Maintenance

.github/pull_request_template.md

@@ -1,5 +1,5 @@
 - [ ] Tag issue being addressed
 - [ ] Add [tests](https://github.com/openforcefield/openff-toolkit/tree/master/openff/toolkit/tests)
 - [ ] Update docstrings/[documentation](https://github.com/openforcefield/openff-toolkit/tree/master/docs), if applicable
-- [ ] [Lint](https://open-forcefield-toolkit.readthedocs.io/en/latest/developing.html#style-guide) codebase
-- [ ] Update [changelog](https://github.com/openforcefield/openff-toolkit/blob/master/docs/releasehistory.rst)
+- [ ] [Lint](https://docs.openforcefield.org/projects/toolkit/en/stable/users/developing.html#style-guide) codebase
+- [ ] Update [changelog](https://github.com/openforcefield/openff-toolkit/blob/master/docs/releasehistory.md)

.github/workflows/CI.yml

@@ -15,89 +15,77 @@ on:
     #   (from https://help.github.com/en/actions/reference/events-that-trigger-workflows#scheduled-events-schedule)
     - cron: "0 0 * * *"
 
+defaults:
+  run:
+    shell: bash -l {0}
+
 jobs:
   test:
     if: (github.event_name == 'schedule' && github.repository == 'openforcefield/openff-toolkit') || (github.event_name != 'schedule')
-    name: Test on ${{ matrix.os }}, Python ${{ matrix.cfg.python-version }}, RDKit=${{ matrix.cfg.rdkit }}, OpenEye=${{ matrix.cfg.openeye }}
+    name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }}, RDKit=${{ matrix.rdkit }}, OpenEye=${{ matrix.openeye }}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        os:
-          - ubuntu-latest
-          - macos-latest
-        cfg:
-          - python-version: 3.7
-            rdkit: "true"
-            openeye: "false"
-
-          - python-version: 3.7
-            rdkit: "false"
-            openeye: "true"
-
-          - python-version: 3.7
-            rdkit: "true"
-            openeye: "true"
-
-          - python-version: 3.8
-            rdkit: "true"
-            openeye: "false"
-
-          - python-version: 3.9
-            rdkit: "true"
-            openeye: "false"
+        os: [ubuntu-latest, macos-latest]
+        python-version: [3.7, 3.8, 3.9]
+        rdkit: [true, false]
+        openeye: [true, false]
+        exclude:
+          - rdkit: false
+            openeye: false
+          - openeye: true
+            python-version: 3.8
+          - openeye: true
+            python-version: 3.9
 
     env:
-      CI_OS: ${{ matrix.os }}
-      RDKIT: ${{ matrix.cfg.rdkit }}
-      OPENEYE: ${{ matrix.cfg.openeye }}
-      PYVER: ${{ matrix.cfg.python-version }}
       OE_LICENSE: ${{ github.workspace }}/oe_license.txt
       PACKAGE: openff
       PYTEST_ARGS: -r fE --tb=short --cov=openff --cov-config=setup.cfg --cov-append --cov-report=xml
       NB_ARGS: -v --nbval-lax --ignore=examples/deprecated
 
     steps:
-      - uses: actions/checkout@v2.3.5
+      - uses: actions/checkout@v3
         with:
           fetch-depth: 2
 
-      - uses: conda-incubator/[email protected]
-        name: Install both RDKit and OpenEye toolkits
-        if: ${{ matrix.cfg.rdkit == 'TRUE' && matrix.cfg.openeye == 'TRUE' }}
-        with:
-          python-version: ${{ matrix.cfg.python-version }}
-          activate-environment: test
-          environment-file: devtools/conda-envs/test_env.yaml
-          auto-activate-base: false
-          miniforge-version: latest
-          miniforge-variant: Mambaforge
-          use-mamba: true
-      - uses: conda-incubator/[email protected]
-        name: Install only RDKit
-        if: ${{ matrix.cfg.rdkit == 'TRUE' && matrix.cfg.openeye == 'FALSE' }}
-        with:
-          python-version: ${{ matrix.cfg.python-version }}
-          activate-environment: test
-          environment-file: devtools/conda-envs/rdkit.yaml
-          auto-activate-base: false
-          miniforge-version: latest
-          miniforge-variant: Mambaforge
-          use-mamba: true
-      - uses: conda-incubator/[email protected]
-        name: Install with OpenEye toolkits
-        if: ${{ matrix.cfg.rdkit == 'FALSE' && matrix.cfg.openeye == 'TRUE' }}
+      - name: Set environment variables
+        run: |
+          if [[ ${{ matrix.openeye }} == true && ${{ matrix.rdkit }} == true ]]; then
+              echo "ENVFILE=test_env" >> $GITHUB_ENV
+              echo "JOBNAME=RDKit and OpenEye" >> $GITHUB_ENV
+              echo "TOOLKIT_CHECKS=RDKIT OPENEYE" >> $GITHUB_ENV
+              echo "PACKAGES_TO_REMOVE=" >> $GITHUB_ENV
+          fi
+
+          if [[ ${{ matrix.openeye }} == true && ${{ matrix.rdkit }} == false ]]; then
+              echo "ENVFILE=openeye" >> $GITHUB_ENV
+              echo "JOBNAME=OpenEye" >> $GITHUB_ENV
+              echo "TOOLKIT_CHECKS=OPENEYE" >> $GITHUB_ENV
+              echo "PACKAGES_TO_REMOVE=ambertools rdkit" >> $GITHUB_ENV
+          fi
+
+          if [[ ${{ matrix.openeye }} == false && ${{ matrix.rdkit }} == true ]]; then
+              echo "ENVFILE=rdkit" >> $GITHUB_ENV
+              echo "JOBNAME=RDKit" >> $GITHUB_ENV
+              echo "TOOLKIT_CHECKS=RDKIT" >> $GITHUB_ENV
+              echo "PACKAGES_TO_REMOVE=openeye-toolkits" >> $GITHUB_ENV
+          fi
+
+
+      - name: Install environment with ${{ env.JOBNAME }}
+        uses: conda-incubator/[email protected]
         with:
           python-version: ${{ matrix.cfg.python-version }}
           activate-environment: test
-          environment-file: devtools/conda-envs/openeye.yaml
+          environment-file: devtools/conda-envs/${{ env.ENVFILE }}.yaml
           auto-activate-base: false
           miniforge-version: latest
           miniforge-variant: Mambaforge
           use-mamba: true
 
