Use bundled package in deployment tests

.github/workflows/CI.yml

@@ -1,14 +1,6 @@
 name: CI
 
 on:
-  push:
-    branches:
-      - "main"
-      - "maintenance/.*"
-  pull_request:
-    branches:
-      - "main"
-      - "maintenance/.*"
   schedule:
     # Nightly tests run on main by default:
     #   Scheduled workflows run on the latest commit on the default or base branch.
@@ -41,7 +33,6 @@ jobs:
 
     env:
       OE_LICENSE: ${{ github.workspace }}/oe_license.txt
-      PACKAGE: openff
       PYTEST_ARGS: -r fE --tb=short -nauto
       COV: --cov=openff/toolkit --cov-config=setup.cfg --cov-append --cov-report=xml
 
@@ -151,7 +142,7 @@ jobs:
           PYTEST_ARGS+=" --ignore=openff/toolkit/_tests/test_examples.py"
           PYTEST_ARGS+=" --ignore=openff/toolkit/_tests/test_links.py"
           if [[ "$GITHUB_EVENT_NAME" == "schedule" ]]; then
-            PYTEST_ARGS+=" --runslow"
+            PYTEST_ARGS+=" -m 'slow or not slow'"
           fi
 
           python -m pytest $PYTEST_ARGS $COV

.github/workflows/beta_rc.yaml

@@ -77,7 +77,7 @@ jobs:
         run: |
           PYTEST_ARGS+=" --ignore=openff/toolkit/_tests/test_examples.py"
           PYTEST_ARGS+=" --ignore=openff/toolkit/_tests/test_links.py"
-          PYTEST_ARGS+=" --runslow"
+          PYTEST_ARGS+=" -m 'slow or not slow'"
           pytest $PYTEST_ARGS $COV
 
       - name: Run code snippets in docs

.github/workflows/conda.yml

@@ -1,6 +1,7 @@
 name: Conda latest
 
 on:
+  push:
   release:
     types:
       - released
@@ -20,59 +21,46 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, macos-latest]
-        python-version: ["3.9", "3.10"]
+        os: [ubuntu-latest]
+        python-version: ["3.11"]
         openeye: ["true", "false"]
 
     env:
-      CI_OS: ${{ matrix.os }}
       OPENEYE: ${{ matrix.openeye }}
-      PYVER: ${{ matrix.python-version }}
       OE_LICENSE: ${{ github.workspace }}/oe_license.txt
-      PACKAGE: openff-toolkit
+      PYTEST_ARGS: -r fE --tb=short -n logical --durations=20
 
     steps:
       - uses: actions/checkout@v4
 
       - name: Vanilla install from conda
         uses: mamba-org/setup-micromamba@v1
-        if: ${{ matrix.openeye == 'false' }}
         with:
-          environment-file: devtools/conda-envs/conda.yaml
-          create-args: >-
-            python=${{ matrix.python-version }}
-      - name: Install from conda with OpenEye
-        uses: mamba-org/setup-micromamba@v1
-        if: ${{ matrix.openeye == 'true' }}
-        with:
-          environment-file: devtools/conda-envs/conda_oe.yaml
+          environment-name: latest-deployment
           create-args: >-
             python=${{ matrix.python-version }}
+            openff-toolkit-examples
+            smirnoff-plugins=2024
+            pytest-xdist
+            pytest-rerunfailures
 
-      - name: Additional info about the build
-        run: |
-          uname -a
-          df -h
-          ulimit -a
+      - name: Install OpenEye Toolkits
+        if: ${{ matrix.openeye == 'true' }}
+        run: micromamba install openeye-toolkits -c openeye
 
       - name: Make oe_license.txt file from GH org secret "OE_LICENSE"
+        if: ${{ matrix.openeye == 'true' }}
         env:
           OE_LICENSE_TEXT: ${{ secrets.OE_LICENSE }}
         run: |
           echo "${OE_LICENSE_TEXT}" > ${OE_LICENSE}
 
       - name: Environment Information
-        run: |
-          conda info
-          conda list
+        run: micromamba info && micromamba list
 
