your flower Dashboard. From 6e4ab16da385f135200cdab8af1f411d2dbb42c8 Mon Sep 17 00:00:00 2001 From: "Sean P. Goggins" Date: Tue, 1 Jul 2025 19:08:03 -0500 Subject: [PATCH 22/66] Update new-install.rst fixing `uv run` and `nohup` order in docs. Signed-off-by: Sean P. Goggins --- docs/source/getting-started/new-install.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/source/getting-started/new-install.rst b/docs/source/getting-started/new-install.rst index 2fe380993b..c472c7a920 100644 --- a/docs/source/getting-started/new-install.rst +++ b/docs/source/getting-started/new-install.rst @@ -466,7 +466,7 @@ report any failed processes as issues on the Augur GitHub site. The error rate for tasks is currently 0.04%, and most errors involve unhandled platform API timeouts. We continue to identify and add fixes to handle these errors through additional retries. Starting Flower: -``(nohup uv run celery -A augur.tasks.init.celery_app.celery_app flower --port=8400 --max-tasks=1000000 &)`` +``(uv run nohup celery -A augur.tasks.init.celery_app.celery_app flower --port=8400 --max-tasks=1000000 &)`` NOTE: You can use any open port on your server, and access the dashboard in a browser with http://servername-or-ip:8400 in the example above (assuming you have access to that port, and its open on your network.) @@ -480,7 +480,7 @@ disable Hyper-V, and afterward AVX should pass to the VM. Starting your Augur Instance ---------------------------- -Start Augur: ``(nohup uv run augur backend start &)`` +Start Augur: ``(uv run nohup augur backend start &)`` When data collection is complete you will see only a single task running in your flower Dashboard. From cb449d2f31632883a013f39e70df83e8dbc1dc54 Mon Sep 17 00:00:00 2001 From: Adrian Edwards Date: Wed, 25 Jun 2025 16:26:15 -0400 Subject: [PATCH 23/66] update docs refs in CONTRIBUTING Signed-off-by: Adrian Edwards --- CONTRIBUTING.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 6fed03731b..99d09cae9d 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -90,8 +90,8 @@ git push origin master ## Community Resources ### Augur -- [Stable documentation (`main` branch)](https://oss-augur.readthedocs.io/en/main/) -- [Nightly/developer build documentation (`dev` branch)](https://oss-augur.readthedocs.io/en/dev/) (warning: this is should be considered an unstable branch and should not be used for production) +- [Stable documentation (`release` branch)](https://oss-augur.readthedocs.io/en/release/) +- [Nightly/developer build documentation (`main` branch)](https://oss-augur.readthedocs.io/en/main/) (warning: this is should be considered an unstable branch and should not be used for production) - [Live Augur demo](https://ai.chaoss.io) ### CHAOSS From 43f07d2461e0a125e5a0f905260896fe4ef17379 Mon Sep 17 00:00:00 2001 From: Adrian Edwards Date: Wed, 25 Jun 2025 16:34:06 -0400 Subject: [PATCH 24/66] update badges Signed-off-by: Adrian Edwards --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 9567757aad..b8667a82fb 100644 --- a/README.md +++ b/README.md @@ -6,7 +6,7 @@ The primary way of looking at Augur data is through [8Knot](https://github.com/o [![first-timers-only](https://img.shields.io/badge/first--timers--only-friendly-blue.svg?style=flat-square)](https://www.firsttimersonly.com/) We follow the [First Timers Only](https://www.firsttimersonly.com/) philosophy of tagging issues for first timers only, and walking one newcomer through the resolution process weekly. You can find these issues tagged with [first timers only](https://github.com/chaoss/augur/labels/first-timers-only) on our issues list. -[![standard-readme compliant](https://img.shields.io/badge/standard--readme-OK-green.svg?style=flat-square)](https://github.com/RichardLitt/standard-readme) [![Build Docker images](https://github.com/chaoss/augur/actions/workflows/build_docker.yml/badge.svg)](https://github.com/chaoss/augur/actions/workflows/build_docker.yml) [![Hits-of-Code](https://hitsofcode.com/github/chaoss/augur?branch=main)](https://hitsofcode.com/github/chaoss/augur/view?branch=main) [![CII Best Practices](https://bestpractices.coreinfrastructure.org/projects/2788/badge)](https://bestpractices.coreinfrastructure.org/projects/2788) +[![standard-readme compliant](https://img.shields.io/badge/standard--readme-OK-green.svg?style=flat-square)](https://github.com/RichardLitt/standard-readme) [![Build Docker images](https://github.com/chaoss/augur/actions/workflows/build_docker.yml/badge.svg)](https://github.com/chaoss/augur/actions/workflows/build_docker.yml) [![Hits-of-Code](https://hitsofcode.com/github/chaoss/augur?branch=release)](https://hitsofcode.com/github/chaoss/augur/view?branch=release) [![CII Best Practices](https://bestpractices.coreinfrastructure.org/projects/2788/badge)](https://bestpractices.coreinfrastructure.org/projects/2788) ## NEW RELEASE ALERT! **If you want to jump right in, the updated docker, docker-compose and bare metal installation instructions are available [here](docs/new-install.md)**. From b3656b71beaca322e74ba0fdfa5ba0113d174478 Mon Sep 17 00:00:00 2001 From: Adrian Edwards Date: Wed, 25 Jun 2025 16:34:19 -0400 Subject: [PATCH 25/66] update some branch names Signed-off-by: Adrian Edwards --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index b8667a82fb..f494873148 100644 --- a/README.md +++ b/README.md @@ -11,10 +11,10 @@ We follow the [First Timers Only](https://www.firsttimersonly.com/) philosophy o ## NEW RELEASE ALERT! **If you want to jump right in, the updated docker, docker-compose and bare metal installation instructions are available [here](docs/new-install.md)**. -Augur is now releasing a dramatically improved new version to the ```main``` branch. It is also available [here](https://github.com/chaoss/augur/releases/tag/v0.89.3). +Augur is now releasing a dramatically improved new version. It is also available [here](https://github.com/chaoss/augur/releases/tag/v0.89.3). -- The `main` branch is a stable version of our new architecture, which features: +- The `release` branch is a stable version of our new architecture, which features: - Dramatic improvement in the speed of large scale data collection (100,000+ repos). All data is obtained for 100k+ repos within 2 weeks. - A new job management architecture that uses Celery and Redis to manage queues, and enables users to run a Flower job monitoring dashboard. - Materialized views to increase the snappiness of API’s and Frontends on large scale data. From c00361dbeab7496f4d3e465b14f9b9d25cc6e949 Mon Sep 17 00:00:00 2001 From: Adrian Edwards Date: Fri, 27 Jun 2025 15:17:56 -0400 Subject: [PATCH 26/66] add an outline for a procedures section of the docs Signed-off-by: Adrian Edwards --- docs/source/index.rst | 1 + docs/source/procedures/creating-releases.rst | 0 docs/source/procedures/toc.rst | 11 +++++++++++ 3 files changed, 12 insertions(+) create mode 100644 docs/source/procedures/creating-releases.rst create mode 100644 docs/source/procedures/toc.rst diff --git a/docs/source/index.rst b/docs/source/index.rst index 8ab9491d68..f6760617d7 100755 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -16,6 +16,7 @@ Welcome! docker/toc schema/toc login + procedures/toc .. library-documentation/toc .. diff --git a/docs/source/procedures/creating-releases.rst b/docs/source/procedures/creating-releases.rst new file mode 100644 index 0000000000..e69de29bb2 diff --git a/docs/source/procedures/toc.rst b/docs/source/procedures/toc.rst new file mode 100644 index 0000000000..4c1183da70 --- /dev/null +++ b/docs/source/procedures/toc.rst @@ -0,0 +1,11 @@ +==================================== +Augur Standard Operating Procedures +==================================== + +This section of the documentation is where the various procedures that help the project run smoothly are documented. If you are unsure of why we do things a certain way, or want to get more involved in the process of helping maintain Augur this may be the place for you. + + +.. toctree:: + :maxdepth: 1 + + creating-releases From 8e2d430c85492b04f35f78d993b3289591a7b2a4 Mon Sep 17 00:00:00 2001 From: Adrian Edwards Date: Fri, 27 Jun 2025 15:39:19 -0400 Subject: [PATCH 27/66] first pass at content for releases procedure document Signed-off-by: Adrian Edwards --- docs/source/procedures/creating-releases.rst | 38 ++++++++++++++++++++ 1 file changed, 38 insertions(+) diff --git a/docs/source/procedures/creating-releases.rst b/docs/source/procedures/creating-releases.rst index e69de29bb2..a142c822d2 100644 --- a/docs/source/procedures/creating-releases.rst +++ b/docs/source/procedures/creating-releases.rst @@ -0,0 +1,38 @@ +The Augur Release Process +========================= + + +Development: + +1. Developer (dev) creates a feature branch +2. dev creates PR proposing this against main +3. code gets reviewed (by humans and CI bots) + - DCO check, tests pass + - no merge commits present in the feature branch + - there are no dependent PRs that need to be merged first (enforced by a bot like mergify) +4. If the PR branch falls behind main [enough to create a merge conflict and/or at all(?)], the author should rebase it to resolve the conflict before merging (super simple cases can probably be resolved in the merge commit, but if its not an obvious resolution it probably requires deeper look in a better set of git tooling than GH's UI anyway) +5. If everything looks ok, merge gets approved and merges into main + + +Special case: Hotfixes +if the fix was a hotfix: +- changelog updates and other metadata changes should be included as part of the PR +- this is where mergeify or something helps re-create the PR targeting the release branch directly. at which point the release process is followed + + +Release process + +preparation + +when the next release is set to be cut (pre-release/release prep): +1. a PR is created to the main branch to update any applicable metadata (such as version information and Changelogs) + - if the fx being released is a hotfix, this will have been part of the hotfix PR itself +2. Once this metadata PR merges the preparation is complete for release + +release +1. a new PR is manually created from the main branch to the release branch +2. CI jobs are allowed to run to ensure that the merge didnt cause any issues + - this will likely be a faster human review since the changes already were thoroughly reviewed when they made it into main + - This is an opportunity for some additional, more stringent CI checks to run +3. once the PR is merged to the release branch, a tag is created for that commit, labeling it as the version being released + - This causes CI to build augur and push it to the registry From f15eb3fa1405ead9c83b6d47ee8d6cf2c7ef9829 Mon Sep 17 00:00:00 2001 From: Adrian Edwards Date: Fri, 27 Jun 2025 16:30:15 -0400 Subject: [PATCH 28/66] Second pass most sections are "done" except the "why" and "hotfixes" sections at the end Signed-off-by: Adrian Edwards --- docs/source/procedures/creating-releases.rst | 64 ++++++++++++-------- 1 file changed, 38 insertions(+), 26 deletions(-) diff --git a/docs/source/procedures/creating-releases.rst b/docs/source/procedures/creating-releases.rst index a142c822d2..24e645adb3 100644 --- a/docs/source/procedures/creating-releases.rst +++ b/docs/source/procedures/creating-releases.rst @@ -1,38 +1,50 @@ The Augur Release Process ========================= +The first step to releasing any changes is to have changes in the first place. +Augur's `CONTRIBUTING.md `__ file contains all the information that is needed to get started with topics like reporting issues, contributing code, and understanding the code review process. -Development: +This document outlines how these changes end up in an Augur release after they are merged into the `main` branch. -1. Developer (dev) creates a feature branch -2. dev creates PR proposing this against main -3. code gets reviewed (by humans and CI bots) - - DCO check, tests pass - - no merge commits present in the feature branch - - there are no dependent PRs that need to be merged first (enforced by a bot like mergify) -4. If the PR branch falls behind main [enough to create a merge conflict and/or at all(?)], the author should rebase it to resolve the conflict before merging (super simple cases can probably be resolved in the merge commit, but if its not an obvious resolution it probably requires deeper look in a better set of git tooling than GH's UI anyway) -5. If everything looks ok, merge gets approved and merges into main -Special case: Hotfixes -if the fix was a hotfix: -- changelog updates and other metadata changes should be included as part of the PR -- this is where mergeify or something helps re-create the PR targeting the release branch directly. at which point the release process is followed +Release workflow: +Starting after version 0.89.3, Augur follows a workflow similar to those you may already be familiar with (such as github flow and git flow). The Augur workflow has two long-lived branches, `main` and `release` and is designed such that changes only flow in one direction - from main into release. + +Branches + +`main` +The `main` branch is the primary development branch that is the target for all new pull requests. At any given point in time, this branch represents the best approximation of what the next upcoming release will look like. Since this is the active development branch, changes happen more frequently and this branch should be considered to be less stable than the `release` branch due to the possibility of breaking changes being made (and potentially reverted) between releases. It is not recommended for production deployment and is primarily intended for use by Augur contributors running their own copies against test data for development purposes. + +`release` +The `release` branch is where all augur versions (after 0.89.3) are tagged. Each commit on this branch represents either a hotfix to the prior release or a new major or minor version. + +Currently, Augur only officially supports the last-released version represented by the latest commit on the `release` branch. + +.. note:: + + If future needs require supporting multiple Augur versions concurrently, individual numbered release branches may be made from this central `release`` branch to allow any hotfixes to be applied to each supported version independently of the others. -Release process +The Release Process -preparation +When the next release is set to be cut, there are some preparation steps need to take place first, these include: +- Ensuring all features planned for that release are merged and any unrelated changes are delayed (as appropriate) until after the release. +- Creating a Pull Request to update any applicable metadata (such as version information and Changelogs) on the `main` branch. -when the next release is set to be cut (pre-release/release prep): -1. a PR is created to the main branch to update any applicable metadata (such as version information and Changelogs) - - if the fx being released is a hotfix, this will have been part of the hotfix PR itself -2. Once this metadata PR merges the preparation is complete for release +Once all release preparation has been completed, a new Pull Request can be created to merge the the main branch into the `release`` branch. This creates a final review opportunity and allows for another run of (potentially more stringent) CI jobs compared to those ran on `main` catching issues that may have come up throughout the various merges or in the process of preparing for release. -release -1. a new PR is manually created from the main branch to the release branch -2. CI jobs are allowed to run to ensure that the merge didnt cause any issues - - this will likely be a faster human review since the changes already were thoroughly reviewed when they made it into main - - This is an opportunity for some additional, more stringent CI checks to run -3. once the PR is merged to the release branch, a tag is created for that commit, labeling it as the version being released - - This causes CI to build augur and push it to the registry +After this PR is merged, a tag is created pointing to that commit on the `release` branch, effectively labeling it so that it can be returned to later if needed. This labeling process can also be the basis for additional CI jobs that build and upload the released code to distribution platforms such as Docker Hub or the GitHub Container Registry + + +Why? + +This is done to solve a number of problems: +- having changes moving in two directions at once (i.e. features coming from main, and hotfixes coming from release) was often confusing and increased the odds that a change would be missed, such as being shipped as a hotfix but not merged into the main codebase - leading to a regression in the next release. + + + +Special case: Hotfixes +if the fix was a hotfix: +- changelog updates and other metadata changes should be included as part of the PR +- this is where mergeify or something helps re-create the PR targeting the release branch directly. at which point the release process is followed From 706e5dcd217d096b0400e657be97979dbabaa5db Mon Sep 17 00:00:00 2001 From: John Strunk Date: Tue, 27 May 2025 14:34:27 -0400 Subject: [PATCH 29/66] Fix warnings/errors in docs Signed-off-by: John Strunk --- docs/source/conf.py | 5 +- .../source/deployment/nginx-configuration.rst | 6 +- docs/source/docker/docker.rst | 5 +- docs/source/docker/getting-started.rst | 41 ++-- docs/source/docker/toc.rst | 4 +- docs/source/getting-started/Welcome.rst | 63 ++--- docs/source/getting-started/database.rst | 2 + .../getting-started/dev-osx-install.rst | 2 - docs/source/getting-started/installation.rst | 34 +-- docs/source/getting-started/new-install.rst | 2 - docs/source/getting-started/using-docker.rst | 30 +-- docs/source/index.html | 1 - docs/source/index.rst | 28 +-- docs/source/login.rst | 4 +- docs/source/quick-start.rst | 4 - docs/source/schema/regularly_used_data.rst | 224 +++++++++--------- docs/source/schema/table_data.rst | 2 +- docs/source/schema/used_data.rst | 2 - docs/source/schema/working_tables.rst | 12 +- 19 files changed, 230 insertions(+), 241 deletions(-) delete mode 100644 docs/source/index.html delete mode 100644 docs/source/schema/used_data.rst diff --git a/docs/source/conf.py b/docs/source/conf.py index 548d6d450b..45966f19ec 100755 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -49,7 +49,6 @@ 'sphinx_rtd_theme', 'sphinxcontrib.openapi', 'sphinxcontrib.redoc', - 'sphinx.ext.autosectionlabel' ] redoc = [ @@ -96,7 +95,7 @@ # # This is also used if you do content translation via gettext catalogs. # Usually you set "language" from the command line for these cases. -language = None +language = "en" # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. @@ -193,4 +192,4 @@ # Example configuration for intersphinx: refer to the Python standard library. -intersphinx_mapping = {'https://docs.python.org/': None} +intersphinx_mapping = {'python': ('https://docs.python.org/3', None)} diff --git a/docs/source/deployment/nginx-configuration.rst b/docs/source/deployment/nginx-configuration.rst index c4aa07c92d..5abc030c65 100644 --- a/docs/source/deployment/nginx-configuration.rst +++ b/docs/source/deployment/nginx-configuration.rst @@ -155,13 +155,13 @@ HTTPS is an extension of HTTP. It is used for secure communications over a compu This guide will start on a fully configured EC2 Ubuntu 20.04 instance, meaning it is assumed to already have Augur installed and running with all of its dependencies(PostgreSQL, Nginx, etc). -~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~ Let's Encrypt/Certbot -~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~ The easiest way to get an HTTPS server up is to make use of `Let's Encrypt `_'s `Certbot `_ tool. It is an open source tool that is so good and it will even alter the nginx configuration for you automatically to enable HTTPS. Following their guide for ``Ubuntu 20.04``, run ``sudo snap install --classic certbot``, ``sudo ln -s /snap/bin/certbot /usr/bin/certbot``, and then ``sudo certbot --nginx``. -.. code-block:: bash +.. code-block:: text # Example Certificate Response Using Certbot diff --git a/docs/source/docker/docker.rst b/docs/source/docker/docker.rst index 60142122dc..65ddfe4d31 100644 --- a/docs/source/docker/docker.rst +++ b/docs/source/docker/docker.rst @@ -1,11 +1,11 @@ Docker Image Breakdown -================= +====================== Augur provides a separate Docker image for each layer of our application (database, backend, and frontend). This section details how to build and run these images locally for testing, and also describes how to set up our test environment using Docker. .. note:: - This page is primarily targeted at developers. + This page is primarily targeted at developers. Building the images -------------------- @@ -42,4 +42,3 @@ To start a container, use the command below. ```` can be whateve # in the root augur/ directory $ docker run -p : --name - diff --git a/docs/source/docker/getting-started.rst b/docs/source/docker/getting-started.rst index aa72dc4b97..e747bbb304 100644 --- a/docs/source/docker/getting-started.rst +++ b/docs/source/docker/getting-started.rst @@ -1,7 +1,7 @@ Getting Started ================ -For the Docker Savvy Who Want to Understand How the Sausage is Made: +For the Docker Savvy Who Want to Understand How the Sausage is Made: -------------------------------------------------------------------- Augur provides several Docker images designed to get you started with our software as quickly as possible. They are: @@ -21,17 +21,17 @@ The rest of this section of the documentation assumes you have a working install If you are less familiar with Docker, or experience issues you cannot resolve attempting our "quick start", please follow the instructions in this section, and the next few pages, to set up your environment. Docker Compose ------------- +-------------- For quickest start up, set up Docker or Podman desktop with a machine with roughly the following resources (or more): -- 8 CPUs +- 8 CPUs - 100 GB disk - 10 GB RAM -Clone the Augur repository and create a .env file in the top level directory -with the following fields: +Clone the Augur repository and create a .env file in the top level directory +with the following fields: .. code:: python @@ -46,38 +46,38 @@ with the following fields: Then run: -.. code:: shell +.. code:: shell + + docker compose up --build - docker compose up --build +or -or +.. code:: shell -.. code:: shell - - podman compose up --build + podman compose up --build -And augur should be up and running! +And augur should be up and running! Credentials ------------ -If you want to create a DB outside of using Docker/Podman Compose, you'll need to set up a PostgreSQL instance either locally or using a remote host. +If you want to create a DB outside of using Docker/Podman Compose, you'll need to set up a PostgreSQL instance either locally or using a remote host. .. note:: Make sure your database is configured to listen to all addresses to work with the containers while running locally. These settings can be edited in your ``postgresql.conf``. Additionally, edit the bottom section of your ``pg_hba.conf`` file with: - -.. code-block:: + +.. code-block:: # TYPE DATABASE USER ADDRESS METHOD host all all 0.0.0.0/0 md5 -If you're interested solely in data collection, we recommend using our test data with the Docker Compose script. This will start up the backend and frontend containers simultaneously, well as an optional database container; however, if you are looking to collect data long term, we **strongly suggest setting up a persistent database instance**; you can find instructions for doing so `here <../getting-started/database.html>`_. Remember to save off the credentials for your newly minted database; you'll need them shortly. +If you're interested solely in data collection, we recommend using our test data with the Docker Compose script. This will start up the backend and frontend containers simultaneously, well as an optional database container; however, if you are looking to collect data long term, we **strongly suggest setting up a persistent database instance**; you can find instructions for doing so `here <../getting-started/database.html>`_. Remember to save off the credentials for your newly minted database; you'll need them shortly. -If you don't care if your data doesn't get persisted or are doing local development, you can use the database containers we provide. +If you don't care if your data doesn't get persisted or are doing local development, you can use the database containers we provide. .. warning:: - There are conflicting opinions on using Docker for a production database. + There are conflicting opinions on using Docker for a production database. If you're more interested in doing local development, we recommend using our Docker testing environment image - more on that later. @@ -100,9 +100,9 @@ Your database credentials and other environment variables used at runtime are st You can provide your own ``.env`` file to pull from. The file should have the below format and set all the variables to some value. - .. code:: + .. code:: - AUGUR_GITHUB_API_KEY=xxxxxxxxxxxxxxxxxxxxxxx + AUGUR_GITHUB_API_KEY=xxxxxxxxxxxxxxxxxxxxxxx AUGUR_GITHUB_USERNAME=usernameGithub AUGUR_GITLAB_API_KEY=xxxxxxxxxxxxxxxxxxxxxxx AUGUR_GITLAB_USERNAME=usernameGitlab @@ -110,4 +110,3 @@ You can provide your own ``.env`` file to pull from. The file should have the be Now that you've created your config file or are ready to generate it yourself, you're ready to `get going `_ . - diff --git a/docs/source/docker/toc.rst b/docs/source/docker/toc.rst index 2fc42a4e9e..2ff55c7b56 100644 --- a/docs/source/docker/toc.rst +++ b/docs/source/docker/toc.rst @@ -7,7 +7,5 @@ Docker quick-start getting-started docker - docker compose + docker-compose usage - - diff --git a/docs/source/getting-started/Welcome.rst b/docs/source/getting-started/Welcome.rst index c26b871ca0..aaec004651 100644 --- a/docs/source/getting-started/Welcome.rst +++ b/docs/source/getting-started/Welcome.rst @@ -1,53 +1,56 @@ -Hi Newcomer! Welcome to CHAOSS! -=============== +================== CHAOSS is an open source community dedicated to creating software/metrics/programs that measures and maintains