Add base tests (#150)

.github/workflows/base-ci.yaml

@@ -0,0 +1,77 @@
+name: Base tests
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+  schedule:
+    # weekly tests, Sundays at midnight
+    - cron: "0 0 * * 0"
+
+concurrency:
+  # Specific group naming so CI is only cancelled
+  # within same PR or on merge to main
+  group: ${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}
+  cancel-in-progress: true
+
+defaults:
+  run:
+    shell: bash -l {0}
+
+env:
+  OE_LICENSE: ${{ github.workspace }}/oe_license.txt
+
+jobs:
+  main_tests:
+    name: CI (${{ matrix.os }}, py-${{ matrix.python-version }}, openeye=${{ matrix.include-openeye }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+        fail-fast: false
+        matrix:
+          os: [macOS-13, macOS-latest, ubuntu-latest]
+          python-version: ["3.10", "3.11", "3.12"]
+          include-openeye: [false, true]
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Build information
+      run: |
+        uname -a
+        df -h
+        ulimit -a
+
+    - name: Install environment
+      uses: mamba-org/setup-micromamba@v2
+      with:
+        environment-file: devtools/conda-envs/base.yaml
+        create-args: >-
+          python=${{ matrix.python-version }}
+
+    - name: Install package
+      run: |
+        python -m pip install . --no-deps
+
+    - uses: ./.github/actions/include-openeye
+      if: matrix.include-openeye == true
+      with:
+        openeye-license-text: ${{ secrets.OE_LICENSE }}
+        openeye-license-file: ${{ env.OE_LICENSE }}
+
+
+    - name: Uninstall OpenEye
+      if: matrix.include-openeye == false
+      run: conda remove --force openeye-toolkits --yes || echo "openeye not installed"
+
+    - name: Check toolkit installations
+      shell: bash -l -c "python -u {0}"
+      run: |
+        from openff.toolkit.utils.toolkits import OPENEYE_AVAILABLE, RDKIT_AVAILABLE
+        assert str(OPENEYE_AVAILABLE).lower() == '${{ matrix.include-openeye }}'
+        assert str(RDKIT_AVAILABLE).lower() == 'true'
+
+    - name: Run tests
+      run: |
+        python -m pytest -n 4 -v --cov=openff/nagl --cov-config=setup.cfg --cov-append --cov-report=xml --color=yes openff/nagl/

devtools/conda-envs/base.yaml

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+name: openff-nagl-test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+    # Base depends
+  - python
+  - pip
+  - importlib_resources
+
+  # UI
+  - click
+  - click-option-group
+  - rich
+  - tqdm
+
+  # chemistry
+  - openff-toolkit-base >=0.11.1
+  - openff-units
+  - pydantic <3
+  - rdkit
+  - scipy
+
+  # files
+  - pyyaml
+
+  # gcn
+  - pytorch >=2.0
+  - pytorch-lightning
+
+  # Testing
+  - pytest
+  - pytest-cov
+  - pytest-xdist
+  - codecov