multiqc-pivot 0.1.0__tar.gz

multiqc_pivot-0.1.0/.github/CODEOWNERS

@@ -0,0 +1 @@
+* @clintval

multiqc_pivot-0.1.0/.github/workflows/publish_multiqc_pivot.yml

@@ -0,0 +1,133 @@
+name: publish multiqc-pivot
+
+on:
+  push:
+    tags: '[0-9]+.[0-9]+.[0-9]+'
+
+permissions: {}
+
+env:
+  UV_VERSION: 0.11.16
+
+jobs:
+  on-main-branch-check:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+    outputs:
+      on_main: ${{ steps.contains_tag.outputs.retval }}
+    steps:
+      # action-contains-tag lists remote branches to find the tag; current git follows the remote
+      # HEAD by default, which breaks that lookup: https://github.com/rickstaa/action-contains-tag/pull/18
+      - name: git config --global remote.origin.followRemoteHEAD never
+        shell: bash
+        run: git config --global remote.origin.followRemoteHEAD never
+
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1  # v7.0.1
+        with:
+          fetch-depth: 0
+          persist-credentials: false
+
+      - uses: rickstaa/action-contains-tag@a9ff27d505ba2bf074a2ebb48b208e76d35ff308  # v1.2.10
+        id: contains_tag
+        with:
+          reference: "main"
+          tag: "${{ github.ref_name }}"
+
+  unit-tests:
+    needs: on-main-branch-check
+    if: ${{ needs.on-main-branch-check.outputs.on_main == 'true' }}
+    permissions:
+      contents: read
+    uses: "./.github/workflows/tests.yml"
+
+  build-wheels:
+    needs: unit-tests
+    permissions:
+      contents: read
+    uses: "./.github/workflows/wheels.yml"
+
+  build-sdist:
+    name: build source distribution
+    needs: unit-tests
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1  # v7.0.1
+        with:
+          fetch-depth: 0
+          persist-credentials: false
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@20cfd1bf945f4377ade1205e4dbc17946fc9a30d  # v10.0.1
+        with:
+          version: ${{ env.UV_VERSION }}
+          python-version: "3.11"
+          enable-cache: 'false'
+
+      - name: Build package
+        run: uv build --sdist --out-dir dist
+
+      - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a  # v7.0.1
+        with:
+          name: multiqc-pivot-sdist
+          path: dist/*.tar.gz
+
+  publish-to-pypi:
+    runs-on: ubuntu-latest
+    needs: [build-wheels, build-sdist]
+    environment: pypi
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c  # v8.0.1
+        with:
+          path: packages
+          pattern: 'multiqc-pivot-*'
+          merge-multiple: true
+
+      - uses: pypa/gh-action-pypi-publish@dc37677b2e1c63e2034f94d8a5b11f265b73ba33  # v1.14.2
+        with:
+          packages-dir: packages/
+          skip-existing: true
+          verbose: true
+
+  make-changelog:
+    runs-on: ubuntu-latest
+    needs: publish-to-pypi
+    permissions:
+      contents: read
+    outputs:
+      release_body: ${{ steps.git-cliff.outputs.content }}
+    steps:
+      - name: Checkout the Repository at the Tagged Commit
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1  # v7.0.1
+        with:
+          fetch-depth: 0
+          ref: ${{ github.ref_name }}
+          persist-credentials: false
+
+      - name: Generate a Changelog
+        uses: orhun/git-cliff-action@3d96a18cc4ec17e9dc69ddcc424ccafaf1f78ce2  # v4.9.0
+        id: git-cliff
+        with:
+          config: pyproject.toml
+          args: --latest --verbose
+        env:
+          GITHUB_REPO: ${{ github.repository }}
+
+  make-github-release:
+    runs-on: ubuntu-latest
+    environment: github
+    permissions:
+      contents: write
+      pull-requests: read
+    needs: make-changelog
+    steps:
+      - name: Create Release
+        env:
+          GH_TOKEN: ${{ github.token }}
+          TAG: ${{ github.ref_name }}
+          NOTES: ${{ needs.make-changelog.outputs.release_body }}
+        run: gh release create "$TAG" --repo "$GITHUB_REPOSITORY" --title "$TAG" --notes "$NOTES"

