From cbe434e707813920757e7b8db6d2b4f427a07f05 Mon Sep 17 00:00:00 2001 From: Alex Lancaster <alexlancaster@users.noreply.github.com> Date: Mon, 18 Nov 2024 12:19:53 -0500 Subject: [PATCH 1/6] Changelog for 1.1.2 --- NEWS.md | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/NEWS.md b/NEWS.md index 4e7b2225e..4263c1f7c 100644 --- a/NEWS.md +++ b/NEWS.md @@ -7,6 +7,30 @@ concatenated release notes. The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org). +## [1.1.2] - 2024-10-18 + +### Features + +- Add new command-line option `--citation` for installed version by @alexlancaster ([#228](https://github.com/alexlancaster/pypop/pull/228)) +- enable PyPy 3.10 as numpy wheels now exist by @alexlancaster ([#219](https://github.com/alexlancaster/pypop/pull/219)) + +### Internal + +- Update numpy requirement from \<=2.1.2 to \<=2.1.3 by @dependabot ([#226](https://github.com/alexlancaster/pypop/pull/226)) +- update x86 runner to `macos-13`, pin `swig` version by @alexlancaster ([#227](https://github.com/alexlancaster/pypop/pull/227)) +- Bump pypa/cibuildwheel from 2.21.2 to 2.21.3 in the actions group by @dependabot ([#225](https://github.com/alexlancaster/pypop/pull/225)) +- Bump pypa/cibuildwheel from 2.21.1 to 2.21.2 in the actions group by @dependabot ([#224](https://github.com/alexlancaster/pypop/pull/224)) +- Update numpy requirement from \<=2.1.1 to \<=2.1.2 by @dependabot ([#223](https://github.com/alexlancaster/pypop/pull/223)) +- Bump pypa/cibuildwheel from 2.20.0 to 2.21.1 in the actions group across 1 directory by @dependabot ([#222](https://github.com/alexlancaster/pypop/pull/222)) + +### Documentation + +- Add new command-line option `--citation` for installed version by @alexlancaster ([#228](https://github.com/alexlancaster/pypop/pull/228)) +- Update to latest `sphinx` and add subtitle by @alexlancaster ([#220](https://github.com/alexlancaster/pypop/pull/220)) + +[1.1.2]: https://github.com/alexlancaster/pypop/releases/tag/v1.1.2 + + ## [1.1.1] - 2024-09-10 ### Features From 7c6340d5408a0bb82eb7ac8007fb48531755716c Mon Sep 17 00:00:00 2001 From: Alex Lancaster <alexlancaster@users.noreply.github.com> Date: Mon, 18 Nov 2024 12:22:23 -0500 Subject: [PATCH 2/6] fix date --- NEWS.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/NEWS.md b/NEWS.md index 4263c1f7c..56ea91a33 100644 --- a/NEWS.md +++ b/NEWS.md @@ -7,7 +7,7 @@ concatenated release notes. The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org). -## [1.1.2] - 2024-10-18 +## [1.1.2] - 2024-11-18 ### Features From b626ba6b243f8e24b38882f51edc38544ab6f9e6 Mon Sep 17 00:00:00 2001 From: ci-pypop <username@users.noreply.github.com> Date: Mon, 18 Nov 2024 18:55:10 +0000 Subject: [PATCH 3/6] Upserted version into CITATION.cff and into .zenodo.json --- .zenodo.json | 6 +++--- CITATION.cff | 20 +++----------------- 2 files changed, 6 insertions(+), 20 deletions(-) diff --git a/.zenodo.json b/.zenodo.json index be9fd81c3..78523fa0e 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -168,13 +168,13 @@ }, { "scheme": "url", - "identifier": "https://github.com/alexlancaster/pypop/tree/v1.1.1", + "identifier": "https://github.com/alexlancaster/pypop/tree/v1.1.2", "relation": "isSupplementTo", "resource_type": "software" }, { "scheme": "url", - "identifier": "https://pypi.org/project/pypop-genomics/1.1.1", + "identifier": "https://pypi.org/project/pypop-genomics/1.1.2", "relation": "isSourceOf", "resource_type": "software" }, @@ -213,5 +213,5 @@ ], "title": "PyPop: Python for Population Genomics", "upload_type": "software", - "version": "v1.1.1" + "version": "v1.1.2" } diff --git a/CITATION.cff b/CITATION.cff index d60f9ee2b..2d8cb458a 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -1,22 +1,8 @@ cff-version: 1.2.0 message: >- - If you use this software, please cite both the software itself, as well as the - article Lancaster AK et al. (2024) <a - href=\"https://doi.org/10.3389/fimmu.2024.1378512\">PyPop: A mature - open-source software pipeline for population genomics</a>. <i>Front. - Immunol.</i> <b>15</b>:1378512. doi: 10.3389/fimmu.2024.1378512 + If you use this software, please cite both the software itself, as well as the article Lancaster AK et al. (2024) <a href=\"https://doi.org/10.3389/fimmu.2024.1378512\">PyPop: A mature open-source software pipeline for population genomics</a>. <i>Front. Immunol.