diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index b3be079f..917563de 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -14,7 +14,6 @@ on: - "zensical.toml" - ".readthedocs.yaml" - "dev/render_example_notebooks.py" - - "dev/render_marimo_notebooks.py" - ".github/workflows/docs.yml" pull_request: paths: @@ -22,7 +21,6 @@ on: - "zensical.toml" - ".readthedocs.yaml" - "dev/render_example_notebooks.py" - - "dev/render_marimo_notebooks.py" - ".github/workflows/docs.yml" jobs: diff --git a/.gitignore b/.gitignore index 5d068dfa..b5c7ce94 100644 --- a/.gitignore +++ b/.gitignore @@ -35,7 +35,6 @@ dev_utils/BioLogic.py_tmp dev_utils/.ipynb_checkpoints *.ipynb_checkpoints -__marimo__/ # Distribution / packaging .Python diff --git a/.issueflows/04-designs-and-guides/marimo-docs.md b/.issueflows/04-designs-and-guides/marimo-docs.md index 6a99998a..e52f6ea9 100644 --- a/.issueflows/04-designs-and-guides/marimo-docs.md +++ b/.issueflows/04-designs-and-guides/marimo-docs.md @@ -1,12 +1,17 @@ # Marimo notebooks in the docs -**Context:** Issue #724 — prove marimo can ship alongside Jupyter tutorials under Zensical. +**Context:** Issue #724 — spike to ship marimo alongside Jupyter tutorials under Zensical. -**Decision:** Keep Jupyter’s committed-markdown pipeline. For marimo, sources live in `docs/examples/marimo/*.py` and are exported with `marimo-md-export` via `dev/render_marimo_notebooks.py`; commit the generated `.md`. No Pyodide / live Python in the site. +**Decision (final):** **Do not ship marimo pages in the Zensical docs for now.** +The sample “Hello cellpy (marimo)” page and `dev/render_marimo_notebooks.py` +pipeline were removed. Keep Jupyter’s committed-markdown path. -**Alternatives considered:** Native Zensical marimo plugin (none yet); generate-at-RTD instead of committing (rejected for this spike — match Jupyter); convert existing `.ipynb` set (out of scope). +**Why withdrawn:** `marimo-md-export` flattens `mo.ui.table` to plain Markdown. +Plotly inline scripts break under Material instant navigation. Reactive marimo +islands / Pyodide hang in the docs embed. Client-side stand-ins (Tabulator, +Plotly iframes) work but are no longer “marimo”. -**Ops:** `uv run --group docs python dev/render_marimo_notebooks.py` then `zensical build`. Keep figures light (base64 size). Ignore `__marimo__/` session dirs. +**Revisit when:** Zensical (or a host plugin) supports marimo islands cleanly, +or marimo ships a reliable Python-free static reactive export that fits docs. -**Landing:** Docs-only PRs (including this spike) target the long-lived -`v2-docs-stable` branch; merge that into `master` when ready to publish. +**Landing:** docs work continues on `v2-docs-stable`. diff --git a/HISTORY.md b/HISTORY.md index 0cc6a10c..88dbffab 100644 --- a/HISTORY.md +++ b/HISTORY.md @@ -2,7 +2,9 @@ ## [Unreleased] -* Include marimo notebooks in the docs (sample under `docs/examples/marimo/`, `marimo-md-export` render path). (#724). +* Tried shipping marimo notebooks in the docs (#724); withdrawn — Zensical + embeds could not keep a real marimo table/plot experience without hanging + Pyodide or replacing widgets with non-marimo UI. * Clarify Neware docs: binary `.nda`/`.ndax` via `neware_nda` (bundled fastnda) vs exported `neware_txt` models. diff --git a/dev/render_marimo_notebooks.py b/dev/render_marimo_notebooks.py deleted file mode 100644 index cb327523..00000000 --- a/dev/render_marimo_notebooks.py +++ /dev/null @@ -1,69 +0,0 @@ -"""Render marimo example notebooks to committed markdown pages (#724). - -Zensical builds from Markdown and does not execute marimo. Sources under -``docs/examples/marimo/`` are exported with ``marimo-md-export`` (markdown