decoupler 2.2.0__tar.gz → 2.3.1__tar.gz

{decoupler-2.2.0 → decoupler-2.3.1}/.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-2.2.0 → decoupler-2.3.1}/.editorconfig

@@ -8,7 +8,7 @@ charset = utf-8
 trim_trailing_whitespace = true
 insert_final_newline = true
 
-[{*.{yml,yaml,toml},.cruft.json}]
+[{*.yml,*.yaml,*.toml,.cruft.json}]
 indent_size = 2
 
 [Makefile]

{decoupler-2.2.0 → decoupler-2.3.1}/.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-2.3.1/.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-2.2.0 → decoupler-2.3.1}/.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-2.3.1/.github/workflows/notebooks.yaml

@@ -0,0 +1,62 @@
+name: Test notebooks
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        # to fail on error in multiline statements (-e), in pipes (-o pipefail), and on unset variables (-u).
+        shell: bash -euo pipefail {0}
+
+    env:
+      NOTEBOOK_PATH: docs/notebooks
+
+    strategy:
+      fail-fast: false
+      matrix:
+        notebook:
+          [
+            "example.ipynb",
+            "bench/rna.ipynb",
+            "bulk/rna.ipynb",
+            "omnipath/licenses.ipynb",
+            "omnipath/orthologs.ipynb",
+            "scell/rna_psbk.ipynb",
+            "scell/rna_pstime.ipynb",
+            "scell/rna_sc.ipynb",
+            "spatial/rna_visium.ipynb",
+          ]
+
+    steps:
+      - 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@6d4fd22b20465ccc0f7354476588e8df7c9ca0e0 # v7.1.0
+        with:
+          python-version: "3.13"
+      - name: Install uv
+        uses: astral-sh/setup-uv@1c37ad07a6a961277cf70c0d37d6f313000f5884 # v10.3.0
+      - name: Install dependencies
+        run: |
+          uv pip install --system .
+          uv pip install --system --group dev --group test
+          uv pip install --system nbconvert ipykernel
+      - name: Run ${{ matrix.notebook }} Notebook
+        run: jupyter nbconvert --to notebook --execute ${{ env.NOTEBOOK_PATH }}/${{ matrix.notebook }}

{decoupler-2.2.0 → decoupler-2.3.1}/.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-2.2.0 → decoupler-2.3.1}/.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@v6
+        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
-          with:
-            allowed-failures: ${{ needs.get-environments.outputs.allowed-failures }}
-            jobs: ${{ toJSON(needs) }}
+      - uses: re-actors/alls-green@b5b5b37504aa4183270bd3d855c52a67f212be35 # v1.3.0
+        with:
+          allowed-failures: ${{ needs.get-environments.outputs.allowed-failures }}
+          jobs: ${{ toJSON(needs) }}

{decoupler-2.2.0 → decoupler-2.3.1}/.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: v2.5.2
+    rev: v2.6.3
     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: v2.25.1
+    rev: v2.30.3
     hooks:
       - id: pyproject-fmt
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.15.20
+    rev: v0.17.2
     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: v1.31.1
+    hooks:
+      - id: zizmor
+        args: [--no-progress, --fix]

{decoupler-2.2.0 → decoupler-2.3.1}/.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-2.2.0 → decoupler-2.3.1}/CHANGELOG.md

@@ -8,15 +8,46 @@ 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
 
+## 2.3.1
+
+### Bugfixes
+
+- Fixed `mt.zscore` swapping the `KSEA` and `RoKAI` flavors, restoring the behaviour of `decoupler<2`. Scores from the default `RoKAI` flavor change (#382)
+- Fixed `mt.gsea` giving p-values of 0 when no permutation reached the observed score. The observed score is now counted as one of the permutations, as in `mt.waggr` (#383)
+- Fixed `mt.waggr` aborting the Python process with numba's `workqueue` threading layer (default when TBB/OpenMP are unavailable, e.g. macOS arm64) due to nested parallel regions
+
+## 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
+
 - Fixed `op.translate` (and every `op.resource` call for non-human organisms) failing with HTTP 404 after HGNC dropped the `genenames/` subtree from the EBI FTP mirror; the HCOP fifteen-column files are now fetched from the new HGNC Google Cloud Storage bucket (#303)
 - Removed a redundant `pd.read_csv` call in `op.translate` that re-downloaded the HCOP file a second time and bypassed the retry logic in `_download`
 - Fixed `bm.benchmark` ground-truth matrix row order not matching score matrix after `pivot`, which silently misaligned perturbation labels when obs names sort differently from their original order (#302)
@@ -24,29 +55,35 @@ and this project adheres to [Semantic Versioning][].
 ## 2.1.5
 
