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Fix CI #366

Merged
merged 9 commits into from
May 1, 2024
Merged

Fix CI #366

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11392cf
Fix CI
IAlibay Apr 27, 2024
a1d4035
unpin dask
IAlibay Apr 27, 2024
2eb7043
remove explicit python version
IAlibay Apr 27, 2024
648fdd7
temp branch switch
IAlibay Apr 27, 2024
580031a
fix hole2 notebook
IAlibay Apr 27, 2024
e64bf1c
skip problematic cells
IAlibay Apr 27, 2024
092d857
move tags around a bit
IAlibay Apr 27, 2024
1c4fc87
fix additional comma
IAlibay Apr 27, 2024
1bcb073
Update environment.yml
IAlibay Apr 28, 2024
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3 changes: 1 addition & 2 deletions .github/workflows/pre-commit.yaml
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Expand Up @@ -23,15 +23,14 @@ jobs:
pre-commit:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4

- name: setup micromamba
uses: mamba-org/setup-micromamba@v1
with:
environment-file: environment.yml
environment-name: mda-user-guide
create-args: >-
python=3.9
pip
condarc: |
channels:
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2 changes: 1 addition & 1 deletion doc/source/examples/analysis/polymers_and_membranes/hole2.ipynb
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Expand Up @@ -293,7 +293,7 @@
"outputs": [
{
"data": {
"text/plain": "<MDAnalysis.analysis.hole2.hole.HoleAnalysis at 0x7f1a146af610>"
"text/plain": "<mdahole2.analysis.hole.HoleAnalysis at 0x7f1a146af610>"
},
"execution_count": 7,
"metadata": {},
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6 changes: 4 additions & 2 deletions doc/source/examples/analysis/reduced_dimensions/diffusion_map.ipynb
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Expand Up @@ -137,7 +137,8 @@
"ExecuteTime": {
"end_time": "2023-12-01T15:45:48.442257804Z",
"start_time": "2023-12-01T15:45:48.414223207Z"
}
},
"tags": ["nbval-ignore-output"]
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},
"outputs": [
{
Expand Down Expand Up @@ -239,7 +240,8 @@
"ExecuteTime": {
"end_time": "2023-12-01T15:46:16.586512021Z",
"start_time": "2023-12-01T15:46:16.569047940Z"
}
},
"tags": ["nbval-ignore-output"]
},
"outputs": [
{
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10 changes: 5 additions & 5 deletions environment.yml
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Expand Up @@ -36,14 +36,14 @@ dependencies:
- scikit-image
- seaborn>=0.12.1
# parallelization
- distributed==2021.1.0
- dask==2021.1.0
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keeping these pinned would prevent us from increasing the python version

- distributed
- dask
# used for visualising/making movies of molecules;
- nglview
- moviepy
# used for notebook testing
- pytest
- python=3.9
- python=3.10
- pip
- pip:
# extensions
Expand All @@ -55,7 +55,7 @@ dependencies:
# doc generation dependency
- pygithub
# mdanalysis and its tests and test data
- git+https://github.com/MDAnalysis/mdanalysis@develop#egg=mdanalysis&subdirectory=package
- git+https://github.com/MDAnalysis/mdanalysis@develop#egg=MDAnalysisTests&subdirectory=testsuite
- git+https://github.com/MDAnalysis/mdanalysis@fix-discovery#egg=mdanalysis&subdirectory=package
- git+https://github.com/MDAnalysis/mdanalysis@fix-discovery#egg=MDAnalysisTests&subdirectory=testsuite
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- git+https://github.com/MDAnalysis/MDAnalysisData@master#egg=MDAnalysisData
- syrupy # snapshot tests
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