the overall health of open source community health. Health in the aspect of community engagement, good code metrics, inclusivity, etc. - -Now, as a new member, it can be overwhelming to navigate and sift through all that information -it was for me, so I’m writing this as a guide since the steps helped me out. I'm hoping it helps you and makes your onboarding a little easier. + +Now, as a new member, it can be overwhelming to navigate and sift through all that information -it was for me, so I'm writing this as a guide since the steps helped me out. I'm hoping it helps you and makes your onboarding a little easier. A few first things to do: -1) Join the slack channel, that's the fastest way to join and be a part of the community. +1. Join the slack channel, that's the fastest way to join and be a part of the community. + .. image:: images/slack.jpg - :width: 400 - :alt: "Slack image" + :width: 400 + :alt: "Slack logo" + +2. Introduce yourself to the #newcomers channel. Say hi, it'd help others get to know you and point you in the right direction. In case you're unsure, here's a format you can use: + + * Name + * If you're participating/contributing through an organization mention it here. + * What you think you'd like to contribute to + * Whatever other sentiments you'd like to add. -2) Introduce yourself to the #newcomers channel. Say hi, it’d help others get to know you and point you in the right direction. In case you’re unsure, here’s a format you can use: -· Name -· If you’re participating/contributing through an organization mention it here. -· What you think you’d like to contribute to -· Whatever other sentiments you’d like to add. -Example: Hi, my name is Precious Onyewuchi. I’m an outreachy intern contributing to the documentation. It’s super exciting to figure out the value I can get from being a member of this community and how much value I can contribute too. + Example: Hi, my name is Precious Onyewuchi. I'm an outreachy intern contributing to the documentation. It's super exciting to figure out the value I can get from being a member of this community and how much value I can contribute too. .. image:: images/chaoss_slack_workspace.png - :width: 400 - :alt: "Slack image" + :width: 400 + :alt: "Slack #newcomers channel" -This is a picture of my own introduction. Some parts of the image were blurred for privacy reasons + This is a picture of my own introduction. Some parts of the image were blurred for privacy reasons + +3. As a follow-up for number two (2), if you're contributing from a program (e.g Outreachy, or GSOC), find the respective channel for your program and join it. It'd be easier to get questions regarding that program answered and you can see other people like you in the same program to interact with and get help from. The channel for GSOC is #gsoc, and the channel for Outreachy is #outreachy, #general is for general questions and #augur is for stuff designated to augur, (e.g Installation (i figured that last part a little later. So, you're welcome!) -3) As a follow-up for number two (2), if you’re contributing from a program (e.g Outreachy, or GSOC), find the respective channel for your program and join it. It’d be easier to get questions regarding that program answered and you can see other people like you in the same program to interact with and get help from. The channel for GSOC is #gsoc, and the channel for Outreachy is #outreachy, #general is for general questions and #augur is for stuff designated to augur, (e.g Installation (i figured that last part a little later. So, you’re welcome!) .. image:: images/channels.PNG - :width: 400 - :alt: "Slack image" + :width: 400 + :alt: "Slack #newcomers channel" + +4. When in these channels, links to what is expected of you would be posted (it'd mostly lead to a Github repo). Read it carefully, and understand what is expected of you. The words in bold are important because as a new person, it's completely normal to get lost in the community and end up doing what isn't expected of you (i did it); especially for Outreachy and GSOC participants. Truth is, as much as the project is an interesting one and might make you have a bunch of interests you want to contribute to, your time as a contributor under these programs is limited, so for the duration of the program, you want to at least make sure you do what is expected of you. After the program, you can decide to fully be a contributor. -4) When in these channels, links to what is expected of you would be posted (it’d mostly lead to a Github repo). Read it carefully, and understand what is expected of you. The words in bold are important because as a new person, it’s completely normal to get lost in the community and end up doing what isn’t expected of you (i did it); especially for Outreachy and GSOC participants. Truth is, as much as the project is an interesting one and might make you have a bunch of interests you want to contribute to, your time as a contributor under these programs is limited, so for the duration of the program, you want to at least make sure you do what is expected of you. After the program, you can decide to fully be a contributor. .. image:: images/project_description.PNG - :width: 400 - :alt: "Slack image" ---------------------Picture of my cohort’s instructions----------------------- + :width: 400 + :alt: "Outreachy expectations" + +5. After understanding the expectations, try your best to do them. -5) After understanding the expectations, try your best to do them. .. image:: images/contribution.png - :width: 400 - :alt: "Slack image" ---------------------Pictures of expectations during my time.-------------------- + :width: 400 + :alt: "Outreachy project description" -6) The mentors are available to help you on the slack channels if you have any questions or there is some form of confusion. They might change at program intervals, but they’d definitely be communicated to you on the project description of your program page. Also, if you’re unsure, just ask your question on the Slack channel, someone will definitely give you an answer. +6. The mentors are available to help you on the slack channels if you have any questions or there is some form of confusion. They might change at program intervals, but they'd definitely be communicated to you on the project description of your program page. Also, if you're unsure, just ask your question on the Slack channel, someone will definitely give you an answer. Thank you, i hope this helps and makes your open source journey a little easier and more enjoyable! WELCOME TO CHAOSS!🎉 .. image:: images/chaoss.png - :width: 400 - :alt: "Slack image" \ No newline at end of file + :width: 400 + :alt: "CHAOSS logo" diff --git a/docs/source/getting-started/database.rst b/docs/source/getting-started/database.rst index 8eee00416a..42cf4b5a65 100644 --- a/docs/source/getting-started/database.rst +++ b/docs/source/getting-started/database.rst @@ -17,6 +17,8 @@ Before you can install our schema, you will need to make sure you have **write a If you're a newcomer to PostgreSQL, you can follow their excellent instructions `here `_ to set it up for your machine of choice. We recommend using ``Postgres.app`` if you're on macOS, but if you're running UNIX or are looking for an alternative to ``Postgres.app`` then pgAdmin is a great open-source alternative. +.. _Creating a Database: + Creating a Database ~~~~~~~~~~~~~~~~~~~~~ diff --git a/docs/source/getting-started/dev-osx-install.rst b/docs/source/getting-started/dev-osx-install.rst index b899ac92ec..dbb2dfd0de 100644 --- a/docs/source/getting-started/dev-osx-install.rst +++ b/docs/source/getting-started/dev-osx-install.rst @@ -535,8 +535,6 @@ Specifically, you may find this error in your augur logs: GRUB_DISABLE_OS_PROBER=true -.. _postgresql-configuration-1: - Postgresql Configuration ------------------------ diff --git a/docs/source/getting-started/installation.rst b/docs/source/getting-started/installation.rst index 25837e2b34..d2a79c4f71 100644 --- a/docs/source/getting-started/installation.rst +++ b/docs/source/getting-started/installation.rst @@ -30,7 +30,7 @@ Required: - `Python 3.6 - 3.8 `__ - + **Python 3.9 is not yet supported because TensorFlow, which we use in our machine learning workers, does not yet support Python 3.9.** Our REST API & data collection workers write in Python 3.6. We query the GitHub & GitLab API to collect data about issues, pull requests, contributors, and other information about a repository, so GitLab and GitHub access tokens are **required** for data collection. @@ -42,18 +42,18 @@ Optional: The ``value_worker`` uses a Go package called `scc `_ to run COCOMO calculations. Once you've installed Go, follow the appropriate steps for your system to install the ``scc`` package. -- Install gcc OpenMP Support: ``sudo apt-get install libgomp1`` -- Ubuntu +- Install gcc OpenMP Support: ``sudo apt-get install libgomp1`` -- Ubuntu The ``message_insights_worker`` uses a system-level package called OpenMP. You will need this installed at the system level for that worker to work. Caching System (Redis) ----------------- +---------------------- * `Linux Installation `__ * `Mac Installation `__ * `Windows Installation `__ Message Broker (RabbitMQ) ----------------- +------------------------- * `Linux Installation `__ * `Mac Installation `__ * `Windows Installation `__ @@ -74,7 +74,7 @@ After installation, you must also set up your rabbitmq instance by running the b it is important to have a static hostname when using rabbitmq as it uses hostname to communicate with nodes. -Then, start rabbitmq server with +Then, start rabbitmq server with .. code-block:: bash @@ -93,7 +93,7 @@ If you're interested in using our visualizations, you can optionally install the - `Node `__ - `npm `__ -- `Vue.js `__ +- `Vue.js `__ - `Vue-CLI `__ We use Vue.js as our frontend web framework and ``npm`` as our package manager. @@ -104,12 +104,12 @@ Visualization API calls On Ubuntu and other Linux flavors: if you want to use the new Augur API Calls that generate downloadable graphics developed in the `https://github.com/chaoss/augur-community-reports` repository, you need to install the `firefox-geckodriver` (on Ubuntu or Red Hat Fedora) or `geckodriver` on Mac OSX, at the system level. This dependency exists because the Bokeh libraries we use for these APIs require a web browser engine. -For Ubuntu you can use: +For Ubuntu you can use: .. code-block:: bash - which firefox-geckodriver - - if nothing returned, then: + - if nothing returned, then: - sudo apt install firefox-geckodriver For Fedora you can use @@ -117,10 +117,10 @@ For Fedora you can use .. code-block:: bash - which firefox-geckodriver - - if nothing returned, then: + - if nothing returned, then: - sudo dnf install firefox-geckodriver -For Mac OSX you can use: +For Mac OSX you can use: .. code-block:: bash @@ -129,13 +129,13 @@ For Mac OSX you can use: - brew install geckodriver .. note:: - If you have BOTH Firefox-geckodriver AND ChromeDriver installed the visualization API will not work. - - We have fully tested with Firefox-gecko driver on Linux platforms, and geckodriver on OSX. If you have ONLY ChromeDriver installed, it will probably work. Open an issue if you have a functioning ChromeDriver implementation. + If you have BOTH Firefox-geckodriver AND ChromeDriver installed the visualization API will not work. + + We have fully tested with Firefox-gecko driver on Linux platforms, and geckodriver on OSX. If you have ONLY ChromeDriver installed, it will probably work. Open an issue if you have a functioning ChromeDriver implementation. =================== -Installation +Installation =================== Now you're ready to build! The steps below outline how to create a virtual environment (**required**) and start the installation process, after which you'll move on to the next section to configure the workers. The instructions are written in a way that you can follow for your respective Operating System. @@ -155,7 +155,7 @@ If you’re running Augur on macOS, we strongly suggest updating your shell’s In a terminal, open the script: nano .bash_profile - + Add the following line to the end of the file: export OBJC_DISABLE_INITIALIZE_FORK_SAFETY=YES @@ -178,7 +178,7 @@ macOS takes "helpful" measures to prevent Python subprocesses (which Augur uses) General Augur Installation Steps (Irrespective of Operating System) --------------------------------------------------------------- +------------------------------------------------------------------- 1. Clone the repository and change to the newly-created directory. @@ -194,7 +194,7 @@ General Augur Installation Steps (Irrespective of Operating System) pip install --user uv -3. Set AUGUR_DB environment variable with a postgres database connection string (if you have not setup a database yet, refer to :ref:`database setup`) Note: Three terminals will be needed to collect data for augur, and AUGUR_DB needs to be set for 2 out of the 3. If you don't want to add it to both terminals you can add it permanently in your .bashrc file if running bash, or .zshrc file if in running zsh. +3. Set AUGUR_DB environment variable with a postgres database connection string (if you have not setup a database yet, refer to :ref:`database setup`) Note: Three terminals will be needed to collect data for augur, and AUGUR_DB needs to be set for 2 out of the 3. If you don't want to add it to both terminals you can add it permanently in your .bashrc file if running bash, or .zshrc file if in running zsh. .. code-block:: bash diff --git a/docs/source/getting-started/new-install.rst b/docs/source/getting-started/new-install.rst index c472c7a920..d51516c15a 100644 --- a/docs/source/getting-started/new-install.rst +++ b/docs/source/getting-started/new-install.rst @@ -436,8 +436,6 @@ Specifically, you may find this error in your augur logs: GRUB_DISABLE_OS_PROBER=true -.. _postgresql-configuration-1: - Postgresql Configuration ------------------------ diff --git a/docs/source/getting-started/using-docker.rst b/docs/source/getting-started/using-docker.rst index ce4e84032f..cc5e23896c 100644 --- a/docs/source/getting-started/using-docker.rst +++ b/docs/source/getting-started/using-docker.rst @@ -1,16 +1,16 @@ Docker Compose -=========== +============== For quickest start up, set up Docker or Podman desktop with a machine with roughly the following resources (or more). -- 8 CPUs +- 8 CPUs - 100 GB disk - 10 GB RAM 1. Clone the Augur repository https://github.com/chaoss/augur -2. Create a .env file in the top level directory with the following fields: +2. Create a .env file in the top level directory with the following fields: .. code:: python @@ -25,32 +25,32 @@ the following resources (or more). 3. Build the container using one of the following commands: -.. code:: shell +.. code:: shell - docker compose up --build + docker compose up --build or -.. code:: shell +.. code:: shell - podman compose up --build + podman compose up --build -And augur should be up and running! Over time, you may decide that you want to download and run newer releases of Augur. It is critical that your `.env` file remains configured to use the same database name and password; though you can change the password if you understand how to connect to a database running inside a Docker container on your computer. +And augur should be up and running! Over time, you may decide that you want to download and run newer releases of Augur. It is critical that your `.env` file remains configured to use the same database name and password; though you can change the password if you understand how to connect to a database running inside a Docker container on your computer. Rebuilding Augur in Docker ---------------------------- -We do not recommend running the augur database in a Docker container in production, though for light installations (~ < 2,000 repos) it is OK as long as you understand that your data exists inside of a Docker container, and you will **need to back that up** if you want to avoid data loss. +We do not recommend running the augur database in a Docker container in production, though for light installations (~ < 2,000 repos) it is OK as long as you understand that your data exists inside of a Docker container, and you will **need to back that up** if you want to avoid data loss. -You can identify the physical location of your Docker database file system using these commands: +You can identify the physical location of your Docker database file system using these commands: .. code:: shell docker volume ls docker volume inspect -For example: +For example: -.. code:: shell +.. code:: shell ➜ augur-demo git:(docker-docs-patch-12) ✗ docker volume inspect augur-demo_augurpostgres [ @@ -82,11 +82,11 @@ To rebuild a fresh Augur database in Docker, follow these steps: .. code:: shell - docker system prune -af - docker volume prune -af + docker system prune -af + docker volume prune -af 3. **Rebuild and start the containers**: .. code:: shell - docker compose up --build \ No newline at end of file + docker compose up --build diff --git a/docs/source/index.html b/docs/source/index.html deleted file mode 100644 index 8b13789179..0000000000 --- a/docs/source/index.html +++ /dev/null @@ -1 +0,0 @@ - diff --git a/docs/source/index.rst b/docs/source/index.rst index 8ab9491d68..bee404d52b 100755 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -1,13 +1,13 @@ Augur Documentation ================================== -Welcome! -~~~~~~~~ -~~~~~~~~ +:doc:`Welcome! ` +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. toctree:: :maxdepth: 2 + getting-started/Welcome quick-start deployment/toc getting-started/toc @@ -16,16 +16,16 @@ Welcome! docker/toc schema/toc login -.. +.. library-documentation/toc -.. +.. deployment/toc -.. +.. schema/toc .. image:: development-guide/images/augur-architecture-2.png :width: 700 - :alt: Development guide image overview of augur + :alt: Development guide image overview of augur What is Augur? @@ -33,14 +33,14 @@ What is Augur? Augur is a software suite for collecting and measuring structured data about free and open-source software (FOSS) communities. -Augur’s main focus is to measure the overall health and sustainability of open source projects, as these types of projects are system critical for nearly every software organization or company. We do this by gathering data about project repositories and normalizing that into our data model to provide useful metrics about your project’s health. For example, one of our metrics is Burstiness. Burstiness – how are short timeframes of intense activity, followed by a corresponding return to a typical pattern of activity, observed in a project? This can paint a picture of a project’s focus and gain insight into the potential stability of a project and how its typical cycle of updates occurs. There are many more useful metrics, and you can find a full list of them `here `_. +Augur's main focus is to measure the overall health and sustainability of open source projects, as these types of projects are system critical for nearly every software organization or company. We do this by gathering data about project repositories and normalizing that into our data model to provide useful metrics about your project's health. For example, one of our metrics is Burstiness. Burstiness - how are short timeframes of intense activity, followed by a corresponding return to a typical pattern of activity, observed in a project? This can paint a picture of a project's focus and gain insight into the potential stability of a project and how its typical cycle of updates occurs. There are many more useful metrics, and you can find a full list of them `here `__. Augur gathers trace data for a group of repositories, normalize it into our data model, and provide a variety of metrics about that data. -This software is developed as part of the CHAOSS (Community Health Analytics Open Source Software) project. Many of our metrics are implementations of the metrics defined by our community. You can find more information about how to get involved on the `CHAOSS website `_. +This software is developed as part of the CHAOSS (Community Health Analytics Open Source Software) project. Many of our metrics are implementations of the metrics defined by our community. You can find more information about how to get involved on the `CHAOSS website `_. -If you want to see augur in action, you can view CHAOSS’s augur instance `here `_. +If you want to see augur in action, you can view CHAOSS's augur instance `here `_. Current maintainers @@ -48,8 +48,8 @@ Current maintainers - `Derek Howard `_ - `Andrew Brain `_ - `Isaac Milarsky `_ -- `John McGinnes `_ -- `Sean P. Goggins `_ +- `John McGinnes `_ +- `Sean P. Goggins `_ @@ -77,13 +77,13 @@ GSoC 2022 participants - `Mabel F `_ - `Priya Srivastava `_ - `Ramya Kappagantu `_ -- `Yash Prakash `_ +- `Yash Prakash `__ GSoC 2021 participants ----------------------- - `Dhruv Sachdev `_ - `Rashmi K A `_ -- `Yash Prakash `_ +- `Yash Prakash `__ - `Anuj Lamoria `_ - `Yeming Gu `_ - `Ritik Malik `_ diff --git a/docs/source/login.rst b/docs/source/login.rst index f549751186..7bbf3a46f8 100644 --- a/docs/source/login.rst +++ b/docs/source/login.rst @@ -73,7 +73,7 @@ The Client Application must make the following request in order to facilitate th The authorization server will respond with the following on success: -.. code:: json +.. code:: text { "status": "Validated", @@ -107,7 +107,7 @@ The application may also attempt automatic reauthorization using the previously The authorization server will respond with the following on success: -.. code:: json +.. code:: text { "status": "Validated", diff --git a/docs/source/quick-start.rst b/docs/source/quick-start.rst index 9dbfb1cdcd..61615f7887 100644 --- a/docs/source/quick-start.rst +++ b/docs/source/quick-start.rst @@ -92,8 +92,6 @@ Specifically, you may find this error in your augur logs: GRUB_DISABLE_OS_PROBER=true -.. _postgresql-configuration-1: - Postgresql Configuration ------------------------ @@ -154,5 +152,3 @@ You can stop augur with ``augur backend stop``, followed by so Augur can shutdown more gently. There is no issue with data integrity if you issue them seconds apart, its just that stopping is nicer than killing. - - diff --git a/docs/source/schema/regularly_used_data.rst b/docs/source/schema/regularly_used_data.rst index 826b0c8200..bba90755cb 100644 --- a/docs/source/schema/regularly_used_data.rst +++ b/docs/source/schema/regularly_used_data.rst @@ -3,71 +3,71 @@ List of Regularly Used Data Tables In Augur **This is a list of data tables in augur that are regularly used and the various tasks attached to them.