Merge remote-tracking branch 'upstream/main' into more-gromacs-import…

…-tests
openforcefield · Jan 13, 2025 · 64975c9 · 64975c9
2 parents 29acdc0 + 271caed
commit 64975c9
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Showing 27 changed files with 374 additions and 160 deletions.
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:
@@ -21,8 +21,7 @@ jobs:
         python-version:
           - "3.10"
           - "3.11"
-        pydantic-version:
-          - "2"
+          - "3.12"
         openeye:
           - true
           - false
@@ -37,25 +36,30 @@ 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/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
-
-    - 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:

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:
       fail-fast: false
@@ -30,8 +28,6 @@ jobs:
         python-version:
           - "3.10"
           - "3.11"
-        pydantic-version:
-          - "2"
         openeye:
           - true
           - false
@@ -49,13 +45,11 @@ 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/test_env.yaml
         create-args: >-
           python=${{ matrix.python-version }}
-          pydantic=${{ matrix.pydantic-version }}
 
     - name: Install package
       run: |

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:
@@ -28,6 +26,7 @@ jobs:
           - macos-latest
         python-version:
           - "3.10"
+          - "3.11"
 
     env:
       OE_LICENSE: ${{ github.workspace }}/oe_license.txt
@@ -39,9 +38,8 @@ 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 }}
@@ -50,11 +48,6 @@ jobs:
       run: |
         python -m pip install .
 
-    - name: Environment Information
-      run: |
-        micromamba info
-        micromamba list
-
     - name: License OpenEye
       run: |
         echo "${SECRET_OE_LICENSE}" > ${OE_LICENSE}

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: v0.8.6
   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
@@ -9,12 +9,12 @@ 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
+  - openff-nagl ~=0.5
+  - openff-nagl-models ~=0.3
   - mbuild ~=0.18
   - foyer =1
   - gmso ~=0.12

diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
@@ -8,7 +8,7 @@ dependencies:
   - numpy
   - pydantic =2
   # OpenFF stack
-  - openff-toolkit-base ~=0.16.4
+  - openff-toolkit-base ~=0.16.6
   - openff-units
   - ambertools =23
   # Needs to be explicitly listed to not be dropped when AmberTools is removed
@@ -17,9 +17,9 @@ dependencies:
   - openmm =8.1.2
   # smirnoff-plugins =2024
   # de-forcefields  # add back after smirnoff-plugins update
-  - openff-nagl
-  - openff-nagl-models
-  - mbuild ~=0.18
+  - openff-nagl ~=0.5
+  - openff-nagl-models ~=0.3
+  - mbuild =1
   - foyer =1
   - gmso ~=0.12
   - nglview