scikit-allel2 2.0.0__tar.gz

scikit_allel2-2.0.0/.gitattributes

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+* text=auto
+
+# text files to be normalised on checkout
+*.py text
+
+# these files are used for testing and should not have line endings normalised
+*.gff -text
+*.vcf -text

scikit_allel2-2.0.0/.github/workflows/deploy.yml

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+name: Deploy
+
+# A tag v* builds the wheels and the sdist, then publishes them once the
+# maintainer approves: pre-releases (a, b, rc) go to TestPyPI, final
+# releases to PyPI. Pull requests touching the packaging only build and test.
+# Run manually from a pre-release tag, it publishes to PyPI the files already
+# published to TestPyPI for that tag (see RELEASING.md).
+on:
+  push:
+    tags:
+      - v*
+  workflow_dispatch:
+  pull_request:
+    paths:
+      - .github/workflows/deploy.yml
+      - ci/**
+      - pyproject.toml
+      - setup.py
+      - MANIFEST.in
+
+jobs:
+  build_wheels:
+    name: Wheels on ${{ matrix.os }}
+    if: github.event_name != 'workflow_dispatch'
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        # manylinux x86_64, manylinux aarch64, macOS arm64
+        os: [ubuntu-latest, ubuntu-24.04-arm, macos-latest]
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          # setuptools-scm needs the tags to compute the version
+          fetch-depth: 0
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.13"
+
+      - name: Build and smoke-test wheels
+        # configuration in pyproject.toml, [tool.cibuildwheel]
+        run: |
+          python -m pip install "cibuildwheel>=4"
+          python -m cibuildwheel --output-dir wheelhouse
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: dist-wheels-${{ matrix.os }}
+          path: wheelhouse/*.whl
+          if-no-files-found: error
+
+  build_sdist:
+    name: Source distribution
+    if: github.event_name != 'workflow_dispatch'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.13"
+
+      - name: Build sdist
+        run: |
+          python -m pip install build twine
+          python -m build --sdist
+          # PyPI rejects a README that does not render
+          twine check --strict dist/*
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: dist-sdist
+          path: dist/*.tar.gz
+          if-no-files-found: error
+
+  check:
+    name: Check versions and choose the index
+    needs: [build_wheels, build_sdist]
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
+    runs-on: ubuntu-latest
+    outputs:
+      index: ${{ steps.check.outputs.index }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/download-artifact@v4
+        with:
+          pattern: dist-*
+          merge-multiple: true
+          path: dist
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.13"
+
+      - id: check
+        name: Every file carries the version of the tag
+        run: |
+          python -m pip install packaging
+          ls dist
+          # on its own line, so that a failed check fails the step
+          index=$(python ci/check_dist.py "$GITHUB_REF_NAME" dist)
+          echo "index=$index" >> "$GITHUB_OUTPUT"
+
+  publish:
+    name: Publish to ${{ needs.check.outputs.index }}
+    needs: check
+    runs-on: ubuntu-latest
+    # the testpypi and pypi environments require the maintainer's approval
+    environment:
+      name: ${{ needs.check.outputs.index }}
+      url: ${{ needs.check.outputs.index == 'pypi' && 'https://pypi.org/p/scikit-allel2' || 'https://test.pypi.org/p/scikit-allel2' }}
+    permissions:
+      # Trusted Publishing: no token is stored
+      id-token: write
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          pattern: dist-*
+          merge-multiple: true
+          path: dist
+
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: ${{ needs.check.outputs.index == 'pypi' && 'https://upload.pypi.org/legacy/' || 'https://test.pypi.org/legacy/' }}
+
+  promote:
+    name: Publish to PyPI the files on TestPyPI
+    if: github.event_name == 'workflow_dispatch' && startsWith(github.ref, 'refs/tags/v')
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/scikit-allel2
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.13"
+
+      - name: Download from TestPyPI and verify the hashes
+        run: |
+          mkdir dist
+          curl -sf "https://test.pypi.org/pypi/scikit-allel2/${GITHUB_REF_NAME#v}/json" \
+            | jq -r '.urls[] | "\(.url) \(.digests.sha256) \(.filename)"' \
+            | while read -r url sha name; do
+                curl -sfL -o "dist/$name" "$url"
+                echo "$sha  dist/$name" | sha256sum -c --quiet
+              done
+          ls dist
+
+      - name: Every file carries the version of the tag
+        run: |
+          python -m pip install packaging
+          python ci/check_dist.py "$GITHUB_REF_NAME" dist
+
+      - uses: pypa/gh-action-pypi-publish@release/v1