multiqc_pivot-0.1.0/.github/workflows/tests.yml

@@ -0,0 +1,37 @@
+name: tests
+
+on:
+  push:
+    branches:
+      - "**"
+    tags:
+      - "!**"
+  workflow_call:
+
+permissions:
+  contents: read
+
+env:
+  UV_VERSION: 0.11.16
+
+jobs:
+  unit-tests:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        PYTHON_VERSION: ["3.10", "3.11", "3.12", "3.13"]
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1  # v7.0.1
+        with:
+          persist-credentials: false
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@20cfd1bf945f4377ade1205e4dbc17946fc9a30d  # v10.0.1
+        with:
+          version: ${{ env.UV_VERSION }}
+          python-version: ${{ matrix.PYTHON_VERSION }}
+          enable-cache: 'false'
+
+      - name: Test the library
+        run: |
+          uv run --locked poe check-all

multiqc_pivot-0.1.0/.github/workflows/wheels.yml

@@ -0,0 +1,37 @@
+name: wheels
+
+on:
+  pull_request:
+  workflow_call:
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+env:
+  UV_VERSION: 0.11.16
+
+jobs:
+  build-wheels:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1  # v7.0.1
+        with:
+          persist-credentials: false
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@20cfd1bf945f4377ade1205e4dbc17946fc9a30d  # v10.0.1
+        with:
+          version: ${{ env.UV_VERSION }}
+          python-version: "3.11"
+          enable-cache: 'false'
+
+      - name: Build wheels
+        run: uv build --wheel --out-dir wheelhouse
+
+      - name: Upload wheels
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a  # v7.0.1
+        with:
+          name: multiqc-pivot-wheels
+          path: ./wheelhouse/multiqc_pivot*.whl
+          if-no-files-found: error

multiqc_pivot-0.1.0/.gitignore

@@ -0,0 +1,161 @@
+*.html
+.DS_Store
+.vscode/
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+venv/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+.idea/

multiqc_pivot-0.1.0/CONTRIBUTING.md

@@ -0,0 +1,125 @@
+# Development and Testing
+
+## Primary Development Commands
+
+To check and resolve linting issues in the codebase, run:
+
+```console
+uv run ruff check --fix
+```
+
+To check and resolve formatting issues in the codebase, run:
+
+```console
+uv run ruff format
+```
+
+To check the unit tests in the codebase, run:
+
+```console
+uv run pytest
+```
+
+To check the typing in the codebase, run:
+
+```console
+uv run mypy
+```
+
+To generate a code coverage report after testing locally, run:
+
+```console
+uv run coverage html
+```
+
+To check the lock file is up to date:
+
+```console
+uv lock --check
+```
+
+The lock file is resolved without any user-level uv configuration, which is how CI resolves it. If your `~/.config/uv/uv.toml` sets `exclude-newer` or similar, uv will want to re-resolve and will rewrite `uv.lock`. Set `UV_NO_CONFIG=1` in your shell while working here to match CI; the environment variable matters because `poe` runs each task through its own `uv run`, which a `--no-config` flag on the outer command does not reach.
+
+## Shortcut Task Commands
+
+###### For Running Individual Checks
+
+```console
+uv run poe check-format
+uv run poe check-lint
+uv run poe check-tests
+uv run poe check-typing
+```
+
+###### For Running All Checks
+
+```console
+uv run poe check-all
+```
+
+###### For Running Individual Fixes
+
+```console
+uv run poe fix-format
+uv run poe fix-lint
+```
+
+###### For Running All Fixes
+
+```console
+uv run poe fix-all
+```
+
+###### For Running All Fixes and Checks
+
+```console
+uv run poe fix-and-check-all
+```
+
+## Trying a change against a real report
+
+Point MultiQC at any directory of QC outputs with a config that has a `sample_pivot` block. The
+plugin is picked up automatically once the package is installed in the same environment:
+
+```console
+uv run multiqc --config my_config.yml ./path-to-data
+```
+
+## Creating a release on PyPI
+
+> [!NOTE]
+> This project follows [Semantic Versioning](https://semver.org/), aka SemVer. In brief:
+>
+> - MAJOR version when you make incompatible API changes
+> - MINOR version when you add functionality in a backwards compatible manner
+> - PATCH version when you make backwards compatible bug fixes
+
+> [!IMPORTANT]
+> Consider editing the changelog if there are any errors or necessary enhancements.
+
+1. Clone the repository, ensure you are on the main branch, and that the working directory is clean.
+2. Check out a new branch to prepare the library for release.
+3. Bump the version of the library to the desired SemVer, e.g.:
+    ```console
+    # Increment the minor segment
+    uv version --bump minor
+
+    # Update to a specific version number
+    uv version 0.2.0
+    ```
+4. Commit the version bump changes with a Git commit message like `chore(release): bump to #.#.#`.
+5. Push the commit, open a PR, ensure tests pass, and seek reviews.
+6. Squash merge the PR into the `main` branch.
+7. Tag the new commit on the main branch with the bumped version number.
+
+> [!WARNING]
+> The tag **must** be a valid SemVer version number and **must** match the version set in (3). The [publishing GitHub Action](.github/workflows/publish_multiqc_pivot.yml) is activated by a new tag on the `main` branch containing a valid SemVer version.
+
+GitHub Actions will take care of the remainder of the deployment and release process:
+
+1. Unit tests will be re-run.
+2. A source distribution will be built.
+3. A wheel distribution will be built.
+4. Assets will be deployed to PyPI with the new version.
+5. A [Conventional Commit](https://www.conventionalcommits.org/en/v1.0.0/)-aware changelog will be drafted.
+6. A GitHub release will be created with the new version tag and the drafted changelog.

