theislab · pre-commit-ci · Dec 15, 2025 · Dec 15, 2025
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -11,19 +11,19 @@ repos:
     hooks:
       - id: prettier
   - repo: https://github.com/tox-dev/pyproject-fmt
-    rev: v2.5.0
+    rev: v2.11.1
     hooks:
       - id: pyproject-fmt
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.2
+    rev: v0.14.9
     hooks:
       - id: ruff
         types_or: [python, pyi, jupyter]
         args: [--fix, --exit-non-zero-on-fix]
       - id: ruff-format
         types_or: [python, pyi, jupyter]
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       - id: detect-private-key
       - id: check-ast

diff --git a/README.md b/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

diff --git a/docs/.ipynb_checkpoints/index-checkpoint.md b/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
 
-```
+```
diff --git a/docs/.ipynb_checkpoints/references-checkpoint.bib b/docs/.ipynb_checkpoints/references-checkpoint.bib
@@ -38,4 +38,4 @@ @article{blampey2024sopa
   pages={4981},
   year={2024},
   publisher={Nature Publishing Group UK London}
-}
+}
diff --git a/docs/api/.ipynb_checkpoints/plotting-checkpoint.md b/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
 ```
-
-
-
diff --git a/docs/api/.ipynb_checkpoints/preprocessing-checkpoint.md b/docs/api/.ipynb_checkpoints/preprocessing-checkpoint.md
@@ -15,3 +15,4 @@
     pp.define_urna
     pp.filter_urna
     pp.format_adata
+```
diff --git a/docs/api/.ipynb_checkpoints/tools-checkpoint.md b/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
 ```
-
diff --git a/docs/api/plotting.md b/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
 ```
-
-
-
diff --git a/docs/api/preprocessing.md b/docs/api/preprocessing.md
@@ -15,3 +15,4 @@
     pp.define_urna
     pp.filter_urna
     pp.format_adata
+```
diff --git a/docs/api/tools.md b/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
 ```
-
diff --git a/docs/index.md b/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
 
-```
+```
diff --git a/docs/references.bib b/docs/references.bib
@@ -38,4 +38,4 @@ @article{blampey2024sopa
   pages={4981},
   year={2024},
   publisher={Nature Publishing Group UK London}
-}
+}
diff --git a/pyproject.toml b/pyproject.toml
@@ -21,6 +21,7 @@ classifiers = [
   "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
   "Programming Language :: Python :: 3.13",
+  "Programming Language :: Python :: 3.14",
 ]
 
 dependencies = [
@@ -34,7 +35,7 @@ dependencies = [
   "sainsc",                # Version not specified; verify if necessary
   "scikit-learn>=1.6.1",
   "seaborn",
-  "sopa[cellpose,baysor]",
+  "sopa[baysor,cellpose]",
   "spatialdata",
   "spatialdata-io",
   "spatialdata-plot",

diff --git a/src/troutpy/pl/__init__.py b/src/troutpy/pl/__init__.py
@@ -1,6 +1,6 @@
 from .basic import crosstab, histogram, pie
 from .colors import get_colormap, get_palette
-from .communication import  cell_type_contacts, gene_communication, target_score_by_celltype
+from .communication import cell_type_contacts, gene_communication, target_score_by_celltype
 from .factor_analysis import factors_in_cells, rank_factor_genes_loadings, rank_factor_genes_loadings_matrixplot
 from .metric_analysis import gene_metric_heatmap, logfoldratio_over_noise, metric_scatter, top_bottom_probes
 from .plotting import (