decoupler 2.1.6__tar.gz → 2.3.0__tar.gz

{decoupler-2.1.6 → decoupler-2.3.0}/.cruft.json

@@ -1,7 +1,7 @@
 {
   "template": "https://github.com/scverse/cookiecutter-scverse",
-  "commit": "6ff5b92b5d44ea6d8a88e47538475718d467db95",
-  "checkout": "v0.7.0",
+  "commit": "6518dfa1abde7379ea7255daf0ce09c23f2b4c94",
+  "checkout": "v0.8.0",
   "context": {
     "cookiecutter": {
       "project_name": "decoupler",
@@ -13,6 +13,7 @@
       "github_repo": "decoupler",
       "license": "BSD 3-Clause License",
       "ide_integration": true,
+      "issue_categorization": "",
       "_copy_without_render": [
         ".github/workflows/build.yaml",
         ".github/workflows/test.yaml",
@@ -36,8 +37,10 @@
         "trim_blocks": true
       },
       "_template": "https://github.com/scverse/cookiecutter-scverse",
-      "_commit": "d383d94fadff9e4e6fdb59d77c68cb900d7cedec"
-    }
+      "_commit": "4d6aa34fd5be7523ca3bd49fbd81a882dde01d1f"
+    },
+    "_commit": "6518dfa1abde7379ea7255daf0ce09c23f2b4c94",
+    "_template": "https://github.com/scverse/cookiecutter-scverse"
   },
   "directory": null
 }

{decoupler-2.1.6 → decoupler-2.3.0}/.github/ISSUE_TEMPLATE/bug_report.yml

@@ -9,8 +9,7 @@ body:
         detailing how to provide the necessary information for us to reproduce your bug. In brief:
           * Please provide exact steps how to reproduce the bug in a clean Python environment.
           * In case it's not clear what's causing this bug, please provide the data or the data generation procedure.
-          * Sometimes it is not possible to share the data, but usually it is possible to replicate problems on publicly
-            available datasets or to share a subset of your data.
+          * Replicate problems on public datasets or share data subsets when full sharing isn't possible.
 
   - type: textarea
     id: report

decoupler-2.3.0/.github/dependabot.yml

@@ -0,0 +1,12 @@
+version: 2
+updates:
+  - package-ecosystem: github-actions
+    directory: /
+    schedule:
+      interval: weekly
+    cooldown:
+      default-days: 7
+    groups:
+      actions-deps:
+        patterns:
+          - "*"

{decoupler-2.1.6 → decoupler-2.3.0}/.github/workflows/build.yaml

@@ -10,16 +10,20 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
+permissions:
+  contents: read
+
 jobs:
   package:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
         with:
           filter: blob:none
           fetch-depth: 0
+          persist-credentials: false
       - name: Install uv
-        uses: astral-sh/setup-uv@v7
+        uses: astral-sh/setup-uv@1c37ad07a6a961277cf70c0d37d6f313000f5884 # v10.3.0
       - name: Build package
         run: uv build
       - name: Check package

{decoupler-2.1.6 → decoupler-2.3.0}/.github/workflows/notebooks.yaml

@@ -10,6 +10,9 @@ concurrency:
     group: ${{ github.workflow }}-${{ github.ref }}
     cancel-in-progress: true
 
+permissions:
+    contents: read
+
 jobs:
     test:
         runs-on: ubuntu-latest
@@ -37,17 +40,18 @@ jobs:
                     ]
 
         steps:
-            - uses: actions/checkout@v5
+            - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
               with:
                 filter: blob:none
                 fetch-depth: 0
                 submodules: "true"
+                persist-credentials: false
             - name: Set up Python
-              uses: actions/setup-python@v5
+              uses: actions/setup-python@6d4fd22b20465ccc0f7354476588e8df7c9ca0e0 # v7.1.0
               with:
                   python-version: "3.13"
             - name: Install uv
-              uses: astral-sh/setup-uv@v7
+              uses: astral-sh/setup-uv@1c37ad07a6a961277cf70c0d37d6f313000f5884 # v10.3.0
             - name: Install dependencies
               run: |
                   uv pip install --system .

