decoupler 1.9.2__tar.gz → 2.0.0__tar.gz

decoupler-2.0.0/.codecov.yaml

@@ -0,0 +1,17 @@
+# Based on pydata/xarray
+codecov:
+  require_ci_to_pass: no
+
+coverage:
+  status:
+    project:
+      default:
+        # Require 1% coverage, i.e., always succeed
+        target: 1
+    patch: false
+    changes: false
+
+comment:
+  layout: diff, flags, files
+  behavior: once
+  require_base: no

decoupler-2.0.0/.cruft.json

@@ -0,0 +1,43 @@
+{
+  "template": "https://github.com/scverse/cookiecutter-scverse",
+  "commit": "5842d5cb8510e1d4a037a8f772630d51ec86de96",
+  "checkout": null,
+  "context": {
+    "cookiecutter": {
+      "project_name": "decoupler",
+      "package_name": "decoupler",
+      "project_description": "Python package to perform enrichment analysis from omics data.",
+      "author_full_name": "Pau Badia i Mompel",
+      "author_email": "pau.badia@uni-heidelberg.de",
+      "github_user": "PauBadiaM",
+      "github_repo": "decoupler",
+      "license": "BSD 3-Clause License",
+      "ide_integration": true,
+      "_copy_without_render": [
+        ".github/workflows/build.yaml",
+        ".github/workflows/test.yaml",
+        "docs/_templates/autosummary/**.rst"
+      ],
+      "_exclude_on_template_update": [
+        "CHANGELOG.md",
+        "LICENSE",
+        "README.md",
+        "docs/api.md",
+        "docs/index.md",
+        "docs/notebooks/example.ipynb",
+        "docs/references.bib",
+        "docs/references.md",
+        "src/**",
+        "tests/**"
+      ],
+      "_render_devdocs": false,
+      "_jinja2_env_vars": {
+        "lstrip_blocks": true,
+        "trim_blocks": true
+      },
+      "_template": "https://github.com/scverse/cookiecutter-scverse",
+      "_commit": "5842d5cb8510e1d4a037a8f772630d51ec86de96"
+    }
+  },
+  "directory": null
+}

decoupler-2.0.0/.editorconfig

@@ -0,0 +1,15 @@
+root = true
+
+[*]
+indent_style = space
+indent_size = 4
+end_of_line = lf
+charset = utf-8
+trim_trailing_whitespace = true
+insert_final_newline = true
+
+[{*.{yml,yaml,toml},.cruft.json}]
+indent_size = 2
+
+[Makefile]
+indent_style = tab

decoupler-2.0.0/.github/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,94 @@
+name: Bug report
+description: Report something that is broken or incorrect
+labels: bug
+body:
+  - type: markdown
+    attributes:
+      value: |
+        **Note**: Please read [this guide](https://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports)
+        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.
+
+  - type: textarea
+    id: report
+    attributes:
+      label: Report
+      description: A clear and concise description of what the bug is.
+    validations:
+      required: true
+
+  - type: textarea
+    id: versions
+    attributes:
+      label: Versions
+      description: |
+        Which version of packages.
+
+        Please install `session-info2`, run the following command in a notebook,
+        click the “Copy as Markdown” button, then paste the results into the text box below.
+
+        ```python
+        In[1]: import session_info2; session_info2.session_info(dependencies=True)
+        ```
+
+        Alternatively, run this in a console:
+
+        ```python
+        >>> import session_info2; print(session_info2.session_info(dependencies=True)._repr_mimebundle_()["text/markdown"])
+        ```
+      render: python
+      placeholder: |
+        anndata	0.11.3
+        ----	----
+        charset-normalizer	3.4.1
+        coverage	7.7.0
+        psutil	7.0.0
+        dask	2024.7.1
+        jaraco.context	5.3.0
+        numcodecs	0.15.1
+        jaraco.functools	4.0.1
+        Jinja2	3.1.6
+        sphinxcontrib-jsmath	1.0.1
+        sphinxcontrib-htmlhelp	2.1.0
+        toolz	1.0.0
+        session-info2	0.1.2
+        PyYAML	6.0.2
+        llvmlite	0.44.0
+        scipy	1.15.2
+        pandas	2.2.3
+        sphinxcontrib-devhelp	2.0.0
+        h5py	3.13.0
+        tblib	3.0.0
+        setuptools-scm	8.2.0
+        more-itertools	10.3.0
+        msgpack	1.1.0
+        sparse	0.15.5
+        wrapt	1.17.2
+        jaraco.collections	5.1.0
+        numba	0.61.0
+        pyarrow	19.0.1
+        pytz	2025.1
+        MarkupSafe	3.0.2
+        crc32c	2.7.1
+        sphinxcontrib-qthelp	2.0.0
+        sphinxcontrib-serializinghtml	2.0.0
+        zarr	2.18.4
+        asciitree	0.3.3
+        six	1.17.0
+        sphinxcontrib-applehelp	2.0.0
+        numpy	2.1.3
+        cloudpickle	3.1.1
+        sphinxcontrib-bibtex	2.6.3
+        natsort	8.4.0
+        jaraco.text	3.12.1
+        setuptools	76.1.0
+        Deprecated	1.2.18
+        packaging	24.2
+        python-dateutil	2.9.0.post0
+        ----	----
+        Python	3.13.2 | packaged by conda-forge | (main, Feb 17 2025, 14:10:22) [GCC 13.3.0]
+        OS	Linux-6.11.0-109019-tuxedo-x86_64-with-glibc2.39
+        Updated	2025-03-18 15:47