** -Commits +Commits ------- - This is where a record for every file in every commit in every repository in an Augur instance is kept. - - * Task: Facade tasks collect, and also stores platform user information in the commits table. - + This is where a record for every file in every commit in every repository in an Augur instance is kept. + + * Task: Facade tasks collect, and also stores platform user information in the commits table. + .. image:: images/commits.png :width: 200 Contributor_affiliations ------------------------ - A list of emails and domains, with start and end dates for individuals to have an organizational affiliation. - + A list of emails and domains, with start and end dates for individuals to have an organizational affiliation. + * Populated by default when augur is installed - * Can be edited so that an Augur instance can resolve a larger list of affiliations. - * These mappings are summarized in the dm_ tables. + * Can be edited so that an Augur instance can resolve a larger list of affiliations. + * These mappings are summarized in the ``dm_*`` tables. .. image:: images/contributor_affiliations.png :width: 200 -Contributor_repo ----------------- +Contributor_repo +----------------- + + Storage of a snowball sample of all the repositories anyone in your schema has accessed on GitHub. So, for example, if you wanted to know all the repositories that people on your project contributed to, this would be the table. - Storage of a snowball sample of all the repositories anyone in your schema has accessed on GitHub. So, for example, if you wanted to know all the repositories that people on your project contributed to, this would be the table. - * contributor_breadth_model populates this table - * Population of this table happens last, and can take a long time. + * Population of this table happens last, and can take a long time. .. image:: images/contributor_repo.png :width: 200 -Contributors ------------- +Contributors +------------- -These are all the contributors to a project/repo. In Augur, all types of contributions create a contributor record. This includes issue comments, pull request comments, label addition, etc. This is different than how GitHub counts contributors; they only include committers. - - * Tasks Adding Contributors: +These are all the contributors to a project/repo. In Augur, all types of contributions create a contributor record. This includes issue comments, pull request comments, label addition, etc. This is different than how GitHub counts contributors; they only include committers. + + * Tasks Adding Contributors: * Github Issue Tasks * Pull Request Tasks * GitLab Issue Tasks * GitLab Merge Request Tasks - * Facade Tasks + * Facade Tasks .. image:: images/contributors.png :width: 200 -Contributors_aliases +Contributors_aliases -------------------- - These are all the alternate emails that the same contributor might use. These records arise almost entirely from the commit log. For example, if I have two different emails on two different computers that I use when I make a commit, then an alias is created for whatever the 2nd to nth email Augur runs across. If a user’s email cannot be resolved, it is placed in the unresolved_commit_emails table. Coverage is greater than 98% since Augur 1.2.4. - - * Tasks: - + These are all the alternate emails that the same contributor might use. These records arise almost entirely from the commit log. For example, if I have two different emails on two different computers that I use when I make a commit, then an alias is created for whatever the 2nd to nth email Augur runs across. If a user's email cannot be resolved, it is placed in the unresolved_commit_emails table. Coverage is greater than 98% since Augur 1.2.4. + + * Tasks: + * Facade Tasks - + .. image:: images/contributors_aliases.png :width: 200 -Discourse_insights ------------------- +Discourse_insights +------------------- -There are nine specific discourse act types identified by the computational linguistic algorithm that underlies the discourse insights task. This task analyzes each comment on each issue or pull request sequentially so that context is applied when determining the discourse act type. These types are: +There are nine specific discourse act types identified by the computational linguistic algorithm that underlies the discourse insights task. This task analyzes each comment on each issue or pull request sequentially so that context is applied when determining the discourse act type. These types are: * negative-reaction * answer @@ -79,15 +79,15 @@ There are nine specific discourse act types identified by the computational ling * announcement * appreciation - * Tasks: - + * Tasks: + * Discourse Insights Task .. image:: images/discourse_insights.png :width: 200 -issue_assignees || issue_events || issue_labels ----------------------------------------------- +issue_assignees || issue_events || issue_labels +------------------------------------------------ * Task: * Github or Gitlab Issues Task @@ -95,8 +95,8 @@ issue_assignees || issue_events || issue_labels .. image:: images/issue_assignees.png :width: 200 -issue_message_ref ------------------ +issue_message_ref +------------------ A link between the issue and each message stored in the message table. @@ -107,32 +107,32 @@ issue_message_ref .. image:: images/issue_message_ref.png :width: 200 -issues +issues ------ Is all the data related to a GitHub Issue. - * Task: + * Task: * Github or Gitlab Issues Task .. image:: images/issues.png :width: 200 -Message +Message ------- Every pull request or issue related message. These are then mapped back to either pull requests, or issues, using the __msg_ref tables - + .. image:: images/message.png :width: 200 Message_analysis ---------------- - Two factors evaluated for every pull request on issues message: What is the sentiment of the message (positive or negative), and what is the novelty of the message in the context of other messages in that repository. + Two factors evaluated for every pull request on issues message: What is the sentiment of the message (positive or negative), and what is the novelty of the message in the context of other messages in that repository. - * Task: + * Task: * Message Insights Task @@ -140,21 +140,21 @@ Message_analysis :width: 200 Message_analysis_summary ----------------------- +------------------------ - A summary level representation of the granular data in message_analysis. + A summary level representation of the granular data in message_analysis. - * Task: - - * Message Insights Task + * Task: + + * Message Insights Task .. image:: images/message_analysis_summary.png :width: 200 Platform ---------- +-------- - Reference data with two rows: one for GitHub, one for GitLab. + Reference data with two rows: one for GitHub, one for GitLab. Pull_request_analysis @@ -162,41 +162,42 @@ Pull_request_analysis A representation of the probability of a pull request being merged into a repository, based on analysis of the properties of previously merged pull requests in a repository. (Machine learning tasks) - * Task: - + * Task: + * Pull request analysis task .. image:: images/pull_request_analysis.png :width: 200 -pull_request_assignees || pull_request_commits || pull_request_events || pull_request_files || pull_request_labels || pull_request_message_ref -------------------------------------------------------------- +pull_request_assignees || pull_request_commits || pull_request_events || pull_request_files || pull_request_labels || pull_request_message_ref +---------------------------------------------------------------------------------------------------------------------------------------------- All the data related to pull requests. Every pull request will be in the pull_requests data. .. image:: images/pull_request_assignees.png :width: 200 - + .. image:: images/pull_request_commits.png :width: 200 .. image:: images/pull_request_events.png :width: 200 - + .. image:: images/pull_request_files.png :width: 200 .. image:: images/pull_request_labels.png :width: 200 - .. image:: images/pull_request_ref.png + .. image:: images/pull_request_message_ref.png :width: 200 -pull_request_meta || pull_request_repo || pull_request_review_message_ref || pull_request_reviewers || pull_request_reviews || pull_request_teams || pull_requests -------------------------- +pull_request_meta || pull_request_repo || pull_request_review_message_ref || pull_request_reviewers || pull_request_reviews || pull_request_teams || pull_requests +------------------------------------------------------------------------------------------------------------------------------------------------------------------ + All the data related to pull requests. Every pull request will be in the pull_requests data. - .. image:: images/pull_request.png + .. image:: images/pull_requests.png :width: 200 .. image:: images/pull_request_meta.png @@ -220,11 +221,11 @@ pull_request_meta || pull_request_repo || pull_request_review_message_ref || pul Releases -------- - Github declared software releases or release tags. For example: https://github.com/chaoss/augur/releases + Github declared software releases or release tags. For example: https://github.com/chaoss/augur/releases + + * Task: - * Task: - - * Release Task. + * Release Task. .. image:: images/releases.png :width: 200 @@ -240,15 +241,15 @@ Repo Repo_badging ------------ - A list of CNCF badging information for a project. Reads this api endpoint: https://bestpractices.coreinfrastructure.org/projects.json - + A list of CNCF badging information for a project. Reads this api endpoint: https://bestpractices.coreinfrastructure.org/projects.json + Repo_cluster_messages --------------------- - Identifying which messages and repositories are clustered together. Identifies project similarity based on communication patterns. - - * Task: + Identifying which messages and repositories are clustered together. Identifies project similarity based on communication patterns. + + * Task: * Clustering task @@ -258,10 +259,10 @@ Repo_cluster_messages Repo_dependencies ----------------- - Enumerates every dependency, including dependencies that are not package managed. - - * Task: - + Enumerates every dependency, including dependencies that are not package managed. + + * Task: + * process_dependency_metrics .. image:: images/repo_dependencies.png @@ -270,43 +271,43 @@ Repo_dependencies Repo_deps_libyear ----------------- - (enumerates every package managed dependency) Looks up the latest release of any library that is imported into a project. Then it compares that release date, the release version of the library version in your project (and its release date), and calculates how old your version is, compared to the latest version. The resulting statistic is “libyear”. This task runs with the facade tasks, so over time, you will see if your libraries are being kept up to date, or not. + (enumerates every package managed dependency) Looks up the latest release of any library that is imported into a project. Then it compares that release date, the release version of the library version in your project (and its release date), and calculates how old your version is, compared to the latest version. The resulting statistic is “libyear”. This task runs with the facade tasks, so over time, you will see if your libraries are being kept up to date, or not. - * Scenarios: - * If a library is updated, but you didn’t change your version, the libyear statistic gets larger - * If you updated a library and it didn’t get older, the libyear statistic gets smaller. + * Scenarios: + * If a library is updated, but you didn't change your version, the libyear statistic gets larger + * If you updated a library and it didn't get older, the libyear statistic gets smaller. + + * Task: - * Task: - * process_libyear_dependency_metrics .. image:: images/repo_deps_libyear.png :width: 200 Repo_deps_scorecard ---------------- +------------------- - Runs the OSSF Scorecard over every repository ( https://github.com/ossf/scorecard ) : There are 16 factors that are explained at that repository location. + Runs the OSSF Scorecard over every repository ( https://github.com/ossf/scorecard ) : There are 16 factors that are explained at that repository location. - * Task: - - * process_ossf_scorecard_metrics + * Task: + + * process_ossf_scorecard_metrics .. image:: images/repo_deps_scorecard.png :width: 200 Repo_groups ---------- +----------- Reference data. The repo groups in an augur instance. - + .. image:: images/repo_groups.png :width: 200 Repo_info --------- - This task gathers metadata from the platform API that includes things like “number of stars”, “number of forks”, etc. AND it also gives us : Number of issues, number of pull requests, etc. .. THAT information we use to determine if we have collected all of the PRs and Issues associated with a repository. + This task gathers metadata from the platform API that includes things like “number of stars”, “number of forks”, etc. AND it also gives us : Number of issues, number of pull requests, etc. .. THAT information we use to determine if we have collected all of the PRs and Issues associated with a repository. * Task: @@ -315,45 +316,44 @@ Repo_info .. image:: images/repo_info.png :width: 200 -Repo_insights ------------ +Repo_insights +------------- + + * Task: - * Task: - * Insight task .. image:: images/repo_insights.png :width: 200 Repo_insights_records ----------- +--------------------- + + * Task: - * Task: - * Insight task .. image:: images/repo_insights_records.png :width: 200 - Repo_meta --------- - Exists to capture repo data that may be useful in the future. Not currently populated. + Exists to capture repo data that may be useful in the future. Not currently populated. .. image:: images/repo_meta.png :width: 200 Repo_sbom_scans ------------ +--------------- + + This table links the augur_data schema to the augur_spdx schema to keep a list of repositories that need licenses scanned. (These are for file level license declarations, which are common in Linux Foundation projects, but otherwise not in wide use). - This table links the augur_data schema to the augur_spdx schema to keep a list of repositories that need licenses scanned. (These are for file level license declarations, which are common in Linux Foundation projects, but otherwise not in wide use). - .. image:: images/repo_sbom_scans.png :width: 200 Repo_stats ---------- +---------- Exists to capture repo data that may be useful in the future. Not currently populated. @@ -361,37 +361,37 @@ Repo_stats :width: 200 Repo_topic -------- +---------- - Identifies probable topics of conversation in discussion threads around issues and pull requests. + Identifies probable topics of conversation in discussion threads around issues and pull requests. - * Task: - - * Clustering task + * Task: + + * Clustering task .. image:: images/repo_topic.png :width: 200 Topic_words ---------- +----------- - Unigrams, bigrams, and trigrams associated with topics in the repo_topic table. + Unigrams, bigrams, and trigrams associated with topics in the repo_topic table. - * Task: + * Task: * Clustering task .. image:: images/topic_words.png :width: 200 -Unresolved_commit_emails ------------------------ +Unresolved_commit_emails +------------------------ + + Emails from commits that were not initially able to be resolved using automated mechanisms. - Emails from commits that were not initially able to be resolved using automated mechanisms. + * Task: - * Task: - - * Facade Tasks. + * Facade Tasks. .. image:: images/unresolved_commit_emails.png :width: 200 diff --git a/docs/source/schema/table_data.rst b/docs/source/schema/table_data.rst index 6ecafbd562..2eae707bb1 100644 --- a/docs/source/schema/table_data.rst +++ b/docs/source/schema/table_data.rst @@ -1,5 +1,5 @@ Descriptions of Tables & Purposes -============================== +================================= .. toctree:: :maxdepth: 2 diff --git a/docs/source/schema/used_data.rst b/docs/source/schema/used_data.rst deleted file mode 100644 index 7956826548..0000000000 --- a/docs/source/schema/used_data.rst +++ /dev/null @@ -1,2 +0,0 @@ -List of Used Data Tables In Augur -=================================== \ No newline at end of file diff --git a/docs/source/schema/working_tables.rst b/docs/source/schema/working_tables.rst index ffd3b2c08d..381c231406 100644 --- a/docs/source/schema/working_tables.rst +++ b/docs/source/schema/working_tables.rst @@ -1,13 +1,13 @@ List of Working Data Tables In Augur -=================================== +==================================== **This Is A List of Working Tables In Augur and The Tasks Attached to Them.** They are in lowercase to represent exactly how they look like on the actual table. * analysis_log - this table is a record of the analysis steps the facade tasks have taken on an augur instance. A listing of all the analysis steps taken for every repository is recorded as they are completed. - - * Tasks Associated With It? + + * Tasks Associated With It? * Facade Tasks @@ -19,14 +19,14 @@ List of Working Data Tables In Augur .. image:: images/commit_parents.png :width: 200 - Other working tables are: + Other working tables are: - * exclude + * exclude .. image:: images/exclude.png :width: 200 * repos_fetch_log - + .. image:: images/repos_fetch_log.png :width: 200 From a20aa6962145cd646b7ab62ff5d9cd084c262085 Mon Sep 17 00:00:00 2001 From: John Strunk Date: Wed, 11 Jun 2025 15:47:23 -0400 Subject: [PATCH 30/66] Add docs check Added a new job to check if documentation builds cleanly, using sphinx- build with extra options to ensure all documentation is generated correctly. Signed-off-by: John Strunk --- .github/workflows/checks.yml | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/.github/workflows/checks.yml b/.github/workflows/checks.yml index 0163ea755c..8b2606fbf0 100644 --- a/.github/workflows/checks.yml +++ b/.github/workflows/checks.yml @@ -4,6 +4,17 @@ on: branches: [main, release] jobs: + check-docs: + name: runner / check docs + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v2 + - name: Install uv + uses: astral-sh/setup-uv@v6 + - name: Ensure docs build cleanly + # Setting `O` to pass extra options to the sphinx-build command. + run: O="-a -E -n -W --keep-going" make docs + run-pylint: name: runner / pylint permissions: write-all From 8acb61cb18c58f36852c05cf87a409b5019e22f6 Mon Sep 17 00:00:00 2001 From: John Strunk Date: Wed, 11 Jun 2025 16:00:58 -0400 Subject: [PATCH 31/66] Fix trailing whitespace Signed-off-by: John Strunk --- .../source/deployment/nginx-configuration.rst | 2 +- docs/source/deployment/server-deployment.rst | 22 +++++----- docs/source/deployment/toc.rst | 7 +--- docs/source/development-guide/cli.rst | 6 +-- .../configuration-file-reference.rst | 4 +- .../create-a-metric/api-development.rst | 41 +++++++++---------- .../create-a-metric/metrics-steps.rst | 36 ++++++++-------- .../development-guide/create-a-metric/toc.rst | 2 +- .../development-guide/documentation.rst | 2 +- .../development-guide/make/development.rst | 6 +-- .../development-guide/make/documentation.rst | 2 +- .../source/development-guide/make/testing.rst | 2 +- docs/source/development-guide/make/toc.rst | 2 +- docs/source/development-guide/testing/toc.rst | 2 +- docs/source/development-guide/toc.rst | 3 -- .../workers/clustering_worker.rst | 2 +- .../workers/creating_a_new_worker.rst | 24 +++++------ .../workers/discourse_analysis_worker.rst | 4 +- .../workers/insight_worker.rst | 34 +++++++-------- .../workers/message_insights_worker.rst | 10 ++--- .../workers/pull_request_analysis_worker.rst | 4 +- docs/source/docker/docker-compose.rst | 12 +++--- docs/source/docker/quick-start.rst | 39 +++++++++--------- docs/source/docker/usage.rst | 1 - .../getting-started/collecting-data.rst | 6 +-- .../command-line-interface/backend.rst | 6 +-- .../command-line-interface/db.rst | 8 ++-- docs/source/getting-started/database.rst | 6 +-- .../getting-started/dev-osx-install.rst | 24 +++++------ docs/source/getting-started/frontend.rst | 8 ++-- docs/source/getting-started/new-install.rst | 24 +++++------ docs/source/quick-start.rst | 2 +- docs/source/schema/commits.rst | 2 +- docs/source/schema/contributors.rst | 2 +- docs/source/schema/dependencies.rst | 4 +- docs/source/schema/issues.rst | 2 +- docs/source/schema/overview.rst | 8 ++-- docs/source/schema/pull-requests.rst | 2 +- docs/source/schema/toc.rst | 2 - docs/source/schema/unused_data.rst | 8 ++-- 40 files changed, 186 insertions(+), 197 deletions(-) diff --git a/docs/source/deployment/nginx-configuration.rst b/docs/source/deployment/nginx-configuration.rst index 5abc030c65..6247f5f065 100644 --- a/docs/source/deployment/nginx-configuration.rst +++ b/docs/source/deployment/nginx-configuration.rst @@ -146,7 +146,7 @@ This file will be located in the ``/etc/nginx/sites-enabled`` directory on most access_log /var/log/nginx/augur.censusscienceosshealth.access.log; } - + -------------------- Enabling HTTPS -------------------- diff --git a/docs/source/deployment/server-deployment.rst b/docs/source/deployment/server-deployment.rst index c966594905..922f126d33 100644 --- a/docs/source/deployment/server-deployment.rst +++ b/docs/source/deployment/server-deployment.rst @@ -3,13 +3,13 @@ Setting up an Augur Server --------------------------- -High-Level Steps to Server Installation of Augur +High-Level Steps to Server Installation of Augur ------------------------------------------------ -1. Have a list of repositories and groups you want them to be in, following the format in the files `schema/repo_group_load_sample.csv` and `schema/repo_load_sample.csv`. +1. Have a list of repositories and groups you want them to be in, following the format in the files `schema/repo_group_load_sample.csv` and `schema/repo_load_sample.csv`. 2. Have access to a server that meets the augur installation pre-requisites (Python, NodeJS, etc). 3. Have nginx installed for front-end service. You can use another HTTP server, but we have instructions for nginx. -4. Make sure you have a database available, owned by a user who has the right to create tables. +4. Make sure you have a database available, owned by a user who has the right to create tables. 5. Have a GitHub API Key handy. Detailed Steps @@ -18,18 +18,18 @@ Detailed Steps 1. Login to your server. 2. If you have not already done so, clone Augur. 3. Change into that directory. -4. ``git checkout main``, if you want to deploy the latest features, otherwise remain in the main branch. -5. You need a database owned by an Augur user. +4. ``git checkout main``, if you want to deploy the latest features, otherwise remain in the main branch. +5. You need a database owned by an Augur user. 6. ``make install`` ... now is a good time to go get some tea. -7. When you return with your tea, follow the prompts: - - respond to the SERVER prompt with localhost. +7. When you return with your tea, follow the prompts: + - respond to the SERVER prompt with localhost. - the current standard is to put the repos in a repos/ directory in the root augur directory (these will never get checked in to VC). 8. Load repos, following instructions in docs. 9. If you have more than one instance of Augur or another service on port 5000, you need to edit the ``augur.config.json`` to update the server port: - ``sudo lsof -i -P -n | grep LISTEN`` shows you ports in use if you are not sure. - ``sudo ufw status`` lets you know if the port you are looking for is available as open through your firewall. - ``sudo ufw status | grep 5005`` checks to see if port 5005 is open, for example: - + +---------------+--------+---------------------------------------------+ | 5005 | ALLOW | Anywhere (this line is the most important) | +---------------+--------+---------------------------------------------+ @@ -43,8 +43,8 @@ Detailed Steps +---------------+--------+---------------------------------------------+ | 5005/udp (v6) | ALLOW | Anywhere (v6) | +---------------+--------+---------------------------------------------+ - -10. In the Frontend block of ``augur.config.json``, set the host value to be the domain you want the front end compiled for. + +10. In the Frontend block of ``augur.config.json``, set the host value to be the domain you want the front end compiled for. For example, we set ours to ``test.augurlabs.io``. .. code-block:: json @@ -53,7 +53,7 @@ For example, we set ours to ``test.augurlabs.io``. "Frontend": { "host": "test.augurlabs.io", "port": "5003" - } + } } 11. Then do a ``make rebuild``. diff --git a/docs/source/deployment/toc.rst b/docs/source/deployment/toc.rst index a6bda24ff7..2474aa0664 100644 --- a/docs/source/deployment/toc.rst +++ b/docs/source/deployment/toc.rst @@ -1,7 +1,7 @@ -Deployment +Deployment ================ -This section details describes production deployment of Augur. +This section details describes production deployment of Augur. .. toctree:: @@ -16,6 +16,3 @@ This section details describes production deployment of Augur. If you have questions or would like to help please open an issue on GitHub_. .. _GitHub: https://github.com/chaoss/augur - - - diff --git a/docs/source/development-guide/cli.rst b/docs/source/development-guide/cli.rst index 49348d9518..3ead5e70d4 100644 --- a/docs/source/development-guide/cli.rst +++ b/docs/source/development-guide/cli.rst @@ -1,7 +1,7 @@ CLI (Command Line Interface) =============================== -To learn what's available in Augur's command line interface (CLI), simply use this set of commands: +To learn what's available in Augur's command line interface (CLI), simply use this set of commands: .. code-block:: bash @@ -9,8 +9,8 @@ To learn what's available in Augur's command line interface (CLI), simply use th augur db --help augur backend --help augur config --help - augur logging --help + augur logging --help If you have questions or would like to help please open an issue on GitHub_. -.. _GitHub: https://github.com/chaoss/augur/issues \ No newline at end of file +.. _GitHub: https://github.com/chaoss/augur/issues diff --git a/docs/source/development-guide/configuration-file-reference.rst b/docs/source/development-guide/configuration-file-reference.rst index 6e9a10e021..48c5cd1576 100644 --- a/docs/source/development-guide/configuration-file-reference.rst +++ b/docs/source/development-guide/configuration-file-reference.rst @@ -1,8 +1,8 @@ Configuration file reference =============================== -Augur's configuration template file, which generates your locally deployed ``augur.config.json`` file, is found at ``augur/config.py``. You will notice a small collection of workers are turned on to start with, by examining the ``switch`` variable within the ``Workers`` block of the config file. You can also specify the number of processes to spawn for each worker using the ``workers`` command. The default is one, and we recommend you start here. If you are going to spawn multiple workers, be sure you have enough credentials cached in the ``augur_operations.worker_oath`` table for the platforms you use. +Augur's configuration template file, which generates your locally deployed ``augur.config.json`` file, is found at ``augur/config.py``. You will notice a small collection of workers are turned on to start with, by examining the ``switch`` variable within the ``Workers`` block of the config file. You can also specify the number of processes to spawn for each worker using the ``workers`` command. The default is one, and we recommend you start here. If you are going to spawn multiple workers, be sure you have enough credentials cached in the ``augur_operations.worker_oath`` table for the platforms you use. If you have questions or would like to help please open an issue on GitHub_. -.. _GitHub: https://github.com/chaoss/augur/issues \ No newline at end of file +.. _GitHub: https://github.com/chaoss/augur/issues diff --git a/docs/source/development-guide/create-a-metric/api-development.rst b/docs/source/development-guide/create-a-metric/api-development.rst index 039f308df7..834b42e8e0 100644 --- a/docs/source/development-guide/create-a-metric/api-development.rst +++ b/docs/source/development-guide/create-a-metric/api-development.rst @@ -2,25 +2,25 @@ Parts of an Augur API Endpoint ===================================== 1. Develop the query that will produce data needed to deliver the endpoint, usually parameterized by a `repo_id`. -2. Determine if the endpoint will be a "standard endpoint", or a custom endpoint. +2. Determine if the endpoint will be a "standard endpoint", or a custom endpoint. -Where Are the Endpoints? +Where Are the Endpoints? --------------------------- -JSON Metrics are here: +JSON Metrics are here: .. code-block:: bash $ AUGUR_HOME/augur/metrics -Visualization Metrics are here: +Visualization Metrics are here: .. code-block:: bash $ AUGUR_HOME/augur/routes -Existing metrics files (JSON Metric) "Standard Metrics": +Existing metrics files (JSON Metric) "Standard Metrics": --------------------------------------------------------- 1. commit.py @@ -31,41 +31,41 @@ Existing metrics files (JSON Metric) "Standard Metrics": 6. message.py 7. platform.py 8. release.py -9. repo_meta.py +9. repo_meta.py All "Standard Metrics" files generally share a set of imports -.. code-block:: python +.. code-block:: python import datetime import sqlalchemy as s import pandas as pd from augur.util import register_metric -You can see that one of the imports is our standard metric import from the util file, which is located in: +You can see that one of the imports is our standard metric import from the util file, which is located in: -.. code-block:: python +.. code-block:: python AUGUR_HOME/augur/routes/util.py All "Standard Metrics" share declaration and a method signature -Declaration: +Declaration: -.. code-block:: python +.. code-block:: python @register_metric() -Method Signature: +Method Signature: -.. code-block:: python +.. code-block:: python def contributors(self, repo_group_id, repo_id=None, period='day', begin_date=None, end_date=None): -Standard metrics also, generally, include default setting blocks for date range, in the event parameters are not passed. +Standard metrics also, generally, include default setting blocks for date range, in the event parameters are not passed. -.. code-block:: python +.. code-block:: python if not begin_date: begin_date = '1970-1-1 00:00:01' @@ -74,7 +74,7 @@ Standard metrics also, generally, include default setting blocks for date range, There is also, generally, a block in a standard metric for pulling data by a repo_id or a repo_group_id. The default is a repo_group_id. Here is an abrdiged example from the contributors endpoint in `contributor.py` -.. code-block:: python +.. code-block:: python if repo_id: contributorsSQL = s.sql.text(""" @@ -133,12 +133,12 @@ There is also, generally, a block in a standard metric for pulling data by a rep 'begin_date': begin_date, 'end_date': end_date}) return results -Existing Visualization Metrics Files: +Existing Visualization Metrics Files: -------------------------------------------- 1. augur/routes/contributor_reports.py 2. augur/routes/pull_request_reports.py -Existing Metrics Files: +Existing Metrics Files: -------------------------------------------- 1. augur/metrics/commit.py @@ -151,8 +151,7 @@ Existing Metrics Files: 8. augur/metrics/platform.py 9. augur/metrics/pull_request.py 10. augur/metrics/release.py -11. augur/metrics/repo_meta.py +11. augur/metrics/repo_meta.py -These files are not intended to be all inclusive. Rather, they are what we have developed, or imagined, based on existing CHAOSS metrics to date. New CHAOSS metrics are likely to result in the inclusion of new files under metrics, or routes, depending if they are standard metrics or not. - +These files are not intended to be all inclusive. Rather, they are what we have developed, or imagined, based on existing CHAOSS metrics to date. New CHAOSS metrics are likely to result in the inclusion of new files under metrics, or routes, depending if they are standard metrics or not. diff --git a/docs/source/development-guide/create-a-metric/metrics-steps.rst b/docs/source/development-guide/create-a-metric/metrics-steps.rst index fe0138871c..ab6bda8ef5 100644 --- a/docs/source/development-guide/create-a-metric/metrics-steps.rst +++ b/docs/source/development-guide/create-a-metric/metrics-steps.rst @@ -5,39 +5,39 @@ Steps to Create a Metric API Endpoint Summary --------------------------------------------------------------------------- -There are many paths, but we usually follow something along these lines: +There are many paths, but we usually follow something along these lines: -1. What is the CHAOSS metric we want to develop? +1. What is the CHAOSS metric we want to develop? 