feat: add OpenRouter provider support #71
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Member
There was a problem hiding this comment. [blocking] Please rework the tutorial to match the style of the existing tutorials (see Three specific points:
The notebook already gets picked up by the |
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| "cells": [ | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "# OpenRouter sample annotation with Leiden clusters\n", | ||
| "\n", | ||
| "This tutorial shows how to annotate one or more samples with `CellAnnotator`\n", | ||
| "using an OpenRouter model and a user-provided Leiden key." | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "import scanpy as sc\n", | ||
| "from cell_annotator import CellAnnotator" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "## Configuration\n", | ||
| "\n", | ||
| "- `OPENROUTER_API_KEY`: your OpenRouter API key\n", | ||
| "- `OPENROUTER_MODEL`: model slug (e.g. `openai/gpt-4o-mini`)\n", | ||
| "- `LEIDEN_KEY`: cluster column in `adata.obs`\n", | ||
| "- `SAMPLE_KEY`: sample column in `adata.obs`, or `None` for a single sample\n", | ||
| "- `ADATA_PATH`: path to your `.h5ad` dataset" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "OPENROUTER_API_KEY = \"\" # e.g. sk-or-v1-...\n", | ||
| "OPENROUTER_MODEL = \"openai/gpt-4o-mini\"\n", | ||
| "LEIDEN_KEY = \"leiden\"\n", | ||
| "ADATA_PATH = \"path/to/your_data.h5ad\"\n", | ||
| "\n", | ||
| "SPECIES = \"human\"\n", | ||
| "TISSUE = \"pancreas\"\n", | ||
| "STAGE = \"adult\"\n", | ||
| "SAMPLE_KEY = \"sample\" # set to None for single-sample datasets\n", | ||
| "\n", | ||
| "if not OPENROUTER_API_KEY:\n", | ||
| " raise ValueError(\"Set OPENROUTER_API_KEY before continuing.\")\n", | ||
| "if not OPENROUTER_MODEL:\n", | ||
| " raise ValueError(\"Set OPENROUTER_MODEL before continuing.\")" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "## Load data" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "adata = sc.read_h5ad(ADATA_PATH)\n", | ||
| "\n", | ||
| "if LEIDEN_KEY not in adata.obs.columns:\n", | ||
| " raise KeyError(f\"Column '{LEIDEN_KEY}' was not found in adata.obs\")\n", | ||
| "if SAMPLE_KEY is not None and SAMPLE_KEY not in adata.obs.columns:\n", | ||
| " raise KeyError(f\"Column '{SAMPLE_KEY}' was not found in adata.obs\")\n", | ||
| "\n", | ||
| "print(adata)\n", | ||
| "print(\"Leiden key:\", LEIDEN_KEY)\n", | ||
| "print(\"Sample key:\", SAMPLE_KEY)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "## Initialize annotator" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "cell_ann = CellAnnotator(\n", | ||
| " adata=adata,\n", | ||
| " species=SPECIES,\n", | ||
| " tissue=TISSUE,\n", | ||
| " stage=STAGE,\n", | ||
| " cluster_key=LEIDEN_KEY,\n", | ||
| " sample_key=SAMPLE_KEY,\n", | ||
| " provider=\"openrouter\",\n", | ||
| " model=OPENROUTER_MODEL,\n", | ||
| " api_key=OPENROUTER_API_KEY,\n", | ||
| ")\n", | ||
| "\n", | ||
| "cell_ann" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "## Run annotation" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "cell_ann.get_expected_cell_type_markers(n_markers=3)\n", | ||
| "cell_ann.get_cluster_markers()\n", | ||
| "cell_ann.annotate_clusters(key_added=\"cell_type_predicted\")" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "## Inspect and save results" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "adata.obs[[LEIDEN_KEY, \"cell_type_predicted\"]].head(10)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "if \"X_umap\" in adata.obsm:\n", | ||
| " sc.pl.umap(adata, color=[LEIDEN_KEY, \"cell_type_predicted\"], wspace=0.35)\n", | ||
| "else:\n", | ||
| " print(\"No UMAP embedding found; skipping plot.\")\n", | ||
| "\n", | ||
| "output_path = ADATA_PATH.replace(\".h5ad\", \"_annotated.h5ad\")\n", | ||
| "adata.write(output_path)\n", | ||
| "print(f\"Saved annotated object to: {output_path}\")" | ||
| ] | ||
| } | ||
| ], | ||
| "metadata": { | ||
| "kernelspec": { | ||
| "display_name": "Python 3", | ||
| "language": "python", | ||
| "name": "python3" | ||
| }, | ||
| "language_info": { | ||
| "name": "python" | ||
| } | ||
| }, | ||
| "nbformat": 4, | ||
| "nbformat_minor": 5 | ||
| } | ||
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Since OpenRouter forwards requests to a chosen upstream provider under OpenRouter's own ToS, the effective attack surface for OpenRouter users is wider than for the other three providers. Could you strengthen this paragraph along the lines of: