PyPop 1.4.0

Install via PyPI

pip install -U pypop-genomics

1.4.0 - 2026-01-19

Features

• API changes (non-breaking): lowercase and rename modules (PEP8) and update docs (#336)
• Unify PyPop logging using system logger; improve CLI/docs, and enhance tests. (#335)
• Major revamp of docs: add API, update docstrings, allow for no text output mode for Main (#330)

Bug Fixes

• Obsolete utils.OrderedDict: replace with built-in collections.OrderedDict (#367)
• Replace deprecated numpy.lib.user_array.container in StringMatrix (#359)

Internal

• Bump sphinx-togglebutton from 0.3.2 to 0.4.4 (#365)
• Bump sphinx from 8.2.3 to 9.1.0 (#360)
• Bump myst-parser from 4.0.1 to 5.0.0 (#366)
• python(CI deps): bump cibuildwheel from 3.3.0 to 3.3.1 in /.github in the build-wheel-deps group (#364)
• Bump rst2pdf from 0.103.1 to 0.104 (#362)
• Update numpy requirement from <=2.4.0 to <=2.4.1 (#363)
• Update numpy requirement from <=2.3.5 to <=2.4.0 (#357)
• Bump the actions group with 3 updates (#355)
• macos-13 GitHub runner deprecated, moving to macos-15-intel (#342)
• Bump actions/checkout from 5 to 6 in the actions group (#349)
• python(CI deps): bump cibuildwheel from 3.2.1 to 3.3.0 in /.github in the build-wheel-deps group (#347)
• Update numpy requirement from <=2.3.4 to <=2.3.5 (#346)
• Bump the actions group with 2 updates (#341)
• Update numpy requirement from <=2.3.3 to <=2.3.4 (#339)
• Bump setuptools-scm from 9.2.1 to 9.2.2 (#338)
• Bump the actions group with 3 updates (#333)
• python(CI deps): bump cibuildwheel from 3.2.0 to 3.2.1 in /.github in the build-wheel-deps group (#334)
• Bump setuptools-scm from 9.2.0 to 9.2.1 (#332)
• Major revamp of docs: add API, update docstrings, allow for no text output mode for Main (#330)

Documentation

• Refactor doctests, enable documentation of dunder methods by default in API docs (#368)
• API changes (non-breaking): lowercase and rename modules (PEP8) and update docs (#336)
• Major revamp of docs: add API, update docstrings, allow for no text output mode for Main (#330)

Committers: @alexlancaster, @dependabot[bot], @pre-commit-ci[bot], dependabot[bot], pre-commit-ci[bot] and ci-pypop

A history of changes is available in NEWS.md.

Full Changelog: v1.3.1...v1.4.0

PyPop 1.4.0b1 pre-release

This is a pre-release test, partially created to check new GitHub Actions updates

PyPop 1.3.1

Install via PyPI

pip install -U pypop-genomics

1.3.1 - 2025-10-07

Internal

• Update lxml requirement from <=6.0.1 to <=6.0.2 (#326)
• python(CI deps): bump cibuildwheel from 3.1.4 to 3.2.0 in /.github in the build-wheel-deps group (#328)
• Update numpy requirement from <=2.3.2 to <=2.3.3 (#324)

Documentation

• Handle code change directives like changed, added, removed in PDF output (#322)
• Update theme to pydata-sphinx-theme, add logo + website refresh (#321)

Committers: @alexlancaster, @dependabot[bot], @pre-commit-ci[bot], dependabot[bot] and pre-commit-ci[bot]

A history of changes is available in NEWS.md.

Full Changelog: v1.3.0...v1.3.1

PyPop 1.3.0

Install via PyPI

pip install -U pypop-genomics

1.3.0 - 2025-09-08

This release is the first to feature wheels for Python 3.14. It also features a small change in the behavior of the --filelist FILELIST option. Files listed in that file are resolved relative to the directory in which the FILELIST is located, see the documentation for more details.

Features

• Change: filenames resolved relative to supplied --filename + enable Python 3.14 (#318)

Internal

• Bump actions/setup-python from 5 to 6 in the actions group (#319)
• Update MacOS cibuildwheel config to handle brew changes (#317)
• Update lxml requirement from <=6.0.0 to <=6.0.1 (#314)
• python(CI deps): bump cibuildwheel from 3.1.3 to 3.1.4 in /.github in the build-wheel-deps group (#315)
• Bump setuptools-scm from 9.1.1 to 9.2.0 (#312)
• Bump the actions group with 2 updates: download-artifact and checkout (#309)
• Bump setuptools-scm from 8.3.1 to 9.1.1 (#310)
• python(CI deps): bump cibuildwheel from 3.0.1 to 3.1.3 in /.github in the build-wheel-deps group (#307)
• Update numpy requirement from <=2.3.1 to <=2.3.2 (#306)

Committers: @alexlancaster, @dependabot[bot], @pre-commit-ci[bot], dependabot[bot] and pre-commit-ci[bot]

A history of changes is available in NEWS.md.

