V2/default task weights

.bumpversion.cfg

@@ -1,11 +1,9 @@
 [bumpversion]
-current_version = 1.5.1
+current_version = 2.0.0b1
 commit = True
 tag = True
 
-[bumpversion:file:setup.cfg]
-
-[bumpversion:file:setup.py]
+[bumpversion:file:pyproject.toml]
 
 [bumpversion:file:chemprop/__init__.py]
 

.flake8

@@ -0,0 +1,8 @@
+[flake8]
+ignore = E203, E266, E501, F403, E741, W503, W605
+max-line-length = 100
+max-complexity = 18
+per-file-ignores =
+    __init__.py: F401
+    chemprop/nn/predictors.py: F405
+    chemprop/nn/metrics.py: F405

.github/ISSUE_TEMPLATE/todo.md

@@ -0,0 +1,11 @@
+---
+name: to-do
+about: Add an item to the to-do list. More generic than a feature request
+title: "[TODO]: "
+labels: todo
+assignees: ''
+
+---
+
+**Notes**
+_these could be implementation or more specific details to keep in mind, if they'll be helpful for issue tracking_

.github/ISSUE_TEMPLATE/v1_bug_report.md

@@ -0,0 +1,35 @@
+---
+name: v1 Bug Report
+about: Report a bug in v1 (will not be fixed)
+title: "[v1 BUG]: "
+labels: bug, v1-wontfix
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**Example(s)**
+Provide some examples of where the current code fails. Feel free to share your actual code for additional context, but a minimal and isolated example is preferred.
+
+**Expected behavior**
+A clear and concise description of what you expected to happen. If there is correct, expected output, include that here as well.
+
+**Error Stack Trace**
+If the bug is resulting in an error message, provide the _full_ stack trace (not just the last line). This is helpful for debugging, especially in cases where you aren't able to provide a minimum/isolated working example with accompanying files.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Environment**
+- python version
+- package versions: `conda list` or `pip list`
+- OS
+
+**Checklist**
+- [ ] all dependencies are satisifed: `conda list` or `pip list` shows the packages listed in the `pyproject.toml`
+- [ ] the unit tests are working: `pytest -v` reports no errors
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/question.md → .github/ISSUE_TEMPLATE/v1_question.md

@@ -1,7 +1,7 @@
 ---
-name: Question
-about: Have a question about how to use Chemprop?
-title: "[QUESTION]: "
+name: v1 Question
+about: Have a question about how to use Chemprop v1?
+title: "[v1 QUESTION]: "
 labels: question
 assignees: ''
 

.github/ISSUE_TEMPLATE/bug_report.md → .github/ISSUE_TEMPLATE/v2_bug_report.md

@@ -1,7 +1,7 @@
 ---
-name: Bug report
+name: v2 Bug Report
 about: Create a report to help us improve
-title: "[BUG]: "
+title: "[v2 BUG]: "
 labels: bug
 assignees: ''
 
@@ -16,6 +16,9 @@ Provide some examples of where the current code fails. Feel free to share your a
 **Expected behavior**
 A clear and concise description of what you expected to happen. If there is correct, expected output, include that here as well.
 
+**Error Stack Trace**
+If the bug is resulting in an error message, provide the _full_ stack trace (not just the last line). This is helpful for debugging, especially in cases where you aren't able to provide a minimum/isolated working example with accompanying files.
+
 **Screenshots**
 If applicable, add screenshots to help explain your problem.
 
@@ -25,7 +28,7 @@ If applicable, add screenshots to help explain your problem.
 - OS
 
 **Checklist**
-- [ ] all dependencies are satisifed: `conda list` shows the packages listed in the `README`
+- [ ] all dependencies are satisifed: `conda list` or `pip list` shows the packages listed in the `pyproject.toml`
 - [ ] the unit tests are working: `pytest -v` reports no errors
 
 **Additional context**

.github/ISSUE_TEMPLATE/feature_request.md → .github/ISSUE_TEMPLATE/v2_feature_request.md

@@ -1,7 +1,7 @@
 ---
-name: Feature request
+name: v2 Feature Request
 about: Suggest an idea for this project
-title: "[FEATURE]: "
+title: "[v2 FEATURE]: "
 labels: enhancement
 assignees: ''
 

.github/ISSUE_TEMPLATE/v2_question.md

@@ -0,0 +1,17 @@
+---
+name: v2 Question
+about: Have a question about how to use Chemprop v2?
+title: "[v2 QUESTION]: "
+labels: question
+assignees: ''
+
+---
+
+**What are you trying to do?**
+Please tell us what you're trying to do with Chemprop, providing as much detail as possible
+
+**Previous attempts**
+If possible, provide some examples of what you've already tried and what the output was.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.

