Update configuration

.github/workflows/CI.yml

@@ -142,7 +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

@@ -28,7 +28,7 @@ jobs:
     env:
       OPENEYE: ${{ matrix.openeye }}
       OE_LICENSE: ${{ github.workspace }}/oe_license.txt
-      PYTEST_ARGS: -r fE --tb=short -n logical
+      PYTEST_ARGS: -r fE --tb=short -n logical --durations=20
 
     steps:
       - name: Vanilla install from conda
@@ -87,12 +87,15 @@ jobs:
 
       - name: Test the package
         run: |
+
+          # Act like we're testing with this patch deployed ...
+          python -m pip install -e . 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+=" -x --trace-config"
           PYTEST_ARGS+=" --ignore-glob='*_links.py'"
           PYTEST_ARGS+=" --ignore-glob='*_examples.py'"
           PYTEST_ARGS+=" --ignore-glob='*_nagl.py'"
@@ -101,4 +104,4 @@ jobs:
 
           python -m pytest $PYTEST_ARGS \
             --pyargs "openff.toolkit" \
-            $CONDA_PREFIX/lib/python3.11/site-packages/openff/toolkit/_tests/conftest.py
+            -m "slow or not slow"

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))

openff/toolkit/_tests/test_forcefield.py

@@ -1347,7 +1347,7 @@ def test_parameterize_large_system(
         force_field,
     ):
         """Test parameterizing a large system of several distinct molecules.
-        This test is very slow, so it is only run if the --runslow option is provided to pytest.
+        This test is very slow, so it is only run if the slow marker option is provided to pytest.
         """
         box_file_path = get_data_file_path(
             os.path.join("systems", "packmol_boxes", box)

pytest.ini

@@ -0,0 +1,4 @@
+[pytest]
+markers =
+    slow: marks tests as slow (deselect with '-m "not slow"')
+addopts = -m "not slow"