Add 3.12 and cron to test matrix (#87)

* add 3.12 to test matrix

* fix typo

* update metadata for 3.10+

* add scipy to dependencies

* add cron

* exclude openeye from 3.12

* move openeye install

* switch to micromamba

.github/actions/include-openeye/action.yaml

@@ -16,6 +16,11 @@ inputs:
 runs:
   using: "composite"
   steps:
+    - name: Install OpenEye
+      shell: ${{ inputs.shell }}
+      run: |
+        micromamba install -y -c openeye openeye-toolkits
+
     - name: Make oe_license.txt file from GH org secret "OE_LICENSE"
       shell: ${{ inputs.shell }}
       run: |

.github/workflows/gh-ci.yaml

@@ -6,6 +6,9 @@ on:
   pull_request:
     branches:
       - main
+  schedule:
+    # weekly tests, Sundays at midnight
+    - cron: "0 0 * * 0"
 
 concurrency:
   # Specific group naming so CI is only cancelled
@@ -28,20 +31,23 @@ jobs:
         fail-fast: false
         matrix:
           os: [macOS-latest, ubuntu-latest]
-          python-version: ["3.9", "3.10"]
+          python-version: ["3.10", "3.11", "3.12"]
           pydantic-version: ["1", "2"]
           include-rdkit: [true, false]
           include-openeye: [true, false]
           include-dgl: [true, false]
           exclude:
             - include-rdkit: false
               include-openeye: false
-              # broken OpenMM build for Mac on 3.10
+            # broken OpenMM build for Mac on 3.10
             - os: "macOS-latest"
               python-version: "3.10"
-            # - os: "macOS-latest"
-            #   python-version: "3.9"
-            #   include-dgl: false
+            # no dgl for 3.12 yet
+            - include-dgl: true
+              python-version: "3.12"
+            # no openeye for 3.12 yet
+            - include-openeye: true
+              python-version: "3.12"
 
 
     steps:
@@ -56,7 +62,7 @@ jobs:
     - name: Install environment
       uses: mamba-org/setup-micromamba@v1
       with:
-        environment-file: devtools/conda-envs/test_env.yaml
+        environment-file: devtools/conda-envs/test_env_dgl_${{ matrix.include-dgl }}.yaml
         create-args: >-
           python=${{ matrix.python-version }}
           pydantic=${{ matrix.pydantic-version }}
@@ -86,10 +92,6 @@ jobs:
       if: matrix.include-rdkit == false
       run: conda remove --force rdkit --yes || echo "rdkit not installed"
 
-    - name: Uninstall DGL
-      if: matrix.include-dgl == false
-      run: conda remove --force dgl --yes || echo "dgl not installed"
-
     - name: Check toolkit installations
       shell: bash -l -c "python -u {0}"
       run: |
@@ -166,7 +168,7 @@ jobs:
     strategy:
         fail-fast: false
         matrix:
-          python-version: ["3.9", "3.10"]
+          python-version: ["3.10", "3.11", "3.12"]
 
     steps:
     - uses: actions/checkout@v3
@@ -189,7 +191,7 @@ jobs:
         conda activate openff-nagl
         conda list
     
-        mamba env update --name openff-nagl --file devtools/conda-envs/test_env.yaml
+        mamba env update --name openff-nagl --file devtools/conda-envs/test_env_dgl_false.yaml
         mamba env update --name openff-nagl --file devtools/conda-envs/docs_env.yaml
         python --version
         python -m pip install . --no-deps

devtools/conda-envs/test_env_dgl_false.yaml

@@ -0,0 +1,43 @@
+name: openff-nagl-test
+channels:
+  - openeye
+  - conda-forge
+  - defaults
+dependencies:
+    # Base depends
+  - python
+  - pip
+
+  # UI
+  - click
+  - click-option-group
+  - tqdm
+  - rich
+
+  # chemistry
+  - openff-recharge
+  - openff-toolkit-base >=0.11.1
+  - openff-units
+  - pydantic <3
+  - rdkit
+  - scipy
+
+  # database
+  - pyarrow
+
+  # gcn
+  - pytorch >=2.0
+  - pytorch-lightning
+
+  # parallelism
+  - dask-jobqueue
+
+  # Testing
+  - pytest
+  - pytest-cov
+  - pytest-xdist
+  - codecov
+
+  # Pip-only installs
+  - pip:
+    - rich

devtools/conda-envs/test_env.yaml → devtools/conda-envs/test_env_dgl_true.yaml

@@ -21,7 +21,7 @@ dependencies:
   - openff-units
   - pydantic <3
   - rdkit
-  - openeye-toolkits
+  - scipy
 
   # database
   - pyarrow

setup.py

@@ -40,7 +40,7 @@
     # Customize MANIFEST.in if the general case does not suit your needs
     # Comment out this line to prevent the files from being packaged with your software
     include_package_data=True,
-    python_requires=">=3.8",          # Python version restrictions
+    python_requires=">=3.10",          # Python version restrictions
     # Allows `setup.py test` to work correctly with pytest
     setup_requires=[] + pytest_runner,
     # Required packages, pulls from pip if needed
@@ -51,7 +51,7 @@
         "tqdm",
         "openff-toolkit",
         "openff-units",
-        "pydantic<2.0",
+        "pydantic",
         "rdkit",
     ],
     # Additional entries you may want simply uncomment the lines you want and fill in the data