plus -embedded outputs) and the result is committed, mirroring the Jupyter path in -``dev/render_example_notebooks.py``. - -Usage: - -```shell -uv run --group docs python dev/render_marimo_notebooks.py -``` - -Re-run and commit the output whenever a marimo notebook changes. This **does** -execute the notebooks (via ``marimo export``) so cellpy and its deps must be -importable in the environment. -""" - -from __future__ import annotations - -import shutil -import subprocess -from pathlib import Path - -REPO_ROOT = Path(__file__).resolve().parents[1] -MARIMO_DIR = REPO_ROOT / "docs" / "examples" / "marimo" - - -def _exporter() -> str: - """Return the ``marimo-md-export`` executable path, or raise a clear error.""" - exe = shutil.which("marimo-md-export") - if exe: - return exe - raise SystemExit( - "marimo-md-export is not on PATH. " - "Install/run via the docs group: uv run --group docs python " - "dev/render_marimo_notebooks.py" - ) - - -def render(notebook_path: Path, exporter: str) -> None: - """Export one marimo notebook to a sibling ``.md`` file.""" - notebook_path = notebook_path.resolve() - output = notebook_path.with_suffix(".md") - cmd = [exporter, str(notebook_path), str(output)] - - print(f"exporting {notebook_path.relative_to(REPO_ROOT)} -> {output.name}") - subprocess.run(cmd, check=True, cwd=REPO_ROOT) - size_kb = output.stat().st_size / 1024 - print(f" wrote {output.relative_to(REPO_ROOT)} ({size_kb:.0f} KB)") - - -def main() -> None: - if not MARIMO_DIR.is_dir(): - raise SystemExit(f"missing marimo examples dir: {MARIMO_DIR}") - - notebooks = sorted( - p for p in MARIMO_DIR.glob("*.py") if not p.name.startswith("_") - ) - if not notebooks: - raise SystemExit(f"no marimo notebooks under {MARIMO_DIR}") - - exporter = _exporter() - for notebook in notebooks: - render(notebook, exporter) - - -if __name__ == "__main__": - main() diff --git a/docs/contributing/developers_guide/dev_docs.md b/docs/contributing/developers_guide/dev_docs.md index 289fcd72..003e58c4 100644 --- a/docs/contributing/developers_guide/dev_docs.md +++ b/docs/contributing/developers_guide/dev_docs.md @@ -90,23 +90,6 @@ The `.ipynb` files stay in the tree as the interactive source. It renders the outputs already stored in the notebooks; it does **not** execute them. -### Example notebooks (marimo) - -Marimo sources live under `docs/examples/marimo/` (``.py`` notebooks). Zensical -does not execute them either; export to committed markdown with -[`marimo-md-export`](https://jmarshrossney.github.io/marimo-md-export/): - -```shell -uv run --group docs python dev/render_marimo_notebooks.py -``` - -Unlike the Jupyter path, this **does** run the notebooks (via `marimo export`), -so cellpy must be importable. Keep figures light — the exporter embeds images -as base64 and large plotly-style blobs bloat the committed pages. Prefer -matplotlib (or `# @suppress` on heavy cells). No Pyodide / live Python in the -docs site; readers who want to edit interactively should open the ``.py`` with -`marimo edit`. - ### Doc-strings - Use Google-style doc-strings diff --git a/docs/examples/index.md b/docs/examples/index.md index 54dffbb8..e3887330 100644 --- a/docs/examples/index.md +++ b/docs/examples/index.md @@ -23,7 +23,6 @@ folder](https://github.com/jepegit/cellpy/tree/master/examples) in the cellpy Gi - [GITT](05_GITT.md) - [Batch processing](batch_utility/cellpy_batch_processing_docs.md) - [Templates](templates/tutorial_templates.md) -- [Hello cellpy (marimo)](marimo/01_hello_cellpy.md) ## About these pages @@ -38,13 +37,3 @@ To re-render after changing a Jupyter notebook: ```shell uv run --group docs python dev/render_example_notebooks.py ``` - -There is also