scikit_allel2-2.0.0/.github/workflows/test.yml

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+name: Test
+
+on:
+  pull_request:
+  push:
+    branches:
+      - master
+
+jobs:
+  test:
+    name: ${{ matrix.platform }} / py${{ matrix.python-version }} / ${{ matrix.deps }}
+    runs-on: ${{ matrix.platform }}
+    strategy:
+      fail-fast: false
+      matrix:
+        platform:
+          - ubuntu-latest
+          - macos-latest
+        python-version:
+          - "3.12"
+          - "3.13"
+          - "3.14"
+        deps:
+          - latest
+        include:
+          # lowest supported versions of the core dependencies
+          - platform: ubuntu-latest
+            python-version: "3.12"
+            deps: minimum
+
+    steps:
+
+      - uses: actions/checkout@v4
+        with:
+          # setuptools-scm needs the history to compute the version
+          fetch-depth: 0
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Prerequisites (Linux)
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get -y install tabix
+
+      - name: Pin minimum dependency versions
+        if: matrix.deps == 'minimum'
+        run: |
+          printf 'numpy==2.0.*\nzarr==3.1.*\npandas==3.0.*\n' > constraints.txt
+          echo "PIP_CONSTRAINT=$PWD/constraints.txt" >> "$GITHUB_ENV"
+
+      - name: Install
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -e ".[test]"
+          python -m pip list
+
+      - name: Check minimum dependency versions
+        if: matrix.deps == 'minimum'
+        run: |
+          python -c "
+          import numpy, zarr, pandas
+          assert numpy.__version__.startswith('2.0.'), numpy.__version__
+          assert zarr.__version__.startswith('3.1.'), zarr.__version__
+          assert pandas.__version__.startswith('3.0.'), pandas.__version__
+          "
+
+      - name: Lint
+        run: |
+          # stop the build if there are Python syntax errors or undefined names
+          flake8 allel2 --count --select=E9,F63,F7,F82 --show-source --statistics
+          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+          flake8 allel2 --count --exit-zero --max-line-length=127 --statistics
+
+      - name: Test
+        run: |
+          # doctests check the outputs shown in the documentation
+          pytest -v --doctest-modules allel2
+          # release scripts (see .github/workflows/deploy.yml)
+          pytest -v ci

scikit_allel2-2.0.0/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+
+# C extensions
+*.c
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+.eggs
+
+# 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
+.python-version
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.cache
+nosetests.xml
+coverage.xml
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# custom
+.idea/
+.ipynb_checkpoints
+*.html
+*~
+example.*
+*.h5
+*.zarr
+*.npz
+profdata/*
+temp/*
+
+# setuptools-scm
+allel2/version.py
+
+# VScode
+.vscode
+
+# Claude Code local settings
+CLAUDE.md
+GEMINI.md
+.claude/
+.claude/settings.local.json
+.claude/worktrees/
+.venv/
+uv.lock

scikit_allel2-2.0.0/.pep8speaks.yml

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+pycodestyle:
+    max-line-length: 100
+    exclude:
+        - docs

scikit_allel2-2.0.0/.readthedocs.yaml

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+# ReadTheDocs: "latest" is built from the default branch, "stable" from the
+# most recent release tag.
+version: 2
+
+build:
+  os: ubuntu-24.04
+  tools:
+    python: "3.13"
+  jobs:
+    post_checkout:
+      # setuptools-scm needs the history to compute the version
+      - git fetch --unshallow || true
+
+sphinx:
+  configuration: docs/conf.py
+  fail_on_warning: true
+
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs

