Make marimo notebooks MoLab-compatible with pinned polyplot install

.github/workflows/ci.yml

@@ -0,0 +1,21 @@
+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v5
+
+      - uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: true
+
+      - run: uv sync --extra test
+      - run: uv run pytest
+      - run: uv build

.github/workflows/publish-test.yml

@@ -0,0 +1,35 @@
+name: Publish (TestPyPI)
+
+on:
+  push:
+    tags:
+      - "v*-test"
+  workflow_dispatch:
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+    environment: testpypi
+    permissions:
+      id-token: write
+      contents: read
+    steps:
+      - uses: actions/checkout@v5
+
+      - uses: astral-sh/setup-uv@v5
+
+      - name: Show package metadata
+        run: |
+          python3 - <<'PY'
+          import tomllib
+          from pathlib import Path
+          project = tomllib.loads(Path("pyproject.toml").read_text(encoding="utf-8"))["project"]
+          assert project["name"] == "polyplot", project["name"]
+          print("package:", project["name"])
+          print("version:", project["version"])
+          PY
+
+      - run: uv sync --extra test
+      - run: uv run pytest
+      - run: uv build
+      - run: uv publish --publish-url https://test.pypi.org/legacy/

.github/workflows/publish.yml

@@ -0,0 +1,41 @@
+name: Publish (PyPI)
+
+on:
+  push:
+    tags:
+      - "v0.1"
+  workflow_dispatch:
+    inputs:
+      confirm_publish:
+        description: "Type 'publish' to upload to PyPI"
+        required: true
+        type: string
+
+jobs:
+  publish:
+    if: ${{ inputs.confirm_publish == 'publish' }}
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      id-token: write
+      contents: read
+    steps:
+      - uses: actions/checkout@v5
+
+      - uses: astral-sh/setup-uv@v5
+
+      - name: Show package metadata
+        run: |
+          python3 - <<'PY'
+          import tomllib
+          from pathlib import Path
+          project = tomllib.loads(Path("pyproject.toml").read_text(encoding="utf-8"))["project"]
+          assert project["name"] == "polyplot", project["name"]
+          print("package:", project["name"])
+          print("version:", project["version"])
+          PY
+
+      - run: uv sync --extra test
+      - run: uv run pytest
+      - run: uv build
+      - run: uv publish

README.md

@@ -19,6 +19,19 @@ From the repository root:
 uv sync
 ```
 
+Optional extras:
+
+```bash
+# test dependencies
+uv sync --extra test
+
+# docs tooling
+uv sync --extra docs
+
+# local development group (pytest + zensical)
+uv sync --group dev
+```
+
 ## Quick start (marimo)
 
 ```bash
@@ -39,12 +52,12 @@ po.plot(gdf)  # meshifies from cache if needed; wireframe / opacity / BG in the
 - **`meshify`**: preprocess a GeoDataFrame (`cell_id`, `ZIndex`, `geometry`), write `tiles/` and `tiles.json` under `.polyplot/<content hash>/` by default (override with `out_dir=...`). Use `smooth=False` for no Taubin smoothing, `use_cache=False` to force a rebuild.
 - **`plot`**: calls `meshify` when needed, starts or reuses a local tile server, and returns a marimo `anywidget` viewer. Wireframe, opacity, and background are adjusted in the widget toolbar, not via Python.
 
-## Full demo
+## Full demo (development notebook)
 
-The longer example is `notebook.py` (a marimo app):
+The longer example is `dev/full_demo.py` (a marimo app for development/benchmarking):
 
 ```bash
-uv run marimo edit notebook.py
+uv run marimo edit dev/full_demo.py
 ```
 
 ## Sample data
@@ -63,4 +76,4 @@ The Python package lives in the `polyplot/` directory. Optional: install [gltfpa
 
 [github.com/ckmah/polyplot](https://github.com/ckmah/polyplot)
 
-To publish pre-rendered molab sessions, run from the repo root: `uvx marimo export session quickstart.py` (and similarly for `notebook.py` if desired).
+To publish pre-rendered molab sessions, run from the repo root: `uvx marimo export session quickstart.py` (and similarly for `dev/full_demo.py` if desired).

autoresearch/README.md

@@ -4,7 +4,7 @@ Experiment drivers and benchmarks for the meshify pipeline. This tree is **not**
 
 | Path | Role |
 |------|------|
-| `scripts/meshify_benchmark_measure.py` | Runs `notebook.py`, prints seconds per cell |
+| `scripts/meshify_benchmark_measure.py` | Runs `dev/full_demo.py`, prints seconds per cell |
 | `scripts/run_experiments.py` | Main commit / measure / revert loop |
 | `scripts/autoresearch_alg.py` | Fixed catalog of algorithmic experiments |
 | `scripts/autoresearch_1k.py` | Structural grid over mesh knobs |

autoresearch/scripts/meshify_benchmark_measure.py

@@ -1,5 +1,5 @@
 #!/usr/bin/env python3
-"""Run ``notebook.py`` once and print meshify wall time **per cell** (seconds).
+"""Run ``dev/full_demo.py`` once and print meshify wall time per cell.
 