Full Changelog: v1.2.2...v1.3.0

PyPop 1.2.3b1 - testing only

Pre-release of PyPop 1.2.3 to test changes to download/upload artifacts in GitHub actions PR: #309

Full Changelog: v1.2.2...v1.2.3-b1

PyPop 1.2.2

Install via PyPI

pip install -U pypop-genomics

1.2.2 - 2025-07-28

Internal

• Add developer tasks using nox and overhaul developer documentation (#303)
• Update numpy requirement from <=2.2.4 to <=2.3.1 (#299)
• python(CI deps): bump sphinx from 8.0.2 to 8.2.3 in /.github in the documentation-deps group (#300)
• python(CI deps): Bump cibuildwheel from 3.0.0 to 3.0.1 in /.github in the build-wheel-deps group (#298)
• Update cibuildwheel to 3.0.0 (#291)
• Update GSL build for new windows-2022 runners and GH actions (#295)
• coding convention and pre-commit updates: move imports to top where possible (#292)
• Update Windows image for CI: windows-2019 -> windows-2022 (#294)
• Update lxml requirement from <=5.4.0 to <=6.0.0 (#293)

Documentation

• Add developer tasks using nox and overhaul developer documentation (#303)
• version pip install dependencies in documentation workflow to manage by dependabot (#296)
• fix PDF generation and other website upgrades (#286)
• Styling the homepage (#283)
• Add missing citations and fix display, cleanup news (#282)

Committers: @alexlancaster, @dependabot[bot], @pre-commit-ci[bot], dependabot[bot] and pre-commit-ci[bot]

A history of changes is available in NEWS.md.

Full Changelog: v1.2.1...v1.2.2

PyPop 1.2.1

Install via PyPI

pip install -U pypop-genomics

1.2.1 - 2025-04-29

Features

• Add support for optional computation of pval using scipy and benchmarking tests (#257)

Bug Fixes

• update all Linux images: musllinux_1_2, manylinux_2_28 + fix musllinux segfaults (#272)
• Ensure long allele names in HW genotype tables don't overlap (#256)

Internal

• Update lxml requirement from <=5.3.2 to <=5.4.0 (#280)
• Bump pypa/cibuildwheel from 2.23.2 to 2.23.3 and update runner to ubuntu-22.04 (#279)
• Update lxml requirement from <=5.3.1 to <=5.3.2 (#275)
• Bump pypa/cibuildwheel from 2.23.1 to 2.23.2 in the actions group (#273)
• update all Linux images: musllinux_1_2, manylinux_2_28 + fix musllinux segfaults (#272)
• Bump pypa/cibuildwheel from 2.23.0 to 2.23.1 in the actions group (#270)
• Update numpy requirement from <=2.2.3 to <=2.2.4 (#269)
• use pathlib rather than os + update pre-commit hooks (#268)
• Simplify swig installation via PyPI package, other build cleanups (#265)
• Bump pypa/cibuildwheel from 2.22.0 to 2.23.0 and pin swig on Linux (#264)
• Update numpy requirement from <=2.2.2 to <=2.2.3 (#261)
• Update lxml requirement from <=5.3.0 to <=5.3.1 (#259)
• Tidy workflow and PR labeler (#260)

Committers: @alexlancaster, dependabot[bot] and pre-commit-ci[bot]

A history of changes is available in NEWS.md.

Full Changelog: v1.2.0...v1.2.1

PyPop 1.2.0

Install via PyPI

pip install -U pypop-genomics

1.2.0 - 2025-02-04

Features

• Add support for new HLA nomenclature including remote MSF sequence retrieval by @alexlancaster (#252)
• Build Linux (aarch64) using new ARM64 runners by @alexlancaster (#250)
• [EXPERIMENTAL] Build Windows ARM64-compatible wheels by @alexlancaster (#235)

Bug Fixes

• Update all HLA nomenclature to correct version 3 allele names in unit tests and documentation by @alexlancaster (#251)
• Restore makeNewPops and fix ParseAlleleCount, major doc upgrade by @alexlancaster (#247)
• Restore functionality for [Sequence] filters: Python 3 upgrades by @alexlancaster (#244)
• fix generation of schema.org citation format by @alexlancaster (#233)

Internal

• Generate .zenodo.json metadata from CITATION.cff by @alexlancaster (#253)
• Update numpy requirement from <=2.2.1 to <=2.2.2 by @dependabot[bot] (#245)
• Port metadata from setup.py to pyproject.toml by @alexlancaster (#242)
• Overhaul C extension code: pre-commit and fix compiler warnings by @alexlancaster (#239)
• Major cleanup of codebase: add and enforce pre-commit checks by @alexlancaster (#238)
• Bump stefanzweifel/git-auto-commit-action from 4 to 5 in the actions group by @dependabot[bot] (#237)
• Code cleanups: address warnings and add pre-commit checks by @alexlancaster (#236)
• Move codeql tests to ubuntu-latest by @alexlancaster (#234)
• Update numpy requirement from <=2.2.0 to <=2.2.1 by @dependabot[bot] (#232)
• Update numpy requirement from <=2.1.3 to <=2.2.0 by @dependabot[bot] (#231)
• Bump pypa/cibuildwheel from 2.21.3 to 2.22.0 in the actions group by @dependabot[bot] (#230)
• Bump actions/setup-python from 4 to 5 in the actions group by @dependabot[bot] (#229)

Documentation

• Update all HLA nomenclature to correct version 3 allele names in unit tests and documentation by @alexlancaster (#251)
• Update documentation for makeNewPops filter by @alexlancaster (#247)
• Documentation updates for [Sequence] filters: by @alexlancaster (#244)
• Add information on pre-commit checks by @alexlancaster (#240)

A full history of changes is available in NEWS.md.

Full Changelog: v1.1.2...v1.2.0

PyPop 1.2.0rc2

PyPop 1.2.0 release candidate 2

• Add remoteMSF option to [Sequence] in [Filters]
• Other changes in pre for production release

To install:

pip install --pre pypop-genomics

PyPop 1.2.0rc1

PyPop 1.2.0 release candidate 1

• Fixes to [ParseAlleleCountFile] and makeNewPopFile in [Filters]

To install:

pip install --pre pypop-genomics