{decoupler-2.1.6 → decoupler-2.3.0}/.github/workflows/release.yaml

@@ -5,6 +5,8 @@ on:
     types: [published]
 
 # Use "trusted publishing", see https://docs.pypi.org/trusted-publishers/
+permissions: {}
+
 jobs:
   release:
     name: Upload release to PyPI
@@ -13,15 +15,19 @@ jobs:
       name: pypi
       url: https://pypi.org/p/decoupler
     permissions:
+      contents: read
       id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
         with:
           filter: blob:none
           fetch-depth: 0
+          persist-credentials: false
       - name: Install uv
-        uses: astral-sh/setup-uv@v7
+        uses: astral-sh/setup-uv@1c37ad07a6a961277cf70c0d37d6f313000f5884 # v10.3.0
+        with:
+          enable-cache: false
       - name: Build package
         run: uv build
       - name: Publish package distributions to PyPI
-        uses: pypa/gh-action-pypi-publish@release/v1
+        uses: pypa/gh-action-pypi-publish@dc37677b2e1c63e2034f94d8a5b11f265b73ba33 # v1.14.2

{decoupler-2.1.6 → decoupler-2.3.0}/.github/workflows/test.yaml

@@ -13,7 +13,7 @@ concurrency:
   cancel-in-progress: true
 
 permissions:
-  id-token: write
+  contents: read
 
 jobs:
   # Get the test environment from hatch as defined in pyproject.toml.
@@ -22,17 +22,18 @@ jobs:
   # Check [[tool.hatch.envs.hatch-test.matrix]] in pyproject.toml and https://hatch.pypa.io/latest/environment/ for
   # more details.
   get-environments:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-slim
     outputs:
       envs: ${{ steps.get-envs.outputs.envs }}
       allowed-failures: ${{ steps.get-envs.outputs.allowed-failures }}
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
         with:
           filter: blob:none
           fetch-depth: 0
+          persist-credentials: false
       - name: Install uv
-        uses: astral-sh/setup-uv@v7
+        uses: astral-sh/setup-uv@1c37ad07a6a961277cf70c0d37d6f313000f5884 # v10.3.0
       - name: Get test environments
         id: get-envs
         run: |
@@ -52,6 +53,9 @@ jobs:
   # Run tests through hatch. Spawns a separate runner for each environment defined in the hatch matrix obtained above.
   test:
     needs: get-environments
+    permissions:
+       id-token: write  # for codecov OIDC
+       contents: read
 
     strategy:
       fail-fast: false
@@ -61,19 +65,22 @@ jobs:
 
     name: ${{ matrix.env.label }}
     runs-on: ${{ matrix.os }}
-    continue-on-error: ${{ contains(matrix.env.name, 'pre') }}
+    continue-on-error: ${{ contains(matrix.env.name, 'pre') }}  # make "all-green" pass even if pre-release job fails
 
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
         with:
           filter: blob:none
           fetch-depth: 0
+          persist-credentials: false
       - name: Install uv
-        uses: astral-sh/setup-uv@v7
+        uses: astral-sh/setup-uv@1c37ad07a6a961277cf70c0d37d6f313000f5884 # v10.3.0
         with:
           python-version: ${{ matrix.env.python }}
       - name: create hatch environment
         run: uvx hatch env create ${{ matrix.env.name }}
+      - name: list all all installed package versions
+        run: uvx hatch run ${{ matrix.env.name }}:uv pip list
       - name: run tests using hatch
         env:
           MPLBACKEND: agg
@@ -82,12 +89,12 @@ jobs:
         run: uvx hatch run ${{ matrix.env.name }}:run-cov -v --color=yes -n auto
       - name: generate coverage report
         run: |
-          # See https://coverage.readthedocs.io/en/latest/config.html#run-patch
+          # See https://coverage.readthedocs.io/page/config.html#run-patch
           test -f .coverage || uvx hatch run ${{ matrix.env.name }}:cov-combine
           uvx hatch run ${{ matrix.env.name }}:cov-report   # report visibly
           uvx hatch run ${{ matrix.env.name }}:coverage xml # create report for upload
       - name: Upload coverage
-        uses: codecov/codecov-action@v5
+        uses: codecov/codecov-action@303a32d7a59b442fa8d48b6a1cc6825c09c847a5 # v7.1.1
         with:
           fail_ci_if_error: true
           use_oidc: true
@@ -102,7 +109,7 @@ jobs:
       - test
     runs-on: ubuntu-latest
     steps:
-        - uses: re-actors/alls-green@release/v1
+        - uses: re-actors/alls-green@b5b5b37504aa4183270bd3d855c52a67f212be35 # v1.3.0
           with:
             allowed-failures: ${{ needs.get-environments.outputs.allowed-failures }}
             jobs: ${{ toJSON(needs) }}

