Merge branch 'MDAnalysis:develop' into frankenatom_fix

.github/workflows/deploy.yaml

@@ -142,7 +142,7 @@ jobs:
           mv dist/MDAnalysisTests-* testsuite/dist
 
       - name: upload_source_and_wheels
-        uses: pypa/gh-action-pypi-publish@v1.9.0
+        uses: pypa/gh-action-pypi-publish@v1.10.0
         with:
           skip_existing: true
           repository_url: https://test.pypi.org/legacy/
@@ -171,7 +171,7 @@ jobs:
           mv dist/MDAnalysisTests-* testsuite/dist
 
       - name: upload_tests
-        uses: pypa/gh-action-pypi-publish@v1.9.0
+        uses: pypa/gh-action-pypi-publish@v1.10.0
         with:
           packages_dir: testsuite/dist
           skip_existing: true
@@ -201,7 +201,7 @@ jobs:
           mv dist/MDAnalysisTests-* testsuite/dist
 
       - name: upload_source_and_wheels
-        uses: pypa/gh-action-pypi-publish@v1.9.0
+        uses: pypa/gh-action-pypi-publish@v1.10.0
 
   upload_pypi_mdanalysistests:
     if: |
@@ -227,7 +227,7 @@ jobs:
           mv dist/MDAnalysisTests-* testsuite/dist
 
       - name: upload_tests
-        uses: pypa/gh-action-pypi-publish@v1.9.0
+        uses: pypa/gh-action-pypi-publish@v1.10.0
         with:
           packages_dir: testsuite/dist
 

azure-pipelines.yml

@@ -101,7 +101,7 @@ jobs:
     displayName: 'pin to older NumPy (wheel test)'
     condition: and(succeeded(), ne(variables['NUMPY_MIN'], ''))
   - script: >-
-      python -m pip install
+      python -m pip install -vvv
       biopython
       "chemfiles>=0.10,<0.10.4"
       duecredit
@@ -112,8 +112,8 @@ jobs:
       networkx
       parmed
       pytng>=0.2.3
-      tidynamics>=1.0.0
       rdkit>=2020.03.1
+      tidynamics>=1.0.0
     displayName: 'Install additional dependencies for 64-bit tests'
     condition: and(succeeded(), eq(variables['PYTHON_ARCH'], 'x64'))
   - script: >-

package/CHANGELOG

@@ -17,7 +17,7 @@ The rules for this file:
 ??/??/?? IAlibay, HeetVekariya, marinegor, lilyminium, RMeli,
          ljwoods2, aditya292002, pstaerk, PicoCentauri, BFedder,
          tyler.je.reddy, SampurnaM, leonwehrhan, kainszs, orionarcher,
-         yuxuanzhuang, PythonFZ, laksh-krishna-sharma
+         yuxuanzhuang, PythonFZ, laksh-krishna-sharma, orbeckst
 
  * 2.8.0
 
@@ -55,6 +55,7 @@ Fixes
 Enhancements
  * Introduce parallelization API to `AnalysisBase` and to `analysis.rms.RMSD` class
    (Issue #4158, PR #4304)
+ * explicitly mark `analysis.pca.PCA` as not parallelizable (Issue #4680)
  * Improve error message for `AtomGroup.unwrap()` when bonds are not present.(Issue #4436, PR #4642)
  * Add `analysis.DSSP` module for protein secondary structure assignment, based on [pydssp](https://github.com/ShintaroMinami/PyDSSP)
  * Added a tqdm progress bar for `MDAnalysis.analysis.pca.PCA.transform()`

package/MDAnalysis/analysis/pca.py

@@ -143,7 +143,7 @@ class PCA(AnalysisBase):
     generates the principal components of the backbone of the atomgroup and
     then transforms those atomgroup coordinates by the direction of those
     variances. Please refer to the :ref:`PCA-tutorial` for more detailed
-    instructions. When using mean selections, the first frame of the selected 
+    instructions. When using mean selections, the first frame of the selected
     trajectory slice is used as a reference.
 
     Parameters
@@ -239,6 +239,7 @@ class PCA(AnalysisBase):
        incorrectly handle cases where the ``frame`` argument
        was passed.
     """
+    _analysis_algorithm_is_parallelizable = False
 
     def __init__(self, universe, select='all', align=False, mean=None,
                  n_components=None, **kwargs):

package/MDAnalysis/converters/RDKit.py

@@ -87,7 +87,6 @@
 from io import StringIO
 
 import numpy as np
-from numpy.lib import NumpyVersion
 
 from . import base
 from ..coordinates import memory
@@ -96,13 +95,8 @@
 from ..exceptions import NoDataError
 
 try:
-    # TODO: remove this guard when RDKit has a release
-    # that supports NumPy 2
-    if NumpyVersion(np.__version__) < "2.0.0":
-        from rdkit import Chem
-        from rdkit.Chem import AllChem
-    else:
-        raise ImportError
+    from rdkit import Chem
+    from rdkit.Chem import AllChem
 except ImportError:
     pass
 else:

testsuite/MDAnalysisTests/analysis/test_pca.py

@@ -23,6 +23,7 @@
 import numpy as np
 import MDAnalysis as mda
 from MDAnalysis.analysis import align
+import MDAnalysis.analysis.pca
 from MDAnalysis.analysis.pca import (PCA, cosine_content,
                                      rmsip, cumulative_overlap)
 
@@ -384,3 +385,23 @@ def test_pca_attr_warning(u, attr):
     wmsg = f"The `{attr}` attribute was deprecated in MDAnalysis 2.0.0"
     with pytest.warns(DeprecationWarning, match=wmsg):
         getattr(pca, attr) is pca.results[attr]
+
+@pytest.mark.parametrize(
+    "classname,is_parallelizable",
+    [
+        (MDAnalysis.analysis.pca.PCA, False),
+    ]
+)
+def test_class_is_parallelizable(classname, is_parallelizable):
+    assert classname._analysis_algorithm_is_parallelizable == is_parallelizable
+
+
+@pytest.mark.parametrize(
+    "classname,backends",
+    [
+        (MDAnalysis.analysis.pca.PCA,  ('serial',)),
+    ]
+)
+def test_supported_backends(classname, backends):
+    assert classname.get_supported_backends() == backends
+

testsuite/MDAnalysisTests/util.py

@@ -117,7 +117,7 @@ def import_not_available(module_name):
     # TODO: remove once these packages have a release
     # with NumPy 2 support
     if NumpyVersion(np.__version__) >= "2.0.0":
-        if module_name in {"rdkit", "parmed"}:
+        if module_name == "parmed":
             return True
     try:
         test = importlib.import_module(module_name)