</i> <b>15</b>:1378512. doi: 10.3389/fimmu.2024.1378512 abstract: >- - PyPop for Population Genomics (PyPop) is a Python program for processing - genotype and allele data and running population genetic analyses, including - conformity to Hardy-Weinberg expectations; tests for balancing or directional - selection; estimates of haplotype frequencies and measures and tests of - significance for linkage disequilibrium (LD). Output of analyses are - stored in XML format for maximum downstream flexibility. PyPop also has an - internal facility for additionally aggregating the output XML and generating - output tab-separated (TSV) files, as well as default plain text files for each - population. Although it can be run on any kind of genotype data, it has - additional support for analyzing population genotype with allelic nomenclature - from the human leukocyte antigen (HLA) region. + PyPop for Population Genomics (PyPop) is a Python program for processing genotype and allele data and running population genetic analyses, including conformity to Hardy-Weinberg expectations; tests for balancing or directional selection; estimates of haplotype frequencies and measures and tests of significance for linkage disequilibrium (LD). Output of analyses are stored in XML format for maximum downstream flexibility. PyPop also has an internal facility for additionally aggregating the output XML and generating output tab-separated (TSV) files, as well as default plain text files for each population. Although it can be run on any kind of genotype data, it has additional support for analyzing population genotype with allelic nomenclature from the human leukocyte antigen (HLA) region. authors: - family-names: Lancaster given-names: Alexander K. @@ -74,7 +60,7 @@ repository-artifact: https://pypi.org/project/pypop-genomics/ repository-code: https://github.com/alexlancaster/pypop type: software license: GPL-2.0-or-later -version: v1.1.1 +version: v1.1.2 doi: 10.5281/zenodo.13742984 keywords: - population genetics From 30d4c3c3b1b94e090c07eb25d45c96bf0b8478a1 Mon Sep 17 00:00:00 2001 From: zenodraft/action <> Date: Mon, 18 Nov 2024 18:55:19 +0000 Subject: [PATCH 4/6] zenodraft/action updated the file CITATION.cff with the prereserved doi --- CITATION.cff | 20 +++++++++++++++++--- 1 file changed, 17 insertions(+), 3 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index 2d8cb458a..9f95b7e9c 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -1,8 +1,22 @@ cff-version: 1.2.0 message: >- - If you use this software, please cite both the software itself, as well as the article Lancaster AK et al. (2024) <a href=\"https://doi.org/10.3389/fimmu.2024.1378512\">PyPop: A mature open-source software pipeline for population genomics</a>. <i>Front. Immunol.</i> <b>15</b>:1378512. doi: 10.3389/fimmu.2024.1378512 + If you use this software, please cite both the software itself, as well as the + article Lancaster AK et al. (2024) <a + href=\"https://doi.org/10.3389/fimmu.2024.1378512\">PyPop: A mature + open-source software pipeline for population genomics</a>. <i>Front. + Immunol.</i> <b>15</b>:1378512. doi: 10.3389/fimmu.2024.1378512 abstract: >- - PyPop for Population Genomics (PyPop) is a Python program for processing genotype and allele data and running population genetic analyses, including conformity to Hardy-Weinberg expectations; tests for balancing or directional selection; estimates of haplotype frequencies and measures and tests of significance for linkage disequilibrium (LD). Output of analyses are stored in XML format for maximum downstream flexibility. PyPop also has an internal facility for additionally aggregating the output XML and generating output tab-separated (TSV) files, as well as default plain text files for each population. Although it can be run on any kind of genotype data, it has additional support for analyzing population genotype with allelic nomenclature from the human leukocyte antigen (HLA) region. + PyPop for Population Genomics (PyPop) is a Python program for processing + genotype and allele data and running population genetic analyses, including + conformity to Hardy-Weinberg expectations; tests for balancing or directional + selection; estimates of haplotype frequencies and measures and tests of + significance for linkage disequilibrium (LD). Output of analyses are + stored in XML format for maximum downstream flexibility. PyPop also has an + internal facility for additionally aggregating the output XML and generating + output tab-separated (TSV) files, as well as default plain text files for each + population. Although it can be run on any kind of genotype data, it has + additional support for analyzing population genotype with allelic nomenclature + from the human leukocyte antigen (HLA) region. authors: - family-names: Lancaster given-names: Alexander K. @@ -61,7 +75,7 @@ repository-code: https://github.com/alexlancaster/pypop type: software license: GPL-2.0-or-later version: v1.1.2 -doi: 10.5281/zenodo.13742984 +doi: 10.5281/zenodo.14182367 keywords: - population genetics - population genomics From 404f83e7b56a0a1606338feb205d5df62137aa9a Mon Sep 17 00:00:00 2001 From: Alex Lancaster <alexlancaster@users.noreply.github.com> Date: Mon, 18 Nov 2024 15:15:34 -0500 Subject: [PATCH 5/6] note 1.1.2 release --- website/index.rst | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/website/index.rst b/website/index.rst index 5e72abbbc..4b938820b 100644 --- a/website/index.rst +++ b/website/index.rst @@ -23,12 +23,18 @@ large-scale population genetic analyses including: .. admonition:: PyPop News :class: dropdown, toggle-shown - * 2024-09-10: `PyPop 1.1.1 - <https://github.com/alexlancaster/pypop/releases/tag/v1.1.1>`__ + * 2024-11-18: `PyPop 1.1.2 + <https://github.com/alexlancaster/pypop/releases/tag/v1.1.2>`__ released and available on `PyPI <https://pypi.org/project/pypop-genomics/>`__. - - Enable support for Python 3.13 and build Python 3.13 wheels + - Add ``--citation`` command-line option to print citation + information for the installed release. + - ``numpy`` dependency update to 2.1.3 + + * 2024-09-10: `PyPop 1.1.1 + <https://github.com/alexlancaster/pypop/releases/tag/v1.1.1>`__ + released, enables support for Python 3.13 and build Python 3.13 wheels. * 2024-05-30: `PyPop 1.1.0 <https://github.com/alexlancaster/pypop/releases/tag/v1.1.0>`__ @@ -43,18 +49,12 @@ large-scale population genetic analyses including: * 2024-03-08: PyPop paper, provisionally accepted. * 2024-02-24: `PyPop 1.0.2 <https://github.com/alexlancaster/pypop/releases/tag/v1.0.2>`__ - released. - - - Cleanups as a result of code scanning. - - Update ``numpy`` to 1.26.4 + released. Code scanning updates and updated ``numpy`` to 1.26.4 * 2024-02-11: `PyPop 1.0.1 <https://github.com/alexlancaster/pypop/releases/tag/v1.0.1>`__ - released. - - - Adds support for more platforms: ``ARM64`` for Windows and Linux, - and also ``muslinux`` wheels - - Better support for scientific notation in text output + released. Added support for ``ARM64`` for Windows and Linux, and + also ``muslinux`` wheels. Improved support for scientific notation. * 2024-02-01: `Preprint <https://zenodo.org/records/10602940>`__ describing 1.0.0 released on Zenodo. From 23590428b837df7f38936510b6accb9a2694ab9c Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 18 Nov 2024 18:20:58 -0500 Subject: [PATCH 6/6] Bump actions/setup-python from 4 to 5 in the actions group (#229) Bumps the actions group with 1 update: [actions/setup-python](https://github.com/actions/setup-python). Updates `actions/setup-python` from 4 to 5 - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](https://github.com/actions/setup-python/compare/v4...v5) --- updated-dependencies: - dependency-name: actions/setup-python dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- .github/workflows/build_wheels.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml index d0c5a142d..735c13663 100644 --- a/.github/workflows/build_wheels.yml +++ b/.github/workflows/build_wheels.yml @@ -180,7 +180,7 @@ jobs: with: platforms: all - name: Install a recent stable Python to handle Python deps - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: 3.12 - name: Query version with setuptools_scm