{decoupler-2.1.6 → decoupler-2.3.0}/.pre-commit-config.yaml

@@ -7,16 +7,16 @@ default_stages:
 minimum_pre_commit_version: 2.16.0
 repos:
   - repo: https://github.com/biomejs/pre-commit
-    rev: v2.4.10
+    rev: v2.5.15
     hooks:
       - id: biome-format
         exclude: ^\.cruft\.json$ # inconsistent indentation with cruft - file never to be modified manually.
   - repo: https://github.com/tox-dev/pyproject-fmt
-    rev: v2.21.0
+    rev: v2.30.3
     hooks:
       - id: pyproject-fmt
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.15.9
+    rev: v0.17.1
     hooks:
       - id: ruff-check
         types_or: [python, pyi, jupyter]
@@ -36,3 +36,9 @@ repos:
       # Check that there are no merge conflicts (could be generated by template sync)
       - id: check-merge-conflict
         args: [--assume-in-merge]
+
+  - repo: https://github.com/zizmorcore/zizmor-pre-commit
+    rev: v1.24.1
+    hooks:
+      - id: zizmor
+        args: [--no-progress, --fix]

{decoupler-2.1.6 → decoupler-2.3.0}/.readthedocs.yaml

@@ -1,9 +1,9 @@
-# https://docs.readthedocs.io/en/stable/config-file/v2.html
+# https://docs.readthedocs.io/page/config-file/v2.html
 version: 2
 build:
   os: ubuntu-24.04
   tools:
-    python: "3.13"
+    python: "3.14"
     nodejs: latest
   jobs:
     create_environment:

{decoupler-2.1.6 → decoupler-2.3.0}/CHANGELOG.md

@@ -8,6 +8,31 @@ 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
 
+## 2.3.0
+
+### Changes
+- Updated the bundled decoupler Agent Skill, and `decoupler-install-skills` now supports multiple agent frameworks
+- `pp.filter_by_prop` now defaults to `min_prop=0.1` (was `0.2`) to match the value used in the vignettes
+- `ds.msvisium` now returns log-normalized data (`sc.pp.normalize_total` + `sc.pp.log1p`), with the log-normalized matrix also stored in `adata.layers["norm"]`, instead of raw counts
+- Dropped support for Python 3.11; decoupler now requires Python 3.12 or newer
+- Updated to the scverse cookiecutter template v0.8.0 (hash-pinned GitHub Actions checked by zizmor, `prek` instead of `pre-commit`, `sphinx-design` instead of `sphinx-tabs`, shared Sphinx extensions from `scverse-misc`)
+
+### Bugfixes
+- Fixed `mt.ora` selecting the bottom `nvar - n_up` features instead of the top `n_up` ones. Ranks are ascending, so the threshold is now `nvar - n_up`, restoring the behaviour of `decoupler<2`. With the default `n_up` (top 5%) this selected 95% of the features as observed, which also made `mt.ora` fail with `invalid contingency table` whenever `nvar - n_up` exceeded `n_bg` (#346)
+- Fixed `n_bm` in `mt.ora` selecting the bottom `n_bm - 1` features instead of `n_bm`
+- `mt.ora` now validates that `n_up` and `n_bm` do not overlap and that `n_bg` is large enough for the number of selected features, instead of failing inside the Fisher exact test
+- `mt.query_set` now raises an informative error when `n_bg` is smaller than the number of features to test, instead of failing inside `scipy.stats.fisher_exact`
+- Fixed `mt.gsea` not shuffling the permutation indices when `seed=0`, which produced identical permutations and invalid p-values (#355)
+- Fixed `mt.waggr` folding its already two-sided permutation p-values as one-sided, which gave scores near 0 the smallest p-value (#373)
+- Fixed `pl.dotplot` showing an empty size legend when all dots have the same size (#370)
+- Fixed `ds.msvisium` failing with HTTP 403 by fetching the spot metadata from `cells.ucsc.edu` instead of the `cells-test.gi.ucsc.edu` mirror
+
+## 2.2.0
+
+### Added
+- Bundled a Claude Code [Agent Skill](https://docs.claude.com/en/docs/claude-code/skills) that teaches coding agents to use decoupler correctly (method selection, calling conventions, output locations, priors, datasets, and benchmarking)
+- Added the `decoupler-install-skills` console script to install the skill into `~/.claude/skills/decoupler/` (use `--force` to refresh after upgrading, or `--print-path` to point `CLAUDE_SKILLS_PATH` at the bundled copy in place)
+
 ## 2.1.6
 
