Merge branch 'main' into fix-methane-charging

openforcefield · Oct 22, 2024 · 4d2fcd8 · 4d2fcd8
2 parents 4e30c47 + 6aef0ed
commit 4d2fcd8
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diff --git a/.github/workflows/base-ci.yaml b/.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/
diff --git a/.github/workflows/dev-ci.yaml b/.github/workflows/dev-ci.yaml
@@ -14,6 +14,10 @@ concurrency:
 defaults:
   run:
     shell: bash -l {0}
+
+env:
+  OE_LICENSE: ${{ github.workspace }}/oe_license.txt
+  DGL_HOME: ${{ github.workspace }}/dgl
 
 jobs:
   nightly_check:
@@ -22,8 +26,8 @@ jobs:
     strategy:
         fail-fast: false
         matrix:
-          os: [macOS-12, ubuntu-latest]
-          python-version: ["3.10", "3.11", "3.12"]
+          os: [macOS-13, macOS-latest, ubuntu-latest]
+          python-version: ["3.11", "3.12"]
 
     steps:
     - uses: actions/checkout@v4
@@ -42,25 +46,63 @@ jobs:
           python=${{ matrix.python-version }}
           pydantic=2
     
-    - name: Install nightly pytorch-lightning and DGL
+    - name: Install nightly pytorch
       run: |
-        python -m pip install --pre dgl -f https://data.dgl.ai/wheels-test/repo.html
-        python -m pip install --pre dglgo -f https://data.dgl.ai/wheels-test/repo.html
-        python -m pip install https://github.com/Lightning-AI/lightning/archive/refs/heads/master.zip -U  
+        python -m pip install https://github.com/Lightning-AI/lightning/archive/refs/heads/master.zip -U 
 
-    - name: Install package
+    - name: Download DGL source
       run: |
-        python -m pip install . --no-deps
+        git clone --recurse-submodules https://github.com/dmlc/dgl.git
+      
+    - name: Set up DGL
+      if: matrix.os != 'ubuntu-latest'
+      run: |
+        # from https://docs.dgl.ai/en/latest/install/index.html#macos
+        cd dgl/
+        mkdir build && cd build
+        cmake -DUSE_OPENMP=off -DUSE_LIBXSMM=OFF ..
+        make -j4
+        cd ../..
+    
+    - name: Set up DGL (Ubuntu)
+      if: matrix.os == 'ubuntu-latest'
+      run: |
+        cd dgl/
+        mkdir build && cd build
+        cmake -DBUILD_TYPE=dev -DUSE_CUDA=OFF -DUSE_LIBXSMM=OFF ..
+        make
+        cd ../..
+    
+    - name: Install DGL Python bindings
+      run: |
+        cd dgl/python
+        python setup.py install
+        python setup.py build_ext --inplace
+        cd ../..
 
-    - name: Python information
+    - uses: ./.github/actions/include-openeye
+      with:
+        openeye-license-text: ${{ secrets.OE_LICENSE }}
+        openeye-license-file: ${{ env.OE_LICENSE }}
+
+    - name: Check toolkit installations
+      shell: bash -l -c "python -u {0}"
       run: |
-        which python
-        conda info
-        conda list
+        from openff.toolkit.utils.toolkits import OPENEYE_AVAILABLE, RDKIT_AVAILABLE
+        assert str(OPENEYE_AVAILABLE).lower() == 'true'
+        assert str(RDKIT_AVAILABLE).lower() == 'true'
 
+    - name: Check Python environment
+      run: |
+        pip list
+    
     - name: Import DGL
       run: |
-        python -c "import dgl"
+        python -c "import dgl; import dgl.nn"
+
+    - name: Install package
+      run: |
+        python -m pip install . --no-deps
 
     - name: Run tests
       run: |

diff --git a/.github/workflows/gh-ci.yaml b/.github/workflows/gh-ci.yaml
@@ -30,7 +30,7 @@ jobs:
     strategy:
         fail-fast: false
         matrix:
-          os: [macOS-12, ubuntu-latest]
+          os: [macOS-13, macOS-latest, ubuntu-latest]
           python-version: ["3.10", "3.11", "3.12"]
           pydantic-version: ["1", "2"]
           include-rdkit: [false, true]
@@ -39,12 +39,6 @@ jobs:
           exclude:
             - include-rdkit: false
               include-openeye: false
-            # no openeye for 3.12 yet
-            - include-openeye: true
-              python-version: "3.12"
-            # no builds?
-            - include-dgl: true
-              python-version: "3.12"
 
 
     steps:
@@ -57,7 +51,7 @@ jobs:
         ulimit -a
 
     - name: Install environment
-      uses: mamba-org/setup-micromamba@v1
+      uses: mamba-org/setup-micromamba@v2
       with:
         environment-file: devtools/conda-envs/test_env_dgl_${{ matrix.include-dgl }}.yaml
         create-args: >-
@@ -77,11 +71,11 @@ jobs:
 
     - name: Uninstall OpenEye
       if: matrix.include-openeye == false
-      run: conda remove --force openeye-toolkits --yes || echo "openeye not installed"
+      run: micromamba remove --force openeye-toolkits --yes || echo "openeye not installed"
 
     - name: Uninstall RDKit
       if: matrix.include-rdkit == false
-      run: conda remove --force rdkit --yes || echo "rdkit not installed"
+      run: micromamba remove --force rdkit --yes || echo "rdkit not installed"
 
     # See https://github.com/openforcefield/openff-nagl/issues/103
     - name: Rewrite DGL config
@@ -90,22 +84,21 @@ jobs:
         mkdir -p ~/.dgl
         echo '{"backend": "pytorch"}' > ~/.dgl/config.json
 
-    - name: Python information
-      run: |
-        which python
-        conda info
-        conda list
-
     - 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() == '${{ matrix.include-openeye }}'
         assert str(RDKIT_AVAILABLE).lower() == '${{ matrix.include-rdkit }}'
 
+    - name: Check DGL installation
+      if: matrix.include-dgl == true
+      run: |
+        python -c "import dgl"
+
     - 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/
+        python -m pytest -v --cov=openff/nagl --cov-config=setup.cfg --cov-append --cov-report=xml --color=yes openff/nagl/
 
     - name: codecov
       uses: codecov/codecov-action@v4
@@ -177,29 +170,19 @@ jobs:
     - uses: actions/checkout@v4
 
     - name: Install conda
-      uses: conda-incubator/setup-miniconda@v3
+      uses: mamba-org/setup-micromamba@v2
       with:
-        python-version: ${{ matrix.python-version }}
-        add-pip-as-python-dependency: true
-        architecture: x64
-        miniforge-variant: Mambaforge
-        use-mamba: true
-        auto-update-conda: true
-        show-channel-urls: true
-        channels: conda-forge, defaults
+        environment-name: openff-nagl
+        create-args: >-
+          python=${{ matrix.python-version }}
 
     - name: Build from source
       run: |
-        conda create --name openff-nagl
-        conda activate openff-nagl
-        conda list
-    
-        mamba env update --name openff-nagl --file devtools/conda-envs/docs_env.yaml
+        micromamba env update --name openff-nagl --file devtools/conda-envs/docs_env.yaml
         python --version
         python -m pip install . --no-deps
-        conda list
+        micromamba list
 
     - name: Check success
       run: |
-        conda activate openff-nagl
         python -c "import openff.nagl ; print(openff.nagl.__version__)"
diff --git a/devtools/conda-envs/base.yaml b/devtools/conda-envs/base.yaml
@@ -0,0 +1,35 @@
+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
diff --git a/devtools/conda-envs/nightly.yaml b/devtools/conda-envs/nightly.yaml
@@ -1,8 +1,8 @@
 name: openff-nagl-test
 channels:
   - openeye
-  - pytorch-nightly
   - conda-forge
+  - pytorch-nightly
   - defaults
 dependencies:
     # Base depends
@@ -18,13 +18,16 @@ dependencies:
   - pydantic <3
   - rdkit
   - scipy
+  - openeye-toolkits
+
+  # gnn
+  - pytorch
+  - torchvision
+  - torchaudio
 
   # database
   - pyarrow
 
-  # gcn
-  - pytorch
-
   # parallelism
   - dask-jobqueue
 
@@ -49,6 +52,11 @@ dependencies:
   - sqlite
   - xmltodict
 
+  # building
+  - make
+  - cmake
+  - cython
+
   # Pip-only installs
   - pip:
     - git+https://github.com/openforcefield/openff-utilities.git@main

diff --git a/devtools/conda-envs/test_env_dgl_false.yaml b/devtools/conda-envs/test_env_dgl_false.yaml
@@ -2,7 +2,6 @@ name: openff-nagl-test
 channels:
   - openeye
   - conda-forge
-  - defaults
 dependencies:
     # Base depends
   - python

diff --git a/devtools/conda-envs/test_env_dgl_true.yaml b/devtools/conda-envs/test_env_dgl_true.yaml
@@ -1,9 +1,7 @@
 name: openff-nagl-test
 channels:
   - openeye
-  - dglteam
   - conda-forge
-  - defaults
 dependencies:
     # Base depends
   - python

diff --git a/docs/CHANGELOG.md b/docs/CHANGELOG.md
@@ -27,6 +27,7 @@ The rules for this file:
 - Removed unused, undocumented code paths, and updated docs (PR #132)
 
 ### Fixed
+- Fixed molecule normalization issues (Issue #119, PR #149)
 - Check lookup tables for allowed molecules before ChemicalDomain for forbidden ones (PR #145, Issue #144)
 - Add support for single atoms (PR #146, Issue #138)