2. Sometimes, there are metrics endpoints that integrate, or visualize several metrics. 3. Determine what tables in the Augur Schema contain the data we need to develop this metric 4. Construct a very basic query that does the work of joining those tables in a minimal way so we have a "baseline query." 5. Refine the query so that it takes the standard inputs for a "standard metric" if that's what type it is; alternatively, look at non-standard metrics as they are defined in ``AUGUR_HOME/augur/routes``, or one of the visualization metrics in ``AUGUR_HOME/augur/routes/contributor.py``, ``AUGUR_HOME/augur/routes/pull_requests.py`` or ``AUGUR_HOME/augur/routes/nonstandard_metrics.py``. (This step is explained in the next section.) -Example Query +Example Query --------------------------------------------------------------------- This is an example query to Get Us Started on a Labor Effort and Cost Endpoint. -1. What tables? +1. What tables? -.. code-block:: python +.. code-block:: python repo repo_group -If we look at the Augur Schema, we can see that effort and cost are contained in the ``repo_labor`` table. +If we look at the Augur Schema, we can see that effort and cost are contained in the ``repo_labor`` table. -2. What might our initial query to explore building the endpoint be? +2. What might our initial query to explore building the endpoint be? -.. code-block:: sql +.. code-block:: sql SELECT C.repo_id, C.repo_name, programming_language, SUM ( estimated_labor_hours ) AS labor_hours, SUM ( estimated_labor_hours * 50 ) AS labor_cost, - analysis_date + analysis_date FROM ( SELECT A @@ -50,33 +50,33 @@ If we look at the Augur Schema, we can see that effort and cost are contained in SUM ( blank_lines ) AS repo_blank_lines, AVG ( code_complexity ) AS repo_lang_avg_code_complexity, AVG ( code_complexity ) * SUM ( code_lines ) + 20 AS estimated_labor_hours, - MAX ( A.rl_analysis_date ) AS analysis_date + MAX ( A.rl_analysis_date ) AS analysis_date FROM repo_labor A, - repo b + repo b WHERE - A.repo_id = b.repo_id + A.repo_id = b.repo_id GROUP BY A.repo_id, programming_language, - repo_name + repo_name ORDER BY repo_name, A.repo_id, - programming_language - ) C + programming_language + ) C GROUP BY repo_id, repo_name, programming_language, - C.analysis_date + C.analysis_date ORDER BY repo_id, programming_language; 3. Over time, as CHAOSS develops a metric for labor investment, the way we calculate hours, and cost in this query will adapt to whatever the CHAOSS community determines is an apt formula. -4. We will fit this metric into one of the different types of metric API Endpoints discussed in the next section. +4. We will fit this metric into one of the different types of metric API Endpoints discussed in the next section. .. note:: - Augur uses https://github.com/boyter/scc to calculate information contained in the ``labor_value`` table, which is populated by the ``value_worker`` tasks. + Augur uses https://github.com/boyter/scc to calculate information contained in the ``labor_value`` table, which is populated by the ``value_worker`` tasks. diff --git a/docs/source/development-guide/create-a-metric/toc.rst b/docs/source/development-guide/create-a-metric/toc.rst index 0b99bc265c..48c9915443 100644 --- a/docs/source/development-guide/create-a-metric/toc.rst +++ b/docs/source/development-guide/create-a-metric/toc.rst @@ -10,6 +10,6 @@ If you have questions or would like to help please open an issue on GitHub_. .. toctree:: :maxdepth: 1 - + metrics-steps api-development diff --git a/docs/source/development-guide/documentation.rst b/docs/source/development-guide/documentation.rst index 59f17427c0..bfecd56117 100644 --- a/docs/source/development-guide/documentation.rst +++ b/docs/source/development-guide/documentation.rst @@ -22,7 +22,7 @@ most commonly used directives. Building ~~~~~~~~ -To see your changes and make sure everything rendered correctly, First activate the python virtual enivroment and run ``make docs`` in the root +To see your changes and make sure everything rendered correctly, First activate the python virtual enivroment and run ``make docs`` in the root ``augur/`` directory, and then open ``docs/build/html/index.html`` in your web browser to view it. .. code-block:: bash diff --git a/docs/source/development-guide/make/development.rst b/docs/source/development-guide/make/development.rst index 2b3d083853..a71bfca84b 100644 --- a/docs/source/development-guide/make/development.rst +++ b/docs/source/development-guide/make/development.rst @@ -37,7 +37,7 @@ The backend output should like something like this (note that your process IDs a [2020-03-22 12:39:53 -0500] [19092] [INFO] Booting worker with pid: 19092 The frontend output should like something like this:: - + # a whole bunch of stuff about compiling ... ... @@ -51,11 +51,11 @@ The frontend output should like something like this:: - Local: http://localhost:8080/ - Network: http://192.168.1.141:8080/ -.. note:: +.. note:: You'll likely see some linting warnings in the frontend section (indicated here by the …). Don’t worry about them: it’s the last 3 lines - that indicate success. Once you see this you’re good to go! Head to the specified URL + that indicate success. Once you see this you’re good to go! Head to the specified URL (in this example it’s ``http://localhost:8080/``) to check it out! -------------- diff --git a/docs/source/development-guide/make/documentation.rst b/docs/source/development-guide/make/documentation.rst index 1310370087..df950903bb 100644 --- a/docs/source/development-guide/make/documentation.rst +++ b/docs/source/development-guide/make/documentation.rst @@ -68,4 +68,4 @@ Example\: .. code-block:: bash - $ make api-docs-view \ No newline at end of file + $ make api-docs-view diff --git a/docs/source/development-guide/make/testing.rst b/docs/source/development-guide/make/testing.rst index a8d4202bd7..ce58bf1558 100644 --- a/docs/source/development-guide/make/testing.rst +++ b/docs/source/development-guide/make/testing.rst @@ -7,7 +7,7 @@ If you have questions or would like to help please open an issue on GitHub_. .. _GitHub: https://github.com/chaoss/augur/issues -These commands are used to run specific subsets of unit tests. We use ``tox`` to manage the test environments, and ``pytest`` as the test runner. Each of these commands except for ``make test-pythons-versions`` will use your default Python version, while ``make test-python-versions`` will test all supported Python versions. +These commands are used to run specific subsets of unit tests. We use ``tox`` to manage the test environments, and ``pytest`` as the test runner. Each of these commands except for ``make test-pythons-versions`` will use your default Python version, while ``make test-python-versions`` will test all supported Python versions. -------------- diff --git a/docs/source/development-guide/make/toc.rst b/docs/source/development-guide/make/toc.rst index b829dd7a2c..8f6e97467a 100644 --- a/docs/source/development-guide/make/toc.rst +++ b/docs/source/development-guide/make/toc.rst @@ -13,4 +13,4 @@ If you have questions or would like to help please open an issue on GitHub_. installation development testing - documentation \ No newline at end of file + documentation diff --git a/docs/source/development-guide/testing/toc.rst b/docs/source/development-guide/testing/toc.rst index c1d658e48c..51111ffbcf 100644 --- a/docs/source/development-guide/testing/toc.rst +++ b/docs/source/development-guide/testing/toc.rst @@ -5,4 +5,4 @@ Testing If you have questions or would like to help please open an issue on GitHub_. -.. _GitHub: https://github.com/chaoss/augur/issues \ No newline at end of file +.. _GitHub: https://github.com/chaoss/augur/issues diff --git a/docs/source/development-guide/toc.rst b/docs/source/development-guide/toc.rst index b2484a13d6..de5c32fce4 100644 --- a/docs/source/development-guide/toc.rst +++ b/docs/source/development-guide/toc.rst @@ -15,6 +15,3 @@ This is the development guide for Augur. See our `Contributing to Augur > index date endpoints1 _ field endpoints2 _ field 0. 2020-03-20 5 8 @@ -66,8 +66,8 @@ Methods inside the Insight_model .. code-block:: bash - - features_set = [ + + features_set = [ [[1], [2]], [[2], @@ -82,20 +82,20 @@ Methods inside the Insight_model #n_features : number of features of columns in dataframe for training #n_predays : next number of days to predict for each entry in features_set - + #tr_days = training_days - anomaly_days (in configuration) - - #here + + #here tr_days = 4, black_days = 2, n_features = 1, - n_predays = 1 + n_predays = 1 - ``lstm_model``\:It is the configuration of the multiple ``BiLSTM`` layers along with single ``dense`` layer and optimisers.This method called inside the ``lstm_keras`` method with ``features_set``, ``n_predays``, ``n_features`` as parameters.Configuation of the model is as follows\: .. code-block:: bash - + model = Sequential() model.add(Bidirectional(LSTM(90, activation='linear',return_sequences=True,input_shape=(features_set.shape[1], n_features)))) model.add(Dropout(0.2)) @@ -109,11 +109,11 @@ Methods inside the Insight_model This configuration is designed to acheive the best possible results for all kind of metrics. - ``lstm_keras``\:This is the most important method in the ``insights_model`` called by the ``lstm_selection`` method with ``entry_info`` , ``repo_id``, and ``dataframe`` as parameters.Here dataframe consists of two columns, one is ``date`` and another one is ``endpoint1 _ field`` .In this method model is trained on ``tr_days`` data and values were predicted for ``anomaly_days`` data.Baesd on the difference on actual and predicted values outliers were discovered. - - If any outliers discovered between the ``anomaly_days`` then those points will be inserted into to the ``repo_insights`` and ``repo_insights_records`` table by calling ``insert_data`` method. + + If any outliers discovered between the ``anomaly_days`` then those points will be inserted into to the ``repo_insights`` and ``repo_insights_records`` table by calling ``insert_data`` method. Before calling the ``insert_data`` method, performance of model on the training as well as test data will be evaluated and its summary will be inserted into the ``lstm_anomaly_results`` table along with the unique model configuration into the ``lstm_anomaly_models`` table. - ``insert_data``\:It is called by the ``lstm_keras`` method with ``entry_info``, ``repo_id``, ``anomaly_df``, ``model`` as parameters.Here ``anomaly_df`` is the dataframe which consists of points which are classified as outliers between the ``anomaly_days``. -Insights\_model consists of multiple independent methods like ``time_series_metrics``, ``insert_data`` etc..These methods can be used independently with other Machine Learning models.Also ``preprocess_data``, ``model_lstm`` methods can be easily modified according to the different LSTM networks configuration. \ No newline at end of file +Insights\_model consists of multiple independent methods like ``time_series_metrics``, ``insert_data`` etc..These methods can be used independently with other Machine Learning models.Also ``preprocess_data``, ``model_lstm`` methods can be easily modified according to the different LSTM networks configuration. diff --git a/docs/source/development-guide/workers/message_insights_worker.rst b/docs/source/development-guide/workers/message_insights_worker.rst index 195ff640ef..fcaa10af51 100644 --- a/docs/source/development-guide/workers/message_insights_worker.rst +++ b/docs/source/development-guide/workers/message_insights_worker.rst @@ -2,9 +2,9 @@ Message Insights Worker ======================= -.. note:: - - If you have an NVidia GPU available, you can install the `cuda` drivers to make this worker run faster. - - On Ubuntu 20.04, use the following commands: +.. note:: + - If you have an NVidia GPU available, you can install the `cuda` drivers to make this worker run faster. + - On Ubuntu 20.04, use the following commands: - On the Ubuntu machine, open a Terminal. Type in the following commands to add the Nvidia ppa repository: - `wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/cuda-ubuntu2004.pin` - `sudo mv cuda-ubuntu2004.pin /etc/apt/preferences.d/cuda-repository-pin-600 && sudo apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/7fa2af80.pub` @@ -61,7 +61,7 @@ When a repo is being analyzed for the first time, the ML models are trained and The ``custom_dataset.xlsx`` is a dataset containing technical code review and commit messages from Oracle & Jira database, and general sentiment, emoji-filled messages from StackOverflow. ``EmoticonLookupTable`` is used in sentiment analysis to parse emojis/emoticons and capture their sentiment. ``doc2vecmodel`` is the trained Doc2Vec model on the custom_dataset, utilized for forming word embeddings in novelty detection. -Novelty Detection +Novelty Detection ^^^^^^^^^^^^^^^^^^ Novelty detection is an unsupervised classification problem to identify abnormal/outlier messages. Since a message that is novel in the context of 1 repo may be normal to another, it is essential to maintain the semantics of the past messages of every repo, to flag an incoming message as novel/normal accurately. Every message is transformed to a 250-dimensional Doc2Vec embedding. Deep Autoencoders are used to compress input data and calculate error thresholds. The architecture of the autoencoder model consists of two symmetrical deep neural networks — an encoder and a decoder that applies backpropagation, setting the target values to be equal to the inputs. It attempts to copy its input to its output and anomalies are harder to reconstruct compared with normal samples. 2 AEs are used, the first one identifies normal data based on the threshold calculated and then the second is trained using only the normal data. The Otsu thresholding technique is used in these steps to get the error threshold. Messages which are at least 10 characters long and have reconstruction error > threshold, get flagged as novel. @@ -72,7 +72,7 @@ The sentiment analysis was modeled as a supervised problem. This uses the SentiC Insights --------- -After these tasks are done, the ``message_analysis`` table is populated with all details are about a message: the id and the sentiment and novelty scores. In order to get a view of these metrics at a repo level, the ``message_analysis_summary`` table is updated with the total ratio of positive/negative sentiment messages and count of novel messages every ``insight_days`` frequency. +After these tasks are done, the ``message_analysis`` table is populated with all details are about a message: the id and the sentiment and novelty scores. In order to get a view of these metrics at a repo level, the ``message_analysis_summary`` table is updated with the total ratio of positive/negative sentiment messages and count of novel messages every ``insight_days`` frequency. The 3 types of insights provided are: diff --git a/docs/source/development-guide/workers/pull_request_analysis_worker.rst b/docs/source/development-guide/workers/pull_request_analysis_worker.rst index b3912f4b9f..03d79d7d44 100644 --- a/docs/source/development-guide/workers/pull_request_analysis_worker.rst +++ b/docs/source/development-guide/workers/pull_request_analysis_worker.rst @@ -51,6 +51,6 @@ After feature engineering, the following features were considered: ├── setup.py └── trained_pr_model.pkl -The ``trained_pr_model.pkl`` is the saved pre-trained model, used for the analysis. +The ``trained_pr_model.pkl`` is the saved pre-trained model, used for the analysis. -After prediction, the ``pull_request_analysis`` table is populated with the predicted probabilities for every open PR. \ No newline at end of file +After prediction, the ``pull_request_analysis`` table is populated with the predicted probabilities for every open PR. diff --git a/docs/source/docker/docker-compose.rst b/docs/source/docker/docker-compose.rst index afac95478b..d96476c392 100644 --- a/docs/source/docker/docker-compose.rst +++ b/docs/source/docker/docker-compose.rst @@ -17,12 +17,12 @@ The default ports for each service are\: psql: could not connect to server: Connection refused Is the server running on host 10.254.254.254 and accepting TCP/IP connections on port 5432? - + Docker Compose =============================== -This section of the documentation details how to use Augur's Docker Compose configuration to get the full stack up and running. +This section of the documentation details how to use Augur's Docker Compose configuration to get the full stack up and running. .. warning:: @@ -30,9 +30,9 @@ This section of the documentation details how to use Augur's Docker Compose conf Don't specify AUGUR_DB if you want the docker database to be used. Example .env: - .. code:: + .. code:: - AUGUR_GITHUB_API_KEY=xxxxxxxxxxxxxxxxxxxxxxx + AUGUR_GITHUB_API_KEY=xxxxxxxxxxxxxxxxxxxxxxx AUGUR_GITHUB_USERNAME=usernameGithub AUGUR_GITLAB_API_KEY=xxxxxxxxxxxxxxxxxxxxxxx AUGUR_GITLAB_USERNAME=usernameGitlab @@ -56,6 +56,6 @@ To run Augur **with** the database container: Stopping the containers ------------------------- -To stop the containers, run ``docker compose down --remove-orphans``. The flag is necessary to stop the database container if you used one; run the command again to delete them. +To stop the containers, run ``docker compose down --remove-orphans``. The flag is necessary to stop the database container if you used one; run the command again to delete them. -Once you've got your container up and running, checkout out `how to use them `_ +Once you've got your container up and running, checkout out `how to use them `_ diff --git a/docs/source/docker/quick-start.rst b/docs/source/docker/quick-start.rst index 4203518919..84fb61a7f0 100644 --- a/docs/source/docker/quick-start.rst +++ b/docs/source/docker/quick-start.rst @@ -1,15 +1,15 @@ Docker Quick Start ================================== -Before you get off to such a quick start, go ahead and +Before you get off to such a quick start, go ahead and 1. Create a fork from augur starting at https://github.com/chaoss/augur 2. Clone that fork locally 3. Checkout the appropriate branch to work on (see notes below): - + .. code-block:: python - - git checkout dev - - 4. Create a .env file in the top level directory with the following fields: + + git checkout dev + + 4. Create a .env file in the top level directory with the following fields: .. code:: python @@ -24,38 +24,38 @@ Before you get off to such a quick start, go ahead and 5. Build the container using one of the following commands: -.. code:: shell +.. code:: shell - docker compose up --build + docker compose up --build -or +or -.. code:: shell +.. code:: shell - podman compose up --build + podman compose up --build -And augur should be up and running! +And augur should be up and running! .. note:: - **Running against an external database**: + **Running against an external database**: - If you want to start running docker against an external database right away: + If you want to start running docker against an external database right away: - 1. Follow the instructions to create a database, and database user (if you have just installed Postgresql locally, you may need to follow instructions to allow access to Postgresql from Docker on the next page. tl;dr, there are edits to the Postgresql `pg_hba.conf` and `postgresql.conf` files): + 1. Follow the instructions to create a database, and database user (if you have just installed Postgresql locally, you may need to follow instructions to allow access to Postgresql from Docker on the next page. tl;dr, there are edits to the Postgresql `pg_hba.conf` and `postgresql.conf` files): + + .. code-block:: postgresql - .. code-block:: postgresql - CREATE DATABASE augur; CREATE USER augur WITH ENCRYPTED PASSWORD 'password'; GRANT ALL PRIVILEGES ON DATABASE augur TO augur; - + 2. Install Docker and docker-compose. If you're not familiar with Docker, their `starting guide `_ is a great resource. 