Add pseudotemporal registration script (#340)

Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>

Author: Zethson

environment.yml

@@ -3,7 +3,9 @@ channels:
   - defaults
   - conda-forge
 dependencies:
-  - conda-forge::python=3.11.8
-  - conda-forge::jupyter-book==1.0.0
-  - conda-forge::jupytext==1.16.1
-  - conda-forge::beautifulsoup4==4.12.3
+  - conda-forge::python=3.13
+  - conda-forge::jupyter-book==1.0.3
+  - conda-forge::jupytext==1.16.7
+  - conda-forge::beautifulsoup4==4.13.3
+  - pip:
+      - lamindb[bionty,jupyter]

scripts/trajectory/pseudotemporal_dataset.ipynb

@@ -0,0 +1,147 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Pseudotemporal dataset"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\u001b[92m→\u001b[0m connected lamindb: theislab/sc-best-practices\n"
+     ]
+    }
+   ],
+   "source": [
+    "import lamindb as ln\n",
+    "import scanpy as sc"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "assert ln.setup.settings.instance.slug == \"theislab/sc-best-practices\""
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\u001b[92m→\u001b[0m loaded Transform('6QcwslTJCWhW0001'), re-started Run('gunbofig...') at 2025-02-19 09:12:59 UTC\n",
+      "\u001b[92m→\u001b[0m notebook imports: lamindb==1.1.0 scanpy==1.11.0\n"
+     ]
+    }
+   ],
+   "source": [
+    "ln.track()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "AnnData object with n_obs × n_vars = 5780 × 27876\n",
+       "    obs: 'clusters', 'palantir_pseudotime', 'palantir_diff_potential'\n",
+       "    var: 'palantir'\n",
+       "    uns: 'clusters_colors', 'palantir_branch_probs_cell_types'\n",
+       "    obsm: 'MAGIC_imputed_data', 'X_tsne', 'palantir_branch_probs'\n",
+       "    layers: 'spliced', 'unspliced'"
+      ]
+     },
+     "execution_count": 4,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "adata = sc.read(\n",
+    "    filename=\"bonemarrow.h5ad\",\n",
+    "    backup_url=\"https://figshare.com/ndownloader/files/35826944\",\n",
+    ")\n",
+    "adata"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\u001b[92m→\u001b[0m found artifact with same hash: Artifact(uid='buvlHZTfCKo60akB0000', is_latest=True, key='trajectory/pseudotemporal.h5ad', description='pseudotemporal dataset', suffix='.h5ad', otype='AnnData', size=388391976, hash='FdzXtifrBdukftwBX2_m5M', space_id=1, storage_id=1, run_id=2, created_by_id=2, created_at=2025-02-19 08:38:20 UTC); to track this artifact as an input, use: ln.Artifact.get()\n"
+     ]
+    },
+    {
+     "data": {
+      "text/plain": [
+       "Artifact(uid='buvlHZTfCKo60akB0000', is_latest=True, key='trajectory/pseudotemporal.h5ad', description='pseudotemporal dataset', suffix='.h5ad', otype='AnnData', size=388391976, hash='FdzXtifrBdukftwBX2_m5M', space_id=1, storage_id=1, run_id=2, created_by_id=2, created_at=2025-02-19 08:38:20 UTC)"
+      ]
+     },
+     "execution_count": 5,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "af = ln.Artifact(\n",
+    "    \"bonemarrow.h5ad\",\n",
+    "    key=\"trajectory/pseudotemporal.h5ad\",\n",
+    "    description=\"pseudotemporal dataset\",\n",
+    ").save()\n",
+    "af"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "ln.finish()"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "bp-pseudotime",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.9"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}