add nbstripout via pre-commit and strip all notebooks

GeigerJ2 · Oct 23, 2025 · Oct 22, 2025 · Oct 22, 2025 · Oct 22, 2025 · Oct 22, 2025
commit 1ecb3f5baa422bf46e806f4b74d0c53e6d2ada77
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,9 @@
+repos:
+  - repo: https://github.com/kynan/nbstripout
+    rev: 0.7.1
+    hooks:
+      - id: nbstripout
+        name: nbstripout - Strip outputs from notebooks
+        args:
+          - --extra-keys
+          - "metadata.kernelspec metadata.language_info"
diff --git a/example_workflows/arithmetic/aiida.ipynb b/example_workflows/arithmetic/aiida.ipynb
diff --git a/example_workflows/arithmetic/cwl.ipynb b/example_workflows/arithmetic/cwl.ipynb
@@ -1,97 +1,66 @@
 {
- "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
-   "language": "python",
-   "name": "python3"
-  },
-  "language_info": {
-   "name": "python",
-   "version": "3.12.8",
-   "mimetype": "text/x-python",
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "pygments_lexer": "ipython3",
-   "nbconvert_exporter": "python",
-   "file_extension": ".py"
-  }
- },
- "nbformat_minor": 5,
- "nbformat": 4,
  "cells": [
   {
-   "id": "377fef56-484d-491c-b19e-1be6931e44eb",
    "cell_type": "code",
-   "source": "import pickle",
-   "metadata": {
-    "trusted": true
-   },
+   "execution_count": null,
+   "id": "0",
+   "metadata": {},
    "outputs": [],
-   "execution_count": 1
+   "source": [
+    "import pickle"
+   ]
   },
   {
-   "id": "92e3921b-2bb8-4333-8cfe-4bd27f785d24",
    "cell_type": "code",
-   "source": "from python_workflow_definition.cwl import write_workflow",
-   "metadata": {
-    "trusted": true
-   },
+   "execution_count": null,
+   "id": "1",
+   "metadata": {},
    "outputs": [],
-   "execution_count": 2
+   "source": [
+    "from python_workflow_definition.cwl import write_workflow"
+   ]
   },
   {
-   "id": "5303c059-8ae4-4557-858e-b4bd64eac711",
    "cell_type": "code",
-   "source": "write_workflow(file_name=\"workflow.json\")",
-   "metadata": {
-    "trusted": true
-   },
+   "execution_count": null,
+   "id": "2",
+   "metadata": {},
    "outputs": [],
-   "execution_count": 3
+   "source": [
+    "write_workflow(file_name=\"workflow.json\")"
+   ]
   },
   {
-   "id": "df302bd2-e9b6-4595-979c-67c46414d986",
    "cell_type": "code",
-   "source": "! cwltool workflow.cwl workflow.yml",
-   "metadata": {
-    "trusted": true
-   },
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": "/srv/conda/envs/notebook/bin/cwltool:11: DeprecationWarning: Nesting argument groups is deprecated.\n  sys.exit(run())\n\u001B[1;30mINFO\u001B[0m /srv/conda/envs/notebook/bin/cwltool 3.1.20250110105449\n\u001B[1;30mINFO\u001B[0m Resolved 'workflow.cwl' to 'file:///home/jovyan/example_workflows/arithmetic/workflow.cwl'\n\u001B[1;30mINFO\u001B[0m [workflow ] start\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step get_prod_and_div_0\n\u001B[1;30mINFO\u001B[0m [step get_prod_and_div_0] start\n\u001B[1;30mINFO\u001B[0m [job get_prod_and_div_0] /tmp/_1apt559$ python \\\n    -m \\\n    python_workflow_definition.cwl \\\n    --workflowfile=/tmp/dyuxg6ka/stgf337bac5-2f8e-4489-bd51-83491b1d5f0e/workflow.py \\\n    --function=workflow.get_prod_and_div \\\n    --arg_x=/tmp/dyuxg6ka/stgd87c2fe4-ca8e-4031-9af0-751d6944cbe7/x.pickle \\\n    --arg_y=/tmp/dyuxg6ka/stg7bcb8ced-0e5b-442e-a0e0-2b3117afe2d8/y.pickle\n\u001B[1;30mINFO\u001B[0m [job get_prod_and_div_0] completed success\n\u001B[1;30mINFO\u001B[0m [step get_prod_and_div_0] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step get_sum_1\n\u001B[1;30mINFO\u001B[0m [step get_sum_1] start\n\u001B[1;30mINFO\u001B[0m [job get_sum_1] /tmp/ysau_yra$ python \\\n    -m \\\n    python_workflow_definition.cwl \\\n    --workflowfile=/tmp/rm6c9qek/stgfef68b90-5d69-4da9-a952-b9c2f2a1eb76/workflow.py \\\n    --function=workflow.get_sum \\\n    --arg_x=/tmp/rm6c9qek/stg35728be7-5a6d-487b-bd02-345581007663/prod.pickle \\\n    --arg_y=/tmp/rm6c9qek/stgc0992786-237e-4308-9d9e-814ebbfb0319/div.pickle\n\u001B[1;30mINFO\u001B[0m [job get_sum_1] completed success\n\u001B[1;30mINFO\u001B[0m [step get_sum_1] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step get_square_2\n\u001B[1;30mINFO\u001B[0m [step get_square_2] start\n\u001B[1;30mINFO\u001B[0m [job get_square_2] /tmp/o3gzya8t$ python \\\n    -m \\\n    python_workflow_definition.cwl \\\n    --workflowfile=/tmp/6a3sltnz/stg58ccf048-a5c3-4ba3-a24f-c64adfff84cd/workflow.py \\\n    --function=workflow.get_square \\\n    --arg_x=/tmp/6a3sltnz/stg70203cec-cbd4-4fea-a3de-70e9373d9c9d/result.pickle\n\u001B[1;30mINFO\u001B[0m [job get_square_2] completed success\n\u001B[1;30mINFO\u001B[0m [step get_square_2] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] completed success\n{\n    \"result_file\": {\n        \"location\": \"file:///home/jovyan/example_workflows/arithmetic/result.pickle\",\n        \"basename\": \"result.pickle\",\n        \"class\": \"File\",\n        \"checksum\": \"sha1$1fd8f217331336b1226b84e351c56fb9a8d93685\",\n        \"size\": 21,\n        \"path\": \"/home/jovyan/example_workflows/arithmetic/result.pickle\"\n    }\n}\u001B[1;30mINFO\u001B[0m Final process status is success\n"
-    }
-   ],
-   "execution_count": 4
+   "execution_count": null,
+   "id": "3",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "! cwltool workflow.cwl workflow.yml"
+   ]
   },
   {
-   "id": "2942dbba-ea0a-4d20-be5c-ed9992d09ff8",
    "cell_type": "code",
-   "source": "with open(\"result.pickle\", \"rb\") as f:\n    print(pickle.load(f))",
-   "metadata": {
-    "trusted": true
-   },
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": "6.25\n"
-    }
-   ],
-   "execution_count": 5
+   "execution_count": null,
+   "id": "4",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "with open(\"result.pickle\", \"rb\") as f:\n",
+    "    print(pickle.load(f))"
+   ]
   },
   {
-   "id": "60e909ee-d0d0-4bd1-81c8-dd5274ae5834",
    "cell_type": "code",
-   "source": "",
-   "metadata": {
-    "trusted": true
-   },
+   "execution_count": null,
+   "id": "5",
+   "metadata": {},
    "outputs": [],
-   "execution_count": null
+   "source": []
   }
- ]
+ ],
+ "metadata": {},
+ "nbformat": 4,
+ "nbformat_minor": 5
 }