decoupler-2.0.0/.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,5 @@
+blank_issues_enabled: false
+contact_links:
+  - name: Scverse Community Forum
+    url: https://discourse.scverse.org/
+    about: If you have questions about “How to do X”, please ask them here.

decoupler-2.0.0/.github/ISSUE_TEMPLATE/feature_request.yml

@@ -0,0 +1,11 @@
+name: Feature request
+description: Propose a new feature for decoupler
+labels: enhancement
+body:
+  - type: textarea
+    id: description
+    attributes:
+      label: Description of feature
+      description: Please describe your suggestion for a new feature. It might help to describe a problem or use case, plus any alternatives that you have considered.
+    validations:
+      required: true

decoupler-2.0.0/.github/workflows/build.yaml

@@ -0,0 +1,33 @@
+name: Check Build
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+defaults:
+  run:
+    # to fail on error in multiline statements (-e), in pipes (-o pipefail), and on unset variables (-u).
+    shell: bash -euo pipefail {0}
+
+jobs:
+  package:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          filter: blob:none
+          fetch-depth: 0
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          cache-dependency-glob: pyproject.toml
+      - name: Build package
+        run: uv build
+      - name: Check package
+        run: uvx twine check --strict dist/*.whl

decoupler-2.0.0/.github/workflows/release.yaml

@@ -0,0 +1,34 @@
+name: Release
+
+on:
+  release:
+    types: [published]
+
+defaults:
+  run:
+    # to fail on error in multiline statements (-e), in pipes (-o pipefail), and on unset variables (-u).
+    shell: bash -euo pipefail {0}
+
+# Use "trusted publishing", see https://docs.pypi.org/trusted-publishers/
+jobs:
+  release:
+    name: Upload release to PyPI
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/decoupler
+    permissions:
+      id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          filter: blob:none
+          fetch-depth: 0
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          cache-dependency-glob: pyproject.toml
+      - name: Build package
+        run: uv build
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

