Merge pull request #63 from microbiomedata/notebook_check_ghaction

Add github workflow for checking notebooks

.github/CONTRIBUTING.md

@@ -85,6 +85,7 @@ _or_
 4. Create a .Rmd and convert it to a Jupyter Notebook. Several methods for this exist and none are perfect, but [this open source method](https://github.com/mkearney/rmd2jupyter) currently works.
 5. Run the entire notebook to ensure it is working as expected and save the *rendered* notebook in the folder.
 6. Update the `README.md` in the folder to include links to the rendered notebook (using [nbviewer](https://nbviewer.org/) and [google colab](https://colab.research.google.com/)).
+7. Add the notebooks to the appropriate github workflow to ensure they are included in the continuous integration process.  See the `.github/workflows` folder for existing workflows (one for the R notebooks and one for the python notebooks). Add the new notebook to the end of the list of notebooks in the workflow file.
 
 
 ## Dependency Management

.github/workflows/notebook_check_python.yml

@@ -0,0 +1,44 @@
+name: Execute python notebooks
+
+on:
+  pull_request:
+  workflow_dispatch:
+  # run once a week
+  schedule:
+    - cron: "0 0 * * 0"
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - id: checkout
+      uses: actions/checkout@v3
+
+    - id: python-setup
+      name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.11'
+
+    - id: python-dependencies
+      name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements_dev.txt
+        pip install jupyter
+
+    - id: execute-bioscales
+      name: Execute bioscales notebook
+      run: |
+        jupyter nbconvert --execute --to notebook --inplace bioscales_biogeochemical_metadata/python/bioscales.ipynb
+
+    - id: execute-neon
+      name: Execute neon notebook
+      run: |
+        jupyter nbconvert --execute --to notebook --inplace NEON_soil_metadata/python/neon_soil_metadata_visual_exploration.ipynb
+
+    - id: execute-taxonomic
+      name: Execute taxonomic notebook
+      run: |
+        jupyter nbconvert --execute --to notebook --inplace taxonomic_dist_by_soil_layer/python/taxonomic_dist_soil_layer.ipynb

.github/workflows/notebook_check_r.yml

@@ -0,0 +1,55 @@
+name: Execute R notebooks
+
+on:
+  pull_request:
+  workflow_dispatch:
+  # run once a week
+  schedule:
+    - cron: "0 0 * * 0"
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - id: checkout
+      uses: actions/checkout@v3
+
+    - id: python-setup
+      name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.11'
+
+    - id: install-juptyer
+      name: Install Juptyer
+      run: |
+        python -m pip install --upgrade pip
+        pip install jupyter
+
+    - id: r-setup
+      name: Set up R
+      uses: r-lib/actions/setup-r@v2
+
+    - id: r-dependencies
+      name: Install r dependencies
+      run: |
+        R -e 'install.packages("renv")'
+        R -e 'renv::restore()'
+        R -e 'install.packages("IRkernel")'
+        R -e 'IRkernel::installspec()'
+
+    - id: execute-bioscales
+      name: Execute bioscales notebook
+      run: |
+        jupyter nbconvert --execute --to notebook --inplace bioscales_biogeochemical_metadata/R/bioscales_metadata.ipynb
+
+    - id: execute-neon
+      name: Execute NEON metadata notebook
+      run: |
+        jupyter nbconvert --execute --to notebook --inplace NEON_soil_metadata/R/NEON_data_exploration.ipynb
+
+    - id: execute-taxonomic
+      name: Execute taxonomic metadata notebook
+      run: |
+        jupyter nbconvert --execute --to notebook --inplace taxonomic_dist_by_soil_layer/R/taxonomic_dist_soil_layer_R.ipynb