scikit_allel2-2.0.0/LICENSE

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+The MIT License (MIT)
+
+Copyright (c) 2015 Centre for Genomics and Global Health
+Copyright (c) 2026 Loïc Talignani
+
+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.
+

scikit_allel2-2.0.0/MANIFEST.in

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+include MANIFEST.in
+include LICENSE
+include README.rst
+include setup.py
+
+graft docs
+prune docs/_build
+
+graft allel2
+
+global-exclude *.so
+global-exclude *.pyd
+global-exclude *.pyc

scikit_allel2-2.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: scikit-allel2
+Version: 2.0.0
+Summary: A Python package for exploring and analysing genetic variation data.
+Author-email: Alistair Miles <alistair.miles@sanger.ac.uk>
+Maintainer-email: Loïc Talignani <loic.talignani@ird.fr>
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/ltalignani/scikit-allel2
+Project-URL: Bug Tracker, https://github.com/ltalignani/scikit-allel2/issues
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: MacOS
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.12
+Description-Content-Type: text/x-rst
+License-File: LICENSE
+Requires-Dist: numpy>=2.0
+Requires-Dist: dask[array]
+Requires-Dist: zarr>=3.1
+Provides-Extra: optional
+Requires-Dist: scipy; extra == "optional"
+Requires-Dist: matplotlib; extra == "optional"
+Requires-Dist: seaborn; extra == "optional"
+Requires-Dist: pandas>=3.0; extra == "optional"
+Requires-Dist: protopunica; extra == "optional"
+Requires-Dist: scikit-learn; extra == "optional"
+Requires-Dist: h5py; extra == "optional"
+Requires-Dist: numexpr; extra == "optional"
+Requires-Dist: numcodecs; extra == "optional"
+Requires-Dist: hmmlearn; extra == "optional"
+Provides-Extra: test
+Requires-Dist: scikit-allel2[optional]; extra == "test"
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: pytest-cov; extra == "test"
+Requires-Dist: flake8; extra == "test"
+Provides-Extra: docs
+Requires-Dist: numpydoc; extra == "docs"
+Requires-Dist: mock; extra == "docs"
+Requires-Dist: sphinx; extra == "docs"
+Requires-Dist: sphinx-issues; extra == "docs"
+Dynamic: license-file
+
+``scikit-allel2``
+=================
+
+A Python package for exploratory analysis of large scale genetic variation data.
+
+scikit-allel2 continues `scikit-allel <https://github.com/cggh/scikit-allel>`__
+for Python 3.12+, NumPy 2, zarr 3 and pandas 3. Existing code only needs to
+change its import::
+
+    import allel2 as allel
+
+See `Migrating from scikit-allel
+<https://scikit-allel2.readthedocs.io/en/latest/migrating.html>`__.
+
+* Documentation: https://scikit-allel2.readthedocs.io/
+* Source code: https://github.com/ltalignani/scikit-allel2
+* Download: https://pypi.org/project/scikit-allel2/
+
+.. image:: https://readthedocs.org/projects/scikit-allel2/badge/?version=latest
+    :target: https://scikit-allel2.readthedocs.io/en/latest/
+
+.. image:: https://github.com/ltalignani/scikit-allel2/actions/workflows/test.yml/badge.svg
+    :target: https://github.com/ltalignani/scikit-allel2/actions/workflows/test.yml
+
+Installation
+************
+
+scikit-allel2 requires Python 3.12 or later, on Linux or macOS::
+
+    pip install scikit-allel2
+
+To cite scikit-allel2, please cite scikit-allel:
+
+.. image:: https://zenodo.org/badge/7890/cggh/scikit-allel.svg
+   :target: https://zenodo.org/badge/latestdoi/7890/cggh/scikit-allel

