Merge pull request #43 from carpentries-incubator/PostTransitionFixes

ENH: Post Workbench transition fixes

.github/workflows/notebook.yml

@@ -0,0 +1,51 @@
+name: Test notebooks
+
+on:
+  push:
+    paths: ["*.ipynb", "requirements.txt", "notebook.yml"]
+
+jobs:
+  test-notebooks:
+    if: "!contains(github.event.head_commit.message, '[skip ci]')"
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.8', '3.9', '3.10', '3.11']
+
+    steps:
+    - name: Checkout GitHub repository
+      uses: actions/checkout@v4
+
+    # Run with multiple Python versions.
+    - name: Setup Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    # Use a cache for the pip install to avoid reinstalling every time this is run.
+    - name: Cache pip install
+      uses: actions/cache@v4
+      id: cache
+      with:
+        path: ${{ env.pythonLocation }}
+        key: ${{ env.pythonLocation }}-${{ hashFiles('requirements.txt') }}
+        restore-keys: |
+          ${{ env.pythonLocation }}-
+
+    # Install all requirements to run these tests.
+    - name: Install requirements
+      if: steps.cache.outputs.cache-hit != 'true'
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt
+        pip install pytest nbval
+
+    # Download the necessary data
+    - name: Download data
+      run: |
+        datalad install
+
+    # Run the actual tests of all the Python Notebooks.
+    - name: Test Notebooks
+      run: |
+        pytest --nbval-lax -v code/*ipynb

README.md

@@ -70,12 +70,12 @@ To cite this lesson, please consult with [CITATION](CITATION)
 [slack_channel_status]: https://img.shields.io/badge/Slack_Channel-neuroimaging-E01563.svg
 [binder_url]: https://mybinder.org/v2/gh/carpentries-incubator/SDC-BIDS-IntroMRI/gh-pages?filepath=code%2F
 [binder_svg]: https://mybinder.org/badge_logo.svg
-[episode01]: https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/before-we-start/index.html
-[episode02]: https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/scanner-to-computer/index.html
-[episode03]: https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/anatomy-of-nifti/index.html
-[episode04]: https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/data-organization-bids/index.html
-[episode05]: https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/open-mri-datasets/index.html
-[episode06]: https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/bids-derivatives/index.html
+[episode01]: https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/before-we-start.html
+[episode02]: https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/scanner-to-computer.html
+[episode03]: https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/anatomy-of-nifti.html
+[episode04]: https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/data-organization-bids.html
+[episode05]: https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/open-mri-datasets.html
+[episode06]: https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/bids-derivatives.html
 [lesson-example]: https://carpentries.github.io/lesson-example
 [link_issues]: https://github.com/conp-pcno-training/SDC-BIDS-IntroMRI/issues
 [michael_joseph]: https://github.com/josephmje