       - name: Additional info about the build
-        shell: bash -l {0}
         run: |
           uname -a
           df -h
@@ -111,58 +99,52 @@ jobs:
           echo "${OE_LICENSE_TEXT}" > ${OE_LICENSE}
 
       - name: Install package
-        shell: bash -l {0}
         run: |
           conda remove --force openff-toolkit openff-toolkit-base
           python setup.py develop --no-deps
 
-      - name: Check installed toolkits
-        shell: bash -l {0}
+      - name: Install test plugins
         run: |
-          if [[ "$OPENEYE" == true ]]; then
-            python -c "from openff.toolkit.utils.toolkits import OPENEYE_AVAILABLE; assert OPENEYE_AVAILABLE, 'OpenEye unavailable'"
-          fi
-          if [[ "$OPENEYE" == false ]]; then
-            if [[ $(conda list | grep openeye-toolkits) ]]; then
-              conda remove --force openeye-toolkits --yes
-            fi
-            python -c "from openff.toolkit.utils.toolkits import OPENEYE_AVAILABLE; assert not OPENEYE_AVAILABLE, 'OpenEye unexpectedly found'"
-          fi
-          if [[ "$RDKIT" == true ]]; then
-            python -c "from openff.toolkit.utils.toolkits import RDKIT_AVAILABLE; assert RDKIT_AVAILABLE, 'RDKit unavailable'"
+          cd utilities/test_plugins
+          python setup.py develop --no-deps
+
+      - name: Remove undesired toolkits
+        run: |
+          if [ ! -z "${{ env.PACKAGES_TO_REMOVE }}" ]; then
+            for cpkg in ${{ env.PACKAGES_TO_REMOVE }}; do
+              if [[ $(conda list | grep $cpkg) ]]; then conda remove --force $cpkg --yes ; fi
+            done
           fi
-          if [[ "$RDKIT" == false ]]; then
-            if [[ $(conda list | grep rdkit) ]]; then
-              conda remove --force rdkit --yes
-            fi
-            if [[ $(conda list | grep ambertools) ]]; then
-              conda remove --force ambertools --yes
-            fi
-            python -c "from openff.toolkit.utils.toolkits import RDKIT_AVAILABLE; assert not RDKIT_AVAILABLE, 'RDKit unexpectedly found'"
+
+      - name: Check installed toolkits
+        run: |
+          for tk in ${{ env.TOOLKIT_CHECKS }}; do
+            python -c "from openff.toolkit.utils.toolkits import ${tk}_AVAILABLE; assert ${tk}_AVAILABLE, '${tk} unavailable'"
+          done
+
+      - name: Check uninstalled toolkits
+        run: |
+          if [ ! -z "${{ env.PACKAGES_TO_REMOVE }}" ]; then
+            for tk in ${{ env.PACKAGES_TO_REMOVE }}; do
+              TK=$(echo ${tk%-*} | tr 'a-z' 'A-Z')
+              python -c "from openff.toolkit.utils.toolkits import ${TK}_AVAILABLE; assert not ${TK}_AVAILABLE, '${TK} available'"
+            done
           fi
 
       - name: Environment Information
-        shell: bash -l {0}
         run: |
           conda info
           conda list
 
       - name: Check links
-        shell: bash -l {0}
-        if: ${{ matrix.cfg.rdkit == 'true' && matrix.cfg.openeye == 'TRUE' }}
-        run: |
-          pytest -r fE --tb=short openff/toolkit/tests/test_links.py
+        if: ${{ matrix.rdkit == true && matrix.openeye == true }}
+        run: pytest -r fE --tb=short openff/toolkit/tests/test_links.py
 