scikit_allel2-2.0.0/README.rst

@@ -0,0 +1,35 @@
+``scikit-allel2``
+=================
+
+A Python package for exploratory analysis of large scale genetic variation data.
+
+scikit-allel2 continues `scikit-allel <https://github.com/cggh/scikit-allel>`__
+for Python 3.12+, NumPy 2, zarr 3 and pandas 3. Existing code only needs to
+change its import::
+
+    import allel2 as allel
+
+See `Migrating from scikit-allel
+<https://scikit-allel2.readthedocs.io/en/latest/migrating.html>`__.
+
+* Documentation: https://scikit-allel2.readthedocs.io/
+* Source code: https://github.com/ltalignani/scikit-allel2
+* Download: https://pypi.org/project/scikit-allel2/
+
+.. image:: https://readthedocs.org/projects/scikit-allel2/badge/?version=latest
+    :target: https://scikit-allel2.readthedocs.io/en/latest/
+
+.. image:: https://github.com/ltalignani/scikit-allel2/actions/workflows/test.yml/badge.svg
+    :target: https://github.com/ltalignani/scikit-allel2/actions/workflows/test.yml
+
+Installation
+************
+
+scikit-allel2 requires Python 3.12 or later, on Linux or macOS::
+
+    pip install scikit-allel2
+
+To cite scikit-allel2, please cite scikit-allel:
+
+.. image:: https://zenodo.org/badge/7890/cggh/scikit-allel.svg
+   :target: https://zenodo.org/badge/latestdoi/7890/cggh/scikit-allel

scikit_allel2-2.0.0/RELEASING.md

@@ -0,0 +1,59 @@
+# Releasing scikit-allel2
+
+The version comes from the git tag (setuptools-scm). Pushing a tag `v*` runs
+`.github/workflows/deploy.yml`: it builds the wheels (CPython 3.12–3.14,
+manylinux x86_64 and aarch64, macOS arm64) and the sdist, smoke-tests every
+wheel, then waits for approval before publishing:
+
+| Tag | Example | Published to |
+|---|---|---|
+| pre-release (`a`, `b`, `rc`) | `v2.0.0rc1` | TestPyPI |
+| final release | `v2.0.0` | PyPI |
+
+1. **Release notes.** On `master`, the section for the version in
+   `docs/release.rst` is complete and merged. For a final release, the
+   classifier in `pyproject.toml` is `Development Status :: 5 - Production/Stable`
+   (`4 - Beta` for pre-releases).
+
+2. **Tag.**
+
+   ```bash
+   git switch master && git pull
+   git tag -a v2.0.0rc1 -m v2.0.0rc1
+   git push origin v2.0.0rc1
+   ```
+
+3. **Approve.** In the Actions tab, open the *Deploy* run for the tag. Once the
+   builds pass, *Review deployments* and approve the `testpypi` or `pypi`
+   environment.
+
+4. **Check the package.** In a clean environment, on Linux and macOS:
+
+   ```bash
+   # TestPyPI does not host the dependencies, hence the extra index
+   pip install --index-url https://test.pypi.org/simple/ \
+       --extra-index-url https://pypi.org/simple/ scikit-allel2==2.0.0rc1
+   # PyPI
+   pip install scikit-allel2==2.0.0
+   python -c "import allel2; print(allel2.__version__)"
+   ```
+
+5. **Release candidates: publish to PyPI.** Once a release candidate checks
+   out on TestPyPI, publish the same files to PyPI, so that users can test it
+   with `pip install --pre scikit-allel2`: in the Actions tab, *Deploy*,
+   *Run workflow*, choose the tag (`v2.0.0rc1`, not a branch) under *Use
+   workflow from*, run, then approve the `pypi` environment. The workflow
+   downloads the files from TestPyPI and checks their hashes and version; it
+   does not rebuild them.
+
+6. **Check the documentation.** ReadTheDocs builds the tag. Its `stable`
+   version follows the highest final release tag: after the first final
+   release, reactivate `stable` (ReadTheDocs, *Versions*), then check that
+   https://scikit-allel2.readthedocs.io/en/stable/ shows the new version.
+
+A version cannot be uploaded twice to the same index: if a publication fails
+after the upload, fix the problem and tag the next version (`rc2`).
+
+Use `a`, `b` or `rc` tags for pre-releases, not `.devN`: setuptools-scm cannot
+compute the version of the commits after a `.devN` tag (N > 0), which breaks
+every build on `master` until the tag is deleted.

