Merge branch 'main' into testing-aws-ci

OpenFreeEnergy · Aug 9, 2024 · a02e729 · a02e729
2 parents 1114298 + 27c9116
commit a02e729
Show file tree

Hide file tree

Showing 10 changed files with 77 additions and 78 deletions.
diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -41,7 +41,6 @@ jobs:
           - "3.11"
           - "3.12"
         openeye: ["no"]
-        ommff-version: [">0.13"]
         include:
           - os: "macos-12"
             python-version: "3.12"
@@ -53,11 +52,6 @@ jobs:
             python-version: "3.11"
             pydantic-version: ">1"
             openeye: "yes"
-          - os: "ubuntu-latest"
-            python-version: "3.10"
-            pydantic-version: ">1"
-            openeye: "no"
-            ommff-version: "0.13"
           - os: "macos-latest"
             python-version: "3.12"
             pydantic-version: ">1"
@@ -88,7 +82,6 @@ jobs:
           create-args: >-
             python=${{ matrix.python-version }}
             pydantic=${{ matrix.pydantic-version }}
-            openmmforcefields=${{ matrix.ommff-version }}
           init-shell: bash
 
       - name: "Install OpenEye"
@@ -129,7 +122,7 @@ jobs:
       - name: codecov-pr
         if: ${{ github.repository == 'OpenFreeEnergy/openfe'
                 && github.event_name == 'pull_request' }}
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           file: coverage.xml
@@ -144,7 +137,7 @@ jobs:
         if: ${{ github.repository == 'OpenFreeEnergy/openfe'  
                 && github.event_name != 'schedule'            
                 && github.event_name != 'pull_request' }}     
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           file: coverage.xml

diff --git a/.github/workflows/conda_cron.yaml b/.github/workflows/conda_cron.yaml
@@ -0,0 +1,67 @@
+name: "conda_cron"
+on:
+  workflow_dispatch:
+  schedule:
+    # At 07:00 UTC every day
+    - cron: "0 7 * * *"
+
+concurrency:
+  group: "${{ github.workflow }}-${{ github.ref }}"
+  cancel-in-progress: true
+
+defaults:
+  run:
+    shell: bash -leo pipefail {0}
+
+jobs:
+  condacheck:
+    runs-on: ${{ matrix.OS }}
+    name: "daily conda check"
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ['ubuntu-latest', 'macos-latest', 'macos-12']
+        python-version:
+          - "3.9"
+          - "3.10"
+          - "3.11"
+          - "3.12"
+        exclude:
+          - os: 'macos-latest'
+            python-version: '3.9'
+
+    steps:
+      - name: Setup Micromamba
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-name: openfe
+          create-args: >-
+            python=${{ matrix.python-version }}
+            pip
+            jq
+          condarc: |
+            channels:
+              - jaimergp/label/unsupported-cudatoolkit-shim
+              - conda-forge
+          init-shell: bash
+
+      - name: "Install openfe + optional deps"
+        run: |
+          # get latest version from conda-forge
+          LATEST_VERSION=$(micromamba search --json openfe | jq '.result.pkgs[0].version')
+          echo "LATEST_VERSION: $LATEST_VERSION"
+          # Removing the quotes from the vesrion number 
+          # https://mywiki.wooledge.org/BashGuide/Parameters#Parameter_Expansion
+          micromamba install openfe=${LATEST_VERSION//\"} pytest -c conda-forge
+          python -m pip install pytest-xdist
+
+      - name: "env info"
+        run: |
+          micromamba info
+          micromamba list
+          pip list
+      - id: run-tests
+        name: "Run tests"
+        run: |
+          # note: this only runs the fast tests
+          pytest -n auto --pyargs openfe openfecli
diff --git a/docs/environment.yaml b/docs/environment.yaml
@@ -26,7 +26,7 @@ dependencies:
   - sphinx-toolbox
   - sphinx<7
   - git+https://github.com/OpenFreeEnergy/gufe@main
-  - git+https://github.com/OpenFreeEnergy/ofe-sphinx-theme@main
+  - git+https://github.com/OpenFreeEnergy/ofe-sphinx-theme@a45f3edd5bc3e973c1a01b577c71efa1b62a65d6
 
 # These are added automatically by RTD, so we include them here 
 # for a consistent environment.

diff --git a/environment.yml b/environment.yml
@@ -15,7 +15,7 @@ dependencies:
   - pytest-xdist
   - pytest-cov
   - pytest-rerunfailures
-  - pydantic >1
+  - pydantic >=1.10.17
   - pyyaml
   - coverage
   - cinnabar ~=0.4.0

diff --git a/openfe/protocols/openmm_afe/equil_afe_settings.py b/openfe/protocols/openmm_afe/equil_afe_settings.py
@@ -33,10 +33,7 @@
 )
 import numpy as np
 