 Reads the last line matching ``^MESHIFY_PER_CELL_SECONDS=(.+)$`` from combined
 stdout/stderr. Also writes the full capture to ``autoresearch/logs/run.log``.
@@ -26,7 +26,7 @@ def main() -> None:
     log_dir = autoresearch_dir / "logs"
     log_dir.mkdir(parents=True, exist_ok=True)
     proc = subprocess.run(
-        ["uv", "run", "python", str(repo_root / "notebook.py")],
+        ["uv", "run", "python", str(repo_root / "dev" / "full_demo.py")],
         cwd=repo_root,
         capture_output=True,
         text=True,

dev/full_demo.py

@@ -0,0 +1,73 @@
+# /// script
+# requires-python = ">=3.12"
+# dependencies = [
+#     "marimo>=0.22",
+#     "geopandas>=1.0",
+#     "pyarrow",
+#     "polyplot @ git+https://github.com/ckmah/polyplot.git@ec17ca181279b30b4b2befddb15d5c15d118b3b0",
+# ]
+# ///
+
+import marimo
+
+__generated_with = "0.23.1"
+app = marimo.App(width="full")
+
+
+@app.cell
+def _():
+    import os
+
+    import geopandas as gpd
+    import polyplot as po
+
+    parquet_url = os.getenv(
+        "POLYPLOT_PARQUET_URL",
+        "https://huggingface.co/datasets/ckmah/polyplot/resolve/92678be92f8e0b06fc2a32b53885c4fdf3419ee3/liver_crop.parquet",
+    )
+    return gpd, parquet_url, po
+
+
+@app.cell
+def _(gpd, parquet_url):
+    """Load dataset from Hugging Face only (no fallbacks)."""
+    import pathlib
+    import tempfile
+    import urllib.parse
+    import urllib.request
+
+    scheme = urllib.parse.urlparse(parquet_url).scheme.lower()
+    if scheme in {"http", "https"}:
+        with urllib.request.urlopen(parquet_url, timeout=120) as response:
+            with tempfile.TemporaryDirectory() as temp_dir:
+                parquet_path = pathlib.Path(temp_dir) / "dataset.parquet"
+                parquet_path.write_bytes(response.read())
+                gdf = gpd.read_parquet(parquet_path)
+    else:
+        gdf = gpd.read_parquet(parquet_url)
+    return (gdf,)
+
+
+@app.cell
+def _(gdf, po):
+    import time
+
+    n_cells = int(gdf["cell_id"].nunique())
+    t0 = time.perf_counter()
+    po.meshify(gdf, use_cache=False)
+    elapsed = time.perf_counter() - t0
+    per_cell = elapsed / n_cells if n_cells else 0.0
+    print(f"MESHIFY_SECONDS={elapsed:.6f}", flush=True)
+    print(f"MESHIFY_PER_CELL_SECONDS={per_cell:.6f}", flush=True)
+    return
+
+
+@app.cell
+def _(gdf, po):
+    viewer = po.plot(gdf, on_demand=True, max_orbit_distance=2000)
+    viewer
+    return
+
+
+if __name__ == "__main__":
+    app.run()

docs/get-started.md

@@ -13,6 +13,19 @@ cd polyplot
 uv sync
 ```
 
+Optional extras:
+
+```bash
+# run tests
+uv sync --extra test
+
+# docs tooling
+uv sync --extra docs
+
+# local development group (pytest + zensical)
+uv sync --group dev
+```
+
 ## Sample data
 
 The repository includes a small **`sample_data/liver_crop_sample.parquet`** (about 50 cells in one spatial patch) for demos and CI. To build a new subset from a local full `liver_crop.parquet`, use:
@@ -35,10 +48,10 @@ A **“Open in molab”** badge in the [README](https://github.com/ckmah/polyplo
 
 ## Full demo
 
-For a longer walkthrough, see `notebook.py`:
+For a longer walkthrough, see `dev/full_demo.py`:
 
 ```bash
-uv run marimo edit notebook.py
+uv run marimo edit dev/full_demo.py
 ```
 
 ## Build this documentation site locally

docs/index.md

@@ -8,7 +8,7 @@ icon: lucide/rocket
 
 - [**Get started**](get-started.md) – install, sample data, and the quickstart notebook.
 - [**User guide**](user-guide.md) – `meshify`, `plot`, and caching.
-- [PyPI / source](https://github.com/ckmah/polyplot) – `uv sync` from the repository root; API docstrings in `polyplot/`.
+- [PyPI / source](https://github.com/ckmah/polyplot) – `uv sync` from the repository root (`--extra test` / `--extra docs` as needed); API docstrings in `polyplot/`.
 
 ## At a glance
 

polyplot/_preprocess.py

@@ -1,7 +1,6 @@
 from __future__ import annotations
 
 import geopandas as gpd
-import pandas as pd
 
 
 def preprocess_gdf(

pyproject.toml

@@ -12,17 +12,23 @@ dependencies = [
     "shapely>=2.0",
     "numpy>=1.26",
     "mapbox-earcut>=1.0",
-    "matplotlib>=3.10.8",
     "pygltflib>=1.15",
     "numba>=0.65.0",
     "trimesh>=4.11.5",
-    "scipy>=1.17.1",
+]
+
+[project.optional-dependencies]
+test = [
+    "pytest>=8.4.0",
+]
+docs = [
     "zensical>=0.0.36",
 ]
 
 [dependency-groups]
 dev = [
     "pytest>=8.4.0",
+    "zensical>=0.0.36",
 ]
 
 [tool.pytest.ini_options]
@@ -37,7 +43,7 @@ packages = ["polyplot"]
 
 [tool.marimo.save]
 # Required for stable `--watch`: otherwise autosave races with external editors
-# (e.g. Cursor) and the browser can show stale code vs notebook.py on disk.
+# (e.g. Cursor) and the browser can show stale code vs on-disk notebook files.
 autosave = "off"
 
 [tool.uv]