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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,9 +1,4 @@ | ||
| from importlib.metadata import PackageNotFoundError, version | ||
| from cev._version import __version__ # noqa | ||
|
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||
| import cev.metrics as metrics # noqa | ||
| import cev.widgets as widgets # noqa | ||
|
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||
| try: | ||
| __version__ = version("cev") | ||
| except PackageNotFoundError: | ||
| __version__ = "uninstalled" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,134 @@ | ||
| import argparse | ||
| import json | ||
| import os | ||
| import shutil | ||
| import sys | ||
| import textwrap | ||
| import zipfile | ||
| from pathlib import Path | ||
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| import pooch | ||
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| from cev._version import __version__ | ||
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| _DEV = True | ||
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| def download_data() -> tuple[Path, Path]: | ||
| archive = pooch.retrieve( | ||
| url="https://figshare.com/ndownloader/articles/23063615/versions/1", | ||
| path=pooch.os_cache("cev"), | ||
| fname="data.zip", | ||
| known_hash=None, | ||
| ) | ||
| archive = Path(archive) | ||
| files = [ | ||
| "mair-2022-tissue-138-umap.pq", | ||
| "mair-2022-tissue-138-ozette.pq", | ||
| ] | ||
| with zipfile.ZipFile(archive, "r") as zip_ref: | ||
| for file in files: | ||
| zip_ref.extract(file, path=archive.parent) | ||
| return ( | ||
| archive.parent / "mair-2022-tissue-138-umap.pq", | ||
| archive.parent / "mair-2022-tissue-138-ozette.pq", | ||
| ) | ||
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| def write_notebook(output: Path): | ||
| umap_path, ozette_path = download_data() | ||
| source = textwrap.dedent( | ||
| f""" | ||
| import pandas as pd | ||
| from cev.widgets import Embedding, EmbeddingComparisonWidget | ||
| umap_embedding = pd.read_parquet("{umap_path}").pipe(Embedding.from_ozette) | ||
| ozette_embedding = pd.read_parquet("{ozette_path}").pipe(Embedding.from_ozette) | ||
| EmbeddingComparisonWidget( | ||
| umap_embedding, | ||
| ozette_embedding, | ||
| titles=("Standard UMAP", "Annotation-Transformed UMAP"), | ||
| metric="confusion", | ||
| selection="synced", | ||
| auto_zoom=True, | ||
| row_height=320, | ||
| ) | ||
| """ | ||
| ).strip() | ||
|
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||
| nb = { | ||
| "cells": [ | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": None, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": source, | ||
| } | ||
| ], | ||
| "metadata": { | ||
| "kernelspec": { | ||
| "display_name": "Python 3", | ||
| "language": "python", | ||
| "name": "python3", | ||
| } | ||
| }, | ||
| "nbformat": 4, | ||
| "nbformat_minor": 5, | ||
| } | ||
| with output.open("w") as f: | ||
| json.dump(nb, f, indent=2) | ||
|
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||
|
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| def check_uv_available(): | ||
| if shutil.which("uv") is None: | ||
| print("Error: 'uv' command not found.", file=sys.stderr) | ||
| print("Please install 'uv' to run `cev demo` entrypoint.", file=sys.stderr) | ||
| print( | ||
| "For more information, visit: https://github.com/astral-sh/uv", | ||
| file=sys.stderr, | ||
| ) | ||
| sys.exit(1) | ||
|
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||
|
|
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| def run_notebook(notebook_path: Path): | ||
| check_uv_available() | ||
| command = [ | ||
| "uvx", | ||
| "--python", | ||
| "3.11", | ||
| "--with", | ||
| "." if _DEV else f"cev=={__version__}", | ||
| "--with", | ||
| "jupyterlab", | ||
| "jupyter", | ||
| "lab", | ||
| str(notebook_path), | ||
| ] | ||
| try: | ||
| os.execvp(command[0], command) | ||
| except OSError as e: | ||
| print(f"Error executing {command[0]}: {e}", file=sys.stderr) | ||
| sys.exit(1) | ||
|
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|
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| def main(): | ||
| parser = argparse.ArgumentParser(prog="cev") | ||
| subparsers = parser.add_subparsers(dest="command", help="Available commands") | ||
| subparsers.add_parser("download", help="Download the demo notebook (and data)") | ||
| subparsers.add_parser("demo", help="Run the demo notebook in JupyterLab") | ||
| args = parser.parse_args() | ||
|
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| notebook_path = Path("cev-demo.ipynb") | ||
| if args.command == "download": | ||
| write_notebook(notebook_path) | ||
| elif args.command == "demo": | ||
| write_notebook(notebook_path) | ||
| run_notebook(notebook_path) | ||
| else: | ||
| parser.print_help() | ||
|
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||
|
|
||
| if __name__ == "__main__": | ||
| main() |