Merge pull request #194 from scverse/fix/ci

Faster RTD & fix CI

Author: Zethson

.readthedocs.yaml

@@ -1,17 +1,18 @@
-# https://docs.readthedocs.io/en/stable/config-file/v2.html
 version: 2
 build:
-  os: ubuntu-20.04
+  os: ubuntu-24.04
   tools:
-    python: "3.10"
-sphinx:
-  configuration: docs/conf.py
-  # disable this for more lenient docs builds
-  fail_on_warning: true
-python:
-  install:
-    - method: pip
-      path: .
-      extra_requirements:
-        - doc
-        - full
+    python: "3.13"
+  jobs:
+    create_environment:
+      - asdf plugin add uv
+      - asdf install uv latest
+      - asdf global uv latest
+      - uv venv
+      - uv pip install .[doc,full]
+    build:
+      html:
+        - uv run sphinx-build -T -W -b html docs $READTHEDOCS_OUTPUT/html
+
+submodules:
+    include: all

CHANGELOG.md

@@ -27,7 +27,7 @@ All functions have been rewritten to follow the new API, errors when running pre
   - `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
 - Databases from Omnipath can now be accessed through the new `op` module
-  - Use `decoupler.op.<resource_name>` to access a database  
+  - Use `decoupler.op.<resource_name>` to access a database
   - Removed the `omnipath` package as a dependancy
   - Fixed `collectri` to the publication version instead of the OmniPath one
   - Made `progeny` only return significant genes by default instead of the top N genes per pathway
@@ -63,7 +63,7 @@ All functions have been rewritten to follow the new API, errors when running pre
   - Added `obsbar` to plot size of metadata columns in `anndata.AnnData.obs`
   - Added `order` to plot sources or features along a continous process such as a trajectory
   - Added `order_targets` to plot the targets of a given source along a continous process
-  - 
+  -
 - New preprocessing functions in the `pp` module
   - Added two functions to format networks, `adjmat` to return an adjacency matrix, and `idxmax` to return a list of sets
   - Added `filter_samples` to filter pseudobulk profiles after running `pseudobulk`

README.md

@@ -1,6 +1,6 @@
 # decoupler - Ensemble of methods to infer enrichment scores
 <img src="https://github.com/saezlab/decoupleR/blob/master/inst/figures/logo.svg?raw=1" align="right" width="120" class="no-scaled-link" />
-   
+
 
 [![Tests][badge-tests]][tests]
 [![Documentation][badge-docs]][documentation]

docs/_static/css/custom.css

@@ -5,10 +5,10 @@ div.cell_output table.dataframe {
 
 /* Adjust the logo size */
 .logo img {
-    width: 50%;   /* or any percentage you want */
+    width: 50%; /* or any percentage you want */
     height: auto; /* maintain aspect ratio */
 }
 
 img.no-scaled-link {
     background: transparent !important;
-}
+}

docs/api/index.md

@@ -21,4 +21,4 @@ pp
 
 pl
 tl
-```
+```

docs/api/mt.md

@@ -30,4 +30,4 @@
 
     mt.decouple
     mt.consensus
-```
+```

docs/api/op.md

@@ -25,4 +25,4 @@
     op.show_resources
     op.show_organisms
     op.translate
-```
+```

docs/api/pl.md

@@ -20,4 +20,4 @@
     pl.order
     pl.source_targets
     pl.volcano
-```
+```

docs/references.bib

@@ -35,7 +35,7 @@ @article{pydeseq
   author = {Muzellec,  Boris and Teleńczuk,  Maria and Cabeli,  Vincent and Andreux,  Mathieu},
   editor = {Ponty,  Yann},
   year = {2023},
-  month = sep 
+  month = sep
 }
 
 @article{limma,
@@ -80,7 +80,7 @@ @article{decoupler
   author = {Badia-i-Mompel,  Pau and Vélez Santiago,  Jesús and Braunger,  Jana and Geiss,  Celina and Dimitrov,  Daniel and M\"{u}ller-Dott,  Sophia and Taus,  Petr and Dugourd,  Aurelien and Holland,  Christian H and Ramirez Flores,  Ricardo O and Saez-Rodriguez,  Julio},
   editor = {Kuijjer,  Marieke Lydia},
   year = {2022},
-  month = jan 
+  month = jan
 }
 