       - name: Check installed toolkits
         run: |
-          # Checkout the state of the repo as of the last release (including RCs)
           export LATEST_TAG=$(git ls-remote --tags https://github.com/openforcefield/openff-toolkit.git | cut -f2 | grep -E "([0-9]+)\.([0-9]+)\.([0-9]+)$" | sort --version-sort | tail -1 | sed 's/refs\/tags\///')
-          git fetch --tags
-          git checkout tags/$LATEST_TAG
-          git log -1 | cat
 
           if [[ "$OPENEYE" == true ]]; then
             python -c "from openff.toolkit.utils.toolkits import OPENEYE_AVAILABLE; assert OPENEYE_AVAILABLE, 'OpenEye unavailable'"
@@ -86,9 +74,6 @@ jobs:
 
       - name: Check that correct OFFTK version was installed
         run: |
-          # Go up one directory to ensure that we don't just load the OFFTK from the checked-out repo
-          cd ../
-
           export LATEST_TAG=$(git ls-remote --tags https://github.com/openforcefield/openff-toolkit.git | cut -f2 | grep -E "([0-9]+)\.([0-9]+)\.([0-9]+)$" | sort --version-sort | tail -1 | sed 's/refs\/tags\///')
           export FOUND_VER=$(python -c "import openff.toolkit; print(openff.toolkit.__version__)")
 
@@ -102,20 +87,23 @@ jobs:
             exit 1
           fi
 
-          cd openff-toolkit
-
       - name: Test the package
         run: |
-          python -m pip install utilities/test_plugins
 
-          pwd
-          ls
+          # Act like we're testing with this patch deployed ...
+          python -m pip install . utilities/test_plugins/
 
           if [[ "$OPENEYE" == true ]]; then
             python -c "import openff.toolkit; print(openff.toolkit.__file__)"
             python -c "import openeye; print(openeye.oechem.OEChemIsLicensed())"
           fi
 
-          PYTEST_ARGS=" -r fE --tb=short --runslow openff/toolkit/_tests/conftest.py"
-          PYTEST_ARGS+=" --ignore=openff/toolkit/_tests/test_links.py"
-          pytest $PYTEST_ARGS openff
+          PYTEST_ARGS+=" --ignore-glob='*_links.py'"
+          PYTEST_ARGS+=" --ignore-glob='*_examples.py'"
+          PYTEST_ARGS+=" --ignore-glob='*_nagl.py'"
+
+          env
+
+          python -m pytest $PYTEST_ARGS \
+            --pyargs "openff.toolkit" \
+            -m "slow or not slow"

.github/workflows/examples.yml

@@ -1,14 +1,6 @@
 name: Examples
 
 on:
-  push:
-    branches:
-      - "main"
-      - "maintenance/.+"
-  pull_request:
-    branches:
-      - "main"
-      - "maintenance/.+"
   schedule:
     - cron: "0 0 * * *"
 
@@ -66,24 +58,13 @@ jobs:
           create-args: >-
             python=${{ matrix.python-version }}
 
-      - name: Additional info about the build
-        run: |
-          uname -a
-          df -h
-          ulimit -a
-
       - name: Make oe_license.txt file from GH org secret "OE_LICENSE"
         env:
           OE_LICENSE_TEXT: ${{ secrets.OE_LICENSE }}
-        run: |
-          echo "${OE_LICENSE_TEXT}" > ${OE_LICENSE}
+        run: echo "${OE_LICENSE_TEXT}" > ${OE_LICENSE}
 
       - name: Install package
-        run: |
-          # Maybe remove the packaged openff-toolkit, installed as a dependency of openmmforcefields
-          # and/or Interchange
-          micromamba remove --force openff-toolkit-base
-          python -m pip install .
+        run: python -m pip install .
 
