Merge remote-tracking branch 'upstream/main' into from-openmm-virtual…

…-sites
openforcefield · Jan 23, 2025 · 6b0b8b9 · 6b0b8b9
2 parents 356718f + acecd06
commit 6b0b8b9
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diff --git a/.codecov.yml b/.codecov.yml
diff --git a/.github/workflows/beta.yaml b/.github/workflows/beta.yaml
@@ -1,9 +1,9 @@
 name: Tests against betas
 
 on:
-  workflow_dispatch:
   schedule:
-    - cron: "0 0 * * *"
+    - cron: "0 3 * * *"
+  workflow_dispatch:
 
 defaults:
   run:
@@ -21,41 +21,42 @@ jobs:
         python-version:
           - "3.10"
           - "3.11"
-        pydantic-version:
-          - "2"
+          - "3.12"
         openeye:
           - true
           - false
 
     env:
       OE_LICENSE: ${{ github.workspace }}/oe_license.txt
-      COV: --cov=openff/interchange --cov-report=xml --cov-config=setup.cfg --cov-append
 
     steps:
     - uses: actions/checkout@v4
       with:
         fetch-depth: 0
 
     - name: Install conda environment
-      uses: mamba-org/setup-micromamba@v1
+      uses: mamba-org/setup-micromamba@v2
       with:
-        micromamba-version: '1.5.10-0'
-        environment-file: devtools/conda-envs/beta_env.yaml
+        environment-file: devtools/conda-envs/test_env.yaml
+        condarc: |
+            channels:
+              - openeye/label/rc
+              - conda-forge/label/openmm_rc
+              - conda-forge/label/mdtraj_rc
+              - conda-forge/label/openff-toolkit_rc
+              - conda-forge/label/openff-interchange_rc
+              - openeye
+              - conda-forge
         create-args: >-
           python=${{ matrix.python-version }}
-          pydantic=${{ matrix.pydantic-version }}
 
     - name: Install package
-      run: |
-        micromamba remove --force openff-interchange openff-interchange-base
-        python -m pip install . plugins/
-
-    - name: Environment Information
-      run: conda info && conda list
+      run: python -m pip install . plugins/
 
-    - name: License OpenEye
+    - name: Install and license OpenEye Toolkits
       if: ${{ matrix.openeye == true }}
       run: |
+        micromamba install "openeye-toolkits =2024.1.0" -c openeye
         echo "${SECRET_OE_LICENSE}" > ${OE_LICENSE}
         python -c "from openeye import oechem; assert oechem.OEChemIsLicensed()"
       env:
@@ -67,7 +68,7 @@ jobs:
 
     - name: Run all tests
       if: always()
-      run: python -m pytest -v $COV openff/interchange/
+      run: python -m pytest -v openff/interchange/
 
     - name: Codecov
       uses: codecov/codecov-action@v5

diff --git a/.github/workflows/changes.yaml b/.github/workflows/changes.yaml
diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -4,13 +4,11 @@ on:
   push:
     branches:
       - main
-      - develop
   pull_request:
     branches:
       - main
-      - develop
   schedule:
-    - cron: "0 0 * * *"
+    - cron: "0 5 * * *"
   workflow_dispatch:
 
 defaults:
@@ -19,7 +17,7 @@ defaults:
 
 jobs:
   test:
-    name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }}, OpenMM ${{ matrix.openmm }}, Pydantic ${{ matrix.pydantic-version }}, OpenEye ${{ matrix.openeye }}
+    name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }}, OpenMM ${{ matrix.openmm }}, OpenEye ${{ matrix.openeye }}
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
@@ -29,39 +27,30 @@ jobs:
         python-version:
           - "3.10"
           - "3.11"
-        pydantic-version:
-          - "2"
         openeye:
           - true
           - false
         openmm:
           - true
-          - false
 
     env:
       OE_LICENSE: ${{ github.workspace }}/oe_license.txt
-      COV: --cov=openff/interchange --cov-report=xml --cov-config=setup.cfg --cov-append
+      COV: --cov=openff/interchange --cov-report=xml --cov-config=pyproject.toml --cov-append
 
     steps:
     - uses: actions/checkout@v4
       with:
         fetch-depth: 0
 
     - name: Install conda environment
-      uses: mamba-org/setup-micromamba@v1
+      uses: mamba-org/setup-micromamba@v2
       with:
-        micromamba-version: '1.5.10-0'
         environment-file: devtools/conda-envs/test_env.yaml
         create-args: >-
           python=${{ matrix.python-version }}
-          pydantic=${{ matrix.pydantic-version }}
 
     - name: Install package
-      run: |
-        # These packages are brought in by conda (via the toolkit) and must be removed manually
-        # since pip doesn't know about the -base split and does not uninstall the -base package
-        micromamba remove --force openff-interchange openff-interchange-base
-        python -m pip install . plugins/
+      run: python -m pip install . plugins/
 
     - name: Install and license OpenEye Toolkits
       if: ${{ matrix.openeye == true }}
@@ -90,13 +79,8 @@ jobs:
       # and also uninstalls RDKit
       run: micromamba install rdkit "ambertools =23" "lammps >=2023.08.02" "jax >=0.3" "jaxlib >=0.3" -c conda-forge
 