 @article{grn_review,
@@ -210,7 +210,7 @@ @article{panglaodb
   publisher = {Oxford University Press (OUP)},
   author = {Franzén,  Oscar and Gan,  Li-Ming and Bj\"{o}rkegren,  Johan L M},
   year = {2019},
-  month = jan 
+  month = jan
 }
 
 @article{msvisium,
@@ -254,7 +254,7 @@ @article{hcop
   publisher = {Oxford University Press (OUP)},
   author = {Yates,  Bethan and Gray,  Kristian A and Jones,  Tamsin E M and Bruford,  Elspeth A},
   year = {2021},
-  month = may 
+  month = may
 }
 
 @article{omnipath,
@@ -325,7 +325,7 @@ @article{mofacell
   publisher = {eLife Sciences Publications,  Ltd},
   author = {Ramirez Flores,  Ricardo Omar and Lanzer,  Jan David and Dimitrov,  Daniel and Velten,  Britta and Saez-Rodriguez,  Julio},
   year = {2023},
-  month = nov 
+  month = nov
 }
 
 @article{scanpy,
@@ -339,7 +339,7 @@ @article{scanpy
   publisher = {Springer Science and Business Media LLC},
   author = {Wolf,  F. Alexander and Angerer,  Philipp and Theis,  Fabian J.},
   year = {2018},
-  month = feb 
+  month = feb
 }
 
 @article{paga,
@@ -353,7 +353,7 @@ @article{paga
   publisher = {Springer Science and Business Media LLC},
   author = {Wolf,  F. Alexander and Hamey,  Fiona K. and Plass,  Mireya and Solana,  Jordi and Dahlin,  Joakim S. and G\"{o}ttgens,  Berthold and Rajewsky,  Nikolaus and Simon,  Lukas and Theis,  Fabian J.},
   year = {2019},
-  month = mar 
+  month = mar
 }
 
 @article{pax5,
@@ -412,7 +412,7 @@ @article{gsva
   publisher = {Springer Science and Business Media LLC},
   author = {H\"{a}nzelmann,  Sonja and Castelo,  Robert and Guinney,  Justin},
   year = {2013},
-  month = jan 
+  month = jan
 }
 
 @inproceedings{xgboost,
@@ -470,5 +470,5 @@ @article{zscore
   publisher = {Springer Science and Business Media LLC},
   author = {Yılmaz,  Serhan and Ayati,  Marzieh and Schlatzer,  Daniela and undefinedi\c{c}ek,  A. Erc\"{u}ment and Chance,  Mark R. and Koyut\"{u}rk,  Mehmet},
   year = {2021},
-  month = feb 
+  month = feb
 }

pyproject.toml

@@ -23,21 +23,16 @@ classifiers = [
   "Programming Language :: Python :: 3.13",
 ]
 dependencies = [
+  "adjusttext",
   "anndata",
-  "numba",
   "docrep",
-  "tqdm",
-  "requests",
   "marsilea",
-  "adjustText",
+  "numba",
+  "requests",
+  "scipy<1.16", # https://github.com/statsmodels/statsmodels/issues/9584
   # for debug logging (referenced from the issue template)
   "session-info2",
-]
-optional-dependencies.full = [
-  "igraph",
-  "xgboost",
-  "ipywidgets",
-  "dcor",
+  "tqdm",
 ]
 optional-dependencies.dev = [
   "pre-commit",
@@ -59,16 +54,22 @@ optional-dependencies.doc = [
   "sphinxcontrib-bibtex>=1",
   "sphinxext-opengraph",
 ]
+optional-dependencies.full = [
+  "dcor",
+  "igraph",
+  "ipywidgets",
+  "xgboost",
+]
 optional-dependencies.test = [
   "coverage",
-  "pytest",
-  "statsmodels",
+  "dcor",
   "gseapy",
-  "scanpy",
   "igraph",
-  "xgboost",
   "ipywidgets",
-  "dcor"
+  "pytest",
+  "scanpy",
+  "statsmodels",
+  "xgboost",
 ]
 # https://docs.pypi.org/project_metadata/#project-urls
 urls.Documentation = "https://decoupler.readthedocs.io/"