[WIP] Debug macos tests

.github/workflows/ci.yaml

@@ -58,7 +58,7 @@ jobs:
 
       - name: "Run tests"
         run: |
-          pytest -n auto -v --cov=openfe_analysis --cov-report=xml --durations=10
+          pytest -v --cov=openfe_analysis --cov-report=xml --durations=10
 
       - name: codecov
         if: ${{ github.repository == 'OpenFreeEnergy/openfe_analysis'

environment.yml

@@ -4,7 +4,7 @@ channels:
 dependencies:
   - click
   - MDAnalysis
-  - netCDF4
+  - netCDF4 <1.7.1
   - openff-units
   - pip
   - tqdm

src/openfe_analysis/reader.py

@@ -193,5 +193,7 @@ def _reopen(self):
         self._frame_index = -1
 
     def close(self):
-        if self._dataset_owner:
-            self._dataset.close()
+        if self._dataset is not None:
+            if self._dataset_owner:
+                self._dataset.close()
+                self._dataset = None

src/openfe_analysis/rmsd.py

@@ -179,6 +179,8 @@ def gather_rms_data(
 
         output["time(ps)"] = list(np.arange(len(u.trajectory))[::skip] * u.trajectory.dt)
 
+    ds.close()
+
     return output
 
 

src/openfe_analysis/tests/conftest.py

@@ -3,6 +3,16 @@
 import pathlib
 import pooch
 import pytest
+import urllib.request
+
+
+try:
+    urllib.request.urlopen('https://www.google.com')
+except:  # -no-cov-
+    HAS_INTERNET = False
+else:
+    HAS_INTERNET = True
+
 
 POOCH_CACHE = pooch.os_cache("openfe_analysis")
 ZENODO_RBFE_DATA = pooch.create(
@@ -12,6 +22,7 @@
        "openfe_analysis_simulation_output.tar.gz":"md5:09752f2c4e5b7744d8afdee66dbd1414",
        "openfe_analysis_skipped.tar.gz": "md5:3840d044299caacc4ccd50e6b22c0880",
     },
+    retry_if_failed=5,
 )
 
 @pytest.fixture(scope="session")
@@ -46,7 +57,7 @@ def hybrid_system_skipped_pdb(rbfe_skipped_data_dir)->pathlib.Path:
     return rbfe_skipped_data_dir/"hybrid_system.pdb"
 
 
-@pytest.fixture(scope="session")
+@pytest.fixture(scope='session')
 def mcmc_serialized():
     return (
         "_serialized__class_name: LangevinDynamicsMove\n"

src/openfe_analysis/tests/test_reader.py

@@ -105,6 +105,8 @@ def test_universe_creation(simulation_nc, hybrid_system_pdb):
     )
     assert_allclose(u.dimensions, [82.191055, 82.191055, 82.191055, 90.0, 90.0, 90.0])
 
+    u.trajectory.close()
+
 
 def test_universe_from_nc_file(simulation_nc, hybrid_system_pdb):
     ds = nc.Dataset(simulation_nc)
@@ -116,6 +118,7 @@ def test_universe_from_nc_file(simulation_nc, hybrid_system_pdb):
     assert len(u.atoms) == 4782
     assert len(u.trajectory) == 501
     assert u.trajectory.dt == pytest.approx(1.0)
+    ds.close()
 
 
 def test_universe_creation_noconversion(simulation_nc, hybrid_system_pdb):
@@ -134,6 +137,7 @@ def test_universe_creation_noconversion(simulation_nc, hybrid_system_pdb):
             ]
         ),
     )
+    u.trajectory.close()
 
 
 def test_fereader_negative_state(simulation_nc, hybrid_system_pdb):
@@ -142,6 +146,7 @@ def test_fereader_negative_state(simulation_nc, hybrid_system_pdb):
 
     assert u.trajectory._state_id == 10
     assert u.trajectory._replica_id is None
+    u.trajectory.close()
 
 
 def test_fereader_negative_replica(simulation_nc, hybrid_system_pdb):
@@ -150,10 +155,11 @@ def test_fereader_negative_replica(simulation_nc, hybrid_system_pdb):
 
     assert u.trajectory._state_id is None
     assert u.trajectory._replica_id == 9
+    u.trajectory.close()
 