.github/workflows/ci.yml

@@ -0,0 +1,156 @@
+# ci.yml
+#
+# Continuous Integration for Chemprop - checks build, code formatting, and runs tests for all
+# proposed changes and on a regular schedule
+#
+# Note: this file contains extensive inline documentation to aid with knowledge transfer.
+
+name: Continuous Integration
+
+on:
+  # run on pushes/pull requests to/against main or v2/dev
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main, v2/dev]
+  # run this in the morning on weekdays to catch dependency issues
+  schedule:
+    - cron: "0 8 * * 1-5"
+  # allow manual runs
+  workflow_dispatch:
+
+# cancel previously running tests if new commits are made
+# https://docs.github.com/en/actions/examples/using-concurrency-expressions-and-a-test-matrix
+concurrency:
+  group: actions-id-${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build:
+    name: Check Build
+    runs-on: ubuntu-latest
+    steps:
+      # clone the repo, attempt to build
+      - uses: actions/checkout@v4
+      - run: python -m pip install build
+      - run: python -m build .
+
+  lint:
+    name: Check Formatting
+    needs: build
+    runs-on: ubuntu-latest
+    steps:
+      # clone the repo, run black and flake8 on it
+      - uses: actions/checkout@v4
+      - run: python -m pip install black==23.* flake8
+      - run: black --check .
+      - run: flake8 .
+
+  test:
+    name: Execute Tests
+    needs: lint
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        # run with a login shell (so that the conda environment is activated)
+        # and echo the commands we run as we do them (for debugging purposes)
+        shell: bash -el {0}
+    strategy:
+      # if one platform/python version fails, continue testing the others
+      fail-fast: false
+      matrix:
+        # test on all platforms with both supported versions of Python
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: [3.11, 3.12]
+    steps:
+      - uses: actions/checkout@v4
+      # use a version of the conda virtual environment manager to set up an
+      # isolated environment with the Python version we want
+      - uses: mamba-org/setup-micromamba@main
+        with:
+          environment-name: temp
+          condarc: |
+            channels:
+              - defaults
+              - conda-forge
+            channel_priority: flexible
+          create-args: |
+            python=${{ matrix.python-version }}
+      - name: Install dependencies
+        shell: bash -l {0}
+        run: |
+          python -m pip install nbmake
+          python -m pip install ".[dev,docs,test]"
+      - name: Install hyperopt optional dependencies (Python 3.11 only)
+        if: ${{ matrix.python-version == '3.11' }} 
+        run: |
+          python -m pip install ".[hpopt]"
+      - name: Test with pytest
+        shell: bash -l {0}
+        run: |
+          pytest -v tests
+      - name: Test notebooks
+        shell: bash -l {0}
+        run: |
+          pytest --nbmake examples/training.ipynb
+          pytest --nbmake examples/predicting.ipynb
+          pytest --nbmake examples/convert_v1_to_v2.ipynb
+          pytest --nbmake examples/training_regression_multicomponent.ipynb
+          pytest --nbmake examples/predicting_regression_multicomponent.ipynb
+
+  conda-test:
+    name: Execute Tests with Conda-based Install
+    needs: lint
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        # run with a login shell (so that the conda environment is activated)
+        # and echo the commands we run as we do them (for debugging purposes)
+        shell: bash -el {0}
+    strategy:
+      # if one platform/python version fails, continue testing the others
+      fail-fast: false
+      matrix:
+        python-version: [3.11, 3.12]
+    steps:
+      - uses: actions/checkout@v4
+      # use a version of the conda virtual environment manager to set up an
+      # isolated environment with the Python version we want
+      - uses: mamba-org/setup-micromamba@main
+        with:
+          environment-file: environment.yml
+          condarc: |
+            channels:
+              - defaults
+              - conda-forge
+              - pytorch
+            channel_priority: flexible
+          create-args: |
+            python=${{ matrix.python-version }}
+      - name: Install Testing Dependencies
+        run: conda install -c conda-forge pytest>=6.2 pytest-cov
+      - name: Install Chemprop
+        run: python -m pip install . --no-deps
+      - name: Test with pytest
+        shell: bash -l {0}
+        run: |
+          pytest -v tests
+
+  # GitHub allows you to set checks as required before PRs can be merged, which is annoying to do
+  # for matrix jobs like the one above which have six actual jobs. Instead we have a summary job
+  # like this, which we mark as required.
+  # Copied in part from:
+  # https://github.com/orgs/community/discussions/26822#discussioncomment-3305794
+  ci-report-status:
+    name: report CI status
+    needs: test
+    runs-on: ubuntu-latest
+    steps:
+      - run: |
+          result="${{ needs.test.result }}"
+          if test $result == "success"; then
+            exit 0
+          else
+            exit 1
+          fi
+

.github/workflows/publish.yml

@@ -0,0 +1,34 @@
+name: publish
+
+on:
+  push:
+    tags:
+      - v**
+
+jobs:
+  publish:
+    name: build and publish to PyPI
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: checkout
+        uses: actions/checkout@v2
+
+      - name: Set up python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.8
+
+      - name: Install dependencies
+        run: |
+          pip install --upgrade pip
+          pip install --upgrade build
+
+      - name: build package
+        run: python3 -m build
+
+      - name: Publish package
+        uses: pypa/gh-action-pypi-publish@v1.5.0
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_API_TOKEN }}