decoupler 2.0.1__tar.gz → 2.0.3__tar.gz

{decoupler-2.0.1 → decoupler-2.0.3}/.readthedocs.yaml

@@ -14,3 +14,4 @@ python:
       path: .
       extra_requirements:
         - doc
+        - full

{decoupler-2.0.1 → decoupler-2.0.3}/CHANGELOG.md

@@ -8,7 +8,7 @@ and this project adheres to [Semantic Versioning][].
 [keep a changelog]: https://keepachangelog.com/en/1.0.0/
 [semantic versioning]: https://semver.org/spec/v2.0.0.html
 
-## 2.0.0
+## 2.0.3
 
 Major update to accomodate the scverse template {cite}`scverse`.
 
@@ -22,6 +22,7 @@ All functions have been rewritten to follow the new API, errors when running pre
   - New argument `bsize` allows to run a method with batches in case excessive memory usage is an issue
   - $p_{values}$ of the enrichment scores are now corrected by Benjamini-Hochberg
   - `mdt` and `udt` are now based on `xgboost` instead of `sklearn` for better scalability. `udt` statistic is now the coefficient of determination $R^2$ instead of the importance of a single decision tree.
+  - `mlm` and `ulm` now include a `tval` parameter, which allows returning either the t-value of the slope or the slope itself as the enrichment statistic
   - `ora` now returns the odds ratio of the contingency table as a statistic, and computes a two-sided Fisher exact test instead of a one-sided one
   - `viper` now correctly estimates shadow regulons when network weights are values other than -1 or +1
   - `wsum` and `wmean` are deprecated, instead now the method `waggr` allows to run both methods and any custom function. This makes it easier to quickly test new enrichment methods without having to deal with `decoupler`'s implementation

{decoupler-2.0.1 → decoupler-2.0.3}/LICENSE

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2025, Pau Badia i Mompel
+Copyright (c) 2025, Pau Badia i Mompel, Saez lab
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

{decoupler-2.0.1 → decoupler-2.0.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: decoupler
-Version: 2.0.1
+Version: 2.0.3
 Summary: Python package to perform enrichment analysis from omics data.
 Project-URL: Documentation, https://decoupler.readthedocs.io/
 Project-URL: Homepage, https://github.com/PauBadiaM/decoupler
@@ -9,7 +9,7 @@ Author: Pau Badia i Mompel
 Maintainer-email: Pau Badia i Mompel <pau.badia@uni-heidelberg.de>
 License: BSD 3-Clause License
         
-        Copyright (c) 2025, Pau Badia i Mompel
+        Copyright (c) 2025, Pau Badia i Mompel, Saez lab
         All rights reserved.
         
         Redistribution and use in source and binary forms, with or without
@@ -46,14 +46,11 @@ Requires-Python: >=3.10
 Requires-Dist: adjusttext
 Requires-Dist: anndata
 Requires-Dist: docrep
-Requires-Dist: igraph
 Requires-Dist: marsilea
 Requires-Dist: numba
 Requires-Dist: requests
-Requires-Dist: seaborn
 Requires-Dist: session-info2
 Requires-Dist: tqdm
-Requires-Dist: xgboost
 Provides-Extra: dev
 Requires-Dist: pre-commit; extra == 'dev'
 Requires-Dist: twine>=4.0.2; extra == 'dev'
@@ -71,12 +68,21 @@ Requires-Dist: sphinx-tabs; extra == 'doc'
 Requires-Dist: sphinx>=4; extra == 'doc'
 Requires-Dist: sphinxcontrib-bibtex>=1; extra == 'doc'
 Requires-Dist: sphinxext-opengraph; extra == 'doc'
+Provides-Extra: full
+Requires-Dist: dcor; extra == 'full'
+Requires-Dist: igraph; extra == 'full'
+Requires-Dist: ipywidgets; extra == 'full'
+Requires-Dist: xgboost; extra == 'full'
 Provides-Extra: test
 Requires-Dist: coverage; extra == 'test'
+Requires-Dist: dcor; extra == 'test'
 Requires-Dist: gseapy; extra == 'test'
+Requires-Dist: igraph; extra == 'test'
+Requires-Dist: ipywidgets; extra == 'test'
 Requires-Dist: pytest; extra == 'test'
 Requires-Dist: scanpy; extra == 'test'
 Requires-Dist: statsmodels; extra == 'test'
+Requires-Dist: xgboost; extra == 'test'
 Description-Content-Type: text/markdown
 
 # decoupler - Ensemble of methods to infer enrichment scores
@@ -128,19 +134,25 @@ If you don't have Python installed, we recommend installing [uv][].
 
 There are several alternative options to install decoupler:
 
-1. Install the latest stable version from [PyPI][pypi]:
+1. Install the latest stable release from [PyPI][pypi] with minimal dependancies:
 
 ```bash
 pip install decoupler
 ```
 
-2. Install the latest stable version from [conda-forge][conda] using mamba or conda:
+2. Install the latest stable full release from [PyPI][pypi] with extra dependancies:
+
+```bash
+pip install decoupler[full]
+```
+
+3. Install the latest stable version from [conda-forge][conda] using mamba or conda (pay attention to the `-py` suffix at the end):
 
 ```bash
 mamba create -n=dcp conda-forge::decoupler-py
 ```
 
-3. Install the latest development version:
+4. Install the latest development version:
 
 ```bash
 pip install git+https://github.com/saezlab/decoupler-py.git@main

{decoupler-2.0.1 → decoupler-2.0.3}/README.md

@@ -47,19 +47,25 @@ If you don't have Python installed, we recommend installing [uv][].
 
 There are several alternative options to install decoupler:
 
-1. Install the latest stable version from [PyPI][pypi]:
+1. Install the latest stable release from [PyPI][pypi] with minimal dependancies:
 
 ```bash
 pip install decoupler
 ```
 
-2. Install the latest stable version from [conda-forge][conda] using mamba or conda:
+2. Install the latest stable full release from [PyPI][pypi] with extra dependancies:
+
+```bash
+pip install decoupler[full]
+```
+
+3. Install the latest stable version from [conda-forge][conda] using mamba or conda (pay attention to the `-py` suffix at the end):
 
 ```bash
 mamba create -n=dcp conda-forge::decoupler-py
 ```
 
-3. Install the latest development version:
+4. Install the latest development version:
 
 ```bash
 pip install git+https://github.com/saezlab/decoupler-py.git@main

{decoupler-2.0.1 → decoupler-2.0.3}/docs/api/mt.md

@@ -16,7 +16,6 @@
     mt.mlm
     mt.ora
     mt.udt
-    mt.udt
     mt.ulm
     mt.viper
     mt.waggr

{decoupler-2.0.1 → decoupler-2.0.3}/docs/conf.py

@@ -114,9 +114,9 @@ exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "**.ipynb_checkpoints"]
 html_theme = "sphinx_book_theme"
 html_static_path = ["_static"]
 html_css_files = ["css/custom.css"]
+html_title = project_name
 html_logo = '_static/images/logo.png'
 html_favicon = '_static/images/logo.png'
-#html_title = project_name
 
 html_theme_options = {
     "repository_url": repository_url,