 
 @pytest.mark.parametrize("rep_id, state_id", [[None, None], [1, 1]])
-@pytest.mark.flaky(reruns=3)
+#@pytest.mark.flaky(reruns=3)
 def test_fereader_replica_state_id_error(simulation_nc, hybrid_system_pdb, rep_id, state_id):
     with pytest.raises(ValueError, match="Specify one and only one"):
         _ = mda.Universe(
@@ -178,3 +184,5 @@ def test_simulation_skipped_nc(simulation_skipped_nc, hybrid_system_skipped_pdb)
         assert np.all(u.atoms.positions > 0)
     with pytest.raises(mda.exceptions.NoDataError, match="This Timestep has no velocities"):
         u.atoms.velocities
+
+    u.trajectory.close()

src/openfe_analysis/tests/test_rmsd.py

@@ -6,7 +6,7 @@
 from openfe_analysis.rmsd import gather_rms_data
 
 
-@pytest.mark.flaky(reruns=3)
+#@pytest.mark.flaky(reruns=3)
 def test_gather_rms_data_regression(simulation_nc, hybrid_system_pdb):
     output = gather_rms_data(
         hybrid_system_pdb,
@@ -43,7 +43,7 @@ def test_gather_rms_data_regression(simulation_nc, hybrid_system_pdb):
     )
 
 
-@pytest.mark.flaky(reruns=3)
+#@pytest.mark.flaky(reruns=3)
 def test_gather_rms_data_regression_skippednc(simulation_skipped_nc, hybrid_system_skipped_pdb):
     output = gather_rms_data(
         hybrid_system_skipped_pdb,

src/openfe_analysis/tests/test_transformations.py

@@ -13,15 +13,17 @@
 
 @pytest.fixture
 def universe(hybrid_system_pdb, simulation_nc):
-    return mda.Universe(
+    u = mda.Universe(
         hybrid_system_pdb,
         simulation_nc,
         format="MultiStateReporter",
         state_id=0,
     )
+    yield u
+    u.trajectory.close()
 
 
-@pytest.mark.flaky(reruns=3)
+#@pytest.mark.flaky(reruns=3)
 def test_minimiser(universe):
     prot = universe.select_atoms("protein and name CA")
     lig = universe.select_atoms("resname UNK")
@@ -34,7 +36,7 @@ def test_minimiser(universe):
     assert d == pytest.approx(11.10, abs=0.01)
 
 
-@pytest.mark.flaky(reruns=3)
+#@pytest.mark.flaky(reruns=3)
 def test_nojump(universe):
     # find frame where protein would teleport across boundary and check it
     prot = universe.select_atoms("protein and name CA")
@@ -50,7 +52,7 @@ def test_nojump(universe):
     assert prot.center_of_mass() == pytest.approx(ref, abs=0.01)
 
 
-@pytest.mark.flaky(reruns=3)
+#@pytest.mark.flaky(reruns=3)
 def test_aligner(universe):
     # checks that rmsd is identical with/without center&super
     prot = universe.select_atoms("protein and name CA")

src/openfe_analysis/tests/utils/test_multistate.py

@@ -13,18 +13,25 @@
 )
 
 
-@pytest.fixture(scope="module")
+@pytest.fixture()
 def dataset(simulation_nc):
-    return nc.Dataset(simulation_nc)
+    ds = nc.Dataset(simulation_nc)
+    yield ds
+    ds.close()
+
+
+@pytest.fixture()
+def skipped_dataset(simulation_skipped_nc):
+    ds = nc.Dataset(simulation_skipped_nc)
+    yield ds
+    ds.close()
 
 
-@pytest.mark.flaky(reruns=3)
 @pytest.mark.parametrize("state, frame, replica", [[0, 0, 0], [0, 1, 3], [0, -1, 7], [3, 100, 6]])
 def test_state_to_replica(dataset, state, frame, replica):
     assert _state_to_replica(dataset, state, frame) == replica
 
 
-@pytest.mark.flaky(reruns=3)
 def test_replica_positions_at_frame(dataset):
     pos = _replica_positions_at_frame(dataset, 1, -1)
     assert_allclose(
@@ -69,6 +76,8 @@ def test_create_new_dataset(tmpdir):
         assert ds.variables["cell_angles"].get_dims()[1].name == "cell_angular"
         assert ds.variables["cell_angles"].dtype.name == "float64"
 
+        ds.close()
+
 
 def test_get_unitcell(dataset):
     dims = _get_unitcell(dataset, 7, -1)
@@ -79,9 +88,7 @@ def test_get_unitcell(dataset):
 
 
 def test_simulation_skipped_nc_no_positions_box_vectors_frame1(
-    simulation_skipped_nc,
+    skipped_dataset,
 ):
-    dataset = nc.Dataset(simulation_skipped_nc)
-
-    assert _get_unitcell(dataset, 1, 1) is None
-    assert dataset.variables["positions"][1][0].mask.all()
+    assert _get_unitcell(skipped_dataset, 1, 1) is None
+    assert skipped_dataset.variables["positions"][1][0].mask.all()