 ### Added
+
 - `pl.volcano` now accepts a gene name (`str`) or list of gene names (`list[str]`) for the `top` parameter to annotate specific features on volcano plots
 
 ### Changes
+
 - Refactored `ds.ensmbl_to_symbol` to reuse `_download` and fixed mirror fallback to actually switch between Ensembl mirrors
 - Made `tqdm` progress bar compact in `_download`
 
 ### Bugfixes
+
 - Fixed `pl.dotplot` ignoring `vcenter=0` due to falsy check (#293)
 - Fixed `_log` setting the root logging level to INFO for all packages (#296)
 
 ## 2.1.4
 
 ### Changes
+
 - Added `alternative` argument to `decoupler.mt.query_set`. By default `'greater'`, before it was `'two-sided'`
 - Unpinned `scipy` version limit
 
 ### Bugfixes
+
 - Fixed missing progressbar for `decoupler._download._download`
 - Added missing `decoupler.mt.query_set` documentation
 
 ## 2.1.3
 
 ### Changes
+
 - `pp.adjmat` now returns the same features as used as input instead of the subset of `net`
 - `pp.pseudobulk` now returns the same order features as used as input instead of shuffling them
 - Added a dedicated header and 5 attemps to `_download` to mitigate 429 Client Error from Zenodo downloads
@@ -54,6 +91,7 @@ and this project adheres to [Semantic Versioning][].
 ## 2.1.2
 
 ### Added
+
 - `pp.query_set` to test overlap between a given feature set against a database of sets
 
 ### Changes
@@ -65,10 +103,12 @@ and this project adheres to [Semantic Versioning][].
 ## 2.1.1
 
 ### Added
+
 - mypy checks in CI
 - notebook checks in CI
 
 ### Bugfixes
+
 - Fixed error in `decoupler.pp.pseudobulk` when `adata.obs_names` were not unique, now throws verbose error
 - Fixed corner case in `decoupler.mt.gsea` when p-values were infitite and could not be corrected
 
@@ -81,41 +121,49 @@ and this project adheres to [Semantic Versioning][].
 - Enrichment methods and pseudobulking now work with backed AnnData objects, useful when working with big datasets and memory is limited
 
 ### Bugfixes
+
 - Fixed error in `pl.obsm` where default value of `cmap_obs` was not properly set.
 
 ## 2.0.7
 
 ### Changes
+
 - Added `pre-commit` functionality to the repository
 
 ## 2.0.6
 
 ### Changes
+
 - Modified links and paths to follow scverse's repository
 
 ## 2.0.5
 
 ### Bugfixes
+
 - Fixed error message when extra dependencies where not installed
 
 ## 2.0.4
 
 ### Bugfixes
+
 - Fixed `dcor` import bug as an external dependency
 
 ## 2.0.3
 
 ### Bugfixes
+
 - Fixed error in `pp.pseudobulk` when obs columns were not categorical
 
 ## 2.0.2
 
 ### Changes
+
 - Allowed ordering functions (`pp.bin_order`, `pl.order` and `pl.order_targets`) not to be bound between 0 and 1
 - Added ipywidgets as dependency
 - Silenced xgboost warnings
 
 ### Bugfixes
+
 - Handled corner case in `bm.metric.auc` when scores are all 0
 - Fixed error in `bm.metric.hmean` when metrics were str instead of list
 - Fixed error when `obs` column is a list in `pp.pseudobulk`
@@ -123,6 +171,7 @@ and this project adheres to [Semantic Versioning][].
 ## 2.0.1
 
