Use pytest 8 in CI (#1822)

* Use bundled package in deployment tests

* Skip version check

* Remove some legacy fixtures

* Update deployment test environments

* Turn on CI

* Clean up

* Clean up

* Clean up

* Update docexample

* Run all doctests

* Update doctests

* Use 7.4 in deployment tests

* Cleanup

* Update config

* Fix call

* Revert changes to "conda" tests

* Ensure pytest 8 is used

* Update release history

.github/workflows/CI.yml

@@ -4,15 +4,10 @@ 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.
-    #   (from https://help.github.com/en/actions/reference/events-that-trigger-workflows#scheduled-events-schedule)
     - cron: "21 0 * * *"
 
 defaults:
@@ -41,7 +36,6 @@ jobs:
 
     env:
       OE_LICENSE: ${{ github.workspace }}/oe_license.txt
-      PACKAGE: openff
       PYTEST_ARGS: -r fE --tb=short -nauto
       COV: --cov=openff/toolkit --cov-append --cov-report=xml
 
@@ -149,7 +143,7 @@ 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 --durations=20 $PYTEST_ARGS $COV
@@ -160,7 +154,7 @@ jobs:
 
       - name: Run notebooks in docs
         if: ${{ matrix.rdkit == true && matrix.openeye == true }}
-        run: pytest -v --no-cov --nbval --ignore docs/_build/ docs/
+        run: python -m pytest -v --no-cov --nbval-lax docs/
 
       - name: Run examples in docstrings
         if: ${{ matrix.rdkit == true && matrix.openeye == true }}

.github/workflows/beta_rc.yaml

@@ -78,7 +78,7 @@ 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
 
       - name: Run code snippets in docs

.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: |
@@ -110,6 +91,7 @@ jobs:
               python -c "from openff.toolkit.utils.toolkits import ${TK}_AVAILABLE; assert not ${TK}_AVAILABLE, '${TK} available'"
             done
           fi
+
       - name: Environment Information
         run: |
           micromamba info

devtools/conda-envs/openeye-examples.yaml

@@ -27,7 +27,7 @@ dependencies:
     # Toolkit-specific
   - openeye-toolkits
     # Test-only/optional/dev/typing/examples
-  - pytest
+  - pytest =8
   - pytest-xdist
   - pytest-rerunfailures
   - pyyaml

devtools/conda-envs/openeye.yaml

@@ -26,7 +26,7 @@ dependencies:
     # Toolkit-specific
   - openeye-toolkits
     # Test-only/optional/dev/typing
-  - pytest
+  - pytest =8
   - pytest-cov
   - pytest-xdist
   - pytest-rerunfailures

devtools/conda-envs/rdkit-examples.yaml

@@ -30,7 +30,7 @@ dependencies:
     # https://github.com/rdkit/rdkit/issues/7221 and https://github.com/rdkit/rdkit/issues/7583
   - rdkit =2024
     # Test-only/optional/dev/typing/examples
-  - pytest
+  - pytest =8
   - pytest-xdist
   - pytest-rerunfailures
   - pyyaml

devtools/conda-envs/rdkit.yaml

@@ -27,7 +27,7 @@ dependencies:
     # https://github.com/rdkit/rdkit/issues/7221 and https://github.com/rdkit/rdkit/issues/7583
   - rdkit !=2024.03.6,!=2024.03.5
     # Test-only/optional/dev/typing
-  - pytest
+  - pytest =8
   - pytest-cov
   - pytest-xdist
   - pytest-rerunfailures

devtools/conda-envs/test_env.yaml

@@ -32,7 +32,7 @@ dependencies:
 
   - openeye-toolkits
     # Test-only/optional/dev/typing
-  - pytest
+  - pytest =8
   - pytest-cov
   - pytest-xdist
   - pytest-rerunfailures

docs/releasehistory.md

@@ -28,6 +28,10 @@ Releases follow the `major.minor.micro` scheme recommended by [PEP440](https://w
 
 - [PR #1981](https://github.com/openforcefield/openff-toolkit/pull/1981): Updates documentation to run quicker and use new features, including some in Interchange 0.4.
 