 ### Bugfixes

{decoupler-2.1.6 → decoupler-2.3.0}/PKG-INFO

@@ -1,8 +1,8 @@
-Metadata-Version: 2.4
+Metadata-Version: 2.5
 Name: decoupler
-Version: 2.1.6
+Version: 2.3.0
 Summary: Python package to perform enrichment analysis from omics data.
-Project-URL: Documentation, https://decoupler.readthedocs.io/
+Project-URL: Documentation, https://decoupler.scverse.org/
 Project-URL: Homepage, https://github.com/scverse/decoupler
 Project-URL: Source, https://github.com/scverse/decoupler
 Author: Pau Badia i Mompel
@@ -39,11 +39,11 @@ License: BSD 3-Clause License
         OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 License-File: LICENSE
 Classifier: Programming Language :: Python :: 3 :: Only
-Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
 Classifier: Programming Language :: Python :: 3.14
-Requires-Python: >=3.11
+Classifier: Programming Language :: Python :: 3.15
+Requires-Python: >=3.12
 Requires-Dist: adjusttext
 Requires-Dist: anndata
 Requires-Dist: docrep
@@ -83,10 +83,8 @@ Description-Content-Type: text/markdown
 [badge-adown]: https://static.pepy.tech/badge/decoupler
 [badge-stars]: https://img.shields.io/github/stars/scverse/decoupler?style=flat&logo=github&color=yellow
 
-`decoupler` is a python package containing different enrichment statistical
-methods to extract biologically driven scores
-from omics data within a unified framework. This is its faster and memory efficient Python implementation,
-a deprecated version in R can be found [here](https://github.com/saezlab/decoupler).
+`decoupler` is a python package containing different enrichment statistical methods to extract biologically driven scores from omics data within a unified framework.
+This is its faster and memory efficient Python implementation, a deprecated version in R can be found [here](https://github.com/saezlab/decoupler).
 
 [//]: # (numfocus-fiscal-sponsor-attribution)
 
@@ -109,7 +107,7 @@ in particular, the [API documentation][].
 
 ## Installation
 
-You need to have Python 3.10 or newer installed on your system.
+You need to have Python 3.12 or newer installed on your system.
 If you don't have Python installed, we recommend installing [uv][].
 