-    - name: Install Foyer
-      run: micromamba install "foyer >=0.12.1" -c conda-forge -yq
-
     - name: Run tests
-      if: always()
-      run: |
-        python -m pytest $COV openff/interchange/ -r fExs -n logical --durations=10
+      run: python -m pytest $COV openff/interchange/ -r fExs -n logical --durations=10
 
     - name: Run small molecule regression tests
       if: ${{ matrix.openeye == true && matrix.openmm == true }}

diff --git a/.github/workflows/examples.yaml b/.github/workflows/examples.yaml
@@ -4,13 +4,11 @@ on:
   push:
     branches:
       - main
-      - develop
   pull_request:
     branches:
       - main
-      - develop
   schedule:
-    - cron: "0 0 * * *"
+    - cron: "0 7 * * *"
   workflow_dispatch:
 
 defaults:
@@ -19,15 +17,16 @@ defaults:
 
 jobs:
   test:
+    name: Examples on ${{ matrix.os }}, Python ${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}
     strategy:
-      fail-fast: false
       matrix:
         os:
           - ubuntu-latest
           - macos-latest
         python-version:
           - "3.10"
+          - "3.11"
 
     env:
       OE_LICENSE: ${{ github.workspace }}/oe_license.txt
@@ -39,21 +38,14 @@ jobs:
         fetch-depth: 0
 
     - name: Install conda environment
-      uses: mamba-org/setup-micromamba@v1
+      uses: mamba-org/setup-micromamba@v2
       with:
-        micromamba-version: '1.5.10-0'
         environment-file: devtools/conda-envs/examples_env.yaml
         create-args: >-
           python=${{ matrix.python-version }}
 
     - name: Install package
-      run: |
-        python -m pip install .
-
-    - name: Environment Information
-      run: |
-        micromamba info
-        micromamba list
+      run: python -m pip install .
 
     - name: License OpenEye
       run: |
@@ -63,12 +55,10 @@ jobs:
         SECRET_OE_LICENSE: ${{ secrets.OE_LICENSE }}
 
     - name: Run docexamples
-      run: |
-        python -m pytest --doctest-modules openff/interchange/ --ignore=openff/interchange/_tests
+      run: python -m pytest -c /dev/null/ --doctest-modules openff/interchange/ --ignore=openff/interchange/_tests
 
     - name: Run example notebooks
-      if: always()
       run: |
-        python -m pytest --nbval-lax --dist loadscope -n logical --durations=20 examples/ \
+        python -m pytest -c /dev/null/ --nbval-lax --dist loadscope -n logical --durations=20 examples/ \
           --ignore=examples/deprecated/ \
           --ignore=examples/experimental
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -12,7 +12,7 @@ repos:
   hooks:
   - id: add-trailing-comma
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.8.1
+  rev: v0.9.2
   hooks:
     - id: ruff
       args: ["--fix"]
@@ -40,7 +40,7 @@ repos:
     - id: nbstripout
       files: ^examples
 - repo: https://github.com/asottile/pyupgrade
-  rev: v3.19.0
+  rev: v3.19.1
   hooks:
   - id: pyupgrade
     args:

diff --git a/devtools/conda-envs/beta_env.yaml b/devtools/conda-envs/beta_env.yaml
diff --git a/devtools/conda-envs/dev_env.yaml b/devtools/conda-envs/dev_env.yaml
@@ -4,22 +4,22 @@ channels:
   - openeye
 dependencies:
   # Core
-  - python =3.10
+  - python
   - pip
   - versioningit
   - pip
   - numpy
   - pydantic =2
   # OpenFF stack
-  - openff-toolkit-base ~=0.16.4
+  - openff-toolkit-base ~=0.16.6
   - openff-units
   - ambertools =23
   # Optional features
   - openmm =8.1.2
   # smirnoff-plugins =2024
   # de-forcefields  # add back after smirnoff-plugins update
-  - openff-nagl
-  - openff-nagl-models
+  - openff-nagl ~=0.5
+  - openff-nagl-models ~=0.3
   - mbuild ~=0.18
   - foyer =1
   - gmso ~=0.12

diff --git a/devtools/conda-envs/docs_env.yaml b/devtools/conda-envs/docs_env.yaml
@@ -9,7 +9,7 @@ dependencies:
   - pip
   - numpy =1
   - pydantic =2
-  - openff-toolkit-base ~=0.16.4
+  - openff-toolkit-base ~=0.16.6
   - openmm =8.1.2
   - mbuild
   - foyer =1

diff --git a/devtools/conda-envs/examples_env.yaml b/devtools/conda-envs/examples_env.yaml
@@ -9,15 +9,14 @@ dependencies:
   - numpy
   - pydantic =2
   # OpenFF stack
-  - openff-toolkit-base ~=0.16.4
+  - openff-toolkit-base ~=0.16.6
   - openff-units
   - ambertools =23
   # Optional features
-  - openff-nagl
-  - openff-nagl-models
-  - mbuild ~=0.18
-  - foyer =1
-  - gmso ~=0.12
+  - openff-nagl ~=0.5
+  - openff-nagl-models ~=0.3
+  - mbuild
+  - foyer
   - nglview
   # Drivers
   - gromacs