Packaging of Graphium 3.0

.github/workflows/doc.yml

@@ -25,14 +25,14 @@ jobs:
       - name: Setup mamba
         uses: mamba-org/setup-micromamba@v1
         with:
-          environment-file: env.yml
+          environment-file: requirements/linux_env.yml
           environment-name: graphium
           cache-environment: true
           cache-downloads: true
 
       - name: Install library
         run: |
-          python -m pip install --no-deps .
+          python -m pip install --no-deps --no-build-isolation .
           pip install typer-cli
 
       - name: Configure git
@@ -45,6 +45,9 @@ jobs:
 
           echo "Auto-generating typer docs"
           typer graphium.cli.__main__ utils docs --name graphium --output docs/cli/graphium.md
+
+          echo "Generating Graphium C++ docs"
+          doxygen Doxyfile
 
           echo "Get the gh-pages branch"
           git fetch origin gh-pages

.github/workflows/release.yml

@@ -30,7 +30,7 @@ jobs:
       - name: Setup mamba
         uses: mamba-org/setup-micromamba@v1
         with:
-          environment-file: env.yml
+          environment-file: requirements/linux_env.yml
           environment-name: graphium
           cache-environment: true
           cache-downloads: true
@@ -99,7 +99,7 @@ jobs:
           git push origin "${{ inputs.release-version }}"
 
       - name: Install library
-        run: python -m pip install --no-deps .
+        run: python -m pip install --no-deps --no-build-isolation .
 
       - name: Build the wheel and sdist
         run: python -m build --no-isolation
@@ -112,6 +112,9 @@ jobs:
 
       - name: Deploy the doc
         run: |
+          echo "Generating Graphium C++ docs"
+          doxygen Doxyfile
+
           echo "Get the gh-pages branch"
           git fetch origin gh-pages
 

.github/workflows/test.yml

@@ -16,49 +16,52 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        include:
-          - python-version: "3.10"
-            pytorch-version: "2.0"
-          - python-version: "3.11"
-            pytorch-version: "2.0"
-          - python-version: "3.12"
-            pytorch-version: "2.3"
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ["3.10", "3.11"] # -> Will re-enable support for py312 once pyg is released, "3.10",
 
-    runs-on: "ubuntu-latest"
+    runs-on: ${{ matrix.os }}
     timeout-minutes: 30
 
     defaults:
       run:
         shell: bash -l {0}
 
     name: |
-        regular_env -
-        python=${{ matrix.python-version }} -
-        pytorch=${{ matrix.pytorch-version }}
+      regular_env -
+      python=${{ matrix.python-version }} -
+      os=${{ matrix.os }}
 
     steps:
       - name: Checkout the code
         uses: actions/checkout@v3
+
+      - name: Set OS-specific environment file to use
+        run: |
+          if [ "${{ matrix.os }}" == "windows-latest" ]; then
+            echo "ENV_FILE=windows_env.yml" >> $GITHUB_ENV
+          elif [ "${{ matrix.os }}" == "ubuntu-latest" ]; then
+            echo "ENV_FILE=linux_env.yml" >> $GITHUB_ENV
+          elif [ "${{ matrix.os }}" == "macos-latest" ]; then
+            echo "ENV_FILE=osx_env.yml" >> $GITHUB_ENV
+          fi
 
       - name: Setup mamba
         uses: mamba-org/setup-micromamba@v1
         with:
-          environment-file: env.yml
+          environment-file: requirements/${{ env.ENV_FILE }}
           environment-name: graphium
           cache-environment: true
           cache-downloads: true
           create-args: >-
             python=${{ matrix.python-version }}
-            pytorch=${{ matrix.pytorch-version }}
-
+
       - name: Install library
-        run: python -m pip install --no-deps -e . # `-e` required for correct `coverage` run.
-
-      - name: Install test dependencies
-        run: micromamba install -c conda-forge pytdc  # Required to run the `test_finetuning.py`
+        run: python -m pip install --no-deps --no-build-isolation -e . -v # `-e` required for correct `coverage` run.
 
-      - name: Install C++ library
-        run: cd graphium/graphium_cpp && git clone https://github.com/pybind/pybind11.git && export PYTHONPATH=$PYTHONPATH:./pybind11 && python -m pip install . && cd ../..
+      - name: Run tests
+        run: |
+          python -c "import rdkit; print('RDKit version:', rdkit.__version__)"
+          pytest
 
       - name: Test CLI
         run: graphium --help
@@ -74,4 +77,4 @@ jobs:
           name: codecov-umbrella
           fail_ci_if_error: false
           verbose: false
-          env_vars: ${{ matrix.python-version }},${{ matrix.pytorch-version }}
+          env_vars: ${{ matrix.python-version }}