example data

Author: flying-sheep

.github/workflows/execute-nbs.yaml

@@ -7,10 +7,6 @@ on:
       - "docs/**"
       - "environment.yml"
 
-defaults:
-  run:
-    shell: bash -el {0}
-
 concurrency:
   group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
   cancel-in-progress: true

.gitignore

@@ -4,7 +4,9 @@
 buck-out/
 
 # Compiled files
-.venv/
+/.venv/
+/.pixi/*
+/pixi.*
 __pycache__/
 .ipynb_checkpoints/
 .*cache/

docs/notebooks/anndata_getting_started.ipynb

@@ -66,10 +66,9 @@
    ],
    "source": [
     "datapath = pooch.retrieve(\n",
-    "    url=\"https://figshare.com/ndownloader/files/40067737\",\n",
+    "    path=pooch.os_cache(\"scverse_tutorials\"),\n",
+    "    url=\"https://exampledata.scverse.org/tutorials/scverse-getting-started-anndata-pbmc3k_processed.h5ad\",\n",
     "    known_hash=\"md5:b80deb0997f96b45d06f19c694e46243\",\n",
-    "    path=\"./data\",\n",
-    "    fname=\"scverse-getting-started-anndata-pbmc3k_processed.h5ad\",\n",
     ")"
    ]
   },

docs/notebooks/basic-scrna-tutorial.ipynb

@@ -27,7 +27,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "sc.settings.set_figure_params(dpi=50, facecolor=\"white\")"
+    "sc.set_figure_params(dpi=50, facecolor=\"white\")"
    ]
   },
   {
@@ -42,20 +42,6 @@
     "We are reading in the count matrix into an [AnnData](https://anndata.readthedocs.io/en/latest/tutorials/notebooks/getting-started.html) object, which holds many slots for annotations and different representations of the data."
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": 3,
-   "id": "f0448e97",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "EXAMPLE_DATA = pooch.create(\n",
-    "    path=pooch.os_cache(\"scverse_tutorials\"),\n",
-    "    base_url=\"doi:10.6084/m9.figshare.22716739.v1/\",\n",
-    ")\n",
-    "EXAMPLE_DATA.load_registry_from_doi()"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": 4,
@@ -94,18 +80,21 @@
     }
    ],
    "source": [
-    "samples = {\n",
-    "    \"s1d1\": \"s1d1_filtered_feature_bc_matrix.h5\",\n",
-    "    \"s1d3\": \"s1d3_filtered_feature_bc_matrix.h5\",\n",
-    "}\n",
-    "adatas = {}\n",
-    "\n",
-    "for sample_id, filename in samples.items():\n",
-    "    path = EXAMPLE_DATA.fetch(filename)\n",
+    "def download_sample(sample_id: str, known_hash: str) -> ad.AnnData:\n",
+    "    path = pooch.retrieve(\n",
+    "        path=pooch.os_cache(\"scverse_tutorials\"),\n",
+    "        url=f\"https://exampledata.scverse.org/tutorials/neurips-2021/{sample_id}_filtered_feature_bc_matrix.h5\",\n",
+    "        known_hash=known_hash,\n",
+    "    )\n",
     "    sample_adata = sc.read_10x_h5(path)\n",
     "    sample_adata.var_names_make_unique()\n",
-    "    adatas[sample_id] = sample_adata\n",
+    "    return sample_adata\n",
     "\n",
+    "samples = {\n",
+    "    \"s1d1\": \"md5:a99285913ea3f3d22600d3d2f8a88e34\",\n",
+    "    \"s1d3\": \"md5:825f7f7578e3dc0b8955f5a97a402338\",\n",
+    "}\n",
+    "adatas = {id_: download_sample(id_, known_hash) for id_, known_hash in samples.items()}\n",
     "adata = ad.concat(adatas, label=\"sample\")\n",
     "adata.obs_names_make_unique()"
    ]
@@ -1347,7 +1336,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "\r",
+      "\r\n",
       "  0%|          | 0/1 [00:00<?, ?it/s]"
      ]
     },
@@ -1362,15 +1351,15 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "\r",
+      "\r\n",
       "100%|██████████| 1/1 [00:17<00:00, 17.34s/it]"
      ]
     },
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "\r",
+      "\r\n",
       "100%|██████████| 1/1 [00:17<00:00, 17.34s/it]"
      ]
     },