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Fix notebooks #242

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Merged
flying-sheep merged 2 commits into from
Sep 30, 2025
Merged

Fix notebooks #242

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a5e4c17
Fix notebooks
flying-sheep Sep 30, 2025
bfd482a
Render notebooks
flying-sheep Sep 30, 2025
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22 changes: 11 additions & 11 deletions docs/notebooks/anndata_getting_started.ipynb
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721 changes: 314 additions & 407 deletions docs/notebooks/basic-scrna-tutorial.ipynb
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Binary file removed docs/notebooks/data/pbmc3k_processed.h5ad
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108 changes: 66 additions & 42 deletions docs/notebooks/scverse_data_backed.ipynb
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2 changes: 1 addition & 1 deletion docs/notebooks/scverse_data_interoperability.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -121,7 +121,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.12.5"
"version": "3.12.11"
}
},
"nbformat": 4,
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128 changes: 41 additions & 87 deletions docs/notebooks/tutorial_axes_anndata_mudata.ipynb
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20 changes: 10 additions & 10 deletions docs/notebooks/tutorial_concatenation_anndata_mudata.ipynb
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Expand Up @@ -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,
Expand Down Expand Up @@ -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"
]
}
Expand Down Expand Up @@ -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,
Expand All @@ -491,7 +491,7 @@
{
"data": {
"text/plain": [
"False"
"np.False_"
]
},
"execution_count": 17,
Expand Down Expand Up @@ -948,7 +948,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.12.5"
"version": "3.12.11"
},
"vscode": {
"interpreter": {
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3 changes: 1 addition & 2 deletions environment.yml
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Expand Up @@ -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
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2 changes: 2 additions & 0 deletions pyproject.toml
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Expand Up @@ -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
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