3. Create a file to store all relevant enviroment variables for running docker. Below is an example file. This file should be named ``.env``` - .. code-block:: + .. code-block:: AUGUR_DB=augur AUGUR_DB_USER=augur @@ -72,4 +72,3 @@ And augur should be up and running! sudo docker build -t augur-docker -f docker/backend/Dockerfile . sudo docker compose up - diff --git a/docs/source/docker/usage.rst b/docs/source/docker/usage.rst index 4201f3dc32..3e36ff4bd5 100644 --- a/docs/source/docker/usage.rst +++ b/docs/source/docker/usage.rst @@ -48,4 +48,3 @@ Conclusion ----------- This wraps up the Docker section of the Augur documentation. We hope it was useful! Happy hacking! - diff --git a/docs/source/getting-started/collecting-data.rst b/docs/source/getting-started/collecting-data.rst index 1ca39d6981..ab7ce215c6 100644 --- a/docs/source/getting-started/collecting-data.rst +++ b/docs/source/getting-started/collecting-data.rst @@ -7,7 +7,7 @@ Now that you’ve installed Augur’s application server, it’s time to configu # Terminal Window 1 - # Starts the redis server + # Starts the redis server redis-server @@ -15,10 +15,10 @@ Now that you’ve installed Augur’s application server, it’s time to configu # Terminal Window 3 - # To Start Augur: + # To Start Augur: (uv run nohup augur backend start) - # To Stop Augur: + # To Stop Augur: uv run augur backend stop uv run augur backend kill diff --git a/docs/source/getting-started/command-line-interface/backend.rst b/docs/source/getting-started/command-line-interface/backend.rst index a6b3d84c2a..717ce5c301 100644 --- a/docs/source/getting-started/command-line-interface/backend.rst +++ b/docs/source/getting-started/command-line-interface/backend.rst @@ -18,7 +18,7 @@ This command is for starting Augur's API server & (optionally) data collection w **To start the backend normally:** -.. code-block:: +.. code-block:: uv run augur backend start @@ -52,12 +52,12 @@ This command is for starting Augur's API server & (optionally) data collection w > ... > From this point on, the housekeeper and broker logs detailing the worker's progress will take over -To start the backend as a background process: +To start the backend as a background process: .. code-block:: bash uv run nohup augur backend start >logs/base.log 2>logs/base.err & - + Successful output looks like the generation of standard Augur logfiles in the logs/ directory. To start the backend server without the housekeeper: diff --git a/docs/source/getting-started/command-line-interface/db.rst b/docs/source/getting-started/command-line-interface/db.rst index b544ba7860..b754f2e067 100644 --- a/docs/source/getting-started/command-line-interface/db.rst +++ b/docs/source/getting-started/command-line-interface/db.rst @@ -63,10 +63,10 @@ The ``.csv`` file must have the following format: .. code:: - ,, + ,, ... -where ```` is an **existing** repository group ID, and ```` is the url to the repository's Git repository, e.g. ``https://github.com/chaoss/augur.git``. +where ```` is an **existing** repository group ID, and ```` is the url to the repository's Git repository, e.g. ``https://github.com/chaoss/augur.git``. Each pair of values should be on its own line (indicated by the ...), without quotes, and there should be no column headers. .. note:: @@ -134,7 +134,7 @@ Example usage\: ``print-db-version`` ------------------------- -The ``print-db-version`` command will give user the current version of the configured database on their system. +The ``print-db-version`` command will give user the current version of the configured database on their system. Example usage\: @@ -183,7 +183,7 @@ Example usage\: ``create-schema`` ------------------ -The ``create-schema`` command will attempt to create the Augur schema in the database defined in your config file. +The ``create-schema`` command will attempt to create the Augur schema in the database defined in your config file. Example usage\: diff --git a/docs/source/getting-started/database.rst b/docs/source/getting-started/database.rst index 42cf4b5a65..e3c2b0e171 100644 --- a/docs/source/getting-started/database.rst +++ b/docs/source/getting-started/database.rst @@ -2,7 +2,7 @@ Database setup =============== One of the reasons that Augur is so powerful is because of its `unified data model <../schema/overview.html>`_. -To ensure this data model remains performant with large amounts of data, we use PostgreSQL as our database engine. +To ensure this data model remains performant with large amounts of data, we use PostgreSQL as our database engine. We'll need to set up a PostgreSQL instance and create a database, after which Augur can take care of the rest. Make sure to save off the credentials you use when creating the database; you'll need them again to configure Augur. @@ -24,8 +24,8 @@ Creating a Database After you set up your PostgreSQL instance, you'll need to create a database and user with the correct permissions. You can do this with the SQL commands below, but be sure to change the password! -.. code-block:: postgresql - +.. code-block:: postgresql + CREATE DATABASE augur; CREATE USER augur WITH ENCRYPTED PASSWORD 'password'; GRANT ALL PRIVILEGES ON DATABASE augur TO augur; diff --git a/docs/source/getting-started/dev-osx-install.rst b/docs/source/getting-started/dev-osx-install.rst index dbb2dfd0de..a1b3aec344 100644 --- a/docs/source/getting-started/dev-osx-install.rst +++ b/docs/source/getting-started/dev-osx-install.rst @@ -88,19 +88,19 @@ Executable .. code:: shell - brew update ; - brew upgrade ; - brew install rabbitmq ; + brew update ; + brew upgrade ; + brew install rabbitmq ; brew install redis ; brew install postgresql@14 ; - brew install python3-yq ; + brew install python3-yq ; brew install python@3.11 ; - brew install postgresql@14 ; + brew install postgresql@14 ; brew install go ; #required: Go Needs to be version 1.19.x or higher. brew install nginx ; # required for hosting - brew install geckodriver; + brew install geckodriver; - # You will almost certainly need to reboot after this. + # You will almost certainly need to reboot after this. RabbitMQ Configuration ~~~~~~~~~~~~~~~~~~~~~~ @@ -232,7 +232,7 @@ time to log off the root user. .. code:: shell exit - exit + exit RabbitMQ Developer Note: ~~~~~~~~~~~~~~~~~~~~~~~~ @@ -320,11 +320,11 @@ template: .. code:: sql - UPDATE augur_operations.config + UPDATE augur_operations.config SET value = 2 WHERE - section_name='Redis' - AND + section_name='Redis' + AND setting_name='cache_group'; What does Redis Do? @@ -436,7 +436,7 @@ Silicon, as it is looking for information in MacOS Intel directories** brew update; brew upgrade; brew install certbot; - brew install openssl; + brew install openssl; brew install brew install python-typing-extensions Generate a certificate for the specific domain for which you have a file diff --git a/docs/source/getting-started/frontend.rst b/docs/source/getting-started/frontend.rst index 7d0c9cace6..fba275f5a2 100644 --- a/docs/source/getting-started/frontend.rst +++ b/docs/source/getting-started/frontend.rst @@ -2,10 +2,10 @@ Augur's Frontend ================= To compile Augur's frontend for deployment in a production environment (i.e., behind an nginx server), you must go through the folowing steps - 1. Run ``uv run augur config init-frontend``. - 2. Enter Augur's home directory - 3. Run ``npm install``, and then ``npm run build`` in the frontend directory. - 4. After that, follow the instructions for configuring Augur behind Nginx. + 1. Run ``uv run augur config init-frontend``. + 2. Enter Augur's home directory + 3. Run ``npm install``, and then ``npm run build`` in the frontend directory. + 4. After that, follow the instructions for configuring Augur behind Nginx. Augur's frontend source code can be found at ``/frontend/src/``. It uses Vue.js as its primary architecture framework, and Vega/Vega-Lite for its visualizations. It's configured via the ``frontend.config.json`` file in ``/frontend/``. diff --git a/docs/source/getting-started/new-install.rst b/docs/source/getting-started/new-install.rst index d51516c15a..cc7cf47a60 100644 --- a/docs/source/getting-started/new-install.rst +++ b/docs/source/getting-started/new-install.rst @@ -30,14 +30,14 @@ Executable .. code:: shell - sudo apt update && - sudo apt upgrade && - sudo apt install software-properties-common && - sudo apt install python3-dev && + sudo apt update && + sudo apt upgrade && + sudo apt install software-properties-common && + sudo apt install python3-dev && sudo apt install python3.10-venv && - sudo apt install postgresql postgresql-contrib postgresql-client && - sudo apt install build-essential && - sudo apt install redis-server && # required + sudo apt install postgresql postgresql-contrib postgresql-client && + sudo apt install build-essential && + sudo apt install redis-server && # required sudo apt install erlang && # required sudo apt install rabbitmq-server && #required sudo snap install go --classic && #required: Go Needs to be version 1.19.x or higher. Snap is the package manager that gets you to the right version. Classic enables it to actually be installed at the correct version. @@ -46,7 +46,7 @@ Executable sudo apt install firefox=121.0~b7+build1-0ubuntu0.22.04.1 && sudo apt install firefox-geckodriver - # You will almost certainly need to reboot after this. + # You will almost certainly need to reboot after this. RabbitMQ Configuration ~~~~~~~~~~~~~~~~~~~~~~ @@ -123,7 +123,7 @@ time to log off the root user. .. code:: shell exit - exit + exit Rabbitmq Broker Configuration ----------------------------- @@ -351,11 +351,11 @@ template: .. code:: sql - UPDATE augur_operations.config + UPDATE augur_operations.config SET value = 2 WHERE - section_name='Redis' - AND + section_name='Redis' + AND setting_name='cache_group'; What does Redis Do? diff --git a/docs/source/quick-start.rst b/docs/source/quick-start.rst index 61615f7887..b1ccadb15c 100644 --- a/docs/source/quick-start.rst +++ b/docs/source/quick-start.rst @@ -1,7 +1,7 @@ Quickstart =============== -Select installation instructions from those most closely related to the operating system that you use below. Note that Augur's dependencies do not consistently support python 3.11 at this time. Python 3.8 - Python 3.10 have been tested on each platform. +Select installation instructions from those most closely related to the operating system that you use below. Note that Augur's dependencies do not consistently support python 3.11 at this time. Python 3.8 - Python 3.10 have been tested on each platform. .. toctree:: :maxdepth: 2 diff --git a/docs/source/schema/commits.rst b/docs/source/schema/commits.rst index 5709ec1b42..9bbc9a2549 100644 --- a/docs/source/schema/commits.rst +++ b/docs/source/schema/commits.rst @@ -2,4 +2,4 @@ Focus: Commits =============== .. image:: images/20211011-commits-augur-schema-v0.21.1.png - :width: 1200 \ No newline at end of file + :width: 1200 diff --git a/docs/source/schema/contributors.rst b/docs/source/schema/contributors.rst index 8e2aebb842..f0a457d31e 100644 --- a/docs/source/schema/contributors.rst +++ b/docs/source/schema/contributors.rst @@ -2,4 +2,4 @@ Focus: Contributors =================== .. image:: images/20211011-contributors-augur-schema-v0.21.1.png - :width: 1200 \ No newline at end of file + :width: 1200 diff --git a/docs/source/schema/dependencies.rst b/docs/source/schema/dependencies.rst index ce31e5be90..fb541a39e5 100644 --- a/docs/source/schema/dependencies.rst +++ b/docs/source/schema/dependencies.rst @@ -1,5 +1,5 @@ -Focus: Dependencies +Focus: Dependencies =================== .. image:: images/20211011-dependencies-augur-schema-v0.21.1.png - :width: 1200 \ No newline at end of file + :width: 1200 diff --git a/docs/source/schema/issues.rst b/docs/source/schema/issues.rst index 2ec2c5fb20..8c1eaf360b 100644 --- a/docs/source/schema/issues.rst +++ b/docs/source/schema/issues.rst @@ -2,4 +2,4 @@ Focus: Issues =================== .. image:: images/20211011-issues-augur-schema-v0.21.1.png - :width: 1200 \ No newline at end of file + :width: 1200 diff --git a/docs/source/schema/overview.rst b/docs/source/schema/overview.rst index 32d8900f51..0e7b6bb793 100644 --- a/docs/source/schema/overview.rst +++ b/docs/source/schema/overview.rst @@ -40,9 +40,9 @@ and constructed by Augur. The origin’s of the data inside of augur are from data collection tasks and populate this schema.: 1. ``augur.tasks.github.*``: Tasks that pull data from the GitHub API. -Primarily, pull requests and issues are collected before more complicated -data. Note that all messages are stored in Augur in the ``messages`` table. -This is to facilitate easy analysis of the tone and characteristics of text +Primarily, pull requests and issues are collected before more complicated +data. Note that all messages are stored in Augur in the ``messages`` table. +This is to facilitate easy analysis of the tone and characteristics of text communication in a project from one place. 2. ``augur.tasks.git.facade_tasks``: Based on @@ -50,7 +50,7 @@ http://www.github.com/brianwarner/facade, but substantially modified in the fork located at http://github.com/sgoggins/facade. The modifications include modularization of code, connections to Postgresql data instead of MySQL and other changes noted in the commit logs. Further modifications -have been made to work with augur as well as seemlessly integrate it into +have been made to work with augur as well as seemlessly integrate it into data collection. 3. ``augur.tasks.data_analysis.insight_worker.tasks``: Generates summarizations from raw data diff --git a/docs/source/schema/pull-requests.rst b/docs/source/schema/pull-requests.rst index 1946273161..76925a298a 100644 --- a/docs/source/schema/pull-requests.rst +++ b/docs/source/schema/pull-requests.rst @@ -2,4 +2,4 @@ Focus: Pull Requests ======================= .. image:: images/20211011-pull-requests-augur-schema-v0.21.1.png - :width: 1200 \ No newline at end of file + :width: 1200 diff --git a/docs/source/schema/toc.rst b/docs/source/schema/toc.rst index e75d8e22b4..c3a0f64f9d 100644 --- a/docs/source/schema/toc.rst +++ b/docs/source/schema/toc.rst @@ -12,5 +12,3 @@ Schema pull-requests contributors dependencies - - diff --git a/docs/source/schema/unused_data.rst b/docs/source/schema/unused_data.rst index fbb82ebe93..8b03206e40 100644 --- a/docs/source/schema/unused_data.rst +++ b/docs/source/schema/unused_data.rst @@ -32,7 +32,7 @@ List of Unused Data Tables In Augur .. image:: images/library_version.png :width: 200 - + * lstm_anomaly_models .. image:: images/lstm_anomaly_models.png @@ -53,11 +53,11 @@ List of Unused Data Tables In Augur .. image:: images/message_sentiment_summary.png :width: 200 - * Repo_group_insights + * Repo_group_insights .. image:: images/repo_group_insights.png :width: 200 - + * repo_groups_list_serve .. image:: images/repo_groups_list_serve.png @@ -66,4 +66,4 @@ List of Unused Data Tables In Augur * repo_test_coverage .. image:: images/repo_test_coverage.png - :width: 200 \ No newline at end of file + :width: 200 From e9b8cdfdea2f3e1203e1486dd55e9a94548aa996 Mon Sep 17 00:00:00 2001 From: John Strunk Date: Wed, 2 Jul 2025 11:36:00 -0400 Subject: [PATCH 32/66] Remove duplicate readthedocs config We had 2 config files for RTD in the repo. This deletes one of them. Signed-off-by: John Strunk --- readthedocs.yml | 37 ------------------------------------- 1 file changed, 37 deletions(-) delete mode 100644 readthedocs.yml diff --git a/readthedocs.yml b/readthedocs.yml deleted file mode 100644 index 3b0e387327..0000000000 --- a/readthedocs.yml +++ /dev/null @@ -1,37 +0,0 @@ -#SPDX-License-Identifier: MIT -# .readthedocs.yml -# Read the Docs configuration file -# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details - -# Required -version: 2 -build: - os: ubuntu-22.04 # <- add this line - tools: - python: "3.10" - -# Build documentation in the docs/ directory with Sphinx -sphinx: - configuration: docs/source/conf.py - -# Build documentation with MkDocs -#mkdocs: -# configuration: mkdocs.yml - -# Optionally build your docs in additional formats such as PDF and ePub -formats: all - -# Optionally set the version of Python and requirements required to build your docs -python: - install: - - method: pip - path: . - extra_requirements: - - dev - - method: setuptools - path: . - -# build: -# os: ubuntu-22.04 -# tools: -# python:3.10 From 5c151b63cec4b219ddc13ae985fc9060ac545e3f Mon Sep 17 00:00:00 2001 From: Adrian Edwards Date: Wed, 2 Jul 2025 11:40:54 -0400 Subject: [PATCH 33/66] Adapt copy permissions to work with podman Signed-off-by: Adrian Edwards --- docker/backend/Dockerfile | 35 ++++++++++++++++++++--------------- docker/keyman/Dockerfile | 4 +++- 2 files changed, 23 insertions(+), 16 deletions(-) diff --git a/docker/backend/Dockerfile b/docker/backend/Dockerfile index 7ffeae30ed..aecc8f14f9 100644 --- a/docker/backend/Dockerfile +++ b/docker/backend/Dockerfile @@ -88,19 +88,24 @@ RUN --mount=type=cache,target=/root/.cache/uv \ uv sync --no-install-project --no-dev # Copy in the actual code -# The --chmod flags ensure that permissions are set correctly: +# The RUN line below ensure that permissions are set correctly. +# This is the equivalent of the following docker --chmod flags, but done in a way thats compatible with podman. +# This can be removed once https://github.com/containers/buildah/issues/6066 or relevant equivalent is fixed # - u=rw,u+X: user can read and write all files/dirs and execute directories # - go=r,go+X: group and others can read all files/dirs and execute directories -COPY --chmod=u=rw,u+X,go=r,go+X pyproject.toml . -COPY --chmod=u=rw,u+X,go=r,go+X uv.lock . -COPY --chmod=u=rw,u+X,go=r,go+X .python-version . -COPY --chmod=u=rw,u+X,go=r,go+X README.md . -COPY --chmod=u=rw,u+X,go=r,go+X LICENSE . -COPY --chmod=u=rw,u+X,go=r,go+X alembic.ini . -COPY --chmod=u=rw,u+X,go=r,go+X augur/ augur/ -COPY --chmod=u=rw,u+X,go=r,go+X metadata.py . -COPY --chmod=u=rw,u+X,go=r,go+X scripts/ scripts/ -COPY --chmod=u=rw,u+X,go=r,go+X keyman/ keyman/ +COPY pyproject.toml . +COPY uv.lock . +COPY .python-version . +COPY README.md . +COPY LICENSE . +COPY alembic.ini . +COPY augur/ augur/ +COPY metadata.py . +COPY scripts/ scripts/ +COPY keyman/ keyman/ + +RUN find . -type d -exec chmod u=rwx,go=rx {} + && find . -type f -exec chmod u=rw,go=r {} + + # Install the main project RUN --mount=type=cache,target=/root/.cache/uv \ @@ -111,9 +116,9 @@ RUN --mount=type=cache,target=/root/.cache/uv \ ENV PATH="/augur/.venv/bin:${PATH}" ENV SCC_DIR=/scc -COPY --from=golang-builder --chmod=u=rw,u+X,go=r,go+X "/scc" "/scc/scc" +COPY --from=golang-builder --chmod=755 "/scc" "/scc/scc" ENV SCORECARD_DIR=/scorecard -COPY --from=golang-builder --chmod=u=rw,u+X,go=r,go+X "/scorecard" "/scorecard/scorecard" +COPY --from=golang-builder --chmod=755 "/scorecard" "/scorecard/scorecard" # Verify installations RUN ${SCC_DIR}/scc --version RUN ${SCORECARD_DIR}/scorecard version @@ -122,8 +127,8 @@ RUN mkdir -p repos/ logs/ /augur/facade/ RUN ln -s /cache /augur/augur/static/cache # Copy in the entrypoint and init scripts, ensuring they are executable -COPY --chmod=u=rwx,go=rx ./docker/backend/entrypoint.sh / -COPY --chmod=u=rwx,go=rx ./docker/backend/init.sh / +COPY --chmod=755 ./docker/backend/entrypoint.sh / +COPY --chmod=755 ./docker/backend/init.sh / RUN chmod +x /entrypoint.sh /init.sh ENTRYPOINT ["/bin/bash", "/entrypoint.sh"] CMD ["/init.sh"] diff --git a/docker/keyman/Dockerfile b/docker/keyman/Dockerfile index 52ae677fc4..bd390e68f3 100644 --- a/docker/keyman/Dockerfile +++ b/docker/keyman/Dockerfile @@ -10,6 +10,8 @@ ENV PYTHONPATH="${PYTHONPATH}:/augur" ENV PYTHONUMBUFFERED=1 WORKDIR /augur -COPY --chmod=u=rw,u+X,go=r,go+X ./keyman keyman/ +COPY ./keyman keyman/ +RUN find . -type d -exec chmod u=rwx,go=rx {} + && find . -type f -exec chmod u=rw,go=r {} + + ENTRYPOINT [ "python", "/augur/keyman/Orchestrator.py" ] From 1b78d93023471764de511fda53865c1e8d73bfaa Mon Sep 17 00:00:00 2001 From: Adrian Edwards Date: Wed, 2 Jul 2025 13:06:55 -0400 Subject: [PATCH 34/66] no need to mount files into the container that we are going to copy in later anyway Also I worry that this may cause issues if the mounted files dont get correctly detected when they change, leading to builds with stale cache Signed-off-by: Adrian Edwards --- docker/backend/Dockerfile | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/docker/backend/Dockerfile b/docker/backend/Dockerfile index aecc8f14f9..1a3319f5ea 100644 --- a/docker/backend/Dockerfile +++ b/docker/backend/Dockerfile @@ -80,11 +80,12 @@ ENV UV_LOCKED=1 WORKDIR /augur -# Install augur's dependencies +COPY pyproject.toml . +COPY uv.lock . +COPY .python-version . + +# Install augur's dependencies early to take advantage of build cache RUN --mount=type=cache,target=/root/.cache/uv \ - --mount=type=bind,source=uv.lock,target=uv.lock \ - --mount=type=bind,source=pyproject.toml,target=pyproject.toml \ - --mount=type=bind,source=.python-version,target=.python-version \ uv sync --no-install-project --no-dev # Copy in the actual code @@ -93,9 +94,6 @@ RUN --mount=type=cache,target=/root/.cache/uv \ # This can be removed once https://github.com/containers/buildah/issues/6066 or relevant equivalent is fixed # - u=rw,u+X: user can read and write all files/dirs and execute directories # - go=r,go+X: group and others can read all files/dirs and execute directories -COPY pyproject.toml . -COPY uv.lock . -COPY .python-version . COPY README.md . COPY LICENSE . COPY alembic.ini . From 01a938b2e90ca16751822f6d683fed1555d9f96a Mon Sep 17 00:00:00 2001 From: Adrian Edwards Date: Wed, 2 Jul 2025 14:36:54 -0400 Subject: [PATCH 35/66] limit perms so they only change the directories just copied to avoid messing with downloaded python deps Signed-off-by: Adrian Edwards --- docker/backend/Dockerfile | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/docker/backend/Dockerfile b/docker/backend/Dockerfile index 1a3319f5ea..03cec8e4dd 100644 --- a/docker/backend/Dockerfile +++ b/docker/backend/Dockerfile @@ -102,7 +102,9 @@ COPY metadata.py . COPY scripts/ scripts/ COPY keyman/ keyman/ -RUN find . -type d -exec chmod u=rwx,go=rx {} + && find . -type f -exec chmod u=rw,go=r {} + +RUN find augur -type d -exec chmod u=rwx,go=rx {} + && find augur -type f -exec chmod u=rw,go=r {} + +RUN find keyman -type d -exec chmod u=rwx,go=rx {} + && find keyman -type f -exec chmod u=rw,go=r {} + +RUN find scripts -exec chmod u=rwx,go=rx {} + # Install the main project From f8a542c841a098ab73c9c1bf70eca2956f755d5f Mon Sep 17 00:00:00 2001 From: "Sean P. Goggins" Date: Mon, 7 Jul 2025 10:30:32 -0500 Subject: [PATCH 36/66] Update creating-releases.rst Signed-off-by: Sean P. Goggins --- docs/source/procedures/creating-releases.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/source/procedures/creating-releases.rst b/docs/source/procedures/creating-releases.rst index 24e645adb3..d46feb9f7b 100644 --- a/docs/source/procedures/creating-releases.rst +++ b/docs/source/procedures/creating-releases.rst @@ -28,13 +28,13 @@ Currently, Augur only officially supports the last-released version represented The Release Process -When the next release is set to be cut, there are some preparation steps need to take place first, these include: +When the next release is set to be cut, some preparation steps need to take place first, these include: - Ensuring all features planned for that release are merged and any unrelated changes are delayed (as appropriate) until after the release. - Creating a Pull Request to update any applicable metadata (such as version information and Changelogs) on the `main` branch. -Once all release preparation has been completed, a new Pull Request can be created to merge the the main branch into the `release`` branch. This creates a final review opportunity and allows for another run of (potentially more stringent) CI jobs compared to those ran on `main` catching issues that may have come up throughout the various merges or in the process of preparing for release. +Once all release preparation has been completed, a new Pull Request can be created to merge the main branch into the `release 'branch. This creates a final review opportunity and allows for another run of (potentially more stringent) CI jobs compared to those run on `main`, catching issues that may have come up throughout the various merges or in the process of preparing for release. -After this PR is merged, a tag is created pointing to that commit on the `release` branch, effectively labeling it so that it can be returned to later if needed. This labeling process can also be the basis for additional CI jobs that build and upload the released code to distribution platforms such as Docker Hub or the GitHub Container Registry +After this PR is merged, a tag is created that points to the commit on the `release` branch, effectively labeling it so that it can be returned to later if needed. This labeling process can also be the basis for additional CI jobs that build and upload the released code to distribution platforms such as Docker Hub or the GitHub Container Registry Why? From c6ea7ff554b90952aa389f77fd0e5726e07101fd Mon Sep 17 00:00:00 2001 From: "Sean P. Goggins" Date: Mon, 7 Jul 2025 10:31:54 -0500 Subject: [PATCH 37/66] Update creating-releases.rst Signed-off-by: Sean P. Goggins --- docs/source/procedures/creating-releases.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/procedures/creating-releases.rst b/docs/source/procedures/creating-releases.rst index d46feb9f7b..007db72441 100644 --- a/docs/source/procedures/creating-releases.rst +++ b/docs/source/procedures/creating-releases.rst @@ -19,7 +19,7 @@ The `main` branch is the primary development branch that is the target for all n `release` The `release` branch is where all augur versions (after 0.89.3) are tagged. Each commit on this branch represents either a hotfix to the prior release or a new major or minor version. -Currently, Augur only officially supports the last-released version represented by the latest commit on the `release` branch. +Currently, Augur only officially supports the last-released version represented by the latest **release** tag. In most cases, the latest commit on the `release` branch is made immediately prior to a release, but always rely on the latest tagged release, not the release branch in production. .. note:: From 53f739622a10e058ba255b9ac93f56b4bbdd052f Mon Sep 17 00:00:00 2001 From: John Strunk Date: Mon, 7 Jul 2025 12:56:41 -0400 Subject: [PATCH 38/66] Update login response example to use json5 format Changed the example response format from text to json5 in the login documentation. Added a comment to clarify the `expires` field. This update improves the readability and understanding of the API response structure for users. Signed-off-by: John Strunk --- docs/source/login.rst | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/source/login.rst b/docs/source/login.rst index 7bbf3a46f8..c80e842e47 100644 --- a/docs/source/login.rst +++ b/docs/source/login.rst @@ -73,7 +73,7 @@ The Client Application must make the following request in order to facilitate th The authorization server will respond with the following on success: -.. code:: text +.. code:: json5 { "status": "Validated", @@ -81,7 +81,7 @@ The authorization server will respond with the following on success: "access_token": "the new Bearer token", "refresh_token": "the new refresh token", "token_type": "Bearer", - "expires": [integer: seconds until this access_token expires] + "expires": 99 // integer: seconds until this access_token expires } Success! @@ -107,14 +107,14 @@ The application may also attempt automatic reauthorization using the previously The authorization server will respond with the following on success: -.. code:: text +.. code:: json5 { "status": "Validated", "access_token": "the new Bearer token", "refresh_token": "the new refresh token", "token_type": "Bearer", - "expires": [integer: seconds until this access_token expires] + "expires": 99 // integer: seconds until this access_token expires } The new User Session and refresh tokens should replace the existing tokens, as they may not be the same. From 6ea59d329bd5876d23b5629e48c48156f3de2d20 Mon Sep 17 00:00:00 2001 From: Adrian Edwards Date: Mon, 7 Jul 2025 15:23:30 -0400 Subject: [PATCH 39/66] add podman copy of the E2E test Signed-off-by: Adrian Edwards --- .github/workflows/build_docker.yml | 105 ++++++++++++++++++++++++++++- 1 file changed, 104 insertions(+), 1 deletion(-) diff --git a/.github/workflows/build_docker.yml b/.github/workflows/build_docker.yml index df5f28e5f2..c8c6e478ce 100644 --- a/.github/workflows/build_docker.yml +++ b/.github/workflows/build_docker.yml @@ -52,7 +52,7 @@ jobs: test-e2e: - name: End-to-end test + name: End-to-end test (Docker) runs-on: ubuntu-latest steps: - name: Checkout repository @@ -168,6 +168,109 @@ jobs: # We use tail so that we can see the name of each file as it's printed run: "docker run -t --rm -v augur_logs:/logs bash -c 'find /logs -type f | xargs tail -n +0'" + test-e2e-podman: + name: End-to-end test (Podman) + runs-on: ubuntu-latest + steps: + - name: Checkout repository + uses: actions/checkout@v4 + + - name: Build database container + uses: redhat-actions/buildah-build@v2 + with: + context: . + containerfiles: | + ./docker/database/Dockerfile + platforms: linux/amd64 + tags: ghcr.io/${{ github.repository_owner }}/augur_database:test + + - name: Build keyman container + uses: redhat-actions/buildah-build@v2 + with: + context: . + containerfiles: | + ./docker/keyman/Dockerfile + platforms: linux/amd64 + tags: ghcr.io/${{ github.repository_owner }}/augur_keyman:test + + - name: Build rabbitmq container + uses: redhat-actions/buildah-build@v2 + with: + context: . + containerfiles: | + ./docker/rabbitmq/Dockerfile + platforms: linux/amd64 + tags: ghcr.io/${{ github.repository_owner }}/augur_rabbitmq:test + + - name: Build backend container + uses: redhat-actions/buildah-build@v2 + with: + context: . + containerfiles: | + ./docker/backend/Dockerfile + platforms: linux/amd64 + tags: ghcr.io/${{ github.repository_owner }}/augur_backend:test + + - name: Prepare compose file + run: | + yq eval -i '.services.augur.image = "ghcr.io/${{ github.repository_owner }}/augur_backend:test"' docker-compose.yml + yq eval -i '.services.augur.pull_policy = "never"' docker-compose.yml + yq eval -i '.services.augur.restart = "no"' docker-compose.yml + + yq eval -i '.services.augur-db.image = "ghcr.io/${{ github.repository_owner }}/augur_database:test"' docker-compose.yml + yq eval -i '.services.augur-db.pull_policy = "never"' docker-compose.yml + yq eval -i '.services.augur-db.restart = "no"' docker-compose.yml + + yq eval -i '.services.augur-keyman.image = "ghcr.io/${{ github.repository_owner }}/augur_keyman:test"' docker-compose.yml + yq eval -i '.services.augur-keyman.pull_policy = "never"' docker-compose.yml + yq eval -i '.services.augur-keyman.restart = "no"' docker-compose.yml + + yq eval -i '.services.rabbitmq.image = "ghcr.io/${{ github.repository_owner }}/augur_rabbitmq:test"' docker-compose.yml + yq eval -i '.services.rabbitmq.pull_policy = "never"' docker-compose.yml + yq eval -i '.services.rabbitmq.restart = "no"' docker-compose.yml + + - name: Setup Podman Compose + uses: webgtx/setup-podman-compose@v1 + + - name: Set up list of log lines to match + run: | + cat < /tmp/regex_matches.txt + Gunicorn webserver started + Starting core worker processes + Starting secondary worker processes + Starting facade worker processes + Retrieved \\d+ github api keys for use + Fetching new repos \\(complete\\) + Inserting \\d+ contributors + Inserting \\d+ issues + Inserting prs of length: \\d+ + Querying committers count + Done generating scc data for repo + Sending due task + EOF + + - name: Start services & wait for output + # This starts the system and sends the output to "await_all.py" which + # scans for the regex matches from above. Once all matches are seen at + # least once, the `compose down` will run to shut down the system. If + # this all doesn't happen before the timeout, the job will fail. + run: | + podman compose -f docker-compose.yml up --no-build 2>&1 \ + | (./scripts/ci/await_all.py /tmp/regex_matches.txt \ + && docker compose -f docker-compose.yml down) + timeout-minutes: 3 + env: + AUGUR_GITHUB_API_KEY: ${{ secrets.GITHUB_TOKEN }} + AUGUR_GITHUB_USERNAME: ${{ github.repository_owner }} + AUGUR_GITLAB_API_KEY: dummy + AUGUR_GITLAB_USERNAME: dummy + + - name: Dump logs + # Always run this step to get logs, even if the previous step fails + if: always() + # We use tail so that we can see the name of each file as it's printed + run: "podman run -t --rm -v augur_logs:/logs bash -c 'find /logs -type f | xargs tail -n +0'" + push-image: From f0e228b3138c1e97d0ae4c0ffe5eed41ba0c5b89 Mon Sep 17 00:00:00 2001 From: Adrian Edwards Date: Mon, 7 Jul 2025 16:42:06 -0400 Subject: [PATCH 40/66] enable cache of intermediate layers during the build process Signed-off-by: Adrian Edwards --- .github/workflows/build_docker.