 There are several alternative options to install decoupler:
@@ -138,6 +136,16 @@ mamba create -n=dcp conda-forge::decoupler-py
 pip install git+https://github.com/scverse/decoupler.git@main
 ```
 
+## Agent Skill
+
+decoupler ships an [Agent Skill](https://docs.claude.com/en/docs/claude-code/skills) that teaches coding agents to use the library correctly. Install it into your agent's skills directory by choosing a framework with `--agent {claude,codex,agents,claude-science}` (or an explicit directory with `--dest`):
+
+```bash
+decoupler-install-skills --agent claude
+```
+
+Re-run with `--force` after upgrading, use `--check` to see whether an installed copy is up to date, or `--print-path` to show where the bundled copy lives inside the package.
+
 ## Release notes
 
 See the [changelog][].
@@ -147,6 +155,13 @@ See the [changelog][].
 For questions and help requests, you can reach out in the [scverse discourse][].
 If you found a bug, please use the [issue tracker][].
 
+## License
+Enrichment methods inside decoupler can be used for academic or commercial purposes, except `viper` which holds a non-commercial license.
+
+The data redistributed by OmniPath does not have a single license, each original resource has its own. By default, `decoupler`
+assumes an academic license, but commercial or nonprofit licenses can be specified in the `license` parameter of `decoupler`'s OmniPath functions.
+[Here](https://omnipathdb.org/info) one can find the license information of all the resources in OmniPath.
+
 ## Citation
 
 > Badia-i-Mompel P., Vélez Santiago J., Braunger J., Geiss C., Dimitrov D.,
@@ -160,9 +175,9 @@ to infer biological activities from omics data. Bioinformatics Advances.
 [scverse]: https://scverse.org/
 [issue tracker]: https://github.com/scverse/decoupler/issues
 [tests]: https://github.com/scverse/decoupler/actions/workflows/test.yaml
-[documentation]: https://decoupler.readthedocs.io
-[changelog]: https://decoupler.readthedocs.io/en/latest/changelog.html
-[api documentation]: https://decoupler.readthedocs.io/en/latest/api.html
+[documentation]: https://decoupler.scverse.org/
+[changelog]: https://decoupler.scverse.org/page/changelog.html
+[api documentation]: https://decoupler.scverse.org/page/api.html
 [pypi]: https://pypi.org/project/decoupler
 [down]: https://pepy.tech/project/decoupler
 [conda]: https://anaconda.org/conda-forge/decoupler-py

{decoupler-2.1.6 → decoupler-2.3.0}/README.md

@@ -26,10 +26,8 @@
 [badge-adown]: https://static.pepy.tech/badge/decoupler
 [badge-stars]: https://img.shields.io/github/stars/scverse/decoupler?style=flat&logo=github&color=yellow
 
-`decoupler` is a python package containing different enrichment statistical
-methods to extract biologically driven scores
-from omics data within a unified framework. This is its faster and memory efficient Python implementation,
-a deprecated version in R can be found [here](https://github.com/saezlab/decoupler).
+`decoupler` is a python package containing different enrichment statistical methods to extract biologically driven scores from omics data within a unified framework.
+This is its faster and memory efficient Python implementation, a deprecated version in R can be found [here](https://github.com/saezlab/decoupler).
 
 [//]: # (numfocus-fiscal-sponsor-attribution)
 
@@ -52,7 +50,7 @@ in particular, the [API documentation][].
 
 ## Installation
 
-You need to have Python 3.10 or newer installed on your system.
+You need to have Python 3.12 or newer installed on your system.
 If you don't have Python installed, we recommend installing [uv][].
 
 There are several alternative options to install decoupler:
@@ -81,6 +79,16 @@ mamba create -n=dcp conda-forge::decoupler-py
 pip install git+https://github.com/scverse/decoupler.git@main
 ```
 
+## Agent Skill
+
+decoupler ships an [Agent Skill](https://docs.claude.com/en/docs/claude-code/skills) that teaches coding agents to use the library correctly. Install it into your agent's skills directory by choosing a framework with `--agent {claude,codex,agents,claude-science}` (or an explicit directory with `--dest`):
+
+```bash
+decoupler-install-skills --agent claude
+```
+
+Re-run with `--force` after upgrading, use `--check` to see whether an installed copy is up to date, or `--print-path` to show where the bundled copy lives inside the package.
+
 ## Release notes
 
 See the [changelog][].
@@ -90,6 +98,13 @@ See the [changelog][].
 For questions and help requests, you can reach out in the [scverse discourse][].
 If you found a bug, please use the [issue tracker][].
 
+## License
+Enrichment methods inside decoupler can be used for academic or commercial purposes, except `viper` which holds a non-commercial license.
+
+The data redistributed by OmniPath does not have a single license, each original resource has its own. By default, `decoupler`
+assumes an academic license, but commercial or nonprofit licenses can be specified in the `license` parameter of `decoupler`'s OmniPath functions.
+[Here](https://omnipathdb.org/info) one can find the license information of all the resources in OmniPath.
+
 ## Citation
 