decoupler-2.0.0/.github/workflows/test.yaml

@@ -0,0 +1,99 @@
+name: Test
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+  schedule:
+    - cron: "0 5 1,15 * *"
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+defaults:
+  run:
+    # to fail on error in multiline statements (-e), in pipes (-o pipefail), and on unset variables (-u).
+    shell: bash -euo pipefail {0}
+
+jobs:
+  # Get the test environment from hatch as defined in pyproject.toml.
+  # This ensures that the pyproject.toml is the single point of truth for test definitions and the same tests are
+  # run locally and on continuous integration.
+  # 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
+    outputs:
+      envs: ${{ steps.get-envs.outputs.envs }}
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          filter: blob:none
+          fetch-depth: 0
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+      - name: Get test environments
+        id: get-envs
+        run: |
+          ENVS_JSON=$(uvx hatch env show --json | jq -c 'to_entries
+            | map(
+                select(.key | startswith("hatch-test"))
+                | {
+                    name: .key,
+                    label: (if (.key | contains("pre")) then .key + " (PRE-RELEASE DEPENDENCIES)" else .key end),
+                    python: .value.python
+                  }
+              )')
+          echo "envs=${ENVS_JSON}" | tee $GITHUB_OUTPUT
+
+  # Run tests through hatch. Spawns a separate runner for each environment defined in the hatch matrix obtained above.
+  test:
+    needs: get-environments
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest]
+        env: ${{ fromJSON(needs.get-environments.outputs.envs) }}
+
+    name: ${{ matrix.env.label }}
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          filter: blob:none
+          fetch-depth: 0
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          python-version: ${{ matrix.env.python }}
+          cache-dependency-glob: pyproject.toml
+      - name: create hatch environment
+        run: uvx hatch env create ${{ matrix.env.name }}
+      - name: run tests using hatch
+        env:
+          MPLBACKEND: agg
+          PLATFORM: ${{ matrix.os }}
+          DISPLAY: :42
+        run: uvx hatch run ${{ matrix.env.name }}:run-cov
+      - name: generate coverage report
+        run: uvx hatch run ${{ matrix.env.name }}:coverage xml
+      - name: Upload coverage
+        uses: codecov/codecov-action@v4
+
+  # Check that all tests defined above pass. This makes it easy to set a single "required" test in branch
+  # protection instead of having to update it frequently. See https://github.com/re-actors/alls-green#why.
+  check:
+    name: Tests pass in all hatch environments
+    if: always()
+    needs:
+      - get-environments
+      - test
+    runs-on: ubuntu-latest
+    steps:
+        - uses: re-actors/alls-green@release/v1
+          with:
+            jobs: ${{ toJSON(needs) }}

decoupler-2.0.0/.gitignore

@@ -0,0 +1,23 @@
+# Temp files
+.DS_Store
+*~
+buck-out/
+
+# Compiled files
+.venv/
+__pycache__/
+.*cache/
+
+# Distribution / packaging
+/dist/
+
+# Tests and coverage
+/data/
+/node_modules/
+
+# docs
+/docs/generated/
+/docs/_build/
+
+# jupyter
+.ipynb_checkpoints/

decoupler-2.0.0/.pre-commit-config.yaml

@@ -0,0 +1,47 @@
+fail_fast: false
+default_language_version:
+  python: python3
+default_stages:
+  - pre-commit
+  - pre-push
+minimum_pre_commit_version: 2.16.0
+repos:
+  - repo: https://github.com/biomejs/pre-commit
+    rev: v1.9.4
+    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: v2.5.1
+    hooks:
+      - id: pyproject-fmt
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.11.5
+    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
+    hooks:
+      - id: detect-private-key
+      - id: check-ast
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+        args: [--fix=lf]
+      - id: trailing-whitespace
+      - id: check-case-conflict
+      # Check that there are no merge conflicts (could be generated by template sync)
+      - id: check-merge-conflict
+        args: [--assume-in-merge]
+  - repo: local
+    hooks:
+      - id: forbid-to-commit
+        name: Don't commit rej files
+        entry: |
+          Cannot commit .rej files. These indicate merge conflicts that arise during automated template updates.
+          Fix the merge conflicts manually and remove the .rej files.
+        language: fail
+        files: '.*\.rej$'

decoupler-2.0.0/.readthedocs.yaml

@@ -0,0 +1,16 @@
+# https://docs.readthedocs.io/en/stable/config-file/v2.html
+version: 2
+build:
+  os: ubuntu-20.04
+  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

decoupler-2.0.0/.vscode/extensions.json

@@ -0,0 +1,18 @@
+{
+    "recommendations": [
+        // GitHub integration
+        "github.vscode-github-actions",
+        "github.vscode-pull-request-github",
+        // Language support
+        "ms-python.python",
+        "ms-python.vscode-pylance",
+        "ms-toolsai.jupyter",
+        "tamasfe.even-better-toml",
+        // Dependency management
+        "ninoseki.vscode-mogami",
+        // Linting and formatting
+        "editorconfig.editorconfig",
+        "charliermarsh.ruff",
+        "biomejs.biome",
+    ],
+}

