Fix notebooks (#242)

Co-authored-by: flying-sheep <flying-sheep@users.noreply.github.com>

Author: flying-sheep

docs/notebooks/anndata_getting_started.ipynb

@@ -121,7 +121,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.5"
+   "version": "3.12.11"
   }
  },
  "nbformat": 4,

docs/notebooks/basic-scrna-tutorial.ipynb

@@ -61,11 +61,11 @@
     {
      "data": {
       "text/plain": [
-       "['brain3k_multiome',\n",
-       " 'pbmc3k_multiome',\n",
-       " 'pbmc5k_citeseq',\n",
+       "['pbmc10k_multiome',\n",
        " 'brain9k_multiome',\n",
-       " 'pbmc10k_multiome']"
+       " 'brain3k_multiome',\n",
+       " 'pbmc5k_citeseq',\n",
+       " 'pbmc3k_multiome']"
       ]
      },
      "execution_count": 2,
@@ -119,11 +119,11 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/home/runner/miniconda3/envs/tutorials/lib/python3.12/site-packages/anndata/_core/anndata.py:1756: UserWarning: Variable names are not unique. To make them unique, call `.var_names_make_unique`.\n",
+      "/home/runner/miniconda3/envs/tutorials/lib/python3.12/site-packages/anndata/_core/anndata.py:1793: UserWarning: Variable names are not unique. To make them unique, call `.var_names_make_unique`.\n",
       "  utils.warn_names_duplicates(\"var\")\n",
-      "/home/runner/miniconda3/envs/tutorials/lib/python3.12/site-packages/anndata/_core/anndata.py:1756: UserWarning: Variable names are not unique. To make them unique, call `.var_names_make_unique`.\n",
+      "/home/runner/miniconda3/envs/tutorials/lib/python3.12/site-packages/anndata/_core/anndata.py:1793: UserWarning: Variable names are not unique. To make them unique, call `.var_names_make_unique`.\n",
       "  utils.warn_names_duplicates(\"var\")\n",
-      "/home/runner/miniconda3/envs/tutorials/lib/python3.12/site-packages/mudata/_core/mudata.py:915: UserWarning: var_names are not unique. To make them unique, call `.var_names_make_unique`.\n",
+      "/home/runner/miniconda3/envs/tutorials/lib/python3.12/site-packages/mudata/_core/mudata.py:947: UserWarning: var_names are not unique. To make them unique, call `.var_names_make_unique`.\n",
       "  warnings.warn(\n"
      ]
     }
@@ -471,7 +471,7 @@
        "       ...,\n",
        "       [0., 0., 0., ..., 0., 0., 0.],\n",
        "       [0., 0., 0., ..., 0., 0., 0.],\n",
-       "       [0., 0., 0., ..., 0., 0., 0.]], dtype=float32)"
+       "       [0., 0., 0., ..., 0., 0., 0.]], shape=(700, 1655), dtype=float32)"
       ]
      },
      "execution_count": 16,
@@ -491,7 +491,7 @@
     {
      "data": {
       "text/plain": [
-       "False"
+       "np.False_"
       ]
      },
      "execution_count": 17,
@@ -948,7 +948,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.5"
+   "version": "3.12.11"
   },
   "vscode": {
    "interpreter": {

docs/notebooks/data/pbmc3k_processed.h5ad

@@ -14,8 +14,7 @@ dependencies:
       - scanpy>=1.10
       - scrublet
       - leidenalg
-      # We need this commit: https://github.com/saezlab/decoupler-py/commit/0b3d9a975e06230ebbc32a6f97810be1730b8562
-      - decoupler @ git+https://github.com/saezlab/decoupler-py.git
+      - decoupler
       - celltypist
       - seaborn
       - mudata

docs/notebooks/scverse_data_backed.ipynb

@@ -88,6 +88,8 @@ select = [
     "RUF100",  # Report unused noqa directives
 ]
 ignore = [
+    # dict() syntax is fine
+    "C408",
     # line too long -> we accept long comment lines; formatter gets rid of long code lines
     "E501",
     # Do not assign a lambda expression, use a def -> lambda expression assignments are convenient