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ENH: Fix GitHub actions notebook test workflow #96

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merged 4 commits into from
Mar 27, 2021
Merged

ENH: Fix GitHub actions notebook test workflow #96

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518cbe1
ENH: Download the data to the path expected by the notebooks
jhlegarreta Mar 27, 2021
f763960
ENH: Define explicitly the Jupyter notebooks to be tested
jhlegarreta Mar 27, 2021
bcbbd61
ENH: Change GitHub Actions test workflow to run weekly
jhlegarreta Mar 27, 2021
74da157
ENH: Fix the cache key
jhlegarreta Mar 27, 2021
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18 changes: 13 additions & 5 deletions .github/workflows/build-test.yaml
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Original file line number Diff line number Diff line change
@@ -1,7 +1,8 @@
name: Build, test

on:
push
schedule:
- cron: "0 2 * * sun" # 02:00 UTC every Sunday

jobs:
build:
Expand All @@ -27,9 +28,10 @@ jobs:
id: cache
with:
path: .cache/pip
key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
key: ${{ runner.os }}-pip-${{ matrix.python-version }}-${{ hashFiles('requirements.txt') }}
restore-keys: |
${{ runner.os }}-pip-
${{ runner.os }}-pip-${{ matrix.python-version }}-
${{ runner.os }}-pip-

# Install all requirements to run these tests.
- name: Install requirements
Expand All @@ -44,10 +46,16 @@ jobs:
# Download the necessary data
- name: Download data
run: |
osf -p cmq8a clone ./data
osf -p cmq8a clone ${{ github.workspace }}/data
mv ${{ github.workspace }}/data/osfstorage/* ${{ github.workspace }}/data
rm -rf ${{ github.workspace }}/data/osfstorage

# Run the actual tests of all the Python Notebooks.
- name: Test Notebooks
run: |
source ~/sdc_bids_dmri/bin/activate
pytest --nbval-lax -v code/*/*.ipynb
pytest --nbval-lax -v code/introduction/solutions/introduction_solutions.ipynb
pytest --nbval-lax -v code/diffusion_tensor_imaging/solutions/diffusion_tensor_imaging_solutions.ipynb
pytest --nbval-lax -v code/constrained_spherical_deconvolution/constrained_spherical_deconvolution.ipynb
pytest --nbval-lax -v code/deterministic_tractography/deterministic_tractography.ipynb
pytest --nbval-lax -v code/probabilistic_tractography/probabilistic_tractography.ipynb