decoupler-2.0.0/.vscode/launch.json

@@ -0,0 +1,33 @@
+{
+    // Use IntelliSense to learn about possible attributes.
+    // Hover to view descriptions of existing attributes.
+    // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+    "version": "0.2.0",
+    "configurations": [
+        {
+            "name": "Python: Build Documentation",
+            "type": "debugpy",
+            "request": "launch",
+            "module": "sphinx",
+            "args": ["-M", "html", ".", "_build"],
+            "cwd": "${workspaceFolder}/docs",
+            "console": "internalConsole",
+            "justMyCode": false,
+        },
+        {
+            "name": "Python: Debug Test",
+            "type": "debugpy",
+            "request": "launch",
+            "program": "${file}",
+            "purpose": ["debug-test"],
+            "console": "internalConsole",
+            "justMyCode": false,
+            "env": {
+                "PYTEST_ADDOPTS": "--color=yes",
+            },
+            "presentation": {
+                "hidden": true,
+            },
+        },
+    ],
+}

decoupler-2.0.0/.vscode/settings.json

@@ -0,0 +1,18 @@
+{
+    "[python][json][jsonc]": {
+        "editor.formatOnSave": true,
+    },
+    "[python]": {
+        "editor.defaultFormatter": "charliermarsh.ruff",
+        "editor.codeActionsOnSave": {
+            "source.fixAll": "always",
+            "source.organizeImports": "always",
+        },
+    },
+    "[json][jsonc]": {
+        "editor.defaultFormatter": "biomejs.biome",
+    },
+    "python.analysis.typeCheckingMode": "basic",
+    "python.testing.pytestEnabled": true,
+    "python.testing.pytestArgs": ["-vv", "--color=yes"],
+}

decoupler-2.0.0/CHANGELOG.md

@@ -0,0 +1,76 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog][],
+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
+
+Major update to accomodate the scverse :cite:`scverse` template.
+
+All functions have been rewritten to follow the new API, errors when running previous versions (`1.X.X`) are expected if `decoupler >= 2.0.0` is installed.
+
+### Changes
+
+- Methods are now in the `mt` module and are built from shared class `Method`
+  - Use `decoupler.mt.<method_name>` to call a method
+  - `min_n` argument has been renamed `tmin`
+  - New argument `bsize` allows to run a method with batches in case excessive memory usage is an issue
+  - :math:`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 :math:`R^2` instead of the importance of a single decision tree.
+  - `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
+- Databases from Omnipath can now be accessed through the new `op` module
+  - 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
+- Plots are now in a new `pl` module
+    - 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
+      - `plot_psbulk_samples` to `filter_samples`
+      - `plot_running_score` to `leading_edge`
+      - `plot_associations` to `obsm`
+      - `plot_targets` to `source_targets`
+- Preprocessing functions are now in the new `pp` module
+  - Renamed `check_corr` to `net_corr`, now also returns adjusted :math:`p_{values}`
+  - Renamed `get_acts` to `get_obsm`
+  - Renamed `get_pseudobulk` to `pseudobulk`. Now it does not automatically remove low quality samples, this is now done with the function `filter_samples`
+  - Deprecated `get_contrast`, `get_top_targets` and `format_contrast_results`. `PyDESeq2` should be used instead
+  - Moved `rank_sources_groups` to the new `tl` module as `rankby_group`
+  - Moved `get_metadata_associations` to the new `tl` module as `rankby_obsm`
+- Moved the benchmarking pipeline inside a new `bm` module, with its metrics and plotting functions in further submodules (`bm.metric` and `bm.pl`)
+
+### Added
+
+- `ds` module with functions to download several datasets at different resolutions
+    - Bulk: `hsctgfb` and `knocktf`
+    - Single-cell: `pbmc3k`, `covid5k` and `erygast1k`
+    - Spatial: `msvisium`
+    - Toy data: `toy` and `toy_bench`
+    - Utils: `ensmbl_to_symbol`
+- New database functions in the `op` module
+  - Added `hallmark` as a custom resource
+- New plotting funcitons in the `pl` module
+  - 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`
+  - Added `knn` to calculate K-Nearest Neighbors similarities based on spatial distances
+  - Added `bin_order` to bin features across a continous process
+- `tl` module with functions to perform statistical tests
+  - Added `rankby_order` to test for non-linear associations of features with a continous process
+- New benchmarking metrics and plotting related functions in the `bm` module
+  - Added two more metrics, `F-score` and `qrank`
+  - Added shared plots for metrics, `bm.pl.auc`, `bm.pl.fscore` and `bm.pl.qrank`
+  - Added a summary plot across metrics `bm.pl.summary`

decoupler-2.0.0/LICENSE

@@ -0,0 +1,29 @@
+BSD 3-Clause License
+
+Copyright (c) 2025, Pau Badia i Mompel
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.