multiqc_pivot-0.1.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright © 2026 Clint Valentine
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

multiqc_pivot-0.1.0/PKG-INFO

@@ -0,0 +1,142 @@
+Metadata-Version: 2.5
+Name: multiqc-pivot
+Version: 0.1.0
+Summary: A MultiQC plugin that folds related samples into one General Statistics row per group with labelled metric columns.
+Project-URL: homepage, https://github.com/clintval/multiqc-pivot
+Project-URL: repository, https://github.com/clintval/multiqc-pivot
+Project-URL: Bug Tracker, https://github.com/clintval/multiqc-pivot/issues
+Author-email: Clint Valentine <valentine.clint@gmail.com>
+License-Expression: MIT
+License-File: LICENSE
+Classifier: Development Status :: 3 - Alpha
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Natural Language :: English
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Classifier: Typing :: Typed
+Requires-Python: >=3.10
+Requires-Dist: multiqc<2,>=1.35
+Requires-Dist: pydantic>=2
+Description-Content-Type: text/markdown
+
+# multiqc-pivot
+
+[![CI](https://github.com/clintval/multiqc-pivot/actions/workflows/tests.yml/badge.svg?branch=main)](https://github.com/clintval/multiqc-pivot/actions/workflows/tests.yml?query=branch%3Amain)
+[![Python Versions](https://img.shields.io/badge/python-3.10_|_3.11_|_3.12_|_3.13-blue)](https://github.com/clintval/multiqc-pivot)
+[![basedpyright](https://img.shields.io/badge/basedpyright-checked-42b983)](https://docs.basedpyright.com/latest/)
+[![mypy](https://www.mypy-lang.org/static/mypy_badge.svg)](https://mypy-lang.org/)
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://docs.astral.sh/ruff/)
+
+A [MultiQC](https://multiqc.info) plugin that folds related samples into one General Statistics row per group.
+
+## Installation
+
+```console
+pip install multiqc-pivot
+```
+## Introduction
+
+MultiQC gives every sample its own row.
+When one subject yields several samples that are measured by different methods, say a tumour and a normal, or two tissues and a paired-genotype check, the General Statistics table ends up with a block of half-empty rows per subject.
+MultiQC's own [sample grouping](https://docs.seqera.io/multiqc/reports/customisation#sample-grouping) only fills the group's row for the handful of modules that know how to merge their metrics.
+
+This plugin runs after every module has reported and rebuilds the table:
+
+1. Rows for one group fold into a single row, and every folded column is prefixed by which method it came from.
+2. The original rows stay beneath the group row, so they still can be viewed.
+3. Rows for a level that does not belong in the table, such as per-library read QC, move out into their own table under General Statistics with whatever grouping they already had.
+4. Hover text, color scales, formats and hidden-by-default state carry over from the module that produced each column.
+
+## Example
+
+The report below comes from the [test fixtures](tests/data/report) and the [configuration](tests/data/multiqc_config.yml) shown in the usage section:
+
+![General Statistics with one row per subject and a Library statistics table beneath it](docs/pivot.png)
+
+```yaml
+sample_pivot:
+  group: '^(?P<group>[^. ]+)\.'
+  levels:
+    - match: '\.subject$'
+    - match: '\.(?P<analyte>tissueA|tissueB)$'
+      label: '{analyte}'
+    - match: '\.(?P<analyte>tissueA|tissueB) \(filtered\)$'
+      label: '{analyte} (filtered)'
