Update .ipynb notebooks from .py in pre-commit hook locally

.github/workflows/docs.yml

@@ -14,65 +14,16 @@ defaults:
     shell: bash
 
 jobs:
-  convert_scripts:
-    name: Translate scripts to notebooks
-    runs-on: ubuntu-latest
-    permissions:
-      pull-requests: write
-      contents: write
-    outputs:
-      commit_hash: ${{ steps.add-commit-push.outputs.commit_hash }}
-    container:
-      image: ghcr.io/ptb-mr/mrpro_py311:latest
-      options: --user runner
-    steps:
-      - name: Checkout repo
-        uses: actions/checkout@v4
-        with:
-          token: ${{ secrets.commit }}
-          ref: ${{ github.event.pull_request.head.ref }}
-          fetch-depth: 0
-
-      - name: Install mrpro and dependencies
-        run: pip install --upgrade --upgrade-strategy "eager" .[notebook]
-
-      - name: Translate scripts to notebooks
-        run: |
-          scripts=$(ls ./examples/*.py)
-          for script in $scripts
-            do jupytext --set-kernel "python3" --update --output ${script//.py/.ipynb} $script
-          done
-
-      - name: Check if any notebooks have been changed
-        uses: tj-actions/verify-changed-files@v20
-        id: verify-changed-notebooks
-        with:
-          files: ./examples/*.ipynb
-
-      - name: Commit notebooks
-        if: steps.verify-changed-notebooks.outputs.files_changed == 'true'
-        uses: actions4git/add-commit-push@v1
-        with:
-          commit-message: Notebooks updated
-
-      - name: Get hash of last commit
-        id: add-commit-push
-        run: echo "commit_hash=$(git rev-parse HEAD)" >> $GITHUB_OUTPUT
-
   get_notebooks:
     name: Get list of notebooks
-    needs: convert_scripts
     runs-on: ubuntu-latest
     steps:
       - name: Checkout mrpro repo
         uses: actions/checkout@v4
-        with:
-          ref: ${{ needs.convert_scripts.outputs.commit_hash }}
 
       - id: set-matrix
         run: |
-          cd ./examples/
-          ls
+          cd ./examples/notebooks
           echo "notebooks=$(ls *.ipynb | jq -R -s -c 'split("\n")[:-1]')" >> $GITHUB_OUTPUT
 
       - name: Notebook overview
@@ -83,7 +34,7 @@ jobs:
 
   run_notebook:
     name: Run notebook
-    needs: [convert_scripts, get_notebooks]
+    needs: get_notebooks
     runs-on: ubuntu-latest
     permissions:
       pull-requests: write
@@ -98,8 +49,6 @@ jobs:
     steps:
       - name: Checkout repo
         uses: actions/checkout@v4
-        with:
-          ref: ${{ needs.convert_scripts.outputs.commit_hash }}
 
       - name: Install mrpro and dependencies
         run: pip install --upgrade --upgrade-strategy "eager" .[notebook]
@@ -113,7 +62,7 @@ jobs:
         env:
           RUNNER: ${{ toJson(runner) }}
         with:
-          notebook: ./examples/${{ matrix.notebook }}
+          notebook: ./examples/notebooks/${{ matrix.notebook }}
 
       - name: Get artifact names
         id: artifact_names
@@ -133,7 +82,7 @@ jobs:
 
   create_documentation:
     name: Build and deploy documentation
-    needs: [convert_scripts, run_notebook]
+    needs: run_notebook
     runs-on: ubuntu-latest
     container:
       image: ghcr.io/ptb-mr/mrpro_py311:latest
@@ -144,8 +93,6 @@ jobs:
     steps:
       - name: Checkout
         uses: actions/checkout@v4
-        with:
-          ref: ${{ needs.convert_scripts.outputs.commit_hash }}
 
       - name: Install mrpro and dependencies
         run: pip install --upgrade --upgrade-strategy "eager" .[docs]

.pre-commit-config.yaml

@@ -52,6 +52,28 @@ repos:
           - "--index-url=https://download.pytorch.org/whl/cpu"
           - "--extra-index-url=https://pypi.python.org/simple"
 
+  - repo: https://github.com/kynan/nbstripout
+    rev: 0.8.0
+    hooks:
+    # cleans the .ipynbs (removes outputs, resets all cell-ids to 0..N, cleans steps)
+    # also clean any kernel information left after execution
+    - id: nbstripout
+      name: clean .ipynb output
+      args: [--extra-keys, "metadata.language_info"]
+      files: examples/notebooks
+
+  - repo: https://github.com/mwouts/jupytext
+    rev: v1.16.4
+    hooks:
+     - id: jupytext
+       name: sync .py and .ipynb
+       args:
+         - --sync
+         - --update-metadata
+         - '{"kernelspec": {"display_name": "Python 3 (ipykernel)","language": "python","name": "python3"}}'
+         - --set-formats
+         - examples/notebooks//ipynb,examples/scripts//py:percent
+       files: '^examples/(notebooks/.*\.ipynb|scripts/.*\.py)$'
 ci:
   autofix_commit_msg: |
     [pre-commit] auto fixes from pre-commit hooks

examples/direct_reconstruction.ipynb → examples/notebooks/direct_reconstruction.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "7ce284e1",
+   "id": "0",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -14,7 +14,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "a203bdc2",
+   "id": "1",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -28,7 +28,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "0c08b3fd",
+   "id": "2",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -45,7 +45,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "e0126c1e",
+   "id": "3",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -59,7 +59,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "f041501b",
+   "id": "4",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -80,7 +80,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4108db0a",
+   "id": "5",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -96,7 +96,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "d669bbd9",
+   "id": "6",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -108,7 +108,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "a4afe6b9",
+   "id": "7",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -136,7 +136,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "b558334f",
+   "id": "8",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -148,7 +148,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "d96152f2",
+   "id": "9",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -180,7 +180,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "564c18d7",
+   "id": "10",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -192,7 +192,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "52d306e3",
+   "id": "11",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -206,7 +206,8 @@
  ],
  "metadata": {
   "jupytext": {
-   "cell_metadata_filter": "-all"
+   "cell_metadata_filter": "-all",
+   "formats": "examples/notebooks//ipynb,examples/scripts//py:percent"
   },
   "kernelspec": {
    "display_name": "Python 3 (ipykernel)",