update strip action

CausalAIBook · Jul 22, 2024 · d01e773 · d01e773
1 parent 46f2319
commit d01e773
Show file tree

Hide file tree

Showing 3 changed files with 34 additions and 35 deletions.
diff --git a/.github/workflows/check-and-transform-R-notebooks.yml b/.github/workflows/check-and-transform-R-notebooks.yml
@@ -1,9 +1,6 @@
-name: Check and Transform R Notebooks
+name: Check R Notebooks
 
 on:
-  push:
-    branches:
-      - main
   pull_request:
     branches:
       - main
@@ -203,27 +200,27 @@ jobs:
           rm -rf r_scripts
           rm ${{ matrix.directory }}_r_scripts.zip
 
-      - name: Check out the branch for pull request
-        if: "(github.event_name == 'pull_request') && (env.notebooks_changed == 'true')"
-        run: |
-          git fetch --all
-          git checkout ${{ github.event.pull_request.head.ref }}
-
-      - name: Check if there are any changes
-        if: env.notebooks_changed == 'true'
-        id: verify_diff
-        run: |
-          git pull
-          git diff --quiet ${{ matrix.directory }}/*.irnb ${{ matrix.directory }}/*.Rmd || echo "changed=true" >> $GITHUB_OUTPUT
-
-      - name: Commit and push stripped .irnb and .Rmd files
-        if: "(env.notebooks_changed == 'true') && (steps.verify_diff.outputs.changed == 'true')"
-        run: |
-          git config --global user.name 'github-actions[bot]'
-          git config --global user.email 'github-actions[bot]@users.noreply.github.com'
-          git pull
-          git add ${{ matrix.directory }}/*.irnb ${{ matrix.directory }}/*.Rmd
-          git commit -m 'Strip outputs from .irnb, convert to .Rmd, lint .Rmd files, and execute .R files in ${{ matrix.directory }} [skip ci]'
-          git push --force-with-lease
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      # - name: Check out the branch for pull request
+      #   if: "(github.event_name == 'pull_request') && (env.notebooks_changed == 'true')"
+      #   run: |
+      #     git fetch --all
+      #     git checkout ${{ github.event.pull_request.head.ref }}
+
+      # - name: Check if there are any changes
+      #   if: env.notebooks_changed == 'true'
+      #   id: verify_diff
+      #   run: |
+      #     git pull
+      #     git diff --quiet ${{ matrix.directory }}/*.irnb ${{ matrix.directory }}/*.Rmd || echo "changed=true" >> $GITHUB_OUTPUT
+
+      # - name: Commit and push stripped .irnb and .Rmd files
+      #   if: "(env.notebooks_changed == 'true') && (steps.verify_diff.outputs.changed == 'true')"
+      #   run: |
+      #     git config --global user.name 'github-actions[bot]'
+      #     git config --global user.email 'github-actions[bot]@users.noreply.github.com'
+      #     git pull
+      #     git add ${{ matrix.directory }}/*.irnb ${{ matrix.directory }}/*.Rmd
+      #     git commit -m 'Strip outputs from .irnb, convert to .Rmd, lint .Rmd files, and execute .R files in ${{ matrix.directory }} [skip ci]'
+      #     git push --force-with-lease
+      #   env:
+      #     GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/strip-python-notebooks.yml b/.github/workflows/strip-python-notebooks.yml
@@ -1,14 +1,14 @@
-name: Strip Python and R Notebooks from Outputs
+name: Strip Python and R Notebooks from Outputs and Transform .irnb to .Rmd
 
 on:
   push:
 
 concurrency:
-  group: strip-notebooks-${{ github.ref }}
+  group: strip-transform-notebooks-${{ github.ref }}
   cancel-in-progress: true
 
 jobs:
-  strip-notebooks:
+  strip-transform-notebooks:
     runs-on: ubuntu-latest
 
     steps:
@@ -63,12 +63,12 @@ jobs:
                 fi
             done
             echo "Converting .irnb to .Rmd to update the .Rmd version"
-            R -e '
-              files <- list.files(path = "${{ dir }}", pattern = "\\.irnb$", full.names = TRUE, recursive = FALSE)
+            R -e "
+              files <- list.files(path = '$dir', pattern = '\\.irnb$', full.names = TRUE, recursive = FALSE)
               lapply(files, function(input) {
                 rmarkdown::convert_ipynb(input)
               })
-            '
+            "
         else
             echo "Directory $dir does not exist."
         fi

diff --git a/README.md b/README.md
@@ -9,4 +9,6 @@ pip install -r requirements.txt
 
 # For Contributors
 
-The .Rmd files are auto-generated by a Github Action, whenever one pushes a .irnb (R Jupyter notebook) to one of the main folders of the repo. So .Rmd files, should never be altered directly. Only changes to .irnb files should be made. Any change to a .Rmd file will be over-written by the corresponding .irnb file and will not survive the Github Action.
+The .Rmd files are auto-generated by a Github Action, whenever one pushes a .irnb (R Jupyter notebook) to one of the main folders of the repo on the main branch. So .Rmd files, should never be altered directly. Only changes to .irnb files should be made. Any change to a .Rmd file will be over-written by the corresponding .irnb file and will not survive the Github Action.
+
+Moreover, whenever a push happens to the main branch, all python and R notebooks and all R Markdown files are stripped from their outputs. It is advisable that you always strip the notebooks before pushing to the repo. You can use `nbstripout --install` on your local git directory, which does this automatically for you.