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.github/workflows/build_docker.yml b/.github/workflows/build_docker.yml index c8c6e478ce..72e6c1472c 100644 --- a/.github/workflows/build_docker.yml +++ b/.github/workflows/build_docker.yml @@ -183,6 +183,7 @@ jobs: ./docker/database/Dockerfile platforms: linux/amd64 tags: ghcr.io/${{ github.repository_owner }}/augur_database:test + layers: true - name: Build keyman container uses: redhat-actions/buildah-build@v2 @@ -192,6 +193,7 @@ jobs: ./docker/keyman/Dockerfile platforms: linux/amd64 tags: ghcr.io/${{ github.repository_owner }}/augur_keyman:test + layers: true - name: Build rabbitmq container uses: redhat-actions/buildah-build@v2 @@ -201,6 +203,7 @@ jobs: ./docker/rabbitmq/Dockerfile platforms: linux/amd64 tags: ghcr.io/${{ github.repository_owner }}/augur_rabbitmq:test + layers: true - name: Build backend container uses: redhat-actions/buildah-build@v2 @@ -210,6 +213,7 @@ jobs: ./docker/backend/Dockerfile platforms: linux/amd64 tags: ghcr.io/${{ github.repository_owner }}/augur_backend:test + layers: true - name: Prepare compose file run: | From b6cd049735a7d752bd9250a2cc1a64be80a689c1 Mon Sep 17 00:00:00 2001 From: Adrian Edwards Date: Mon, 7 Jul 2025 17:05:16 -0400 Subject: [PATCH 41/66] attempt to clean files from the base image per online advice https://stackoverflow.com/a/75539500 Signed-off-by: Adrian Edwards --- .github/workflows/build_docker.yml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/.github/workflows/build_docker.yml b/.github/workflows/build_docker.yml index 72e6c1472c..e78ff2fab6 100644 --- a/.github/workflows/build_docker.yml +++ b/.github/workflows/build_docker.yml @@ -172,6 +172,11 @@ jobs: name: End-to-end test (Podman) runs-on: ubuntu-latest steps: + - name: Remove unnecessary files from the base image + run: | + sudo rm -rf /usr/share/dotnet + sudo rm -rf "$AGENT_TOOLSDIRECTORY" + - name: Checkout repository uses: actions/checkout@v4 From 17c6d2b22e0768716d18a88482d4ccdf79441656 Mon Sep 17 00:00:00 2001 From: Andrew Brain Date: Mon, 7 Jul 2025 20:16:14 -0500 Subject: [PATCH 42/66] improve retrieval of repo_info from args --- augur/tasks/init/celery_app.py | 25 +++++++++++++++++++++---- 1 file changed, 21 insertions(+), 4 deletions(-) diff --git a/augur/tasks/init/celery_app.py b/augur/tasks/init/celery_app.py index 04b07bb9a7..a0f7c2aab8 100644 --- a/augur/tasks/init/celery_app.py +++ b/augur/tasks/init/celery_app.py @@ -5,6 +5,7 @@ import os import datetime import traceback +import inspect import celery from celery import Celery from celery import current_app @@ -101,27 +102,43 @@ def augur_handle_task_failure(self,exc,task_id,repo_git,logger_name,collection_h session.commit() def on_failure(self,exc,task_id,args, kwargs, einfo): - repo_git = args[0] + repo_git = extract_repo_git(args, kwargs) # log traceback to error file self.augur_handle_task_failure(exc, task_id, repo_git, "core_task_failure") class AugurSecondaryRepoCollectionTask(AugurCoreRepoCollectionTask): def on_failure(self,exc,task_id,args, kwargs, einfo): - repo_git = args[0] + repo_git = extract_repo_git(args, kwargs) self.augur_handle_task_failure(exc, task_id, repo_git, "secondary_task_failure",collection_hook='secondary') class AugurFacadeRepoCollectionTask(AugurCoreRepoCollectionTask): def on_failure(self,exc,task_id,args, kwargs, einfo): - repo_git = args[0] + repo_git = extract_repo_git(args, kwargs) self.augur_handle_task_failure(exc, task_id, repo_git, "facade_task_failure",collection_hook='facade') class AugurMlRepoCollectionTask(AugurCoreRepoCollectionTask): def on_failure(self,exc,task_id,args,kwargs,einfo): - repo_git = args[0] + repo_git = extract_repo_git(args, kwargs) self.augur_handle_task_failure(exc,task_id,repo_git, "ml_task_failure", collection_hook='ml') +def extract_repo_git(self, args, kwargs): + if 'repo_git' in kwargs: + return kwargs['repo_git'] + + sig = inspect.signature(self.run) + param_names = list(sig.parameters.keys()) + + try: + index = param_names.index('repo_git') + return args[index] + except (ValueError, IndexError): + pass + + return None # If not found + + #task_cls='augur.tasks.init.celery_app:AugurCoreRepoCollectionTask' celery_app = Celery('tasks', broker=BROKER_URL, backend=BACKEND_URL, include=tasks) From 9c462c42ca09a3bddac2fad85d0964f76f965a2b Mon Sep 17 00:00:00 2001 From: Andrew Brain Date: Mon, 7 Jul 2025 20:18:20 -0500 Subject: [PATCH 43/66] extract out diff_refs and author assignment to make it clearer which object is None sometimes --- augur/application/db/data_parse.py | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/augur/application/db/data_parse.py b/augur/application/db/data_parse.py index 6f20fa35a7..08d11c4d02 100644 --- a/augur/application/db/data_parse.py +++ b/augur/application/db/data_parse.py @@ -1088,17 +1088,21 @@ def extract_needed_mr_metadata(mr_dict, repo_id, pull_request_id, tool_source, t Returns: List of dicts of parsed mr metadata """ - head = {'sha': mr_dict['diff_refs']['head_sha'], + + diff_refs = mr_dict['diff_refs'] + author = mr_dict['author'] + + head = {'sha': diff_refs['head_sha'], 'ref': mr_dict['target_branch'], 'label': str(mr_dict['target_project_id']) + ':' + mr_dict['target_branch'], - 'author': mr_dict['author']['username'], + 'author': author['username'], 'repo': str(mr_dict['target_project_id']) } - base = {'sha': mr_dict['diff_refs']['base_sha'], + base = {'sha': diff_refs['base_sha'], 'ref': mr_dict['source_branch'], 'label': str(mr_dict['source_project_id']) + ':' + mr_dict['source_branch'], - 'author': mr_dict['author']['username'], + 'author': author['username'], 'repo': str(mr_dict['source_project_id']) } From 6fa8c01854c5a9e6b05f1758c9c98849bcda098c Mon Sep 17 00:00:00 2001 From: Andrew Brain Date: Mon, 7 Jul 2025 20:25:32 -0500 Subject: [PATCH 44/66] handle NoneType exception --- augur/application/db/data_parse.py | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/augur/application/db/data_parse.py b/augur/application/db/data_parse.py index 08d11c4d02..de0d9aaa81 100644 --- a/augur/application/db/data_parse.py +++ b/augur/application/db/data_parse.py @@ -1089,20 +1089,19 @@ def extract_needed_mr_metadata(mr_dict, repo_id, pull_request_id, tool_source, t List of dicts of parsed mr metadata """ - diff_refs = mr_dict['diff_refs'] - author = mr_dict['author'] + diff_refs = mr_dict.get('diff_refs', {}) - head = {'sha': diff_refs['head_sha'], + head = {'sha': diff_refs.get('head_sha', None), 'ref': mr_dict['target_branch'], 'label': str(mr_dict['target_project_id']) + ':' + mr_dict['target_branch'], - 'author': author['username'], + 'author': mr_dict['author']['username'], 'repo': str(mr_dict['target_project_id']) } - base = {'sha': diff_refs['base_sha'], + base = {'sha': diff_refs.get('base_sha', None), 'ref': mr_dict['source_branch'], 'label': str(mr_dict['source_project_id']) + ':' + mr_dict['source_branch'], - 'author': author['username'], + 'author': mr_dict['author']['username'], 'repo': str(mr_dict['source_project_id']) } From 4f38278a7b1ad8d2ff176e1ee28f4e05b6d831d5 Mon Sep 17 00:00:00 2001 From: Andrew Brain Date: Mon, 7 Jul 2025 20:31:52 -0500 Subject: [PATCH 45/66] fix: need self so it must be in the class --- augur/tasks/init/celery_app.py | 38 +++++++++++++++++----------------- 1 file changed, 19 insertions(+), 19 deletions(-) diff --git a/augur/tasks/init/celery_app.py b/augur/tasks/init/celery_app.py index a0f7c2aab8..db8d2239d4 100644 --- a/augur/tasks/init/celery_app.py +++ b/augur/tasks/init/celery_app.py @@ -102,42 +102,42 @@ def augur_handle_task_failure(self,exc,task_id,repo_git,logger_name,collection_h session.commit() def on_failure(self,exc,task_id,args, kwargs, einfo): - repo_git = extract_repo_git(args, kwargs) + repo_git = self._extract_repo_git(args, kwargs) # log traceback to error file self.augur_handle_task_failure(exc, task_id, repo_git, "core_task_failure") + def _extract_repo_git(self, args, kwargs): + if 'repo_git' in kwargs: + return kwargs['repo_git'] + + sig = inspect.signature(self.run) + param_names = list(sig.parameters.keys()) + + try: + index = param_names.index('repo_git') + return args[index] + except (ValueError, IndexError): + pass + + return None + class AugurSecondaryRepoCollectionTask(AugurCoreRepoCollectionTask): def on_failure(self,exc,task_id,args, kwargs, einfo): - repo_git = extract_repo_git(args, kwargs) + repo_git = self._extract_repo_git(args, kwargs) self.augur_handle_task_failure(exc, task_id, repo_git, "secondary_task_failure",collection_hook='secondary') class AugurFacadeRepoCollectionTask(AugurCoreRepoCollectionTask): def on_failure(self,exc,task_id,args, kwargs, einfo): - repo_git = extract_repo_git(args, kwargs) + repo_git = self._extract_repo_git(args, kwargs) self.augur_handle_task_failure(exc, task_id, repo_git, "facade_task_failure",collection_hook='facade') class AugurMlRepoCollectionTask(AugurCoreRepoCollectionTask): def on_failure(self,exc,task_id,args,kwargs,einfo): - repo_git = extract_repo_git(args, kwargs) + repo_git = self._extract_repo_git(args, kwargs) self.augur_handle_task_failure(exc,task_id,repo_git, "ml_task_failure", collection_hook='ml') -def extract_repo_git(self, args, kwargs): - if 'repo_git' in kwargs: - return kwargs['repo_git'] - - sig = inspect.signature(self.run) - param_names = list(sig.parameters.keys()) - - try: - index = param_names.index('repo_git') - return args[index] - except (ValueError, IndexError): - pass - - return None # If not found - #task_cls='augur.tasks.init.celery_app:AugurCoreRepoCollectionTask' celery_app = Celery('tasks', broker=BROKER_URL, backend=BACKEND_URL, include=tasks) From 91189cb2a1821e8910c0d52a40f0d1a821654aa6 Mon Sep 17 00:00:00 2001 From: Andrew Brain Date: Mon, 7 Jul 2025 21:40:03 -0500 Subject: [PATCH 46/66] Remove redis connection from top level --- augur/api/routes/user.py | 7 +++- augur/application/cli/_cli_util.py | 5 ++- augur/application/cli/backend.py | 4 +- augur/application/cli/cache.py | 5 ++- augur/application/cli/tasks.py | 1 - augur/tasks/init/redis_connection.py | 9 ++++- augur/tasks/util/redis_list.py | 39 ++++++++++--------- augur/tasks/util/redis_scalar.py | 11 +++--- keyman/KeyClient.py | 26 +++++++------ keyman/Orchestrator.py | 18 +++++---- .../test_github_api_key_handler.py | 4 +- .../test_redis/test_redis_list.py | 9 ++++- 12 files changed, 85 insertions(+), 53 deletions(-) diff --git a/augur/api/routes/user.py b/augur/api/routes/user.py index 31f18ce663..3a76aa4071 100644 --- a/augur/api/routes/user.py +++ b/augur/api/routes/user.py @@ -16,7 +16,8 @@ from augur.api.util import ssl_required from augur.application.db.models import User, UserSessionToken, RefreshToken -from augur.tasks.init.redis_connection import redis_connection as redis +from augur.tasks.init.redis_connection import get_redis_connection + from ..server import app logger = logging.getLogger(__name__) @@ -64,6 +65,8 @@ def user_authorize(): code = secrets.token_hex() username = current_user.login_name + redis = get_redis_connection() + redis.set(code, username, ex=300) return jsonify({"status": "Validated", "code": code}) @@ -81,6 +84,8 @@ def generate_session(application): if "code" not in grant_type: return jsonify({"status": "Invalid grant type"}) + + redis = get_redis_connection() username = redis.get(code) redis.delete(code) diff --git a/augur/application/cli/_cli_util.py b/augur/application/cli/_cli_util.py index d5837f9f90..6ab969c6f5 100644 --- a/augur/application/cli/_cli_util.py +++ b/augur/application/cli/_cli_util.py @@ -5,7 +5,7 @@ import signal from urllib.parse import urlparse -from augur.tasks.init.redis_connection import redis_connection +from augur.tasks.init.redis_connection import get_redis_connection def clear_redis_caches(logger): """Clears the redis databases that celery and redis use.""" @@ -13,6 +13,9 @@ def clear_redis_caches(logger): logger.info("Flushing all redis databases this instance was using") celery_purge_command = "celery -A augur.tasks.init.celery_app.celery_app purge -f" subprocess.call(celery_purge_command.split(" ")) + + + redis_connection = get_redis_connection() redis_connection.flushdb() diff --git a/augur/application/cli/backend.py b/augur/application/cli/backend.py index 970c78b525..343c60f823 100644 --- a/augur/application/cli/backend.py +++ b/augur/application/cli/backend.py @@ -22,7 +22,7 @@ from augur.tasks.github.util.github_api_key_handler import GithubApiKeyHandler from augur.tasks.gitlab.gitlab_api_key_handler import GitlabApiKeyHandler from augur.tasks.data_analysis.contributor_breadth_worker.contributor_breadth_worker import contributor_breadth_model -from augur.tasks.init.redis_connection import redis_connection +from augur.tasks.init.redis_connection import get_redis_connection from augur.application.db.models import UserRepo from augur.application.db.session import DatabaseSession from augur.application.logs import AugurLogger @@ -363,6 +363,8 @@ def clear_redis_caches(): logger.info("Flushing all redis databases this instance was using") celery_purge_command = "celery -A augur.tasks.init.celery_app.celery_app purge -f" subprocess.call(celery_purge_command.split(" ")) + + redis_connection = get_redis_connection() redis_connection.flushdb() def clear_all_message_queues(connection_string): diff --git a/augur/application/cli/cache.py b/augur/application/cli/cache.py index 80a25d4dbb..0003419648 100644 --- a/augur/application/cli/cache.py +++ b/augur/application/cli/cache.py @@ -4,7 +4,7 @@ """ import click -from augur.tasks.init.redis_connection import redis_connection as redis_conn +from augur.tasks.init.redis_connection import get_redis_connection from augur.application.logs import AugurLogger from augur.application.cli import test_connection, test_db_connection @@ -30,6 +30,7 @@ def clear_all(): if user_input in ("y", "Y", "Yes", "yes"): logger.info("Clearing call redis databases") + redis_conn = get_redis_connection() redis_conn.flushall() return @@ -46,4 +47,6 @@ def clear(): """Clears the redis cache specified in the config""" print("Clearing redis cache that is specified in the config") + + redis_conn = get_redis_connection() redis_conn.flushdb() diff --git a/augur/application/cli/tasks.py b/augur/application/cli/tasks.py index f760dfddeb..b0a1ac2e6a 100644 --- a/augur/application/cli/tasks.py +++ b/augur/application/cli/tasks.py @@ -13,7 +13,6 @@ from augur import instance_id from augur.application.logs import AugurLogger -from augur.tasks.init.redis_connection import redis_connection from augur.application.cli import test_connection, test_db_connection from augur.application.cli.backend import clear_rabbitmq_messages, raise_open_file_limit diff --git a/augur/tasks/init/redis_connection.py b/augur/tasks/init/redis_connection.py index 0e18bf605f..7860172b39 100644 --- a/augur/tasks/init/redis_connection.py +++ b/augur/tasks/init/redis_connection.py @@ -2,6 +2,11 @@ import redis from augur.tasks.init import get_redis_conn_values -redis_db_number, redis_conn_string = get_redis_conn_values() -redis_connection= redis.from_url(f'{redis_conn_string}{redis_db_number+2}', decode_responses=True) +def get_redis_connection(): + + redis_db_number, redis_conn_string = get_redis_conn_values() + + redis_connection= redis.from_url(f'{redis_conn_string}{redis_db_number+2}', decode_responses=True) + + return redis_connection diff --git a/augur/tasks/util/redis_list.py b/augur/tasks/util/redis_list.py index 8da8f12746..933b041a1f 100644 --- a/augur/tasks/util/redis_list.py +++ b/augur/tasks/util/redis_list.py @@ -4,7 +4,7 @@ from typing import Iterable, Any, Union from collections.abc import MutableSequence -from augur.tasks.init.redis_connection import redis_connection as redis +from augur.tasks.init.redis_connection import get_redis_connection from augur import instance_id @@ -25,6 +25,7 @@ def __init__(self, list_name: str): """ self.redis_list_key = f"{instance_id}_{list_name}" + self.redis = get_redis_connection() def __len__(self) -> int: @@ -34,7 +35,7 @@ def __len__(self) -> int: length of redis list """ - return redis.llen(self.redis_list_key) + return self.redis.llen(self.redis_list_key) def __iter__(self) -> Any: @@ -63,7 +64,7 @@ def __getitem__(self, index: int) -> Any: Item at requested index """ - item = redis.lindex(self.redis_list_key, index) + item = self.redis.lindex(self.redis_list_key, index) if item is None: return None @@ -94,10 +95,10 @@ def __setitem__(self, index: int, data: Union[Any, Iterable[Any]]): """ - if redis.exists(self.redis_list_key): - redis.lset(self.redis_list_key, index, data) + if self.redis.exists(self.redis_list_key): + self.redis.lset(self.redis_list_key, index, data) else: - redis.rpush(self.redis_list_key, data) + self.redis.rpush(self.redis_list_key, data) def __delitem__(self, index: int) -> None: @@ -110,10 +111,10 @@ def __delitem__(self, index: int) -> None: index: index of desired item in list """ - items_before = redis.lpop(self.redis_list_key, index+1) + items_before = self.redis.lpop(self.redis_list_key, index+1) items_before.pop() if items_before: - redis.lpush(self.redis_list_key, *items_before) + self.redis.lpush(self.redis_list_key, *items_before) # def contains(self, value: Any): # """Determiens whether the paramater value is in the list @@ -143,8 +144,8 @@ def insert(self, index: int, value: Any): data: value that will be added """ - value_before = redis.lindex(self.redis_list_key, index-1) - redis.linsert(self.redis_list_key, "after", value_before, value) + value_before = self.redis.lindex(self.redis_list_key, index-1) + self.redis.linsert(self.redis_list_key, "after", value_before, value) def append(self, value): """Adds the paramater value to the end of the list @@ -153,7 +154,7 @@ def append(self, value): value: value that is added to end of list """ - redis.rpush(self.redis_list_key, value) + self.redis.rpush(self.redis_list_key, value) def pop(self, index: int = None): @@ -170,7 +171,7 @@ def pop(self, index: int = None): # This will get a random index from the list and remove it, # decreasing the likelihood of everyone using the same key all the time #redis.rpop(self.redis_list_key) - redis.spop(self.redis_list_key) + self.redis.spop(self.redis_list_key) else: # calls __delitem__ @@ -184,7 +185,7 @@ def remove(self, value): value: item being removed """ - redis.lrem(self.redis_list_key, 0, value) + self.redis.lrem(self.redis_list_key, 0, value) def extend(self, values: Iterable[Any]): @@ -195,27 +196,27 @@ def extend(self, values: Iterable[Any]): """ if values: - redis.rpush(self.redis_list_key, *values) + self.redis.rpush(self.redis_list_key, *values) def clear(self): """Removes all items from the redis list""" - redis.delete(self.redis_list_key) + self.redis.delete(self.redis_list_key) def print_values(self): """Prints all the values in the redis list""" - key_list_length = redis.llen(self.redis_list_key) + key_list_length = self.redis.llen(self.redis_list_key) for i in range(key_list_length): - print(redis.lindex(self.redis_list_key, i)) + print(self.redis.lindex(self.redis_list_key, i)) if __name__ == "__main__": - redis.flushdb() redis_list = RedisList("list") + redis_list.redis.flushdb() # redis_list.append(5) # redis_list.append(15) @@ -225,5 +226,5 @@ def print_values(self): print("List values") redis_list.print_values() - redis.delete("list") + redis_list.redis.delete("list") \ No newline at end of file diff --git a/augur/tasks/util/redis_scalar.py b/augur/tasks/util/redis_scalar.py index 88ebfb3d43..45579689dc 100644 --- a/augur/tasks/util/redis_scalar.py +++ b/augur/tasks/util/redis_scalar.py @@ -4,7 +4,7 @@ from typing import Iterable, Any, Union from collections.abc import MutableSequence -from augur.tasks.init.redis_connection import redis_connection as redis +from augur.tasks.init.redis_connection import get_redis_connection from augur import instance_id from redis import exceptions import numbers @@ -17,14 +17,15 @@ def __init__(self, scalar_name: str, default_value: int = 0, override_existing: self._scalar_name = scalar_name self.__value = default_value + self.redis = get_redis_connection() #Check redis to see if key exists in cache - if 1 != redis.exists(self.redis_scalar_key) or override_existing: + if 1 != self.redis.exists(self.redis_scalar_key) or override_existing: #Set value - redis.set(self.redis_scalar_key,self.__value) + self.redis.set(self.redis_scalar_key,self.__value) else: #else get the value - self.__value = int(float(redis.get(self.redis_scalar_key))) + self.__value = int(float(self.redis.get(self.redis_scalar_key))) @property def value(self): @@ -34,4 +35,4 @@ def value(self): def value(self, otherVal): if isinstance(otherVal, numbers.Number): self.__value = otherVal - redis.set(self.redis_scalar_key,self.__value) + self.redis.set(self.redis_scalar_key,self.