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Merged
jeromedockes merged 6 commits into from
Aug 23, 2025
Merged

update packaging & min deps versions #56

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62f6589
update packaging & min deps versions
jeromedockes Aug 20, 2025
b0a2381
no sparse matrix .A
jeromedockes Aug 20, 2025
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jeromedockes Aug 21, 2025
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jeromedockes Aug 21, 2025
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jeromedockes Aug 23, 2025
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jeromedockes Aug 23, 2025
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96 changes: 19 additions & 77 deletions .github/workflows/testing.yml
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Expand Up @@ -13,108 +13,50 @@ jobs:
name: checks
runs-on: "ubuntu-latest"
steps:
- uses: actions/checkout@v2
- uses: actions/setup-python@v2
- uses: actions/checkout@v4
- uses: actions/setup-python@v5
with:
python-version: "3.10"
python-version: "3.13"
- name: "install"
run: pip install .[dev]
run: pip install ".[dev]"
- name: "mypy"
run: make test_mypy
- name: "flake8"
run: make test_flake8

run_tests:
name: ${{ matrix.os }} with Python ${{ matrix.python-version }}
name: ${{ matrix.os }} ${{ matrix.environment }}
runs-on: ${{ matrix.os }}
strategy:
matrix:
os: ["ubuntu-latest", "windows-latest", "macos-latest"]
python-version: ["3.7", "3.10"]
environment: ["py310-min-deps", "py313-latest-deps"]
steps:
- uses: actions/checkout@v2
- uses: actions/setup-python@v2
- uses: actions/checkout@v4
- uses: prefix-dev/setup-pixi@v0.8.8
with:
python-version: ${{ matrix.python-version }}
name: "setup python"
- name: "install"
run: pip install .[dev]
- name: "run tests"
run: make test_coverage
- uses: codecov/codecov-action@v2
if: success()
name: "upload coverage to CodeCov"

run_tests_ubuntu_old_dependencies:
name: "Ubuntu with Python 3.7 min dependencies"
runs-on: "ubuntu-latest"
steps:
- uses: actions/checkout@v2
- uses: actions/setup-python@v2
with:
python-version: "3.7"
name: "setup python"
- name: "install tox"
run: pip install tox
- name: "run tests"
run: tox -e py37-old

run_tests_with_nimare_installed:
name: "Ubuntu with Python 3.8 and NiMARE"
runs-on: "ubuntu-latest"
steps:
- uses: actions/checkout@v2
- uses: actions/setup-python@v2
with:
python-version: "3.8"
name: "setup python"
- name: "install tox"
run: pip install tox
pixi-version: v0.41.3
environments: ${{ matrix.environment }}
frozen: true
- name: "run tests"
run: tox -e py38-nimare

run_test_plugin:
name: "Test plugin"
runs-on: "ubuntu-latest"
steps:
- uses: actions/checkout@v2
- uses: actions/setup-python@v2
with:
python-version: "3.10"
name: "setup python"
- name: "install tox"
run: pip install tox
- name: "run tests"
run: make test_plugin

run_compare_query_vs_pmcid_list:
name: "Compare query vs PMCID list"
runs-on: "ubuntu-latest"
steps:
- uses: actions/checkout@v2
- uses: actions/setup-python@v2
with:
python-version: "3.10"
name: "setup python"
- name: "install"
run: pip install .[dev]
- name: "run check"
run: make compare_query_vs_pmcid_list
run: pixi run -e ${{ matrix.environment }} test
- name: "upload coverage to CodeCov"
uses: codecov/codecov-action@v5.4.3

build_doc:
name: "build documentation"
runs-on: "ubuntu-latest"
steps:
- uses: actions/checkout@v2
- uses: actions/setup-python@v2
- uses: actions/checkout@v4
- uses: actions/setup-python@v5
with:
python-version: "3.10"
python-version: "3.13"
- name: "install"
run: pip install .[dev]
run: pip install ".[dev]"
- name: "build"
run: make doc
- name: "store doc artifact"
uses: actions/upload-artifact@v2
uses: actions/upload-artifact@v4
with:
name: documentation
path: doc_build/pubget.html
7 changes: 3 additions & 4 deletions Makefile
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Expand Up @@ -7,7 +7,7 @@ pubget_version := $(shell cat src/pubget/_data/VERSION)
test_all: test_mypy test_flake8 test_coverage_strict test test_plugin test_pylint

test:
tox
pytest tests

test_coverage_strict:
pytest --cov=pubget --cov-report=xml --cov-report=term --cov-fail-under=100 tests
Expand All @@ -28,8 +28,7 @@ test_pylint:
pylint ./src

test_plugin:
tox -e run_plugin
tox -c docs/example_plugin/tox.ini
pixi run run_plugin

run_full_pipeline:
python tests/run_full_pipeline.py -o /tmp/
Expand Down Expand Up @@ -58,4 +57,4 @@ clean:
rm -rf doc_build build dist htmlcov .coverage .coverage.*

clean_all: clean
rm -rf .mypy_cache .pytest_cache .tox
rm -rf .mypy_cache .pytest_cache
22 changes: 20 additions & 2 deletions docs/example_plugin/pyproject.toml
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@@ -1,3 +1,21 @@
[build-system]
requires = ["setuptools", "wheel"]
build-backend = "setuptools.build_meta"
requires = ["hatchling"]
build-backend = "hatchling.build"

[project]
name = "pubget_example_plugin"
version = "0.1.0"
requires-python = ">=3.10"
dependencies = [
"pandas",
"matplotlib",
"pubget",
]

[project.optional-dependencies]
dev = [
"pytest",
]

[project.entry-points."pubget.plugin_actions"]
get_pubget_actions = "pubget_example_plugin:get_pubget_actions"
9 changes: 0 additions & 9 deletions docs/example_plugin/tox.ini
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