+### Miscellaneous
+
+- [PR #1822](https://github.com/openforcefield/openff-toolkit/pull/1922): Updates internal tests to use Pytest 8.
+
 ## 0.16.7
 
 ### Bugfixes

openff/toolkit/_tests/conftest.py

@@ -1,9 +1,5 @@
 """
 Configuration file for pytest.
-
-This adds the following command line options.
-- runslow: Run tests marked as slow (default is False).
-
 """
 
 import logging
@@ -20,16 +16,6 @@
     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.

openff/toolkit/_tests/test_examples.py

@@ -36,8 +36,7 @@ def run_script_str(script_str):
 
     """
     with tempfile.TemporaryDirectory() as tmp_dir:
-        temp_file_path = pathlib.Path(tmp_dir, "temp.py").as_posix()
-
+        temp_file_path = (pathlib.Path(tmp_dir) / "temp.py").as_posix()
         # Create temporary python script.
         with open(temp_file_path, "w") as f:
             f.write(script_str)
@@ -57,16 +56,17 @@ def find_example_scripts() -> list[str]:
     example_file_paths : list[str]
         List of full paths to python scripts to execute.
     """
-    # Count on the examples/ path being equivalently accessible as the README file
-    readme_file_path = _get_readme_path()
-
-    if readme_file_path is None:
+    if "site-packages" in __file__:
+        # This test file is being collected from the installed package, which
+        # does not provide the examples folder in the same location
         return list()
 
-    examples_dir_path = pathlib.Path(_get_readme_path().parent, "examples")
+    examples_dir_path = pathlib.Path(__file__).parents[3] / "examples"
 
     # Examples that require RDKit
-    rdkit_examples = {examples_dir_path / "conformer_energies/conformer_energies.py"}
+    rdkit_examples = {
+        examples_dir_path / "conformer_energies/conformer_energies.py",
+    }
 
     example_file_paths = []
     for example_file_path in examples_dir_path.glob("*/*.py"):

openff/toolkit/_tests/test_forcefield.py

@@ -1325,7 +1325,7 @@ 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)
@@ -1882,9 +1882,8 @@ def test_handlers_tracked_if_already_loaded(self):
 
         plugins = load_handler_plugins()
 
-        assert (
-            len(plugins) > 0
-        ), "Test assumes that some ParameterHandler plugins are available"
+        if len(plugins) == 0:
+            pytest.skip("Test assumes that some ParameterHandler plugins are available")
 
         assert ForceField(load_plugins=False)._plugin_parameter_handler_classes == []
         assert ForceField(load_plugins=True)._plugin_parameter_handler_classes == [

openff/toolkit/_tests/test_links.py

@@ -1,10 +1,9 @@
+import pathlib
 import re
 from urllib.request import Request, urlopen
 
 import pytest
 
-from openff.toolkit._tests.utils import _get_readme_path
-
 
 def find_readme_links() -> list[str]:
     """Yield all the links in the main README.md file.
@@ -14,16 +13,23 @@ def find_readme_links() -> list[str]:
     readme_examples : list[str]
         The list of links included in the README.md file.
     """
-    readme_file_path = _get_readme_path()
-
-    if readme_file_path is None:
+    if "site-packages" in __file__:
+        # This test file is being collected from the installed package, which
+        # does not provide the README file.
+        # Note that there will likely be a mis-bundled file
+        # $CONDA_PREFIX/lib/python3.x/site-packages/README.md, but this is not
+        # the toolkit's README file!
         return list()
 
     else:
+        readme_file_path = pathlib.Path(__file__).parents[3] / "README.md"
         with open(readme_file_path.as_posix()) as f:
             readme_content = f.read()
 
-        return re.findall("http[s]?://(?:[0-9a-zA-Z]|[-/.%:_])+", readme_content)
+    with open(readme_file_path.as_posix()) as f:
+        readme_content = f.read()
+
+    return re.findall("http[s]?://(?:[0-9a-zA-Z]|[-/.%:_])+", readme_content)
 
 
 @pytest.mark.parametrize("readme_link", find_readme_links())

openff/toolkit/_tests/test_toolkit_io.py

@@ -3,7 +3,6 @@
 
 """
 
-import os
 import pathlib
 import sys
 import tempfile
@@ -944,14 +943,6 @@ def test_from_file_obj_smi_supports_stringio(self):
         assert mol.name == "CHEMBL113"
 