 > Badia-i-Mompel P., Vélez Santiago J., Braunger J., Geiss C., Dimitrov D.,
@@ -103,9 +118,9 @@ to infer biological activities from omics data. Bioinformatics Advances.
 [scverse]: https://scverse.org/
 [issue tracker]: https://github.com/scverse/decoupler/issues
 [tests]: https://github.com/scverse/decoupler/actions/workflows/test.yaml
-[documentation]: https://decoupler.readthedocs.io
-[changelog]: https://decoupler.readthedocs.io/en/latest/changelog.html
-[api documentation]: https://decoupler.readthedocs.io/en/latest/api.html
+[documentation]: https://decoupler.scverse.org/
+[changelog]: https://decoupler.scverse.org/page/changelog.html
+[api documentation]: https://decoupler.scverse.org/page/api.html
 [pypi]: https://pypi.org/project/decoupler
 [down]: https://pepy.tech/project/decoupler
 [conda]: https://anaconda.org/conda-forge/decoupler-py

decoupler-2.3.0/docs/_static/images/logo.svg

@@ -0,0 +1,35 @@
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+<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
+<svg width="100%" height="100%" viewBox="0 0 882 863" version="1.1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" xml:space="preserve" xmlns:serif="http://www.serif.com/" style="color-scheme:light dark;fill-rule:evenodd;clip-rule:evenodd;stroke-linecap:round;stroke-linejoin:round;stroke-miterlimit:1.5;">
+    <g transform="matrix(1,0,0,1,-1021.15,-508.159)">
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{decoupler-2.1.6 → decoupler-2.3.0}/docs/conf.py

@@ -2,7 +2,7 @@
 
 # This file only contains a selection of the most common options. For a full
 # list see the documentation:
-# https://www.sphinx-doc.org/en/master/usage/configuration.html
+# https://www.sphinx-doc.org/page/usage/configuration.html
 
 # -- Path setup --------------------------------------------------------------
 import shutil
@@ -57,11 +57,12 @@ extensions = [
     "sphinx.ext.autosummary",
     "sphinx.ext.napoleon",
     "sphinxcontrib.bibtex",
-    "sphinx_autodoc_typehints",
-    "sphinx_tabs.tabs",
     "sphinxcontrib.katex",
+    "sphinx_autodoc_typehints",
+    "sphinx_design",
     "IPython.sphinxext.ipython_console_highlighting",
     "sphinxext.opengraph",
+    "scverse_misc.sphinx_ext",
     *[p.stem for p in (HERE / "extensions").glob("*.py")],
 ]
 
@@ -87,6 +88,7 @@ nb_output_stderr = "remove"
 nb_execution_mode = "off"
 nb_merge_streams = True
 typehints_defaults = "braces"
+always_use_bars_union = True  # use `|` instead of `Union` in types even when building with Python ≤3.14
 
 source_suffix = {
     ".rst": "restructuredtext",
@@ -95,10 +97,9 @@ source_suffix = {
 }
 
 intersphinx_mapping = {
-    # TODO: replace `3.13` with `3` once ReadTheDocs supports building with Python 3.14
-    "python": ("https://docs.python.org/3.13", None),
-    "anndata": ("https://anndata.readthedocs.io/en/stable/", None),
-    "scanpy": ("https://scanpy.readthedocs.io/en/stable/", None),
+    "python": ("https://docs.python.org/3", None),
+    "anndata": ("https://anndata.scverse.org/en/stable/", None),
+    "scanpy": ("https://scanpy.scverse.org/en/stable/", None),
     "numpy": ("https://numpy.org/doc/stable/", None),
     "matplotlib": ("https://matplotlib.org/stable/", None),
     "pandas": ("https://pandas.pydata.org/pandas-docs/stable/", None),

{decoupler-2.1.6 → decoupler-2.3.0}/docs/references.bib

@@ -472,3 +472,17 @@
   year = {2021},
   month = feb
 }
+
+@article{phipson2010,
+  title = {Permutation P-values Should Never Be Zero: Calculating Exact P-values When Permutations Are Randomly Drawn},
+  volume = {9},
+  ISSN = {1544-6115},
+  url = {http://dx.doi.org/10.2202/1544-6115.1585},
+  DOI = {10.2202/1544-6115.1585},
+  number = {1},
+  journal = {Statistical Applications in Genetics and Molecular Biology},
+  publisher = {Walter de Gruyter GmbH},
+  author = {Phipson,  Belinda and Smyth,  Gordon K.},
+  year = {2010},
+  month = jan
+}