       - name: Run mypy
-        shell: bash -l {0}
-        # Try to prevent failure from preventing later steps, but also display red X
-        # https://stackoverflow.com/a/62112985/4248961
-        if: ${{ matrix.cfg.rdkit == 'true' && matrix.cfg.openeye == 'TRUE' }}
-        run: |
-          mypy --namespace-packages -p "openff.toolkit"
+        if: ${{ matrix.rdkit == true && matrix.openeye == true }}
+        run: mypy --namespace-packages -p "openff.toolkit"
 
       - name: Run unit tests
-        shell: bash -l {0}
         run: |
           PYTEST_ARGS+=" --ignore=openff/toolkit/tests/test_examples.py"
           PYTEST_ARGS+=" --ignore=openff/toolkit/tests/test_links.py"
@@ -172,13 +154,11 @@ jobs:
           pytest $PYTEST_ARGS openff/toolkit/tests/
 
       - name: Run code snippets in docs
-        shell: bash -l {0}
-        if: ${{ matrix.cfg.rdkit == 'TRUE' && matrix.cfg.openeye == 'TRUE' }}
+        if: ${{ matrix.rdkit == true && matrix.openeye == true }}
         run: |
           pytest -v --doctest-glob="docs/*.rst" docs/
 
       - name: Codecov
-        uses: codecov/codecov-action@v2.1.0
+        uses: codecov/codecov-action@v3
         with:
           file: ./coverage.xml
-          fail_ci_if_error: true

.github/workflows/beta_rc.yaml

@@ -0,0 +1,96 @@
+name: Weekly test against upstream beta and RC builds
+
+on:
+  schedule:
+    - cron: "0 0 * * 0"
+  workflow_dispatch:
+
+jobs:
+  test:
+    name: Test beta and RC builds on on ${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os:
+          - ubuntu-latest
+          - macos-latest
+        python-version:
+          - 3.7
+          - 3.8
+          - 3.9
+
+    env:
+      OE_LICENSE: ${{ github.workspace }}/oe_license.txt
+      PYTEST_ARGS: -r fE --tb=short --cov=openff --cov-config=setup.cfg --cov-append --cov-report=xml
+
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 2
+
+      - uses: conda-incubator/[email protected]
+        name: Install everything with betas and RCs
+        with:
+          python-version: ${{ matrix.python-version }}
+          activate-environment: test
+          environment-file: devtools/conda-envs/beta_rc_env.yaml
+          auto-activate-base: false
+          miniforge-version: latest
+          miniforge-variant: Mambaforge
+          use-mamba: true
+          channel-priority: strict
+
+      - name: Additional info about the build
+        shell: bash -l {0}
+        run: |
+          uname -a
+          df -h
+          ulimit -a
+
+      - name: Make oe_license.txt file from GH org secret "OE_LICENSE"
+        shell: bash
+        env:
+          OE_LICENSE_TEXT: ${{ secrets.OE_LICENSE }}
+        run: |
+          echo "${OE_LICENSE_TEXT}" > ${OE_LICENSE}
+
+      - name: Install package
+        shell: bash -l {0}
+        run: |
+          conda remove --force openff-toolkit openff-toolkit-base
+          python setup.py develop --no-deps
+
+      - name: Environment Information
+        shell: bash -l {0}
+        run: |
+          conda info
+          conda list
+
+      - name: Check links
+        shell: bash -l {0}
+        run: |
+          pytest -r fE --tb=short openff/toolkit/tests/test_links.py
+
+      - name: Run unit tests
+        shell: bash -l {0}
+        run: |
+          PYTEST_ARGS+=" --ignore=openff/toolkit/tests/test_examples.py"
+          PYTEST_ARGS+=" --ignore=openff/toolkit/tests/test_links.py"
+          PYTEST_ARGS+=" --runslow"
+          pytest $PYTEST_ARGS openff/toolkit/tests/
+
+      - name: Run code snippets in docs
+        shell: bash -l {0}
+        run: |
+          pytest -v --doctest-glob="docs/*.rst" docs/
+
+      - name: Run mypy
+        shell: bash -l {0}
+        run: |
+          mypy --namespace-packages -p "openff.toolkit"
+
+      - name: Codecov
+        uses: codecov/codecov-action@v3
+        with:
+          file: ./coverage.xml

.github/workflows/conda.yml

@@ -19,10 +19,7 @@ jobs:
         os:
           - ubuntu-latest
           - macos-latest
-        cfg:
-          - python-version: 3.6
-            openeye: "true"
-
+        cfg:            
           - python-version: 3.7
             openeye: "true"
 
@@ -47,7 +44,7 @@ jobs:
       PACKAGE: openff-toolkit
 
     steps:
-      - uses: actions/checkout@v2.3.5
+      - uses: actions/checkout@v3
 
       - uses: conda-incubator/[email protected]
         name: Vanilla install from conda
@@ -134,6 +131,11 @@ jobs:
           git fetch --tags
           git checkout tags/$LATEST_TAG
           git log -1 | cat
+
+          # Install test plugins
+          cd utilities/test_plugins
+          python setup.py develop --no-deps
+          cd -
 
           pwd
           ls