[pre-commit.ci] auto fixes from pre-commit.com hooks

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Author: pre-commit-ci[bot]

README.md

@@ -22,7 +22,7 @@ If you don't have Python installed, we recommend installing [Mambaforge][].
 
 There are several alternative options to install troutpy:
 
-1) Install the latest release of `troutpy` from [PyPI][]:
+1. Install the latest release of `troutpy` from [PyPI][]:
 
 ```bash
 pip install troutpy
@@ -43,6 +43,7 @@ import troutpy as tp
 ```
 
 ## Reproducibility
+
 Code, notebooks, and instructions to reproduce the results from the paper are available at the [reproducibility repository](https://github.com/theislab/troutpy_reproducibility). This repository also include diverse tutorials and compementary functions that are not core to Troutpy, but are required to reproduce the figures from Marco Salas et al. 2025.
 
 ## Release notes

docs/.ipynb_checkpoints/index-checkpoint.md

@@ -11,6 +11,7 @@ Tools <api/tools.md>
 Plotting  <api/plotting.md>
 
 ```
+
 ```{toctree}
 :maxdepth: 3
 :caption: Tutorials
@@ -26,4 +27,4 @@ changelog.md
 contributing.md
 references.md
 
-```
+```

docs/.ipynb_checkpoints/references-checkpoint.bib

@@ -38,4 +38,4 @@ @article{blampey2024sopa
   pages={4981},
   year={2024},
   publisher={Nature Publishing Group UK London}
-}
+}

docs/api/.ipynb_checkpoints/plotting-checkpoint.md

@@ -8,7 +8,7 @@
 
 .. autosummary::
     :toctree: generated/basic_plots
-    
+
     crosstab
     histogram
     pie
@@ -23,7 +23,7 @@
 ```{eval-rst}
 .. autosummary::
     :toctree: generated/quantification
-    
+
     gene_metric_heatmap
     logfoldratio_over_noise
     metric_scatter
@@ -33,18 +33,15 @@
     moranI_histogram
     diffusion_results
     spatial_inout_expression
-    
-```
-
-
 
+```
 
 ## Source, target and communication
 
 ```{eval-rst}
 .. autosummary::
     :toctree: generated/communication
-    
+
     celltype_communication
     gene_communication
     global_distribution_from_source
@@ -54,25 +51,24 @@
     target_score_by_celltype
     interactions_with_arrows
     spatial_interactions
-    
+
 ```
 
 ## Factor analysis
 
 ```{eval-rst}
 .. autosummary::
     :toctree: generated/factor_analysis
-    
+
     factors_in_cells
     rank_factor_genes_loadings
     rank_factor_genes_loadings_matrixplot
     nmf_factors_exrna_cells_W
     nmf_gene_contributions
     paired_nmf_factors
     apply_exrnaH_to_cellular_to_create_cellularW
- 
-```
 
+```
 
 ## Colormaps & palettes
 
@@ -83,6 +79,3 @@
     get_colormap
     get_palette
 ```
-
-
-

docs/api/.ipynb_checkpoints/preprocessing-checkpoint.md

@@ -15,3 +15,4 @@
     pp.define_urna
     pp.filter_urna
     pp.format_adata
+```

docs/api/.ipynb_checkpoints/tools-checkpoint.md

@@ -35,7 +35,7 @@
     tl.calculate_target_cells
     tl.compute_target_score
     tl.define_target_by_celltype
-    tl.cluster_distribution_from_source 
+    tl.cluster_distribution_from_source
     tl.get_gene_interaction_strength
     tl.communication_strength
     tl.gene_specific_interactions
@@ -46,7 +46,7 @@
 ```{eval-rst}
 .. autosummary::
     :toctree: generated/cell_scores
-    
+
     tl.compute_contribution_score
 ```
 
@@ -55,7 +55,7 @@
 ```{eval-rst}
 .. autosummary::
     :toctree: generated/factors
-    
+
     tl.factors_to_cells
     tl.latent_factor
 ```
@@ -68,15 +68,14 @@
 
     tl.assess_diffusion
     tl.compute_js_divergence
-    
+
 ```
 
 ## Multimodal quantication
 
 ```{eval-rst}
 .. autosummary::
     :toctree: generated/multimodal
-    
+
     tl.image_intensities_per_transcript
 ```
-

docs/api/plotting.md

@@ -8,7 +8,7 @@
 
 .. autosummary::
     :toctree: generated/basic_plots
-    
+
     crosstab
     histogram
     pie
@@ -23,7 +23,7 @@
 ```{eval-rst}
 .. autosummary::
     :toctree: generated/quantification
-    
+
     gene_metric_heatmap
     logfoldratio_over_noise
     metric_scatter
@@ -33,18 +33,15 @@
     moranI_histogram
     diffusion_results
     spatial_inout_expression
-    
-```
-
-
 
+```
 
 ## Source, target and communication
 
 ```{eval-rst}
 .. autosummary::
     :toctree: generated/communication
-    
+
     celltype_communication
     gene_communication
     global_distribution_from_source
@@ -54,25 +51,24 @@
     target_score_by_celltype
     interactions_with_arrows
     spatial_interactions
-    
+
 ```
 
 ## Factor analysis
 
 ```{eval-rst}
 .. autosummary::
     :toctree: generated/factor_analysis
-    
+
     factors_in_cells
     rank_factor_genes_loadings
     rank_factor_genes_loadings_matrixplot
     nmf_factors_exrna_cells_W
     nmf_gene_contributions
     paired_nmf_factors
     apply_exrnaH_to_cellular_to_create_cellularW
- 
-```
 
+```
 
 ## Colormaps & palettes
 
@@ -83,6 +79,3 @@
     get_colormap
     get_palette
 ```
-
-
-

docs/api/preprocessing.md

@@ -15,3 +15,4 @@
     pp.define_urna
     pp.filter_urna
     pp.format_adata
+```

docs/api/tools.md

@@ -35,7 +35,7 @@
     tl.calculate_target_cells
     tl.compute_target_score
     tl.define_target_by_celltype
-    tl.cluster_distribution_from_source 
+    tl.cluster_distribution_from_source
     tl.get_gene_interaction_strength
     tl.communication_strength
     tl.gene_specific_interactions
@@ -46,7 +46,7 @@
 ```{eval-rst}
 .. autosummary::
     :toctree: generated/cell_scores
-    
+
     tl.compute_contribution_score
 ```
 
@@ -55,7 +55,7 @@
 ```{eval-rst}
 .. autosummary::
     :toctree: generated/factors
-    
+
     tl.factors_to_cells
     tl.latent_factor
 ```
@@ -68,15 +68,14 @@
 
     tl.assess_diffusion
     tl.compute_js_divergence
-    
+
 ```
 
 ## Multimodal quantication
 
 ```{eval-rst}
 .. autosummary::
     :toctree: generated/multimodal
-    
+
     tl.image_intensities_per_transcript
 ```
-

docs/index.md

@@ -11,6 +11,7 @@ Tools <api/tools.md>
 Plotting  <api/plotting.md>
 
 ```
+
 ```{toctree}
 :maxdepth: 3
 :caption: Tutorials
@@ -26,4 +27,4 @@ changelog.md
 contributing.md
 references.md
 
-```
+```