 
-@pytest.fixture(scope="class")
-def tmpdir(request):
-    request.cls.tmpdir = tmpdir = tempfile.TemporaryDirectory()
-    with tmpdir:
-        yield
-    request.cls.tmpdir = None
-
-
 def assert_is_ethanol_sdf(f):
     assert f.readline() == "ethanol\n"  # title line
     f.readline()  # ignore next two lines
@@ -973,12 +964,9 @@ def assert_is_ethanol_smiles(smiles):
 
 
 class BaseToFileIO:
-    def get_tmpfile(self, name):
-        return os.path.join(self.tmpdir.name, name)
-
     @pytest.mark.parametrize("format_name", ["SDF", "sdf", "sDf", "mol", "MOL"])
-    def test_to_file_sdf(self, format_name):
-        filename = self.get_tmpfile("abc.xyz")
+    def test_to_file_sdf(self, format_name, tmp_path):
+        filename = tmp_path / "abc.xyz"
         self.toolkit_wrapper.to_file(ETHANOL, filename, format_name)
         with open(filename) as f:
             assert_is_ethanol_sdf(f)
@@ -999,8 +987,8 @@ def test_to_file_obj_sdf_with_bytesio(self):
             self.toolkit_wrapper.to_file_obj(ETHANOL, f, "sdf")
 
     @pytest.mark.parametrize("format_name", ["SMI", "smi", "sMi"])
-    def test_to_file_smi(self, format_name):
-        filename = self.get_tmpfile("abc.xyz")
+    def test_to_file_smi(self, format_name, tmp_path):
+        filename = tmp_path / "abc.xyz"
         self.toolkit_wrapper.to_file(ETHANOL, filename, format_name)
         with open(filename) as f:
             assert_is_ethanol_smi(f)
@@ -1026,19 +1014,19 @@ def test_to_file_qwe_format_raises_exception(self):
                 self.toolkit_wrapper.to_file(ETHANOL, fileobj.name, "QWE")
 
     @pytest.mark.parametrize("format_name", ["smi", "sdf", "mol"])
-    def test_to_file_when_the_file_does_not_exist(self, format_name):
-        filename = self.get_tmpfile("does/not/exist.smi")
+    def test_to_file_when_the_file_does_not_exist(self, format_name, tmp_path):
+        filename = tmp_path / "does/not/exist.smi"
         with pytest.raises(OSError):
             self.toolkit_wrapper.to_file(ETHANOL, filename, format_name)
 
 
-@pytest.mark.usefixtures("init_toolkit", "tmpdir")
+@pytest.mark.usefixtures("init_toolkit")
 @requires_openeye
 class TestOpenEyeToolkitToFileIO(BaseToFileIO):
     toolkit_wrapper_class = OpenEyeToolkitWrapper
 
 
-@pytest.mark.usefixtures("init_toolkit", "tmpdir")
+@pytest.mark.usefixtures("init_toolkit")
 @requires_rdkit
 class TestRDKitToolkitToFileIO(BaseToFileIO):
     toolkit_wrapper_class = RDKitToolkitWrapper

openff/toolkit/topology/topology.py

@@ -1688,12 +1688,7 @@ def from_pdb(
         (24, 23, 29, 36)
         (32, 31, 40, 42)
         >>> [*top.hierarchy_iterator("residues")]
-        [HierarchyElement ('A', '1', ' ', 'ACE') of iterator 'residues' containing 6 atom(s),
-         HierarchyElement ('A', '2', ' ', 'SER') of iterator 'residues' containing 11 atom(s),
-         HierarchyElement ('A', '3', ' ', 'NME') of iterator 'residues' containing 6 atom(s),
-         HierarchyElement ('B', '1', ' ', 'ACE') of iterator 'residues' containing 6 atom(s),
-         HierarchyElement ('B', '2', ' ', 'CYS') of iterator 'residues' containing 11 atom(s),
-         HierarchyElement ('B', '3', ' ', 'NME') of iterator 'residues' containing 6 atom(s)]
+        [HierarchyElement ('A', '1', ' ', 'ACE') of iterator 'residues' containing 6 atom(s), HierarchyElement ('A', '2', ' ', 'SER') of iterator 'residues' containing 11 atom(s), HierarchyElement ('A', '3', ' ', 'NME') of iterator 'residues' containing 6 atom(s), HierarchyElement ('B', '1', ' ', 'ACE') of iterator 'residues' containing 6 atom(s), HierarchyElement ('B', '2', ' ', 'CYS') of iterator 'residues' containing 11 atom(s), HierarchyElement ('B', '3', ' ', 'NME') of iterator 'residues' containing 6 atom(s)]
 
         Polymer systems can also be supported if ``_custom_substructures`` are
         given as a ``dict[str, list[str]]``, where the keys are unique atom
@@ -1716,7 +1711,7 @@ def from_pdb(
         ...          get_data_file_path("systems/test_systems/PE.pdb"),
         ...          _custom_substructures=PE_substructs,
         ...      )
-        """
+        """  # noqa: E501
         import io
         import json