__value) diff --git a/keyman/KeyClient.py b/keyman/KeyClient.py index fba0a5620e..eab94b1a1b 100644 --- a/keyman/KeyClient.py +++ b/keyman/KeyClient.py @@ -1,4 +1,4 @@ -from augur.tasks.init.redis_connection import redis_connection as conn +from augur.tasks.init.redis_connection import get_redis_connection from redis.client import PubSub from logging import Logger from os import getpid @@ -29,8 +29,10 @@ def __init__(self, platform: str, logger: Logger): if not platform: raise ValueError("Platform must not be empty") - self.stdout = conn - self.stdin: PubSub = conn.pubsub(ignore_subscribe_messages = True) + self.conn = get_redis_connection() + + self.stdout = self.conn + self.stdin: PubSub = self.conn.pubsub(ignore_subscribe_messages = True) self.stdin.subscribe(f"{self.REQUEST}-{self.id}") self.platform = platform self.logger = logger @@ -157,7 +159,7 @@ def __init__(self) -> None: setattr(self, channel["name"], channel["id"]) self.id = getpid() - self.stdin: PubSub = conn.pubsub(ignore_subscribe_messages = True) + self.stdin: PubSub = self.conn.pubsub(ignore_subscribe_messages = True) self.stdin.subscribe(f"{self.ANNOUNCE}-{self.id}") def publish(self, key: str, platform: str): @@ -172,7 +174,7 @@ def publish(self, key: str, platform: str): "key_platform": platform } - conn.publish(self.ANNOUNCE, json.dumps(message)) + self.conn.publish(self.ANNOUNCE, json.dumps(message)) def unpublish(self, key: str, platform: str): """ Unpublish a key, and remove it from orchestration @@ -189,7 +191,7 @@ def unpublish(self, key: str, platform: str): "key_platform": platform } - conn.publish(self.ANNOUNCE, json.dumps(message)) + self.conn.publish(self.ANNOUNCE, json.dumps(message)) def wait(self, timeout_seconds = 30, republish = False): """ Wait for ACK from the orchestrator @@ -215,7 +217,7 @@ def wait(self, timeout_seconds = 30, republish = False): } listen_delta = 0.1 - conn.publish(self.ANNOUNCE, json.dumps(message)) + self.conn.publish(self.ANNOUNCE, json.dumps(message)) # Just wait for and consume the next incoming message while timeout_seconds >= 0: @@ -227,7 +229,7 @@ def wait(self, timeout_seconds = 30, republish = False): elif timeout_seconds < listen_delta: break elif republish: - conn.publish(self.ANNOUNCE, json.dumps(message)) + self.conn.publish(self.ANNOUNCE, json.dumps(message)) time.sleep(listen_delta) timeout_seconds -= listen_delta @@ -245,7 +247,7 @@ def list_platforms(self): "requester_id": self.id } - conn.publish(self.ANNOUNCE, json.dumps(message)) + self.conn.publish(self.ANNOUNCE, json.dumps(message)) reply = next(self.stdin.listen()) @@ -272,7 +274,7 @@ def list_keys(self, platform): "key_platform": platform } - conn.publish(self.ANNOUNCE, json.dumps(message)) + self.conn.publish(self.ANNOUNCE, json.dumps(message)) reply = next(self.stdin.listen()) @@ -302,7 +304,7 @@ def list_invalid_keys(self, platform): "key_platform": platform } - conn.publish(self.ANNOUNCE, json.dumps(message)) + self.conn.publish(self.ANNOUNCE, json.dumps(message)) reply = next(self.stdin.listen()) @@ -325,4 +327,4 @@ def shutdown(self): were sent prior to this message, and will then shut down immediately upon processing of the shutdown command """ - conn.publish(self.ANNOUNCE, json.dumps({"type": "SHUTDOWN"})) + self.conn.publish(self.ANNOUNCE, json.dumps({"type": "SHUTDOWN"})) diff --git a/keyman/Orchestrator.py b/keyman/Orchestrator.py index b16ec36ace..7086a43688 100644 --- a/keyman/Orchestrator.py +++ b/keyman/Orchestrator.py @@ -21,14 +21,16 @@ logger.addHandler(handler) # Attach the handler to the logger logger.setLevel(logging.DEBUG) else: - from augur.tasks.init.redis_connection import redis_connection as conn + from augur.tasks.init.redis_connection import get_redis_connection from augur.application.logs import AugurLogger logger = AugurLogger("KeyOrchestrator").get_logger() class KeyOrchestrator: def __init__(self) -> None: - self.stdin = conn.pubsub(ignore_subscribe_messages = True) + + self.conn = get_redis_connection() + self.stdin = self.conn.pubsub(ignore_subscribe_messages = True) self.logger = logger # Load channel names and IDs from the spec @@ -154,18 +156,18 @@ def run(self): elif request["type"] == "UNPUBLISH": self.unpublish_key(request["key_str"], request["key_platform"]) elif request["type"] == "ACK": - conn.publish(stdout, "") + self.conn.publish(stdout, "") self.logger.info(f"ACK; for: {request['requester_id']}") elif request["type"] == "LIST_PLATFORMS": platforms = [ p for p in self.fresh_keys.keys() ] - conn.publish(stdout, json.dumps(platforms)) + self.conn.publish(stdout, json.dumps(platforms)) elif request["type"] == "LIST_KEYS": keys = list(self.fresh_keys[request["key_platform"]]) keys += list(self.expired_keys[request["key_platform"]].keys()) - conn.publish(stdout, json.dumps(keys)) + self.conn.publish(stdout, json.dumps(keys)) elif request["type"] == "LIST_INVALID_KEYS": keys = list(self.invalid_keys[request["key_platform"]]) - conn.publish(stdout, json.dumps(keys)) + self.conn.publish(stdout, json.dumps(keys)) elif request["type"] == "SHUTDOWN": self.logger.info("Shutting down") # Close @@ -196,7 +198,7 @@ def run(self): break except WaitKeyTimeout as w: timeout = w.tiemout_seconds - conn.publish(stdout, json.dumps({ + self.conn.publish(stdout, json.dumps({ "wait": timeout })) continue @@ -206,7 +208,7 @@ def run(self): continue self.logger.debug(f"REPLY; for: {request['requester_id']}, platform: {request['key_platform']}") - conn.publish(stdout, json.dumps({ + self.conn.publish(stdout, json.dumps({ "key": new_key })) diff --git a/tests/test_tasks/test_task_utlities/test_key_handler/test_github_api_key_handler.py b/tests/test_tasks/test_task_utlities/test_key_handler/test_github_api_key_handler.py index 5443b3a733..59bcefbe9e 100644 --- a/tests/test_tasks/test_task_utlities/test_key_handler/test_github_api_key_handler.py +++ b/tests/test_tasks/test_task_utlities/test_key_handler/test_github_api_key_handler.py @@ -9,7 +9,7 @@ from augur.tasks.github.util.github_api_key_handler import GithubApiKeyHandler from augur.application.db.session import DatabaseSession -from augur.tasks.init.redis_connection import redis_connection as redis +from augur.tasks.init.redis_connection import get_redis_connection @pytest.fixture def httpx_client(): @@ -20,6 +20,8 @@ def httpx_client(): @pytest.fixture def key_handler(test_db_session): + + redis = get_redis_connection() redis.flushdb() diff --git a/tests/test_tasks/test_task_utlities/test_redis/test_redis_list.py b/tests/test_tasks/test_task_utlities/test_redis/test_redis_list.py index f57e755268..8e2ab29265 100644 --- a/tests/test_tasks/test_task_utlities/test_redis/test_redis_list.py +++ b/tests/test_tasks/test_task_utlities/test_redis/test_redis_list.py @@ -1,5 +1,5 @@ import pytest -from augur.tasks.init.redis_connection import redis_connection as redis +from augur.tasks.init.redis_connection import get_redis_connection from augur.tasks.util.redis_list import RedisList list_name = "list" @@ -11,10 +11,14 @@ def redis_list(): yield redis_list + redis = get_redis_connection() + redis.flushdb() def test_redis_list_append(redis_list): + redis = get_redis_connection() + string = "Hello world, how are you?" string_array = string.split(" ") @@ -32,6 +36,7 @@ def test_redis_list_append(redis_list): def test_redis_list_length(redis_list, data): # print(f"Data: {data}. Data length: {len(data)}") + redis = get_redis_connection() if data: redis.rpush(redis_list.redis_list_key, *data) @@ -58,6 +63,8 @@ def test_redis_list_length(redis_list, data): @pytest.mark.parametrize("data", [extend_data_1, extend_data_2]) def test_redis_list_extend(redis_list, data): + redis = get_redis_connection() + redis_list.extend(data) for i in range(0, len(data)): From 65cb3789d541a9d0078cf1873e28d7524cd5bc3b Mon Sep 17 00:00:00 2001 From: Adrian Edwards Date: Tue, 8 Jul 2025 14:13:10 -0400 Subject: [PATCH 47/66] start podman socket Signed-off-by: Adrian Edwards --- .github/workflows/build_docker.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/build_docker.yml b/.github/workflows/build_docker.yml index e78ff2fab6..64d69d8357 100644 --- a/.github/workflows/build_docker.yml +++ b/.github/workflows/build_docker.yml @@ -177,6 +177,9 @@ jobs: sudo rm -rf /usr/share/dotnet sudo rm -rf "$AGENT_TOOLSDIRECTORY" + - name: Start Podman socket + run: systemctl --user start podman.socket + - name: Checkout repository uses: actions/checkout@v4 From 93cb8e9a4228d14e2340b613a1cff8b60d39c288 Mon Sep 17 00:00:00 2001 From: "Sean P. Goggins" Date: Tue, 8 Jul 2025 17:59:30 -0500 Subject: [PATCH 48/66] Update KeyClient.py Update to address error message in end to end build. Signed-off-by: Sean P. Goggins --- keyman/KeyClient.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/keyman/KeyClient.py b/keyman/KeyClient.py index eab94b1a1b..21f9daa9fc 100644 --- a/keyman/KeyClient.py +++ b/keyman/KeyClient.py @@ -152,12 +152,13 @@ class KeyPublisher: as the process ID is used for async communication between the publisher and the orchestrator. """ + def __init__(self) -> None: # Load channel names and IDs from the spec for channel in spec["channels"]: # IE: self.ANNOUNCE = "augur-oauth-announce" setattr(self, channel["name"], channel["id"]) - + self.conn = get_redis_connection() self.id = getpid() self.stdin: PubSub = self.conn.pubsub(ignore_subscribe_messages = True) self.stdin.subscribe(f"{self.ANNOUNCE}-{self.id}") From e0eb110f45e1eacb3ea69c4d4ed6c766cfcb5212 Mon Sep 17 00:00:00 2001 From: Andrew Brain Date: Tue, 8 Jul 2025 18:17:22 -0500 Subject: [PATCH 49/66] assign connection at top level since docker orchestrator can't access augur --- keyman/Orchestrator.py | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/keyman/Orchestrator.py b/keyman/Orchestrator.py index 7086a43688..ed29397a9e 100644 --- a/keyman/Orchestrator.py +++ b/keyman/Orchestrator.py @@ -25,12 +25,12 @@ from augur.application.logs import AugurLogger logger = AugurLogger("KeyOrchestrator").get_logger() + conn = get_redis_connection() class KeyOrchestrator: def __init__(self) -> None: - self.conn = get_redis_connection() - self.stdin = self.conn.pubsub(ignore_subscribe_messages = True) + self.stdin = conn.pubsub(ignore_subscribe_messages = True) self.logger = logger # Load channel names and IDs from the spec @@ -156,18 +156,18 @@ def run(self): elif request["type"] == "UNPUBLISH": self.unpublish_key(request["key_str"], request["key_platform"]) elif request["type"] == "ACK": - self.conn.publish(stdout, "") + conn.publish(stdout, "") self.logger.info(f"ACK; for: {request['requester_id']}") elif request["type"] == "LIST_PLATFORMS": platforms = [ p for p in self.fresh_keys.keys() ] - self.conn.publish(stdout, json.dumps(platforms)) + conn.publish(stdout, json.dumps(platforms)) elif request["type"] == "LIST_KEYS": keys = list(self.fresh_keys[request["key_platform"]]) keys += list(self.expired_keys[request["key_platform"]].keys()) - self.conn.publish(stdout, json.dumps(keys)) + conn.publish(stdout, json.dumps(keys)) elif request["type"] == "LIST_INVALID_KEYS": keys = list(self.invalid_keys[request["key_platform"]]) - self.conn.publish(stdout, json.dumps(keys)) + conn.publish(stdout, json.dumps(keys)) elif request["type"] == "SHUTDOWN": self.logger.info("Shutting down") # Close @@ -198,7 +198,7 @@ def run(self): break except WaitKeyTimeout as w: timeout = w.tiemout_seconds - self.conn.publish(stdout, json.dumps({ + conn.publish(stdout, json.dumps({ "wait": timeout })) continue @@ -208,7 +208,7 @@ def run(self): continue self.logger.debug(f"REPLY; for: {request['requester_id']}, platform: {request['key_platform']}") - self.conn.publish(stdout, json.dumps({ + conn.publish(stdout, json.dumps({ "key": new_key })) From a68e7cbf8194a7238f955a594988bc2d34777e4a Mon Sep 17 00:00:00 2001 From: "Sean P. Goggins" Date: Tue, 8 Jul 2025 18:38:00 -0500 Subject: [PATCH 50/66] fixing make clean to preserve uv.lock Signed-off-by: Sean P. Goggins --- scripts/control/clean.sh | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/scripts/control/clean.sh b/scripts/control/clean.sh index 742d9dc36c..934eaa8f20 100755 --- a/scripts/control/clean.sh +++ b/scripts/control/clean.sh @@ -14,7 +14,8 @@ echo "Cleaning output files..." find . -name \*.out -delete find . -name \*.log -delete find . -name \*.err -delete -find . -type f -name "*.lock" -delete +find . -type f -name "*.lock" ! -name "uv.lock" -delete + rm -rf logs/ echo "Removing build files..." From ad865313559d91a9d537dcaa2cc1487097241de5 Mon Sep 17 00:00:00 2001 From: Adrian Edwards Date: Wed, 9 Jul 2025 10:31:52 -0400 Subject: [PATCH 51/66] determine whether to reset logs via a new AUGUR_RESET_LOGS environment variable this defaults to True to avoid infinite log growth unless explicitly opted in Signed-off-by: Adrian Edwards --- augur/application/cli/backend.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/augur/application/cli/backend.py b/augur/application/cli/backend.py index 343c60f823..28ed289033 100644 --- a/augur/application/cli/backend.py +++ b/augur/application/cli/backend.py @@ -32,7 +32,9 @@ from keyman.KeyClient import KeyClient, KeyPublisher -logger = AugurLogger("augur", reset_logfiles=True).get_logger() +reset_logs = os.getenv("AUGUR_RESET_LOGS", 'True').lower() in ('true', '1', 't', 'y', 'yes') + +logger = AugurLogger("augur", reset_logfiles=reset_logs).get_logger() @click.group('server', short_help='Commands for controlling the backend API server & data collection workers') From 00505ceef61986a0eebfbf4ae1f756835b81581f Mon Sep 17 00:00:00 2001 From: John Strunk Date: Fri, 27 Jun 2025 14:19:13 -0400 Subject: [PATCH 52/66] Allow DB connection specification via components Require individual DB config vars when AUGUR_DB is not set and construct AUGUR_DB from them. This allows specifying username, database name, etc. separately if desired. This was added because the postgres operator provides these individually, and by accepting the individual components, the postgres operator's secret can be directly mapped to the env vars on Kubernetes/OpenShift environments. Signed-off-by: John Strunk --- docker/backend/entrypoint.sh | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/docker/backend/entrypoint.sh b/docker/backend/entrypoint.sh index 3f7ae68387..bef5fd213b 100644 --- a/docker/backend/entrypoint.sh +++ b/docker/backend/entrypoint.sh @@ -2,6 +2,16 @@ #SPDX-License-Identifier: MIT set -e +if [[ -z "$AUGUR_DB" ]]; then + # Require AUGUR_DB_HOST, AUGUR_DB_USER, AUGUR_DB_PASSWORD, and AUGUR_DB_NAME to be set + if [[ -z "$AUGUR_DB_HOST" ]] || [[ -z "$AUGUR_DB_USER" ]] || [[ -z "$AUGUR_DB_PASSWORD" ]] || [[ -z "$AUGUR_DB_NAME" ]]; then + echo -e "When AUGUR_DB is not set, you must set AUGUR_DB_HOST, AUGUR_DB_USER,\nAUGUR_DB_PASSWORD, and AUGUR_DB_NAME" + exit 1 + fi + # Construct AUGUR_DB from the individual components + export AUGUR_DB="postgresql+psycopg2://${AUGUR_DB_USER}:${AUGUR_DB_PASSWORD}@${AUGUR_DB_HOST}/${AUGUR_DB_NAME}" +fi + if [[ "$AUGUR_DB" == *"localhost"* ]]; then echo "localhost db connection" export AUGUR_DB="${AUGUR_DB/localhost/host.docker.internal}" From 2a5793e374aad9ea64fe52cfafb661e46827cee0 Mon Sep 17 00:00:00 2001 From: Adrian Edwards Date: Wed, 9 Jul 2025 17:27:07 -0400 Subject: [PATCH 53/66] Adjust globbing for gunicorn template reload so its limited to the augur templates directory Co-authored-by: Ulincsys <28362836a@gmail.com> Signed-off-by: Adrian Edwards --- augur/api/gunicorn_conf.py | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/augur/api/gunicorn_conf.py b/augur/api/gunicorn_conf.py index 09c21161a0..3e7bf5e3a5 100644 --- a/augur/api/gunicorn_conf.py +++ b/augur/api/gunicorn_conf.py @@ -19,7 +19,17 @@ workers = multiprocessing.cpu_count() * 2 + 1 umask = 0o007 reload = True -reload_extra_files = glob(str(Path.cwd() / '**/*.j2'), recursive=True) + +augur_templates_dir = Path.cwd() / "augur/templates" + +if not augur_templates_dir.is_dir(): + logger.critical("Could not locate templates in Gunicorn startup") + exit(-1) + +reload_extra_files = glob(str(augur_templates_dir.resolve() / '**/*.j2'), recursive=True) + +# Don't want to leave extraneous variables in config scope +del augur_templates_dir # set the log location for gunicorn logs_directory = get_value('Logging', 'logs_directory') From bbda22102ee41935330c74dd1e372392491bbf0e Mon Sep 17 00:00:00 2001 From: Adrian Edwards Date: Wed, 9 Jul 2025 17:44:03 -0400 Subject: [PATCH 54/66] surround the template/hot reload config in a check for the AUGUR_DEV environment variable Signed-off-by: Adrian Edwards --- augur/api/gunicorn_conf.py | 20 +++++++++++++------- 1 file changed, 13 insertions(+), 7 deletions(-) diff --git a/augur/api/gunicorn_conf.py b/augur/api/gunicorn_conf.py index 3e7bf5e3a5..ef1295b316 100644 --- a/augur/api/gunicorn_conf.py +++ b/augur/api/gunicorn_conf.py @@ -1,6 +1,7 @@ # from augur import ROOT_AUGUR_DIRECTORY import multiprocessing import logging +import os from pathlib import Path from glob import glob @@ -20,16 +21,21 @@ umask = 0o007 reload = True -augur_templates_dir = Path.cwd() / "augur/templates" +is_dev = os.getenv("AUGUR_DEV", 'False').lower() in ('true', '1', 't', 'y', 'yes') -if not augur_templates_dir.is_dir(): - logger.critical("Could not locate templates in Gunicorn startup") - exit(-1) +if is_dev: -reload_extra_files = glob(str(augur_templates_dir.resolve() / '**/*.j2'), recursive=True) + augur_templates_dir = Path.cwd() / "augur/templates" -# Don't want to leave extraneous variables in config scope -del augur_templates_dir + if not augur_templates_dir.is_dir(): + logger.critical("Could not locate templates in Gunicorn startup") + exit(-1) + + reload_extra_files = glob(str(augur_templates_dir.resolve() / '**/*.j2'), recursive=True) + + # Don't want to leave extraneous variables in config scope + del augur_templates_dir +del is_dev # set the log location for gunicorn logs_directory = get_value('Logging', 'logs_directory') From 161cf0647c1fbef87684577a4a1d19dbc7ef79c2 Mon Sep 17 00:00:00 2001 From: "Sean P. Goggins" Date: Thu, 10 Jul 2025 18:16:48 -0500 Subject: [PATCH 55/66] removed junk Signed-off-by: Sean P. Goggins --- gsoc-ideas.md | 199 --------------------------------------------- gsoc-interest.md | 39 --------- run_http.sh | 4 - schema-updates.sql | 57 ------------- test.md | 1 - 5 files changed, 300 deletions(-) delete mode 100644 gsoc-ideas.md delete mode 100644 gsoc-interest.md delete mode 100755 run_http.sh delete mode 100644 schema-updates.sql delete mode 100644 test.md diff --git a/gsoc-ideas.md b/gsoc-ideas.md deleted file mode 100644 index 3bc2748811..0000000000 --- a/gsoc-ideas.md +++ /dev/null @@ -1,199 +0,0 @@ - -## Idea: Enhance Conversational Topic Modelling Capabilities in CHAOSS Software - -**Hours: 350** - -[Micro-tasks and place for questions](https://github.com/chaoss/augur/issues/1640) - -## Microtasks - -For becoming familiar with Augur, you can start by reading some documentation. You can find useful information at in the links, below. Grimoirelab also has a set of installation instructions and documentation here: https://chaoss.github.io/grimoirelab-tutorial/ - -#### GSoC Students : -Once you're familiar with Augur, you can have a look at the following microtasks. - -Microtask 0: - Download and configure Augur, creating a dev environment using the general cautions noted here: -Augur - https://oss-augur.readthedocs.io/en/dev/getting-started/installation.html and the full documentation here: - https://oss-augur.readthedocs.io/en/dev/development-guide/toc.html -Grimoirelab - https://chaoss.github.io/grimoirelab-tutorial/ - -Microstask 1: - Work on any Augur or Grimoirelab Issue that's Open - -Microtask 2: - Identify new issues you encounter during installation. - -Microstask 3: - Explore data presently captured, develop an experimental visualization using tools of your choice. If Jupyter Notebooks against an Augur database/API endpoint collection, use https://github.com/chaoss/augur-community-reports for development. - -Microtask 4: - Anything you want to show us. Even if you find bugs in our documentation and want to issue a PR for those! - - -This project will add GenSIM logic, and other capabilities to the Clustering Worker inside of Augur Software, and be extended into a generalized Open Source Software Conversational Topic Modeling Instrument. - -CHOASS/augur has several workers that store machine learning information derived from computational linguistic analysis of data in the `message` table. The message table includes messages from issue, pull request, pull request review, and email messages. They are related to their origin with bridge tables like `pull_request_message_ref`. The ML/CL workers are all run against all the messages, regardless of origin. - -1. Clustering Worker (clusters created and topics modeled) -2. message analysis worker (sentiment and novelty analysis) -3. discourse analysis worker (speech act classification (question, answer, approval, etc.) - -Clustering Worker Notes: - -Clustering Worker: 2 Models. - - Models: - - Topic modeling, but it needs a better way of estimating number of topics. - - Tables - - repo_topic - - topic_words - - Computational linguistic clustering - - Tables - - repo_cluster_messages - - Key Needs - - Add GenSim algorithms to topic modeling section https://github.com/chaoss/augur/issues/1199 - - The topics, and associated topic words need to be persisted after each run. At the moment, the topic words get overwritten for each topic modeling run. - - Description/optimization of the parameters used to create the computational linguistic clusters. - - Periodic deletion of models (heuristic: If 3 months pass, OR there’s a 10% increase in the messages, issues, or PRs in a repo, rebuild the models) - - Establish some kind of model archiving with appropriate metadata (lower priority) - -Discourse Analysis Worker Notes: - -discourse_insights table (select max(data_collection_date) for each msg_id) - - sequence is reassembled from the timestamp in the message table (look at msg_timestamp) - - issues_msg_ref, pull_request_message_ref, pull_request_review_msg_ref - -Message Analysis Worker - - message_analysis - - message_analysis_summary - -augur-tech - -The aims of the project are as follows: - - Advance topic modeling of open source software conversations captured in GitHub. - - Integrate this information into clearer, more parsimonious CHAOSS metrics. - - Automate the management machine learning insights, and topic models over time. - - (Stretch Goal) Improve the operation of the overall machine learning insights pipeline in CHAOSS/augur, and generalize these capabilities. - - - -## IDEA: Implement Conversion Rate Metric in CHAOSS Software - -**Hours: 350** - -[Micro-tasks and place for questions](https://github.com/chaoss/augur/issues/2992) - -### Conversion Rate - -Question: What are the rates at which new contributors become more sustained contributors? - -### Description - -The conversion rate metric is primarily aimed at identifying how new community members become more sustained contributors over time. However, the conversion rate metric can also help understand the changing roles of contributors, how a community is growing or declining, and paths to maintainership within an open source community. - -### Objectives (why) - - Observe if new members are becoming more involved with an open source project - - Observe if new members are taking on leadership roles within an open source project - - Observe if outreach efforts are generating new contributors to an open source project - - Observe if outreach efforts are impacting roles of existing community members - - Observe if community conflict results in changing roles within an open source community - - Identify casual, regular, and core contributors - -### Implementation - -This project could be implemented using either the CHAOSS/Augur, or CHAOSS/Grimoirelab (including stack components noted in references) technology stacks. - -The aims of the project are as follows: - - Implement the Conversion Rate Metric in CHAOSS Software - - After discussion, consider which CHAOSS Software Stack you wish to work with - - In collaboration with mentors, define the technology framework, and initial path to a "hello world" version of the metric - - Iterative development of the metric - - Assist in the deployment of this metric for a pre-determined collection of repositories in a publicly viewable website linked to the CHAOSS project. - - Advance the work of the [chaoss metrics models working group](https://github.com/chaoss/wg-metrics-models). - -* _Difficulty:_ Medium -* _Requirements:_ Knowledge of Python is desired. Some knowledge of Javascript or twitter/bootstrap is also desired. Key requirement is a keenness to dig into this challenge! -* _Recommended:_ Python experience. -* _Mentors:_ Sean Goggins - -#### Filters (optional) - - Commits - - Issue creation - - Issue comments - - Change request creation - - Change request comments - - Merged change requests - - Code Reviews - - Code Review Comments - - Reactions (emoji) - - Chat platform messages - - Maillist messages - - Meetup attendance - -#### Visualizations - -![](./images/gsoc-1.png) - -Source: https://chaoss.github.io/grimoirelab-sigils/assets/images/screenshots/sigils/overall-community-structure.png - -![](./images/gsoc-2.png) - -Source: https://opensource.com/sites/default/files/uploads/2021-09-15-developer-level-02.png - -#### Tools Providing the Metric - - Augur - - openEuler Infra - -#### Data Collection Strategies - -The following is an example from the [openEuler](https://www.openeuler.org/en/) community: - - A group of people who attended an offline event A held by the community, can be identified as Group A. Demographic information of Group A could be fetched from an on-line survey when people register for the event. To identify the conversation rate of these participants: - - Some people from Group A started watching and forking the repos, indicating they have shown some interest in this community. We marked them as subgroup D0 (Developer Level 0) as a subset of Group A. - - Conversion rate from the total number of people in Group A to the number of people in subgroup D0 is: D0/Group A - - Some people from subgroup D0 make more contributions beyond just watching or forking, including creating issues, making comments on an issue, or performed a code review. We marked them as subgroup D1 (Developer Level 1) as a subset of D0. - - Conversion rate from the total number of people in Subgroup D0 to the number of people in subgroup D1 is: D1/D0. - - Some people from subgroup D1 continue to make more contributions, like code contributions, to the project. This could include creating merge requests and merging new project code. We marked them as subgroup D2 (Developer Level 2) as a subset of D1. - - Conversion rate from the total number of people in subgroup D1 to the number of people in subgroup D2 is: D2/D1. - -![](./images/gsoc-3.png) - - Definition: - - Developer Level 0 (D0) example: Contributors who have given the project a star, or are watching or have forked the repository - - Developer Level 1 (D1): Contributors who have created issues, made comments on an issue, or performed a code review - - Developer Level 2 (D2): Contributors who have created a merge request and successfully merged code - - Conversion Rate (Group A -> D0): CR (Group A -> D2) = D0/Group A - - Conversion Rate (D0 -> D1): CR (D0 -> D1) = D1/D0 - - Conversion Rate (D1 -> D2): CR (D1 -> D2) = D2/D1 - -### References - - https://opensource.com/article/21/11/data-open-source-contributors - - https://github.com/chaoss/augur - - https://gitee.com/openeuler/website-v2/blob/master/web-ui/docs/en/blog/zhongjun/2021-09-15-developer-level.md - - https://chaoss.github.io/grimoirelab-sigils/common/onion_analysis/ - - https://mikemcquaid.com/2018/08/14/the-open-source-contributor-funnel-why-people-dont-contribute-to-your-open-source-project/ -### Contributors - - Sean Goggins - - Andrew Brain - - John McGinness - -## IDEA: Open Source Software Health Metrics Visualization Exploration - -**Hours: 350** - -[Micro-tasks and place for questions](https://github.com/chaoss/augur/issues/2993) - -The CHAOSS Community currently delivers pre-packaged visualizations of open source software health data through Augur APIs (https://github.com/chaoss/augur/blob/main/augur/routes/pull_request_reports.py and https://github.com/chaoss/augur/blob/main/augur/routes/contributor_reports.py), and the https://github.com/chaoss/augur-community-reports repository. This project seeks to expand, refine, and standardize the visualization of different classes of community health metrics data. Specifically, some analyses are temporal, others are anomaly driven, and in some cases contrasts across repositories and communities are required. In each case, the visualization of data is an essential component for metrics, and what we are now referring to as metrics models (https://github.com/chaoss/wg-metrics-models). - -Additional resources include: http://new.augurlabs.io/ && https://github.com/augurlabs/augur_view which demonsrate the updated twitter/bootstrap Augur frontend. - -The aims of the project are as follows: - - Experiment with standard metrics visualizations using direct Augur database connections, or through the Augur API. - - Refine metrics, and metrics model visualizations using Jupyter Notebooks are similar technology. - - Transform visualizations, as they are completed, into Augur API endpoints, following the pull request, and contributor reports examples. - -* _Difficulty:_ Medium -* _Requirements:_ Strong interest in data visualization. -* _Recommended:_ Experience with Python is desirable, and experience designing, or developing visualizations is desirable. -* _Mentors:_ Isaac Milarsky, Andrew Brain diff --git a/gsoc-interest.md b/gsoc-interest.md deleted file mode 100644 index e737687a01..0000000000 --- a/gsoc-interest.md +++ /dev/null @@ -1,39 +0,0 @@ -# Google Summer of Code 2025 Interested Candidates - -[IDEAS PAGE](https://github.com/chaoss/augur/blob/main/gsoc-ideas.md) - -Hi potential GSoC students, - -You can ask questions and meet the community on Slack here: https://join.slack.com/t/chaoss-workspace/shared_invite/zt-289zxh6tu-3oQaFlutPFY039MjKpnWcA ... look for the `wg-augur-8knot` channel. - -A few details regarding the application process specific to the CHAOSS project: - -1) You must complete one micro-task related to the idea you are interested in. You can find the micro-tasks on the GSoc Idea Page at: [gsoc-ideas.md](./gsoc-ideas.md) - -2) Once you completed one micro-task, create a pull request on this file below to add yourself, your information, and a link to your repository of the completed micro-task. **NOTE:** This repository requires [Developer Certificate of Origin](https://developercertificate.org/) (DCO) sign-off; see [CONTRIBUTING.md](https://github.com/chaoss/governance/blob/master/CONTRIBUTING.md#code-or-document-change-contributions-github-interface) for details on how to sign your commits. - -3) You are welcome to include in your repositories other information that could be of interest, such as open issues or pull requests submitted to the project to which you intend to contribute during GSoC, contributions to other projects, skills, and other related information. - -4) Using and submitting other people's work as your own is not allowed. If you use other people's work, be sure to acknowledge their work in your submission. - -5) Documentation of all code contributions is critical, and expected from all CHAOSS GSoC Students. - -You must complete these things by the GSOC Deadline. Make sure to also [submit the information required by GSoC for applicants](https://summerofcode.withgoogle.com/) (i.e., project proposal), linking to it from your pull request to this file. Here is an [Proposal Template](https://docs.google.com/document/d/1YZez6_hgp2dBybEsMZoQ-ONB9IawK4_OPISLHe9Tjew/edit) to get you started. - -Regards, -GSoC Mentors - ---- - -## Applicants - -**The applicants section will be completed as applicants are added here. At the moment, we are at the very beginning!