Remove GSD from optional test dependencies (#4707)

* Fixed high dimensional GroupBase indexing.

* fixed pep8 issues

* Removed sanitisation

* Fix #4687 -- rdkit values in azure CI (#4688)

* Investigate rdkit issue

* Update azure-pipelines.yml

* fix numpy 2.0 import block

* fix imports

* mark analysis.pca.PCA as not parallelizable (#4684)

- fix #4680
- PCA explicitly marked as not parallelizable (at least not with
  simple split-apply-combine)
- add tests
- update CHANGELOG

* disable gsd

* disable gsd in azure

* reduce timeout and set logical

* fix azure

* restore timeout to 200

---------

Co-authored-by: Matthew Davies <128810112+MattTDavies@users.noreply.github.com>
Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
Co-authored-by: Oliver Beckstein <orbeckst@gmail.com>

Author: 4 people

.github/workflows/gh-ci.yaml

@@ -85,6 +85,8 @@ jobs:
       with:
         micromamba: true
         full-deps: ${{ matrix.full-deps }}
+        # disable GSD because it occasionally introduce hanging in testing #4209
+        gsd: ''
         # in most cases will just default to empty, i.e. pick up max version from other deps
         numpy: ${{ matrix.numpy }}
         extra-pip-deps: ${{ matrix.extra-pip-deps }}
@@ -113,7 +115,7 @@ jobs:
           PYTEST_FLAGS="${PYTEST_FLAGS} --cov-config=.coveragerc --cov=MDAnalysis --cov-report=xml"
         fi
         echo $PYTEST_FLAGS
-        pytest -n auto --timeout=200 testsuite/MDAnalysisTests $PYTEST_FLAGS
+        pytest -n logical --timeout=200 testsuite/MDAnalysisTests $PYTEST_FLAGS
 
     - name: run_asv
       if: contains(matrix.name, 'asv_check')
@@ -161,6 +163,7 @@ jobs:
       with:
         micromamba: true
         full-deps: true
+        gsd: ''
         extra-pip-deps: "docutils sphinx-sitemap sphinxcontrib-bibtex pybtex pybtex-docutils"
         extra-conda-deps: "mdanalysis-sphinx-theme>=1.3.0"
 
@@ -281,4 +284,4 @@ 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
@@ -114,6 +113,8 @@ jobs:
       pytng>=0.2.3
       rdkit>=2020.03.1
       tidynamics>=1.0.0
+    # remove from azure to avoid test hanging #4707
+    # "gsd>3.0.0"
     displayName: 'Install additional dependencies for 64-bit tests'
     condition: and(succeeded(), eq(variables['PYTHON_ARCH'], 'x64'))
   - script: >-
@@ -128,7 +129,7 @@ jobs:
     displayName: 'Check installed packages'
   - powershell: |
       cd testsuite
-      pytest MDAnalysisTests --disable-pytest-warnings -n auto --timeout=200 -rsx --cov=MDAnalysis
+      pytest MDAnalysisTests --disable-pytest-warnings -n logical --timeout=200 -rsx --cov=MDAnalysis
     displayName: 'Run MDAnalysis Test Suite'
   - script: |
       curl -s https://codecov.io/bash | bash