-try:
-    from pydantic.v1 import validator
-except ImportError:
-    from pydantic import validator  # type: ignore[assignment]
+from pydantic.v1 import validator
 
 
 class AlchemicalSettings(SettingsBaseModel):

diff --git a/openfe/protocols/openmm_md/plain_md_settings.py b/openfe/protocols/openmm_md/plain_md_settings.py
@@ -19,10 +19,7 @@
     SettingsBaseModel,
     OpenMMSystemGeneratorFFSettings
 )
-try:
-    from pydantic.v1 import validator
-except ImportError:
-    from pydantic import validator  # type: ignore[assignment]
+from pydantic.v1 import validator
 
 
 class PlainMDProtocolSettings(Settings):

diff --git a/openfe/protocols/openmm_rfe/equil_rfe_settings.py b/openfe/protocols/openmm_rfe/equil_rfe_settings.py
@@ -27,10 +27,7 @@
     OpenFFPartialChargeSettings,
 )
 
-try:
-    from pydantic.v1 import validator
-except ImportError:
-    from pydantic import validator  # type: ignore[assignment]
+from pydantic.v1 import validator
 
 
 class LambdaSettings(SettingsBaseModel):

diff --git a/openfe/protocols/openmm_utils/omm_settings.py b/openfe/protocols/openmm_utils/omm_settings.py
@@ -21,10 +21,7 @@
 )
 
 
-try:
-    from pydantic.v1 import validator
-except ImportError:
-    from pydantic import validator  # type: ignore[assignment]
+from pydantic.v1 import validator
 
 
 class BaseSolvationSettings(SettingsBaseModel):

diff --git a/openfe/tests/protocols/test_openmm_equil_rfe_protocols.py b/openfe/tests/protocols/test_openmm_equil_rfe_protocols.py
@@ -244,32 +244,7 @@ def test_dry_run_gaff_vacuum(benzene_vacuum_system, toluene_vacuum_system,
         mapping=benzene_to_toluene_mapping,
     )
     unit = list(dag.protocol_units)[0]
-
-    # If we do a lot of GAFF testing, this should be refactored so we don't
-    # have to copy it all over the place.
-    # https://github.com/OpenFreeEnergy/openfe/pull/847#issuecomment-2096810453
-
-
-    import openmmforcefields
-    from packaging import version
-
-    ommff_version = openmmforcefields.__version__
-
-    gaff_should_fail = version.parse(
-        ommff_version
-    ) == version.parse("0.13.0")
-
-    if gaff_should_fail:
-        from openmmforcefields.generators.template_generators import (
-            GAFFNotSupportedError,
-        )
-
-        with pytest.raises(GAFFNotSupportedError):
-            with tmpdir.as_cwd():
-                sampler = unit.run(dry=True)["debug"]["sampler"]
-    else:
-        with tmpdir.as_cwd():
-            sampler = unit.run(dry=True)["debug"]["sampler"]
+    sampler = unit.run(dry=True)["debug"]["sampler"]
 
 
 @pytest.mark.slow

diff --git a/openfe/tests/protocols/test_openmm_plain_md_protocols.py b/openfe/tests/protocols/test_openmm_plain_md_protocols.py
@@ -176,31 +176,7 @@ def test_dry_run_gaff_vacuum(benzene_vacuum_system, tmpdir):
         mapping=None,
     )
     unit = list(dag.protocol_units)[0]
-
-    # If we do a lot of GAFF testing, this should be refactored so we don't
-    # have to copy it all over the place.
-    # https://github.com/OpenFreeEnergy/openfe/pull/847#issuecomment-2096810453
-
-    import openmmforcefields
-    from packaging import version
-
-    ommff_version = openmmforcefields.__version__
-
-    gaff_should_fail = version.parse(
-        ommff_version
-    ) == version.parse("0.13.0")
-
-    if gaff_should_fail:
-        from openmmforcefields.generators.template_generators import (
-            GAFFNotSupportedError,
-        )
-
-        with pytest.raises(GAFFNotSupportedError):
-            with tmpdir.as_cwd():
-                system = unit.run(dry=True)["debug"]["system"]
-    else:
-        with tmpdir.as_cwd():
-            system = unit.run(dry=True)["debug"]["system"]
+    system = unit.run(dry=True)["debug"]["system"]
 
 
 @pytest.mark.parametrize('method, backend, ref_key', [