diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml new file mode 100644 index 0000000..4796d5d --- /dev/null +++ b/.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 diff --git a/.github/workflows/publish-test.yml b/.github/workflows/publish-test.yml new file mode 100644 index 0000000..7d830de --- /dev/null +++ b/.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/ diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml new file mode 100644 index 0000000..929ad09 --- /dev/null +++ b/.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 diff --git a/README.md b/README.md index 2f7fdf5..b46d6f9 100644 --- a/README.md +++ b/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//` 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). diff --git a/autoresearch/README.md b/autoresearch/README.md index bc985d8..40cf0f5 100644 --- a/autoresearch/README.md +++ b/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 | diff --git a/autoresearch/scripts/meshify_benchmark_measure.py b/autoresearch/scripts/meshify_benchmark_measure.py index 3587862..d432251 100644 --- a/autoresearch/scripts/meshify_benchmark_measure.py +++ b/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, diff --git a/dev/full_demo.py b/dev/full_demo.py new file mode 100644 index 0000000..723926d --- /dev/null +++ b/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() diff --git a/docs/get-started.md b/docs/get-started.md index 8acbec8..61709fd 100644 --- a/docs/get-started.md +++ b/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 diff --git a/docs/index.md b/docs/index.md index e809db2..7d9bb7f 100644 --- a/docs/index.md +++ b/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 diff --git a/notebook.py b/notebook.py deleted file mode 100644 index 8082c41..0000000 --- a/notebook.py +++ /dev/null @@ -1,64 +0,0 @@ -# /// script -# requires-python = ">=3.12" -# dependencies = [ -# "polyplot", -# "marimo>=0.22", -# "geopandas>=1.0", -# "pyarrow", -# ] -# /// - -import marimo - -__generated_with = "0.23.1" -app = marimo.App(width="full") - - -@app.cell -def _(): - import pathlib - - import geopandas as gpd - import marimo as mo - import polyplot as po - - return gpd, pathlib, po - - -@app.cell -def _(gpd, pathlib): - """Load the 500-cell subset (``scripts/make_liver_subset.py -n 500``).""" - gdf = gpd.read_parquet( - pathlib.Path(__file__).parent / "sample_data" / "liver_crop.parquet" - ) - 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 - - -@app.cell -def _(): - return - - -if __name__ == "__main__": - app.run() diff --git a/polyplot/_preprocess.py b/polyplot/_preprocess.py index 12ebc30..440d3b8 100644 --- a/polyplot/_preprocess.py +++ b/polyplot/_preprocess.py @@ -1,7 +1,6 @@ from __future__ import annotations import geopandas as gpd -import pandas as pd def preprocess_gdf( diff --git a/pyproject.toml b/pyproject.toml index a49ab8d..fd1c2ae 100644 --- a/pyproject.toml +++ b/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] diff --git a/quickstart.py b/quickstart.py index a909331..3fc1e21 100644 --- a/quickstart.py +++ b/quickstart.py @@ -4,10 +4,8 @@ # "marimo>=0.22", # "geopandas>=1.0", # "pyarrow", -# "polyplot", +# "polyplot @ git+https://github.com/ckmah/polyplot.git@ec17ca181279b30b4b2befddb15d5c15d118b3b0", # ] -# [tool.uv.sources] -# polyplot = { path = ".", editable = true } # /// import marimo @@ -18,25 +16,47 @@ @app.cell def _(): - import pathlib + import os import textwrap import geopandas as gpd import marimo as mo import polyplot as po - return gpd, mo, pathlib, po, textwrap + parquet_url = os.getenv( + "POLYPLOT_PARQUET_URL", + "https://huggingface.co/datasets/ckmah/polyplot/resolve/92678be92f8e0b06fc2a32b53885c4fdf3419ee3/liver_crop_sample.parquet", + ) + return gpd, mo, parquet_url, po, textwrap @app.cell -def _(gpd, mo, pathlib, po, textwrap): +def _(gpd, mo, parquet_url, po, textwrap): + 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) + intro = mo.md( textwrap.dedent( - """ + f""" # Polyplot quick start - This notebook uses the tracked `sample_data/liver_crop_sample.parquet`. From - the repository root (so paths resolve) run `uv run marimo edit quickstart.py`. + This notebook loads sample data from Hugging Face only, so it works + in hosted MoLab sessions where only this notebook file is copied. + + Set `POLYPLOT_PARQUET_URL` to any public parquet URL. + Current source: `{parquet_url}` Tip: In `on_demand=True` mode, click a cell in the minimap to build a on-demand tile view. The camera also clamps max zoom-out so you cannot @@ -45,11 +65,6 @@ def _(gpd, mo, pathlib, po, textwrap): """ ).strip() ) - gdf = gpd.read_parquet( - pathlib.Path(__file__).resolve().parent - / "sample_data" - / "liver_crop_sample.parquet" - ) viewer = po.plot(gdf, on_demand=True) return mo.vstack(intro, viewer) diff --git a/sample_data/README.md b/sample_data/README.md index e7db1cc..0f34cc9 100644 --- a/sample_data/README.md +++ b/sample_data/README.md @@ -1,6 +1,6 @@ # Sample data - **`liver_crop_sample.parquet`** (tracked) — small subset (~50 cells in one spatial neighborhood) for docs, CI, and `quickstart.py`. Generated with `uv run python scripts/make_liver_subset.py` from a local full export. -- **`liver_crop.parquet`** (not committed) — full dataset; place it here locally if you use `scripts/make_liver_subset.py` or the full [`notebook.py`](../notebook.py) against the large file. +- **`liver_crop.parquet`** (not committed) — full dataset; place it here locally if you use `scripts/make_liver_subset.py`. 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