** - - -**UPDATE:** This repository requires [Developer Certificate of Origin](https://developercertificate.org/) (DCO) sign-off; see [CONTRIBUTING.md](https://github.com/chaoss/governance/blob/master/CONTRIBUTING.md#code-or-document-change-contributions-github-interface) for details on how to sign your commits. - - -| Name | Email | Idea | Micro-Task Repository | Project Proposal | Submitted on GSOC | -| --- | --- | --- | --- | --- | --- | -| Your Name Here | Your Email Here | Idea You Hoping to Work On | Link to your Mico-task Repo | Link to Your Proposal | YES/NO | - diff --git a/run_http.sh b/run_http.sh deleted file mode 100755 index 1f0fb72d99..0000000000 --- a/run_http.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash -export AUGUR_DEV=1 -(nohup augur backend start &) - diff --git a/schema-updates.sql b/schema-updates.sql deleted file mode 100644 index a09cf0136f..0000000000 --- a/schema-updates.sql +++ /dev/null @@ -1,57 +0,0 @@ --- DO NOT IMPLEMENT YET .. trying to figure out why this happened. Running again. --- --- 10/1/2022: SPG - Got an error on this login constraint, which actually makes no sense. So, trying this change. -/* -Traceback (most recent call last): - File "/home/sean/github/virtualenv/k12/lib/python3.8/site-packages/celery/app/trace.py", line 451, in trace_task - R = retval = fun(*args, **kwargs) - File "/home/sean/github/virtualenv/k12/lib/python3.8/site-packages/celery/app/trace.py", line 734, in __protected_call__ - return self.run(*args, **kwargs) - File "/home/sean/github/rh-augur-new-dev/augur/tasks/start_tasks.py", line 159, in start_task - augur_collection.start_data_collection() - File "/home/sean/github/rh-augur-new-dev/augur/tasks/start_tasks.py", line 139, in start_data_collection - raise e - File "/home/sean/github/rh-augur-new-dev/augur/tasks/start_tasks.py", line 132, in start_data_collection - phaseResult.join() - File "/home/sean/github/virtualenv/k12/lib/python3.8/site-packages/celery/result.py", line 747, in join - value = result.get( - File "/home/sean/github/virtualenv/k12/lib/python3.8/site-packages/celery/result.py", line 224, in get - return self.backend.wait_for_pending( - File "/home/sean/github/virtualenv/k12/lib/python3.8/site-packages/celery/backends/asynchronous.py", line 221, in wait_for_pending - for _ in self._wait_for_pending(result, **kwargs): - File "/home/sean/github/virtualenv/k12/lib/python3.8/site-packages/celery/backends/asynchronous.py", line 287, in _wait_for_pending - for _ in self.drain_events_until( - File "/home/sean/github/virtualenv/k12/lib/python3.8/site-packages/celery/backends/asynchronous.py", line 58, in drain_events_until - on_interval() - File "/home/sean/github/virtualenv/k12/lib/python3.8/site-packages/vine/promises.py", line 160, in __call__ - return self.throw() - File "/home/sean/github/virtualenv/k12/lib/python3.8/site-packages/vine/promises.py", line 157, in __call__ - retval = fun(*final_args, **final_kwargs) - File "/home/sean/github/virtualenv/k12/lib/python3.8/site-packages/celery/result.py", line 237, in _maybe_reraise_parent_error - node.maybe_throw() - File "/home/sean/github/virtualenv/k12/lib/python3.8/site-packages/celery/result.py", line 609, in maybe_throw - result.maybe_throw(callback=callback, propagate=propagate) - File "/home/sean/github/virtualenv/k12/lib/python3.8/site-packages/celery/result.py", line 609, in maybe_throw - result.maybe_throw(callback=callback, propagate=propagate) - File "/home/sean/github/virtualenv/k12/lib/python3.8/site-packages/celery/result.py", line 336, in maybe_throw - self.throw(value, self._to_remote_traceback(tb)) - File "/home/sean/github/virtualenv/k12/lib/python3.8/site-packages/celery/result.py", line 329, in throw - self.on_ready.throw(*args, **kwargs) - File "/home/sean/github/virtualenv/k12/lib/python3.8/site-packages/vine/promises.py", line 234, in throw - reraise(type(exc), exc, tb) - File "/home/sean/github/virtualenv/k12/lib/python3.8/site-packages/vine/utils.py", line 30, in reraise - raise value -Exception: (['(psycopg2.errors.UniqueViolation) duplicate key value violates unique constraint "GL-cntrb-LOGIN-UNIQUE"\nDETAIL: Key (cntrb_login)=(name) already exists.\n']) -*/ - -ALTER TABLE "augur_data"."commits" DROP CONSTRAINT "fk_commits_contributors_3"; - -ALTER TABLE "augur_data"."commits" DROP CONSTRAINT "fk_commits_contributors_4"; - -ALTER TABLE "augur_data"."contributors" - DROP CONSTRAINT "GL-cntrb-LOGIN-UNIQUE", - ADD CONSTRAINT "GL-cntrb-LOGIN-UNIQUE" UNIQUE ("cntrb_login") DEFERRABLE INITIALLY DEFERRED; - -ALTER TABLE "augur_data"."commits" ADD CONSTRAINT "fk_commits_contributors_3" FOREIGN KEY ("cmt_author_platform_username") REFERENCES "augur_data"."contributors" ("cntrb_login") ON DELETE RESTRICT ON UPDATE CASCADE DEFERRABLE INITIALLY DEFERRED; - -ALTER TABLE "augur_data"."commits" ADD CONSTRAINT "fk_commits_contributors_4" FOREIGN KEY ("cmt_author_platform_username") REFERENCES "augur_data"."contributors" ("cntrb_login") ON DELETE RESTRICT ON UPDATE CASCADE DEFERRABLE INITIALLY DEFERRED; diff --git a/test.md b/test.md deleted file mode 100644 index 753e9975dd..0000000000 --- a/test.md +++ /dev/null @@ -1 +0,0 @@ -teh test From 08515de89d1adafb51cb18b50bdc0f5dfe429984 Mon Sep 17 00:00:00 2001 From: Adrian Edwards Date: Wed, 2 Jul 2025 09:34:11 -0400 Subject: [PATCH 56/66] Add an exception case for handling 410 Gone when making requests to github This may happen if requesting issues or issue comments when issues have been disabled for a repo Signed-off-by: Adrian Edwards --- augur/tasks/github/util/github_data_access.py | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/augur/tasks/github/util/github_data_access.py b/augur/tasks/github/util/github_data_access.py index 3e8a8accc6..b8248c02b0 100644 --- a/augur/tasks/github/util/github_data_access.py +++ b/augur/tasks/github/util/github_data_access.py @@ -22,6 +22,17 @@ class UrlNotFoundException(Exception): class NotAuthorizedException(Exception): pass +class ResourceGoneException(Exception): + """Exception class indicating the requested resource (or necessary parent resource) + is intentionally unavailable (such as requesting issues for a repo when they are disabled) + + example: https://api.github.com/repos/openshift/release/issues/4352/comments + + See also: https://httpstatuses.com/410 + """ + def __init__(self, message="Resource returned HTTP 410 Gone. It is likely intentionally removed"): + super().__init__(message) + class GithubDataAccess: def __init__(self, key_manager, logger: logging.Logger, feature="rest"): @@ -124,6 +135,13 @@ def make_request(self, url, method="GET", timeout=100): if response.status_code == 401: raise NotAuthorizedException(f"Could not authorize with the github api") + if response.status_code == 410: + response_msg = response.json().get("message") + if response_msg is not None: + raise ResourceGoneException(response_msg) + else: + raise ResourceGoneException() + response.raise_for_status() try: From 04ef1ef09b373d410c392702df12616345c83fab Mon Sep 17 00:00:00 2001 From: Adrian Edwards Date: Wed, 9 Jul 2025 09:44:02 -0400 Subject: [PATCH 57/66] include ResourceGoneException as one that should be ignored during a retry Signed-off-by: Adrian Edwards --- augur/tasks/github/util/github_data_access.py | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/augur/tasks/github/util/github_data_access.py b/augur/tasks/github/util/github_data_access.py index b8248c02b0..5764880223 100644 --- a/augur/tasks/github/util/github_data_access.py +++ b/augur/tasks/github/util/github_data_access.py @@ -163,13 +163,16 @@ def make_request_with_retries(self, url, method="GET", timeout=100): return self.__make_request_with_retries(url, method, timeout) except RetryError as e: raise e.last_attempt.exception() + + def _decide_retry_policy(exception): + return not isinstance(num, (UrlNotFoundException, ResourceGoneException)) - @retry(stop=stop_after_attempt(10), wait=wait_fixed(5), retry=retry_if_exception(lambda exc: not isinstance(exc, UrlNotFoundException))) + @retry(stop=stop_after_attempt(10), wait=wait_fixed(5), retry=retry_if_exception(_decide_retry_policy)) def __make_request_with_retries(self, url, method="GET", timeout=100): """ What method does? 1. Retires 10 times 2. Waits 5 seconds between retires - 3. Does not rety UrlNotFoundException + 3. Does not retry any exceptions excluded by _decide_retry_policy 4. Catches RatelimitException and waits or expires key before raising exception """ From 99a82235e2c0a86a3c03d3b138e8f982ae17f734 Mon Sep 17 00:00:00 2001 From: Adrian Edwards Date: Wed, 9 Jul 2025 09:54:24 -0400 Subject: [PATCH 58/66] Add docs to _decide_retry_policy Signed-off-by: Adrian Edwards --- augur/tasks/github/util/github_data_access.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/augur/tasks/github/util/github_data_access.py b/augur/tasks/github/util/github_data_access.py index 5764880223..8a8ca57372 100644 --- a/augur/tasks/github/util/github_data_access.py +++ b/augur/tasks/github/util/github_data_access.py @@ -164,7 +164,12 @@ def make_request_with_retries(self, url, method="GET", timeout=100): except RetryError as e: raise e.last_attempt.exception() - def _decide_retry_policy(exception): + def _decide_retry_policy(exception: Exception) -> bool: + """Defines whether or not to retry a failed request based on the exception thrown + + Returns: + bool: Boolean describing whether or not the request should be retried + """ return not isinstance(num, (UrlNotFoundException, ResourceGoneException)) @retry(stop=stop_after_attempt(10), wait=wait_fixed(5), retry=retry_if_exception(_decide_retry_policy)) From 537df456981183ea22e282eb58e51c78942cc666 Mon Sep 17 00:00:00 2001 From: Adrian Edwards Date: Thu, 10 Jul 2025 21:12:33 -0400 Subject: [PATCH 59/66] Address warnings from linter Signed-off-by: Adrian Edwards --- augur/api/gunicorn_conf.py | 2 +- augur/application/cli/collection.py | 29 ++++++++++++++--------------- augur/application/cli/config.py | 2 +- 3 files changed, 16 insertions(+), 17 deletions(-) diff --git a/augur/api/gunicorn_conf.py b/augur/api/gunicorn_conf.py index ef1295b316..4e97d7b465 100644 --- a/augur/api/gunicorn_conf.py +++ b/augur/api/gunicorn_conf.py @@ -5,7 +5,7 @@ from pathlib import Path from glob import glob -from augur.application.db.lib import get_value, get_section +from augur.application.db.lib import get_value from augur.application.db import dispose_database_engine logger = logging.getLogger(__name__) diff --git a/augur/application/cli/collection.py b/augur/application/cli/collection.py index b42f1f3fcc..f18ff03e29 100644 --- a/augur/application/cli/collection.py +++ b/augur/application/cli/collection.py @@ -2,7 +2,6 @@ """ Augur library commands for controlling the backend components """ -import resource import os import time import subprocess @@ -27,7 +26,7 @@ from augur.application.cli import test_connection, test_db_connection, with_database, DatabaseContext from augur.application.cli._cli_util import _broadcast_signal_to_processes, raise_open_file_limit, clear_redis_caches, clear_rabbitmq_messages -from keyman.KeyClient import KeyClient, KeyPublisher +from keyman.KeyClient import KeyPublisher logger = AugurLogger("augur", reset_logfiles=False).get_logger() @@ -81,7 +80,7 @@ def start(ctx, development): worker_vmem_cap = get_value("Celery", 'worker_process_vmem_cap') - processes = start_celery_collection_processes(float(worker_vmem_cap)) + process_list = start_celery_collection_processes(float(worker_vmem_cap)) if os.path.exists("celerybeat-schedule.db"): logger.info("Deleting old task schedule") @@ -110,11 +109,11 @@ def start(ctx, development): try: - processes[0].wait() + process_list[0].wait() except KeyboardInterrupt: logger.info("Shutting down all celery worker processes") - for p in processes: + for p in process_list: if p: p.terminate() @@ -185,9 +184,9 @@ def stop(ctx): """ Sends SIGTERM to all Augur server & worker processes """ - logger = logging.getLogger("augur.cli") + cli_logger = logging.getLogger("augur.cli") - augur_stop(signal.SIGTERM, logger, ctx.obj.engine) + augur_stop(signal.SIGTERM, cli_logger, ctx.obj.engine) @cli.command('kill') @with_database @@ -196,8 +195,8 @@ def kill(ctx): """ Sends SIGKILL to all Augur server & worker processes """ - logger = logging.getLogger("augur.cli") - augur_stop(signal.SIGKILL, logger, ctx.obj.engine) + cli_logger = logging.getLogger("augur.cli") + augur_stop(signal.SIGKILL, cli_logger, ctx.obj.engine) @cli.command('repo-reset') @test_connection @@ -263,7 +262,7 @@ def is_collection_process(process): return False -def augur_stop(signal, logger, engine): +def augur_stop(stop_signal, logger_instance, engine): """ Stops augur with the given signal, and cleans up collection if it was running @@ -271,21 +270,21 @@ def augur_stop(signal, logger, engine): augur_collection_processes = get_augur_collection_processes() - _broadcast_signal_to_processes(augur_collection_processes, logger=logger, broadcast_signal=signal) + _broadcast_signal_to_processes(augur_collection_processes, logger=logger_instance, broadcast_signal=stop_signal) cleanup_after_collection_halt(logger, engine) -def cleanup_after_collection_halt(logger, engine): +def cleanup_after_collection_halt(logger_instance, engine): queues = ['celery', 'core', 'secondary','scheduling','facade'] connection_string = get_value("RabbitMQ", "connection_string") - with DatabaseSession(logger, engine) as session: + with DatabaseSession(logger_instance, engine) as session: clean_collection_status(session) - clear_rabbitmq_messages(connection_string, queues, logger) - clear_redis_caches(logger) + clear_rabbitmq_messages(connection_string, queues, logger_instance) + clear_redis_caches(logger_instance) #Make sure that database reflects collection status when processes are killed/stopped. def clean_collection_status(session): diff --git a/augur/application/cli/config.py b/augur/application/cli/config.py index 1e73698fc3..7156c0561b 100644 --- a/augur/application/cli/config.py +++ b/augur/application/cli/config.py @@ -237,7 +237,7 @@ def config_get_all_json(): for row in session.query(Config).all(): data[row.section_name][row.setting_name] = row.value - except: + except Exception: pass print(json.dumps(data, indent=4)) From d3d1ef480e1b709e53a046aa4266a67d993bcd64 Mon Sep 17 00:00:00 2001 From: John Strunk Date: Fri, 11 Jul 2025 09:59:39 -0400 Subject: [PATCH 60/66] Update entrypoint.sh construction of AUGUR_DB from env vars This changes the test for the DB connection components to not exit with failure if AUGUR_DB can't be constructed. Signed-off-by: John Strunk --- docker/backend/entrypoint.sh | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/docker/backend/entrypoint.sh b/docker/backend/entrypoint.sh index bef5fd213b..4583aa972b 100644 --- a/docker/backend/entrypoint.sh +++ b/docker/backend/entrypoint.sh @@ -3,15 +3,13 @@ set -e if [[ -z "$AUGUR_DB" ]]; then - # Require AUGUR_DB_HOST, AUGUR_DB_USER, AUGUR_DB_PASSWORD, and AUGUR_DB_NAME to be set - if [[ -z "$AUGUR_DB_HOST" ]] || [[ -z "$AUGUR_DB_USER" ]] || [[ -z "$AUGUR_DB_PASSWORD" ]] || [[ -z "$AUGUR_DB_NAME" ]]; then - echo -e "When AUGUR_DB is not set, you must set AUGUR_DB_HOST, AUGUR_DB_USER,\nAUGUR_DB_PASSWORD, and AUGUR_DB_NAME" - exit 1 + # If AUGUR_DB is not set, check for individual environment variables and construct AUGUR_DB connection string + if [[ -n "$AUGUR_DB_HOST" ]] && [[ -n "$AUGUR_DB_USER" ]] && [[ -n "$AUGUR_DB_PASSWORD" ]] && [[ -n "$AUGUR_DB_NAME" ]]; then + export AUGUR_DB="postgresql+psycopg2://${AUGUR_DB_USER}:${AUGUR_DB_PASSWORD}@${AUGUR_DB_HOST}/${AUGUR_DB_NAME}" fi - # Construct AUGUR_DB from the individual components - export AUGUR_DB="postgresql+psycopg2://${AUGUR_DB_USER}:${AUGUR_DB_PASSWORD}@${AUGUR_DB_HOST}/${AUGUR_DB_NAME}" fi + if [[ "$AUGUR_DB" == *"localhost"* ]]; then echo "localhost db connection" export AUGUR_DB="${AUGUR_DB/localhost/host.docker.internal}" From e4f10e1fcdf397396c138659d74b6c7a2fc87138 Mon Sep 17 00:00:00 2001 From: Adrian Edwards Date: Mon, 14 Jul 2025 10:50:22 -0400 Subject: [PATCH 61/66] fix missing docker -> podman in podman CI job --- .github/workflows/build_docker.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build_docker.yml b/.github/workflows/build_docker.yml index 64d69d8357..d37d205da4 100644 --- a/.github/workflows/build_docker.yml +++ b/.github/workflows/build_docker.yml @@ -269,7 +269,7 @@ jobs: run: | podman compose -f docker-compose.yml up --no-build 2>&1 \ | (./scripts/ci/await_all.py /tmp/regex_matches.txt \ - && docker compose -f docker-compose.yml down) + && podman compose -f docker-compose.yml down) timeout-minutes: 3 env: AUGUR_GITHUB_API_KEY: ${{ secrets.GITHUB_TOKEN }} From 08aeca436cdeeac133b143d0105af99e7723c72f Mon Sep 17 00:00:00 2001 From: Adrian Edwards Date: Thu, 17 Jul 2025 16:32:45 -0400 Subject: [PATCH 62/66] use check_output for git log Signed-off-by: Adrian Edwards --- .../facade_worker/analyzecommit.py | 23 +++++++++++-------- 1 file changed, 14 insertions(+), 9 deletions(-) diff --git a/augur/tasks/git/util/facade_worker/facade_worker/analyzecommit.py b/augur/tasks/git/util/facade_worker/facade_worker/analyzecommit.py index d64564bd8b..0426c8372e 100644 --- a/augur/tasks/git/util/facade_worker/facade_worker/analyzecommit.py +++ b/augur/tasks/git/util/facade_worker/facade_worker/analyzecommit.py @@ -149,14 +149,19 @@ def analyze_commit( recordsToInsert: List[Dict[str, Any]] = [] try: - git_log = subprocess.Popen( - ["git --git-dir %s log -p -M %s -n1 " - "--pretty=format:'" - "author_name: %%an%%nauthor_email: %%ae%%nauthor_date:%%ai%%n" - "committer_name: %%cn%%ncommitter_email: %%ce%%ncommitter_date: %%ci%%n" - "parents: %%p%%nEndPatch' " % (repo_loc, commit)], - stdout=subprocess.PIPE, - shell=True + pretty_format = ( + "author_name: %an%n" + "author_email: %ae%n" + "author_date:%ai%n" + "committer_name: %cn%n" + "committer_email: %ce%n" + "committer_date: %ci%n" + "parents: %p%n" + "EndPatch" + ) + git_log = check_output( + [f"git", "--git-dir", repo_loc, "log", "-p", "-M", commit, "-n1", + f"--pretty=format:'{pretty_format}'"] ) except Exception as e: logger.error(f"Failed to run git log for commit {commit}: {e}") @@ -189,7 +194,7 @@ def analyze_commit( } try: - log_output = git_log.stdout.read().decode("utf-8", errors="ignore") + log_output = git_log.decode("utf-8", errors="ignore") except Exception as e: logger.error(f"Failed to read stdout from git process for commit {commit}: {e}") return [], msg_record From df4aeb927dd3e39cece3bffc75c14f9cf9e6f262 Mon Sep 17 00:00:00 2001 From: Adrian Edwards Date: Fri, 18 Jul 2025 10:56:41 -0400 Subject: [PATCH 63/66] correct docs links in error messages relating to keys Signed-off-by: Adrian Edwards --- scripts/install/config.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/scripts/install/config.sh b/scripts/install/config.sh index d3b9695098..0408b0aa09 100755 --- a/scripts/install/config.sh +++ b/scripts/install/config.sh @@ -43,7 +43,7 @@ function get_github_api_key() { echo echo "Please provide a valid GitHub API key." echo "For more information on how to create the key, visit:" - echo "https://oss-augur.readthedocs.io/en/dev/getting-started/installation.html#backend" + echo "https://oss-augur.readthedocs.io/en/main/getting-started/installation.html#backend" echo "** This is required for Augur to gather data ***" read -p "GitHub API Key: " github_api_key blank_confirm github_api_key @@ -63,7 +63,7 @@ function get_gitlab_api_key() { echo echo "Please provide a valid GitLab API key." echo "For more information on how to create the key, visit:" - echo "https://oss-augur.readthedocs.io/en/dev/getting-started/installation.html#backend" + echo "https://oss-augur.readthedocs.io/en/main/getting-started/installation.html#backend" echo "** This is required for Augur to gather data ***" read -p "GitLab API Key: " gitlab_api_key blank_confirm gitlab_api_key From 78cacb13d4940cd51b08a482b68645b2c3fa1ebd Mon Sep 17 00:00:00 2001 From: Adrian Edwards Date: Fri, 18 Jul 2025 11:05:14 -0400 Subject: [PATCH 64/66] another main -> dev from RTD Signed-off-by: Adrian Edwards --- docs/source/docker/quick-start.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/docker/quick-start.rst b/docs/source/docker/quick-start.rst index 84fb61a7f0..b7d7b7cc7e 100644 --- a/docs/source/docker/quick-start.rst +++ b/docs/source/docker/quick-start.rst @@ -7,7 +7,7 @@ Before you get off to such a quick start, go ahead and .. code-block:: python - git checkout dev + git checkout main 4. Create a .env file in the top level directory with the following fields: From c45d53bf35d9766bf0d30eb972543c57c6517397 Mon Sep 17 00:00:00 2001 From: Adrian Edwards <17362949+MoralCode@users.noreply.github.com> Date: Fri, 18 Jul 2025 22:53:50 -0400 Subject: [PATCH 65/66] Fix variable name in _decide_retry_policy Signed-off-by: Adrian Edwards <17362949+MoralCode@users.noreply.github.com> --- augur/tasks/github/util/github_data_access.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/augur/tasks/github/util/github_data_access.py b/augur/tasks/github/util/github_data_access.py index 8a8ca57372..7827282334 100644 --- a/augur/tasks/github/util/github_data_access.py +++ b/augur/tasks/github/util/github_data_access.py @@ -170,7 +170,7 @@ def _decide_retry_policy(exception: Exception) -> bool: Returns: bool: Boolean describing whether or not the request should be retried """ - return not isinstance(num, (UrlNotFoundException, ResourceGoneException)) + return not isinstance(exception, (UrlNotFoundException, ResourceGoneException)) @retry(stop=stop_after_attempt(10), wait=wait_fixed(5), retry=retry_if_exception(_decide_retry_policy)) def __make_request_with_retries(self, url, method="GET", timeout=100): From 69c17385962a173139b08fa1cd3ef0019a6f4fd2 Mon Sep 17 00:00:00 2001 From: Ulincsys Date: Thu, 24 Jul 2025 18:24:31 -0500 Subject: [PATCH 66/66] cache redis connection on first retrieval Signed-off-by: Ulincsys --- augur/tasks/init/redis_connection.py | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/augur/tasks/init/redis_connection.py b/augur/tasks/init/redis_connection.py index 7860172b39..33e0aec3f0 100644 --- a/augur/tasks/init/redis_connection.py +++ b/augur/tasks/init/redis_connection.py @@ -4,9 +4,11 @@ def get_redis_connection(): + global redis_connection - redis_db_number, redis_conn_string = get_redis_conn_values() - - redis_connection= redis.from_url(f'{redis_conn_string}{redis_db_number+2}', decode_responses=True) + # Only load the redis connection values once + if "redis_connection" not in globals(): + redis_db_number, redis_conn_string = get_redis_conn_values() + redis_connection = redis.from_url(f'{redis_conn_string}{redis_db_number+2}', decode_responses=True) return redis_connection