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Remove GSD from optional test dependencies #4707

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merged 12 commits into from
Sep 10, 2024
Merged

Remove GSD from optional test dependencies #4707

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a8bda7b
Fixed high dimensional GroupBase indexing.
MattTDavies Aug 15, 2024
40b0c37
fixed pep8 issues
MattTDavies Aug 15, 2024
be47d85
Removed sanitisation
MattTDavies Aug 21, 2024
acc60b8
Fix #4687 -- rdkit values in azure CI (#4688)
IAlibay Aug 25, 2024
dc9654e
mark analysis.pca.PCA as not parallelizable (#4684)
orbeckst Aug 26, 2024
652efec
merge to main
yuxuanzhuang Sep 8, 2024
a7c7624
Merge remote-tracking branch 'upstream/develop' into develop
yuxuanzhuang Sep 9, 2024
c9ab1c5
disable gsd
yuxuanzhuang Sep 9, 2024
1c447d4
disable gsd in azure
yuxuanzhuang Sep 9, 2024
06ec49a
reduce timeout and set logical
yuxuanzhuang Sep 9, 2024
5dc9f0f
fix azure
yuxuanzhuang Sep 9, 2024
73b68c5
restore timeout to 200
yuxuanzhuang Sep 9, 2024
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7 changes: 5 additions & 2 deletions .github/workflows/gh-ci.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -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: ${{ matrix.extra-pip-deps }}
Expand Down Expand Up @@ -113,7 +115,7 @@ jobs:
PYTEST_FLAGS="${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')
Expand Down Expand Up @@ -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"

Expand Down Expand Up @@ -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
5 changes: 3 additions & 2 deletions azure-pipelines.yml
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Expand Up @@ -105,7 +105,6 @@ jobs:
biopython
"chemfiles>=0.10,<0.10.4"
duecredit
"gsd>3.0.0"
joblib
GridDataFormats
mmtf-python
Expand All @@ -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: >-
Expand All @@ -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
Expand Down
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