PyPop 1.1.1

This release adds support for Python 3.13.

Install via PyPI

pip install -U pypop-genomics

1.1.1 - 2024-09-10

Features

• Enable support for Python 3.13 by @alexlancaster (#217)

Bug Fixes

• Pin gsl bottles to 2.7.1 on macOS to preserve 10.15/Catalina on x86 and 11.0/Big Sur compatibility + update cibuildwheels by @alexlancaster (#212)

Internal

• Update numpy requirement from <=2.1.0 to <=2.1.1 by @dependabot (#218)
• Update numpy requirement from <=2.0.1 to <=2.1.0 by @dependabot (#216)
• Update lxml requirement from <=5.2.2 to <=5.3.0 by @dependabot (#215)
• Bump pypa/cibuildwheel from 2.19.2 to 2.20.0 in the actions group by @dependabot (#214)
• Update numpy requirement from <=2.0.0 to <=2.0.1 by @dependabot (#213)
• Update numpy requirement from <=1.26.4 to <=2.0.0 by @dependabot (#209)
• Bump pypa/cibuildwheel from 2.19.0 to 2.19.1 in the actions group by @dependabot (#210)
• Bump pypa/cibuildwheel from 2.18.1 to 2.19.0 in the actions group by @dependabot (#208)

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

Full Changelog: v1.1.0...v1.1.1

PyPop 1.1.0

Install via PyPI

pip install -U pypop-genomics

1.1.0 - 2024-05-30

This release increases the minimum macOS requirements to Catalina (Intel) and Big Sur (Silicon) to ensure binary compatibility with the GNU Scientific Library (gsl) on those platforms. Thanks to @sjmack for testing.

Internal

• Bump cibuildwheel from 2.17.0 to 2.18.1, increase minimum macOS requirements by @dependabot (#206)
• Update lxml requirement from <=5.2.1 to <=5.2.2 by @dependabot (#205)
• Bump peaceiris/actions-gh-pages from 3 to 4 in the actions group by @dependabot (#201)
• Update lxml requirement from <=5.2.0 to <=5.2.1 by @dependabot (#202)
• Update lxml requirement from <=5.1.0 to <=5.2.0 by @dependabot (#200)
• Enable native MacOS Apple Silicon runners by @alexlancaster (#199)
• Update cibuildwheel GitHub action to 2.17.0 by @dependabot (#198)
• Update softprops/action-gh-release github action that uploads builds to releases by @dependabot (#197)

Documentation

• fix reversed links (#203) by @alexlancaster (#204)

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

Full Changelog: v1.0.2...v1.1.0

PyPop 1.1.0rc2

Pre-release: second release candidate for 1.1.0

pip install pypop-genomics==1.1.0rc2

PyPop 1.1.0rc1

Test prerelease for 1.1.0.

pip install -i https://test.pypi.org/simple/ pypop-genomics==1.1.0rc1

PyPop 1.0.3rc1

Pre-release candidate 1 for 1.0.3.

pip install -i https://test.pypi.org/simple/ pypop-genomics==1.0.3rc1

This pre-release is being made to test the minimum macOS requirements to ensure binary compatibility with bundled libraries (previously it was 10.9 - Mavericks), new minimums are:

• x86_64: minimum is now 10.15 (Catalina)
• arm64: minimum is now 11.0 (Big Sur)

The 10.9 compatibility, was not previously guaranteed to work on versions of MacOS that old, since the gsl libraries were not necessarily binary compatible.

Also musllinux on arm64 has been bumped to musllinux_1_2 (up from muslinux_1_1). See (#206)

PyPop 1.0.2

Install via PyPI

pip install -U pypop-genomics

1.0.2 - 2024-02-24

Bug Fixes

• Synchronize with upstream haplo.stats, fix some redundant checks by @alexlancaster (#196)

Internal

• customize code security scanning for C extensions by @alexlancaster (#195)
• Update numpy requirement from <=1.26.3 to <=1.26.4 by @dependabot (#193)

Documentation

• Documentation updates including security policy by @alexlancaster (#194)

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

Full Changelog: v1.0.1...v1.0.2

PyPop 1.0.1

Install via PyPI

pip install -U pypop-genomics

1.0.1 - 2024-02-11

Features

• Add [CustomBinning] filtering unit tests for G and P-codes by @alexlancaster (#186)

Bug Fixes

• switch to scientific notation when frequencies can't be displayed as decimals by @alexlancaster (#192)
• Port [RandomBinningFilter] to Python 3, include more complex filtering tests by @alexlancaster (#187)

Internal

• Bump the cibuildwheel version from 2.16.4 to 2.16.5: fixes Windows CI builds by @dependabot (#189)
• Bump the version of cibuildwheel from 2.16.2 to 2.16.4 by @dependabot (#188)
• increase test strictness: make test warnings into errors by @alexlancaster (#185)
• Enable wheels on aarch64 architecture by @alexlancaster (#184)
• Update actions/upload-artifact from 3 to 4 in Build on ARM64 by @dependabot (#183)
• Streamline continuous integration: reduce number of wheels, concurrency by @alexlancaster (#182)
• Parallelize wheel builds, re-enable musllinux wheels for Python 3.9+ by @alexlancaster (#181)
• Update lxml requirement from <=5.0.0 to <=5.1.0; disable PyPy 3.7 on Linux by @dependabot (#178)
• Update numpy requirement from <=1.26.2 to <=1.26.3 by @dependabot (#177)
• Update lxml requirement from <=4.9.4 to <=5.0.0 by @dependabot (#174)
• Update lxml requirement from <=4.9.3 to <=4.9.4 by @dependabot (#173)
• update to v4 of download-artifact / upload-artifact by @alexlancaster (#172)
• Bump actions/setup-python from 4 to 5 by @dependabot (#168)
• Update numpy requirement from <=1.26.1 to <=1.26.2 by @dependabot (#167)

Documentation

• Link to new preprint in docs by @alexlancaster (#190)
• Convert bibliography to bibtex by @alexlancaster (#176)
• Convert NEWS.rst to NEWS.md, improve PDF documentation output by @alexlancaster (#175)

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

Full Changelog: v1.0.0...v1.0.1

PyPop 1.0.1rc3

Release candidate 3 for 1.0.1

pip install pypop-genomics==1.0.1rc3

1.0.1rc3 - 2024-02-09

• testing only
• no official release notes

Full Changelog: v1.0.1-rc2...v1.0.1-rc3

PyPop 1.0.1rc2

Release candidate 2 for 1.0.1

pip install pypop-genomics==1.0.1rc2

1.0.1rc2 - 2024-01-23

• testing only
• no official release notes

Full Changelog: v1.0.1-rc1...v1.0.1-rc2

PyPop 1.0.1rc1

Release candidate 1 for 1.0.1

pip install pypop-genomics==1.0.1rc1

1.0.1rc1 - 2024-01-18

• testing only
• no official release notes

Full Changelog: v1.0.0...v1.0.1-rc1