Skip to content

ci: strip notebook outputs with nbstripout #8

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
Marius1311 merged 3 commits into from
Jun 22, 2026
Merged

ci: strip notebook outputs with nbstripout #8

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
b02717b
ci(pre-commit): add nbstripout hook to strip notebook outputs
Marius1311 Jun 19, 2026
2b83cba
chore: strip outputs from tracked notebooks
Marius1311 Jun 19, 2026
c63952c
build(pixi): add nbstripout to the environment
Marius1311 Jun 22, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 4 additions & 0 deletions .pre-commit-config.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -23,6 +23,10 @@ repos:
args: [--fix, --exit-non-zero-on-fix]
- id: ruff-format
types_or: [python, pyi, jupyter]
- repo: https://github.com/kynan/nbstripout
rev: 0.9.1
hooks:
- id: nbstripout
- repo: https://github.com/pre-commit/pre-commit-hooks
rev: v6.0.0
hooks:
Expand Down
23 changes: 3 additions & 20 deletions analysis/XX-2026-01-27_sample_notebook.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -52,13 +52,8 @@
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {
"ExecuteTime": {
"end_time": "2021-05-31T09:25:02.307098Z",
"start_time": "2021-05-31T09:25:02.291254Z"
}
},
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"%load_ext autoreload\n",
Expand All @@ -76,10 +71,6 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
"ExecuteTime": {
"end_time": "2021-05-31T09:25:05.984402Z",
"start_time": "2021-05-31T09:25:02.309195Z"
},
"hidePrompt": true
},
"outputs": [],
Expand Down Expand Up @@ -144,15 +135,7 @@
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"/nas/groups/treutlein/USERS/mlange/github/data\n"
]
}
],
"outputs": [],
"source": [
"print(f\"Data directory: {FilePaths.DATA}\")\n",
"print(f\"Figures directory: {FilePaths.FIGURES}\")"
Expand Down
808 changes: 80 additions & 728 deletions analysis/demo_scRNA_workflow.ipynb
View file
Open in desktop

Large diffs are not rendered by default.

Loading
Loading