       - name: Remove undesired toolkits
         run: |
@@ -92,7 +73,7 @@ jobs:
           # so don't remove it.
           if [ ! -z "${{ env.PACKAGES_TO_REMOVE }}" ]; then
             for cpkg in ${{ env.PACKAGES_TO_REMOVE }}; do
-              if [[ $(conda list | grep $cpkg) ]]; then micromamba remove --force $cpkg --yes ; fi
+              if [[ $(micromamba list | grep $cpkg) ]]; then micromamba remove --force $cpkg --yes ; fi
             done
           fi
 
@@ -119,10 +100,11 @@ jobs:
               python -c "from openff.toolkit.utils.toolkits import ${TK}_AVAILABLE; assert not ${TK}_AVAILABLE, '${TK} available'"
             done
           fi
+
       - name: Environment Information
         run: |
-          conda info
-          conda list
+          micromamba info
+          micromamba list
 
       - name: Run example scripts
         run: |

.github/workflows/lint.yml

@@ -1,7 +1,7 @@
 name: lint
 
 on:
-  push:
+  release:
 
 jobs:
 

openff/toolkit/_tests/conftest.py

@@ -1,15 +1,9 @@
 """
 Configuration file for pytest.
-
-This adds the following command line options.
-- runslow: Run tests marked as slow (default is False).
-
 """
 
 import logging
 
-import pytest
-
 logger = logging.getLogger(__name__)
 
 # Ensure QCPortal is imported before any OpenEye modules, see
@@ -20,16 +14,6 @@
     pass
 
 
-def pytest_configure(config):
-    """
-    Initialization hook to register custom markers without a pytest.ini
-    More info: https://docs.pytest.org/en/latest/reference.html#initialization-hooks
-    """
-    config.addinivalue_line(
-        "markers", "slow: marks tests as slow (deselect with `-m 'not slow'`)"
-    )
-
-
 def untar_full_alkethoh_and_freesolv_set():
     """When running slow tests, we unpack the full AlkEthOH and FreeSolv test
     sets in advance to speed things up.
@@ -48,81 +32,3 @@ def untar_full_alkethoh_and_freesolv_set():
         tarfile_path = os.path.join(molecule_dir_path, tarfile_name)
         with tarfile.open(tarfile_path, "r:gz") as tar:
             tar.extractall(path=molecule_dir_path)
-
-
-def pytest_addoption(parser):
-    """Add the pytest command line option --runslow and --failwip.
-
-    If --runslow is not given, tests marked with pytest.mark.slow are
-    skipped.
-
-    If --failwip is not given, tests marked with pytest.mark.wip are
-    xfailed.
-
-    Parameters
-    ----------
-    parser : argparsing.parser
-        The parser used by pytest to process arguments
-
-    Returns
-    -------
-    None
-
-    """
-
-    # Loaded pytest plugins define their own arguments, and in certain cases
-    # our options use the same name. Although this can define two different
-    # behaviors for the same argument, the two options below are fairly
-    # unambiguous in their interpretation, so we skip any errors and allow
-    # the testing to proceed
-
-    try:
-        parser.addoption(
-            "--runslow", action="store_true", default=False, help="run slow tests"
-        )
-    except ValueError:
-        logger.warning(
-            "Option --runslow already added elsewhere (from a plugin possibly?). Skipping..."
-        )
-
-    try:
-        parser.addoption(
-            "--failwip",
-            action="store_true",
-            default=False,
-            help="fail work in progress tests",
-        )
-    except ValueError:
-        logger.warning(
-            "Option --failwip already added elsewhere (from a plugin possibly?). Skipping..."
-        )
-
-
-def pytest_collection_modifyitems(config, items):
-    if config.getoption("runslow"):
-        # If --runslow is given, we don't have to mark items for skipping,
-        # but we need to extract the whole AlkEthOH and FreeSolv sets (see
-        # test_forcefield::test_alkethoh/freesolv_parameters_assignment).
-        untar_full_alkethoh_and_freesolv_set()
-    else:
-        # Mark for skipping all items marked as slow.
-        skip_slow = pytest.mark.skip(
-            reason="specify --runslow pytest option to run this test."
-        )
-        for item in items:
-            if "slow" in item.keywords:
-                item.add_marker(skip_slow)
-
-    # Mark work-in-progress tests for xfail.
-    if not config.getoption("failwip"):
-        xfail_wip_reason = (
-            "This is a work in progress test. Specify "
-            "--failwip pytest option to make this test fail."
-        )
-        for item in items:
-            if "wip" in item.keywords:
-                # Augment original reason.
-                reason = xfail_wip_reason + item.get_closest_marker("wip").kwargs.get(
-                    "reason", ""
-                )
-                item.add_marker(pytest.mark.xfail(reason=reason))