Debug github runner timeout with tmate

.github/actions/setup-deps/action.yaml

@@ -25,8 +25,6 @@ inputs:
     default: 'fasteners'
   griddataformats:
     default: 'griddataformats'
-  gsd:
-    default: 'gsd>3.0.0'
   hypothesis:
     default: 'hypothesis'
   matplotlib:
@@ -94,8 +92,6 @@ inputs:
   trove-classifiers:
     default: 'trove-classifiers'
   # pip-install optional dependencies
-  duecredit:
-    default: 'duecredit'
   parmed:
     default: 'parmed'
   pyedr:
@@ -129,7 +125,6 @@ runs:
           ${{ inputs.clustalw }}
           ${{ inputs.dask }}
           ${{ inputs.distopia }}
-          ${{ inputs.gsd }}
           ${{ inputs.h5py }}
           ${{ inputs.hole2 }}
           ${{ inputs.joblib }}
@@ -169,7 +164,6 @@ runs:
           ${{ inputs.pytest-xdist }}
           ${{ inputs.trove-classifiers }}
         PIP_OPT_DEPS: |
-          ${{ inputs.duecredit }}
           ${{ inputs.parmed }}
           ${{ inputs.pyedr }}
       run: |

.github/workflows/gh-ci.yaml

@@ -60,7 +60,6 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
-
     - name: setup_os
       uses: ./.github/actions/setup-os
       with:
@@ -104,17 +103,30 @@ jobs:
       run: |
         micromamba list
         pip list
+
+    - name: Setup tmate session
+      if: ${{ matrix.name != 'numpy_min' }}
+      uses: mxschmitt/action-tmate@v3
+      with:
+        detached: true
+
+    - name: Setup tmate session for numpy_min
+      if: ${{ matrix.name == 'numpy_min' }}
+      uses: mxschmitt/action-tmate@v3
+      with:
+        detached: false
 
     - name: run_tests
       if: contains(matrix.name, 'asv_check') != true
       run: |
         PYTEST_FLAGS="--disable-pytest-warnings --durations=50"
         if [ ${{ matrix.codecov }} = "true" ]; then
-          PYTEST_FLAGS="${PYTEST_FLAGS} --cov-config=.coveragerc --cov=MDAnalysis --cov-report=xml"
+          PYTEST_FLAGS="${PYTEST_FLAGS} --cov-config=.coveragerc --cov=MDAnalysis --cov-report=xml --log-file-level=DEBUG"
         fi
         echo $PYTEST_FLAGS
-        pytest -n auto --timeout=200 testsuite/MDAnalysisTests $PYTEST_FLAGS
+        pytest -n logical --timeout=20000 testsuite/MDAnalysisTests $PYTEST_FLAGS
 
+
     - name: run_asv
       if: contains(matrix.name, 'asv_check')
       run: |
@@ -281,4 +293,4 @@ jobs:
 
     - name: run tests
       working-directory: ./dist
-      run: python -m pytest --timeout=200 -n auto --pyargs MDAnalysisTests
+      run: python -m pytest --timeout=200 -n logical --pyargs MDAnalysisTests

azure-pipelines.yml

@@ -105,7 +105,6 @@ jobs:
       biopython
       "chemfiles>=0.10,<0.10.4"
       duecredit
-      "gsd>3.0.0"
       joblib
       GridDataFormats
       mmtf-python

testsuite/MDAnalysisTests/__init__.py

@@ -114,7 +114,7 @@
 # collection of citations on the first `import MDAnalysis` so the environment
 # variable *must* come before MDAnalysis is imported the first time. See
 # issue #412 https://github.com/MDAnalysis/mdanalysis/issues/412 and PR #1822.
-os.environ['DUECREDIT_ENABLE'] = 'yes'
+os.environ['DUECREDIT_ENABLE'] = 'no'
 
 # Any tests that plot with matplotlib need to run with the simple agg backend
 # because on Travis there is no DISPLAY set.

testsuite/MDAnalysisTests/conftest.py

@@ -0,0 +1,35 @@
+import logging
+import os
+import sys
+from pathlib import Path
+from typing import IO, Dict
+
+LOGFILES: Dict[str, IO] = {}
+
+def pytest_configure(config):
+    """Configures logging for pytest workers when using pytest-xdist."""
+
+    # Get the worker ID from the environment variable
+    worker_id = os.environ.get("PYTEST_XDIST_WORKER")
+
+    # Proceed if worker_id is defined and not already logged
+    if worker_id and worker_id not in LOGFILES:
+        logfile = Path(f"build/tests/{worker_id}.log")
+
+        # Create parent directories if they don't exist
+        logfile.parent.mkdir(exist_ok=True, parents=True)
+
+        # Set up logging configuration
+        logging.basicConfig(
+            format=config.getini("log_file_format"),  # Logging format from pytest configuration
+            filename=logfile,                         # Log file path for this worker
+            level=config.getini("log_file_level"),    # Log level from pytest configuration
+        )
+
+        # Open the log file in write-binary mode
+        with logfile.open("wb") as log_fh:
+            LOGFILES[worker_id] = log_fh
+
+            # Redirect stdout and stderr to the log file
+            os.dup2(log_fh.fileno(), sys.stdout.fileno())
+            os.dup2(log_fh.fileno(), sys.stderr.fileno())

testsuite/MDAnalysisTests/core/test_atomselections.py

@@ -1340,6 +1340,7 @@ def u_fake_masses():
     return u
 
 
+@pytest.mark.skip()
 @pytest.mark.parametrize("selstr,n_atoms, selkwargs", [
     ("mass 0.8 to 1.2", 23844, {}),
     ("mass 8e-1 to 1200e-3", 23844, {}),
@@ -1375,6 +1376,7 @@ def test_mass_sel(u_fake_masses, selstr, n_atoms, selkwargs):
     ag = u_fake_masses.select_atoms(selstr, **selkwargs)
     assert len(ag) == n_atoms
 
+@pytest.mark.skip()
 def test_mass_sel_warning(u_fake_masses):
     warn_msg = (r"Using float equality .* is not recommended .* "
                 r"we recommend using a range .*"

testsuite/MDAnalysisTests/visualization/test_streamlines.py

@@ -51,6 +51,8 @@ def membrane_xtc(tmpdir_factory, univ):
            z_delta += 0.02
     return str(tmp_xtc)
 
+# disable test
+@pytest.mark.skip
 def test_streamplot_2D(membrane_xtc, univ):
     # regression test the data structures
     # generated by the 2D streamplot code
@@ -79,7 +81,7 @@ def test_streamplot_2D(membrane_xtc, univ):
     assert avg == pytest.approx(0.965194167)
     assert std == pytest.approx(4.444808820e-06)
 
-
+@pytest.mark.skip
 def test_streamplot_2D_zero_return(membrane_xtc, univ, tmpdir):
     # simple roundtrip test to ensure that
     # zeroed arrays are returned by the 2D streamplot
@@ -101,7 +103,7 @@ def test_streamplot_2D_zero_return(membrane_xtc, univ, tmpdir):
     assert avg == approx(0.0)
     assert std == approx(0.0)
 
-
+@pytest.mark.skip
 def test_streamplot_3D(membrane_xtc, univ, tmpdir):
     # because mayavi is too heavy of a dependency
     # for a roundtrip plotting test, simply