 ### Bugfixes
+
 - Fixed an error in `pp.pseudobulk` when handling empty samples or features
 
 ## 2.0.0
@@ -149,7 +198,7 @@ All functions have been rewritten to follow the new API, errors when running pre
   - 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
 - Plots are now in a new `pl` module
-    - Use `decoupler.pl.<plot_name>` to call a plot
+  - Use `decoupler.pl.<plot_name>` to call a plot
     - They use a common class `Plotter` to make it easier to share arguments between them
     - `plot_violins` has been deprecated
     - Names that have changed
@@ -169,7 +218,7 @@ All functions have been rewritten to follow the new API, errors when running pre
 ### Added
 
 - `ds` module with functions to download several datasets at different resolutions
-    - Bulk: `hsctgfb` and `knocktf`
+  - Bulk: `hsctgfb` and `knocktf`
     - Single-cell: `pbmc3k`, `covid5k` and `erygast1k`
     - Spatial: `msvisium`
     - Toy data: `toy` and `toy_bench`

{decoupler-2.2.0 → decoupler-2.3.1}/PKG-INFO

@@ -1,8 +1,8 @@
-Metadata-Version: 2.4
+Metadata-Version: 2.5
 Name: decoupler
-Version: 2.2.0
+Version: 2.3.1
 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
@@ -56,6 +56,7 @@ Requires-Dist: tqdm
 Description-Content-Type: text/markdown
 
 # decoupler - Ensemble of methods to infer enrichment scores
+
 <img src="https://raw.githubusercontent.com/scverse/decoupler/refs/heads/main/docs/_static/images/logo.svg" align="right" width="120" class="no-scaled-link" />
 
 [![Tests][badge-tests]][tests]
@@ -86,7 +87,7 @@ Description-Content-Type: text/markdown
 `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)
+[//]: # "numfocus-fiscal-sponsor-attribution"
 
 decoupler is part of the scverse® project ([website](https://scverse.org), [governance](https://scverse.org/about/roles)) and is fiscally sponsored by [NumFOCUS](https://numfocus.org/).
 If you like scverse® and want to support our mission, please consider making a tax-deductible [donation](https://numfocus.org/donate-to-scverse) to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.
@@ -107,7 +108,7 @@ in particular, the [API documentation][].
 
 ## Installation
 
-You need to have Python 3.11 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:
@@ -136,19 +137,15 @@ mamba create -n=dcp conda-forge::decoupler-py
 pip install git+https://github.com/scverse/decoupler.git@main
 ```
 
-## Claude Code Skill
+## Agent Skill
 
-decoupler ships an [Agent Skill](https://docs.claude.com/en/docs/claude-code/skills) for [Claude Code](https://claude.com/claude-code) that teaches the agent to use the library correctly. Install it once into your personal skills directory:
+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
+decoupler-install-skills --agent claude
 ```
 
-This copies the skill to `~/.claude/skills/decoupler/`, making it available in **every** project (re-run with `--force` after upgrading). Once installed, just ask Claude Code to do decoupler tasks ("find the most active TFs in this cell cluster", "score hallmark gene sets with ora", "build a consensus across methods") and the skill is consulted automatically. To avoid copying into your home directory, point Claude Code at the bundled copy instead:
-
-```bash
-export CLAUDE_SKILLS_PATH="$(decoupler-install-skills --print-path)"
-```
+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
 
@@ -159,22 +156,30 @@ 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.,
-Müller-Dott S., Taus P., Dugourd A., Holland C.H., Ramirez Flores R.O.
-and Saez-Rodriguez J. 2022. decoupleR: Ensemble of computational methods
-to infer biological activities from omics data. Bioinformatics Advances.
-<https://doi.org/10.1093/bioadv/vbac016>
+> Müller-Dott S., Taus P., Dugourd A., Holland C.H., Ramirez Flores R.O.
+> and Saez-Rodriguez J. 2022. decoupleR: Ensemble of computational methods
+> to infer biological activities from omics data. Bioinformatics Advances.
+> <https://doi.org/10.1093/bioadv/vbac016>
 
 [uv]: https://github.com/astral-sh/uv
 [scverse discourse]: https://discourse.scverse.org/
 [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