Fixed Notebook Tests (#52)

* Added a flag file to differentiate between workflow tests * Made changes in notebook dir path and few minor changes in notebook itself * Added few requirements which were required for staging notebook * Upgraded macOS versions as previous ones are deprecated [read issue here](actions/runner-images#5583) Closes #41 --------- Authored-by: pjflux2001 <cisprashant@gmail.com>
PolyPhyHub · Jun 8, 2023 · ca5297d · ca5297d
1 parent 1d3caf3
commit ca5297d
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diff --git a/.github/workflows/macos_python.yml b/.github/workflows/macos_python.yml
@@ -12,7 +12,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        os: [macOS-10.14, macOS-10.15]
+        os: [macOS-11, macOS-12]
         python-version: ["3.8", "3.9", "3.10"]
     steps:
     - uses: actions/checkout@v3

diff --git a/.github/workflows/ubuntu20_python.yml b/.github/workflows/ubuntu20_python.yml
@@ -30,6 +30,9 @@ jobs:
         python -m pip install flake8 pytest
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
         pip install . -U
+    - name: Create Flag File
+      run: |
+        touch /tmp/flag
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names
@@ -41,4 +44,4 @@ jobs:
         pytest -v
     - name: Test with jupyter notebooks
       run: |
-        pytest --nbmake experiments/jupyter/*.ipynb
+        pytest --nbmake experiments/jupyter/production/*.ipynb
diff --git a/experiments/jupyter/PolyPhy_2D_continuous_data.ipynb b/experiments/jupyter/PolyPhy_2D_continuous_data.ipynb
diff --git a/experiments/jupyter/PolyPhy_2D_discrete_data.ipynb b/experiments/jupyter/PolyPhy_2D_discrete_data.ipynb
diff --git a/experiments/jupyter/PolyPhy_3D_discrete_data.ipynb b/experiments/jupyter/PolyPhy_3D_discrete_data.ipynb
diff --git a/experiments/jupyter/production/PolyPhy_2D_continuous_data.ipynb b/experiments/jupyter/production/PolyPhy_2D_continuous_data.ipynb
diff --git a/experiments/jupyter/production/PolyPhy_2D_discrete_data.ipynb b/experiments/jupyter/production/PolyPhy_2D_discrete_data.ipynb
diff --git a/experiments/jupyter/production/PolyPhy_3D_discrete_data.ipynb b/experiments/jupyter/production/PolyPhy_3D_discrete_data.ipynb
diff --git a/...ts/jupyter/PolyPhy_3D_discrete_mask.ipynb → ...er/testing/PolyPhy_3D_discrete_mask.ipynb b/...ts/jupyter/PolyPhy_3D_discrete_mask.ipynb → ...er/testing/PolyPhy_3D_discrete_mask.ipynb
diff --git a/requirements.txt b/requirements.txt
@@ -15,3 +15,8 @@ taichi==1.0.3
 toml
 tox
 yapf
+ipywidgets
+pyvista
+trimesh
+PyMCubes
+scikit-image