Merge pull request #333 from OpenFreeEnergy/slow-tests

Add pytest filter for slow tests

Author: IAlibay

.github/workflows/ci.yaml

@@ -63,6 +63,9 @@ jobs:
           micromamba list
 
       - name: "Run tests"
+        env:
+          # Set the OFE_SLOW_TESTS to True if running a Cron job
+          OFE_SLOW_TESTS: ${{ fromJSON('{"false":"false","true":"true"}')[github.event_name == 'schedule'] }}
         run: |
           pytest -n auto -v --cov=openfe --cov=openfecli --cov-report=xml
 

.github/workflows/mypy.yaml

@@ -21,14 +21,15 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: conda-incubator/setup-miniconda@v2
+      - name: Setup Micromamba
+        uses: mamba-org/provision-with-micromamba@main
         with:
-            auto-update-conda: true
-            use-mamba: true
-            python-version: 3.9
-            miniforge-variant: Mambaforge
-            environment-file: environment.yml
-            activate-environment: openfe
+          environment-file: environment.yml
+          environment-name: openfe
+          cache-env: true
+          cache-downloads: true
+          extra-specs: |
+            python==3.9
 
       - name: "Install steps"
         run: |
@@ -37,8 +38,8 @@ jobs:
 
       - name: "Environment Information"
         run: |
-          mamba info -a
-          mamba list
+          micromamba info
+          micromamba list
 
       - name: "Lint with mypy"
         run: mypy 

.github/workflows/package-tests.yaml

@@ -40,6 +40,8 @@ jobs:
 
       - name: "run tests"
         working-directory: ./dist
+        env:
+          OFE_SLOW_TESTS: "true"
         run: |
           pytest -n auto -v --pyargs openfe.tests
           pytest -n auto -v --pyargs openfecli.tests

openfe/protocols/openmm_rfe/equil_rfe_methods.py

@@ -436,8 +436,10 @@ def run(self, dry=False, verbose=True, basepath=None) -> dict[str, Any]:
                 smirnoff_stateB.generator)
 
         # 3. Model state A
+        # Note: protein dry run tests are part of the slow tests and don't show
+        # up in coverage reports
         stateA_ligand_topology = stateA_openff_ligand.to_topology().to_openmm()
-        if 'protein' in stateA.components:
+        if 'protein' in stateA.components:  # pragma: no-cover
             pdbfile: gufe.ProteinComponent = stateA['protein']
             stateA_modeller = app.Modeller(pdbfile.to_openmm_topology(),
                                            pdbfile.to_openmm_positions())

openfe/tests/conftest.py

@@ -1,5 +1,6 @@
 # This code is part of OpenFE and is licensed under the MIT license.
 # For details, see https://github.com/OpenFreeEnergy/openfe
+import os
 import importlib
 import pytest
 from importlib import resources
@@ -11,12 +12,39 @@
 from gufe import SmallMoleculeComponent, LigandAtomMapping
 
 
+# allow for optional slow tests
+# See: https://docs.pytest.org/en/latest/example/simple.html
+def pytest_addoption(parser):
+    parser.addoption(
+        "--runslow", action="store_true", default=False, help="run slow tests"
+    )
+
+
+def pytest_configure(config):
+    config.addinivalue_line("markers", "slow: mark test as slow to run")
+
+
+def pytest_collection_modifyitems(config, items):
+    if (config.getoption("--runslow") or
+        os.environ['OFE_SLOW_TESTS'].lower() == 'true'):
+        # --runslow given in cli or OFE_SLOW_TESTS set to True in env vars
+        # do not skip slow tests
+        return
+    msg = ("need --runslow pytest cli option or the environment variable "
+           "`OFE_SLOW_TESTS` set to `True` to run")
+    skip_slow = pytest.mark.skip(reason=msg)
+    for item in items:
+        if "slow" in item.keywords:
+            item.add_marker(skip_slow)
+
+
 def mol_from_smiles(smiles: str) -> Chem.Mol:
     m = Chem.MolFromSmiles(smiles)
     AllChem.Compute2DCoords(m)
 
     return m
 
+
 @pytest.fixture(scope='session')
 def ethane():
     return SmallMoleculeComponent(mol_from_smiles('CC'))

openfe/tests/protocols/test_openmm_equil_rfe_protocols.py

@@ -133,6 +133,7 @@ def test_dry_run_ligand(benzene_system, toluene_system,
         assert sampler.is_periodic
 
 
+@pytest.mark.slow
 @pytest.mark.parametrize('method', ['repex', 'sams', 'independent'])
 def test_dry_run_complex(benzene_complex_system, toluene_complex_system,
                          benzene_to_toluene_mapping, method, tmpdir):
@@ -726,6 +727,7 @@ def tyk2_reference_xml():
     return ET.fromstring(xmldata)
 
 
+@pytest.mark.slow
 class TestTyk2XmlRegression:
     """Generates Hybrid system XML and performs regression test"""
     @staticmethod