Jupyter build

Signed-off-by: Chaichontat Sriworarat <[email protected]>

.github/workflows/render.yml

@@ -15,7 +15,34 @@ on:
 
 
 jobs:
-  build:
+  jupyter-build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          miniforge-version: latest
+          activate-environment: qmn
+          environment-file: environment.yml
+          use-mamba: true
+
+      - name: Execute and export
+        run: |
+          jupytext --to notebook modules/**/*.py
+          jupyter nbconvert --NbConvertApp.recursive_glob=True --output-dir=modules/jupyter --execute --to html modules/**/*.ipynb
+
+      - name: Upload artifacts
+        uses: actions/upload-artifact@v3
+        with:
+          path: modules/jupyter/
+
+  Rmd-build:
+    needs: jupyter-build
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
@@ -36,6 +63,11 @@ jobs:
       - name: Render
         run: Rscript render.R
 
+      - name: Download jupyter artifacts
+        uses: actions/download-artifact@v3
+        with:
+          path: modules/jupyter/
+
       - name: Generate index
         if: matrix.os == 'ubuntu-latest' && github.ref == 'refs/heads/main'
         run: Rscript genIndex.R

.gitignore

@@ -46,3 +46,4 @@ vignettes/*.pdf
 *.pdf
 
 **/data/**
+*.ipynb

environment.yml

@@ -0,0 +1,12 @@
+name: qmn
+
+channels:
+  - conda-forge
+
+dependencies:
+  - python=3.10
+  - jupyterlab
+  - jupytext
+  - scanpy
+  - seaborn
+  - pandas