a small [marimo](https://marimo.io) spike under -[`docs/examples/marimo/`](https://github.com/jepegit/cellpy/tree/master/docs/examples/marimo). -Those pages are exported with -[`marimo-md-export`](https://jmarshrossney.github.io/marimo-md-export/) (markdown -plus embedded outputs — no Pyodide in the docs site). Re-render with: - -```shell -uv run --group docs python dev/render_marimo_notebooks.py -``` diff --git a/docs/examples/marimo/01_hello_cellpy.md b/docs/examples/marimo/01_hello_cellpy.md deleted file mode 100644 index 040d149c..00000000 --- a/docs/examples/marimo/01_hello_cellpy.md +++ /dev/null @@ -1,55 +0,0 @@ ---- -title: 01 Hello Cellpy -marimo-version: 0.23.15 -width: medium ---- - -```python {.marimo} -import marimo as mo -``` - -# Hello cellpy (marimo) - -Tiny spike showing that [marimo](https://marimo.io) notebooks can appear -in the cellpy docs. The page you are reading was exported with -[`marimo-md-export`](https://jmarshrossney.github.io/marimo-md-export/) -— static markdown plus embedded outputs, no Pyodide in the site. - -Source: -[`01_hello_cellpy.py`](https://github.com/jepegit/cellpy/blob/master/docs/examples/marimo/01_hello_cellpy.py) -— run locally with `marimo edit docs/examples/marimo/01_hello_cellpy.py`. - -```python {.marimo} -import matplotlib.pyplot as plt - -from cellpy.utils import example_data -``` - -```python {.marimo} -c = example_data.cellpy_file() -n_cycles = c.get_number_of_cycles() -mo.md(f"Loaded the bundled example cellpy file — **{n_cycles}** cycles.") -``` - - - -Loaded the bundled example cellpy file — 304 cycles. - -```python {.marimo} -# Keep the figure light: a few summary points, PNG-friendly matplotlib. -summary = c.data.summary -cycles = summary[c.schema.summary.cycle_num] -charge = summary[c.schema.summary.charge_capacity] - -fig, ax = plt.subplots(figsize=(6, 3.5)) -ax.plot(cycles, charge, marker="o", markersize=3, linewidth=1) -ax.set_xlabel("Cycle") -ax.set_ylabel("Charge capacity") -ax.set_title("Example cell — charge capacity vs cycle") -fig.tight_layout() -fig -``` - - - -png \ No newline at end of file diff --git a/docs/examples/marimo/01_hello_cellpy.py b/docs/examples/marimo/01_hello_cellpy.py deleted file mode 100644 index 4dc4d5fb..00000000 --- a/docs/examples/marimo/01_hello_cellpy.py +++ /dev/null @@ -1,68 +0,0 @@ -import marimo - -__generated_with = "0.23.15" -app = marimo.App(width="medium") - - -@app.cell -def _(): - import marimo as mo - - return (mo,) - - -@app.cell -def _(mo): - mo.md( - r""" - # Hello cellpy (marimo) - - Tiny spike showing that [marimo](https://marimo.io) notebooks can appear - in the cellpy docs. The page you are reading was exported with - [`marimo-md-export`](https://jmarshrossney.github.io/marimo-md-export/) - — static markdown plus embedded outputs, no Pyodide in the site. - - Source: - [`01_hello_cellpy.py`](https://github.com/jepegit/cellpy/blob/master/docs/examples/marimo/01_hello_cellpy.py) - — run locally with `marimo edit docs/examples/marimo/01_hello_cellpy.py`. - """ - ) - return - - -@app.cell -def _(): - import matplotlib.pyplot as plt - - from cellpy.utils import example_data - - return example_data, plt - - -@app.cell -def _(example_data, mo): - c = example_data.cellpy_file() - n_cycles = c.get_number_of_cycles() - mo.md(f"Loaded the bundled example cellpy file — **{n_cycles}** cycles.") - return (c,) - - -@app.cell -def _(c, plt): - # Keep the figure light: a few summary points, PNG-friendly matplotlib. - summary = c.data.summary - cycles = summary[c.schema.summary.cycle_num] - charge = summary[c.schema.summary.charge_capacity] - - fig, ax = plt.subplots(figsize=(6, 3.5)) - 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