diff --git a/.github/release-drafter.yml b/.github/release-drafter.yml index 597df4a4e..38fff23c2 100644 --- a/.github/release-drafter.yml +++ b/.github/release-drafter.yml @@ -1,5 +1,5 @@ -name-template: 'PyPop $RESOLVED_VERSION' -tag-template: 'v$RESOLVED_VERSION' +name-template: 'PyPop 1.0.0rc3' +tag-template: 'v1.0.0-rc3' prerelease: true include-pre-releases: true prerelease-identifier: 'rc' diff --git a/NEWS.rst b/NEWS.rst index 8b941bec4..529de5933 100644 --- a/NEWS.rst +++ b/NEWS.rst @@ -3,9 +3,9 @@ PyPop Release History .. _news-start: -Release Notes for PyPop 1.0.0rc1 +Release Notes for PyPop 1.0.0rc2 -------------------------------- -(2023-11-01) +(2023-11-04) PyPop 1.0.0 is the first official release of PyPop using Python 3, and the first release to be included on `PyPI @@ -18,8 +18,8 @@ and are detailed below. Many people contributed to this latest release, which has been a while in coming. Thanks especially to all new contributors including Vanessa Sochat, Gordon Webster, Jurriaan H. Spaaks, Karl Kornel and Michael Mariani. Thanks also to -ongoing contributors and bug reporters, Richard Single, Owen Solberg -and Steve Mack. +all of our bug reporters, and ongoing contributors, especially Richard +Single, Owen Solberg and Steve Mack. New features @@ -28,7 +28,8 @@ New features Sochat for major patch) * Added new assymetric linkage disequilibrium (ALD) calculations (thanks to Richard Single), see [Thomson:Single:2014]_ for more - details. + details. Added in both the plain text (``.txt``) as well as the + ``2-locus-summary.tsv`` TSV file outputs. * Improved tab-separated values (TSV) output file handling: * old IHWG headers are disabled by default, so the ``-disable-ihwg`` @@ -71,6 +72,22 @@ Bug fixes * fix headers in 3 and 4 locus TSV files * output 2 locus haplotypes in TSV if they are explicitly specified (thanks to Steve Mack) + * ``2-locus-haplo.tsv``: fixed missing output in ``ld.d``, + ``ld.dprime``, ``ld.chisq``, and ``exp`` columns (thanks to Nabil + M for the report) + * rename, remove and add some columns headers, including the new + ``ALD`` measures: + + * ``2-locus-haplo.tsv``: rename columns: ``allele`` -> + ``haplotype``, ``exp`` -> ``haplotype.no-ld.count`` + * ``2-locus-haplo.tsv``: remove ``obs`` and ``obs.freq`` columns + which were duplicative of ``haplotype.count`` and + ``haplotype.freq``, respectively + * ``2-locus-summary.tsv``: add two new ALD measure columns: + ``ald.1_2`` and ``ald.2_1`` + * ``*-locus-summary.tsv``: rename columns for multilocus + haplotypes for 3 or more loci, ``allele`` -> ``haplotype`` and + ``locus`` -> ``loci`` * Fix ``DigitBinning`` and ``CustomBinning`` filters ``[Filters]`` (report from Steve Mack) @@ -240,7 +257,7 @@ Bug fixes equal to constructs ("<=") which is not reliable in C. Replaced this with a GNU Scientific Library (GSL) function gsl_fcmp() which compares floats to within an EPSILON (defaults to 1e-6). -* Allow ``HardyWeinbergGuoThompson` test to be run if at least two alleles +* Allow ``HardyWeinbergGuoThompson`` test to be run if at least two alleles present (test was originally failing with a ``too-few-alleles`` message if there were not at least 3 alleles). Thanks to Kristie Mather for the report. diff --git a/website/conf.py b/website/conf.py index abf954fab..7fe4bd610 100644 --- a/website/conf.py +++ b/website/conf.py @@ -128,7 +128,7 @@ # html_theme_options = { # these are both piccolo theme-specific "source_url": 'https://github.com/alexlancaster/pypop/', - "banner_text": 'A release candidate for PyPop (1.0.0rc1) is now available via PyPI as package pypop-genomics. See README for more detailed instructions.
' + "banner_text": 'Release candidates for PyPop are now available via PyPI as package pypop-genomics. See README for more detailed instructions.
' } # Add any paths that contain custom static files (such as style sheets) here, diff --git a/website/index.rst b/website/index.rst index 11f32708d..66cd211fd 100644 --- a/website/index.rst +++ b/website/index.rst @@ -8,8 +8,7 @@ PyPop: Python for Population Genomics Please follow the instructions on the GitHub `README.rst `__ for how to - install 1.0.0 release candidate 1 from PyPI (or build PyPop from - source on a modern Python 3 system). A formal 1.0.0 release will + install a 1.0.0 release candidate from PyPI. A formal 1.0.0 release will be made soon. .. _news: @@ -17,8 +16,9 @@ PyPop: Python for Population Genomics .. admonition:: Release summary and news :class: dropdown, toggle-shown - - 2023-11-01: release candidate 1 (1.0.0rc1) is now available on - `PyPI `__. + - 2023-11-04: release candidate 2 (1.0.0rc2) is now available on + `PyPI `__. Fixes some missing TSV output. + - 2023-11-01: release candidate 1 (1.0.0rc1) released. - 2023-10-27: seventh beta pre-release 1.0.0b7, Previous ``arm64`` issues have been resolved. Thanks to Owen Solberg for extensive testing and debugging.