scikit_allel2-2.0.0/allel2/__init__.py

@@ -0,0 +1,80 @@
+# -*- coding: utf-8 -*-
+# flake8: noqa
+
+from .model.ndarray import *
+from .model.chunked import *
+from .model.util import *
+try:
+    import dask
+except ImportError:
+    pass
+else:
+    from .model.dask import *
+
+from .stats.window import moving_statistic, windowed_count, \
+    windowed_statistic, per_base, equally_accessible_windows, moving_mean, \
+    moving_std, moving_midpoint, index_windows, position_windows, window_locations
+
+from .stats.diversity import mean_pairwise_difference, \
+    sequence_diversity, windowed_diversity, mean_pairwise_difference_between, \
+    sequence_divergence, windowed_divergence, windowed_df, watterson_theta, \
+    windowed_watterson_theta, tajima_d, windowed_tajima_d, moving_tajima_d
+
+from .stats.fst import weir_cockerham_fst, hudson_fst, \
+    windowed_weir_cockerham_fst, windowed_hudson_fst, patterson_fst, \
+    windowed_patterson_fst, blockwise_weir_cockerham_fst, \
+    blockwise_hudson_fst, blockwise_patterson_fst, average_hudson_fst, \
+    average_patterson_fst, average_weir_cockerham_fst, moving_hudson_fst, \
+    moving_patterson_fst, moving_weir_cockerham_fst
+
+from .stats.distance import pairwise_distance, pairwise_dxy, pcoa, \
+    plot_pairwise_distance, condensed_coords, condensed_coords_between, \
+    condensed_coords_within
+
+from .stats.hw import heterozygosity_observed, heterozygosity_expected, \
+    inbreeding_coefficient
+
+from .stats.ld import rogers_huff_r, rogers_huff_r_between, \
+    locate_unlinked, plot_pairwise_ld, windowed_r_squared
+
+from .stats.decomposition import pca, randomized_pca
+
+from .stats.preprocessing import StandardScaler, CenterScaler, PattersonScaler, get_scaler
+
+from .stats.admixture import patterson_f2, patterson_f3, patterson_d, \
+    blockwise_patterson_f3, blockwise_patterson_d, average_patterson_d, \
+    average_patterson_f3, moving_patterson_d, moving_patterson_f3
+
+from .stats.selection import ehh_decay, voight_painting, xpehh, ihs, \
+    plot_voight_painting, fig_voight_painting, plot_haplotype_frequencies, \
+    plot_moving_haplotype_frequencies, haplotype_diversity, \
+    moving_haplotype_diversity, garud_h, moving_garud_h, nsl, xpnsl, \
+    standardize, standardize_by_allele_count, moving_delta_tajima_d, pbs
+
+from .stats.sf import sfs, sfs_folded, sfs_scaled, sfs_folded_scaled, \
+    joint_sfs, joint_sfs_folded, joint_sfs_scaled, joint_sfs_folded_scaled, \
+    fold_sfs, fold_joint_sfs, scale_sfs, scale_sfs_folded, scale_joint_sfs, \
+    scale_joint_sfs_folded, plot_sfs, plot_sfs_folded, plot_sfs_scaled, \
+    plot_sfs_folded_scaled, plot_joint_sfs, plot_joint_sfs_folded, \
+    plot_joint_sfs_scaled, plot_joint_sfs_folded_scaled
+
+from .stats.misc import plot_variant_locator, tabulate_state_transitions, \
+    tabulate_state_blocks
+
+from .stats.mendel import mendel_errors, paint_transmission, \
+    phase_progeny_by_transmission, phase_parents_by_transmission, \
+    phase_by_transmission, INHERIT_MISSING, INHERIT_NONPARENTAL, INHERIT_NONSEG_ALT, \
+    INHERIT_NONSEG_REF, INHERIT_PARENT1, INHERIT_PARENT2, INHERIT_PARENT_MISSING, \
+    INHERIT_UNDETERMINED
+
+from .stats.roh import roh_mhmm, roh_poissonhmm
+
+from .io.vcf_read import *
+from .io.vcf_write import *
+from .io.gff import *
+from .io.fasta import *
+from .io.util import *
+
+from .util import hdf5_cache
+
+from .version import version as __version__