Merge pull request #131 from pyiron/pass-kernelname

[patch] optionally pass kernel to papermill (headless notebook execution)
pyiron · Sep 4, 2024 · 72012de · 72012de
2 parents 9e97c10 + 8e21260
commit 72012de
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Showing 3 changed files with 19 additions and 4 deletions.
diff --git a/.github/workflows/push-pull.yml b/.github/workflows/push-pull.yml
@@ -170,6 +170,11 @@ on:
         description: 'The directory containing the tests run with the alternate environment'
         default: tests
         required: false
+      notebooks-kernel:
+        type: string
+        description: 'Name of the kernel to be used by papermill during headless execution'
+        default: python3
+        required: false
 
 
 jobs:
@@ -229,7 +234,7 @@ jobs:
           python-version: ${{ inputs.python-version }}
           env-files: ${{ inputs.notebooks-env-files }}
           exclusion-file: ${{ inputs.notebooks-exclusion-file }}
-
+          kernel: ${{ inputs.notebooks-kernel }}
 
   unit-tests:
     needs: commit-updated-env

diff --git a/.support/build_notebooks.sh b/.support/build_notebooks.sh
@@ -2,18 +2,24 @@
 
 NOTEBOOKS_DIR=$1
 EXCLUSION_FILE=$2
+KERNEL=$3
 
 # Remove excluded notebooks
-if [ ${EXCLUSION_FILE} != "" ]; then
+if [ "${EXCLUSION_FILE}" != "" ]; then
   for f in $(cat ${EXCLUSION_FILE}); do
       rm "${NOTEBOOKS_DIR}/$f";
   done;
 fi
 
+# Set the kernel to be used by papermill to 'python3' if not specified otherwise
+if [ "${KERNEL}" = "" ]; then
+    KERNEL=python3;
+fi
+
 # execute notebooks
 i=0;
 for notebook in $(find ${NOTEBOOKS_DIR} -type f -name '*.ipynb'); do
-    papermill ${notebook} ${notebook%.*}-out.${notebook##*.} || i=$((i+1));
+    papermill  ${notebook} ${notebook%.*}-out.${notebook##*.} -k ${KERNEL} || i=$((i+1));
 done;
 
 # push error to next level

diff --git a/build-notebooks/action.yml b/build-notebooks/action.yml
@@ -20,6 +20,10 @@ inputs:
   exclusion-file:
     description: 'An optional path to a file containing the names of notebooks to NOT build'
     required: false
+  kernel:
+    description: 'Name of the kernel to be used by papermill during headless execution'
+    default: python3
+    required: false
 
 runs:
   using: 'composite'
@@ -31,4 +35,4 @@ runs:
   - uses: pyiron/actions/pyiron-config@main
   - name: Build notebooks
     shell: bash -l {0}
-    run: $GITHUB_ACTION_PATH/../.support/build_notebooks.sh ${{ inputs.notebooks-dir }} ${{ inputs.exclusion-file }}
+    run: $GITHUB_ACTION_PATH/../.support/build_notebooks.sh ${{ inputs.notebooks-dir }} ${{ inputs.exclusion-file }} ${{ inputs.kernel }}