+    - match: '\.library\.'
+      table: Library statistics
+  label_order: [tissueA, tissueB, tissueB (filtered)]
+  tables:
+    Library statistics:
+      description: Per-library read QC.
+```
+
+## Usage
+
+Add a `sample_pivot` block to any MultiQC config, for example with `--config my_config.yml`.
+
+So, with these sample names:
+
+```text
+101.subject
+101.tissueA
+101.tissueB
+101.tissueB (filtered data, though)
+101.tissueA.library.L1
+101.tissueA.library.L2
+```
+
+This configuration produces one row named `101` carrying `Concordance`, `TissueA Median`, `TissueB Median`, `TissueB (filtered) % Aligned` and so on, and moves the library rows into a separate table:
+
+```yaml
+sample_pivot:
+  group: '^(?P<group>[^. ]+)\.'
+  levels:
+    - match: '\.subject$'
+    - match: '\.(?P<analyte>tissueA|tissueB)$'
+      label: '{analyte}'
+    - match: '\.(?P<analyte>tissueA|tissueB) \(filtered\)$'
+      label: '{analyte} (filtered)'
+    - match: '\.library\.'
+      table: Library statistics
+  label_order: [tissueA, tissueB, tissueB (filtered)]
+  tables:
+    Library statistics:
+      description: Per-library read QC; read pairs nest under their library.
+```
+
+### YAML Configuration Reference
+
+| Key | Meaning |
+| --- | --- |
+| `group` | A regular expression searched in every matched sample name. Its `(?P<group>...)` capture names the folded row. Required. |
+| `levels` | An ordered list; the first level whose `match` is found in a sample name wins. Required. |
+| `levels[].match` | A regular expression searched in the sample name. Named captures are available to `label`. |
+| `levels[].label` | A format string built from the captures of `match`. Columns of matching rows are renamed with it and folded onto the group row; the row itself stays beneath. Omit it, and omit `table`, to fold the row's columns onto the group row unchanged. |
+| `levels[].table` | The name of a table that receives matching rows instead of General Statistics. Rows keep their grouping, so paired reads stay nested under their library. |
+| `column_title` | How a pivoted column is titled. `{label}` is the label as written, `{Label}` has its first letter upper-cased, `{title}` is the module's title. Default `{Label} {title}`. |
+| `label_order` | Labels in the order their column blocks should appear. Labels not listed follow in order of first appearance. |
+| `tables` | Presentation of the tables named by `levels[].table`, currently a `description` each. |
+
+> [!TIP]
+> A sample that matches no level is left where it was. 
+> A sample that matches a level but not `group` is left alone as well, with a warning in the log.
+> Columns that a module did not declare a header for are dropped from folded rows, as MultiQC would have dropped them anyway.
+
+### Limitations
+
+1. Sample names are matched after MultiQC has cleaned them, so you must write patterns against the names you see in an un-pivoted report.
+2. Only one level of nesting exists in a MultiQC table. Rows moved into a secondary table keep the nesting they already had; rows folded into a group row become its children, and cannot nest further.
+3. Two rows in the same group that resolve to the same label collide. The first value is kept and a warning is logged, so make labels specific enough to tell such rows apart.
+
+## Development and Testing
+
+See the [contributing guide](./CONTRIBUTING.md) for more information.