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T008/10/15/16/18/20: AttributeError: module 'numpy' has no attribute 'typeDict' #294

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merged 8 commits into from
Dec 27, 2022
Merged

T008/10/15/16/18/20: AttributeError: module 'numpy' has no attribute 'typeDict' #294

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b562bce
CI: Exclude T021 from Windows tests
dominiquesydow Dec 27, 2022
494dcbd
CI: Remove explicit numpy install (#150 resolved)
dominiquesydow Dec 27, 2022
e29f69e
CI: Unpin tensorflow+install last; reverts #265
dominiquesydow Dec 27, 2022
7794cd3
Rm tensorflow from env+T021/22 from CI
dominiquesydow Dec 27, 2022
dc65b41
CI: Add base-ci-env-fix branch
dominiquesydow Dec 27, 2022
8b80929
CI: Rm T021/22 from CI
dominiquesydow Dec 27, 2022
2ed424c
Env: Add numpy<1.24 and tensorflow
dominiquesydow Dec 27, 2022
fdfec11
CI: Fix pytest ignores
dominiquesydow Dec 27, 2022
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9 changes: 5 additions & 4 deletions .github/workflows/ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,11 +4,11 @@ on:
push:
branches:
- "master"
- "maintenance/.+"
- "base-ci-env-fix"
pull_request:
branches:
- "master"
- "maintenance/.+"
- "base-ci-env-fix"
schedule:
# Run a cron job once weekly on Monday
- cron: "0 3 * * 1"
Expand Down Expand Up @@ -76,10 +76,11 @@ jobs:
shell: bash -l {0}
run: |
PYTEST_ARGS="--nbval-lax --current-env --dist loadscope --numprocesses 2"
PYTEST_IGNORE="--ignore=teachopencadd/talktorials/T021_one_hot_encoding/talktorial.ipynb --ignore=teachopencadd/talktorials/T022_ligand_based_screening_neural_network/talktorial.ipynb"
if [ "$RUNNER_OS" != "Windows" ]; then
pytest $PYTEST_ARGS teachopencadd/talktorials/T*/talktorial.ipynb
pytest $PYTEST_ARGS teachopencadd/talktorials/T*/talktorial.ipynb $PYTEST_IGNORE
else
pytest $PYTEST_ARGS teachopencadd/talktorials/ --ignore=teachopencadd/talktorials/T008_md_simulation/talktorial.ipynb --ignore=teachopencadd/talktorials/T019_md_simulation/talktorial.ipynb
pytest $PYTEST_ARGS teachopencadd/talktorials/ --ignore=teachopencadd/talktorials/T019_md_simulation/talktorial.ipynb $PYTEST_IGNORE
fi

format:
Expand Down
11 changes: 6 additions & 5 deletions devtools/test_env.yml
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
name: teachopencadd
name: teachopencadd
channels:
- conda-forge
- defaults
Expand All @@ -10,11 +10,10 @@ dependencies:
- nglview>=3
# https://github.com/volkamerlab/teachopencadd/issues/262
- ipywidgets<8
# Explicitly add numpy because of https://github.com/volkamerlab/teachopencadd/issues/150
- numpy
# New numpy version too young
- numpy<1.24
- tensorflow
- scikit-learn
# API changed after v2.6, see https://github.com/volkamerlab/teachopencadd/issues/265
- tensorflow<=2.6
- seaborn
- matplotlib-venn
# Remove jsonschema once this issue is fixed: https://github.com/Yelp/bravado/issues/478
Expand Down Expand Up @@ -44,6 +43,8 @@ dependencies:
- tqdm
- lxml
- kissim
# API changed after v2.6, see https://github.com/volkamerlab/teachopencadd/issues/265
#- tensorflow
## CI tests
# Workaround for https://github.com/computationalmodelling/nbval/issues/153
- pytest 5.*
Expand Down