PR to bring HLAfreq 0.0.5#1
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This prevents errors when data is unusually formatted, eg sample sizes with commas 1,000
Note that if AF doesn't sum to 1 this gives coverage outside 0-1
adding missing alleles
combineAF now uses the scipy dirichlet distribution means as the combined allele frequency. To do this it calculates c for each row as reported allele freq multiplied by the supplied weights argument, which defaults to 2n (which is also created as sample_size *2). The default prior is [1]*k. This function requires a single loci so this is asserted. The demo files have been updated accordingly. Mostly filtering to single loci, and removing unmeasured_alleles calls because these are handled by combineAF().
This fix is part of the changes made to calculate dirichlet means. Also check that each allele is unique in a dataset when combining. Fixed a bug in unmeasured_alleles.
This doesn't change anything as it sorts by default
Also allows plotting sample estimates onto distribution
Commited code but will imediately delete. Test demo to identify outlier populations based on pdf. However is unsuccessful because the AF pdf peaks are so sharp that effectively all real world populations have pdf zero.
Relsease 0.0.5
Update tests for python 3.13 and 3.14 and update install to conda's :: channel specification
thanks to @usethedata for diving in to this openjournals/joss-reviews#10122 (comment)
Address [reviewers comments](openjournals/joss-reviews#10122) Merge pull request #17 from BarinthusBio/dev - add asserts to test_correct_c_array and test_correct_c_array_alleles - check data type using is_string_dtype to handle pandas 3 update - use https for url links - avoid depreciation warning by setting include_groups for .apply on grouped data
Fill missing values in pivot with zero to match make_c_array where zeros are important.
Fix `test_correct_c_array` test
Bumps [actions/checkout](https://github.com/actions/checkout) from 4 to 6. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@v4...v6) --- updated-dependencies: - dependency-name: actions/checkout dependency-version: '6' dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com>
Bumps [actions/deploy-pages](https://github.com/actions/deploy-pages) from 4 to 5. - [Release notes](https://github.com/actions/deploy-pages/releases) - [Commits](actions/deploy-pages@v4...v5) --- updated-dependencies: - dependency-name: actions/deploy-pages dependency-version: '5' dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com>
Bumps [actions/upload-pages-artifact](https://github.com/actions/upload-pages-artifact) from 3 to 4. - [Release notes](https://github.com/actions/upload-pages-artifact/releases) - [Commits](actions/upload-pages-artifact@v3...v4) --- updated-dependencies: - dependency-name: actions/upload-pages-artifact dependency-version: '4' dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com>
…tions/checkout-6 Bump actions/checkout from 4 to 6
…tions/upload-pages-artifact-4 Bump actions/upload-pages-artifact from 3 to 4
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 3 to 6. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@v3...v6) --- updated-dependencies: - dependency-name: actions/setup-python dependency-version: '6' dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com>
…tions/deploy-pages-5 Bump actions/deploy-pages from 4 to 5
…tions/setup-python-6 Bump actions/setup-python from 3 to 6
Bumps [actions/upload-pages-artifact](https://github.com/actions/upload-pages-artifact) from 4 to 5. - [Release notes](https://github.com/actions/upload-pages-artifact/releases) - [Commits](actions/upload-pages-artifact@v4...v5) --- updated-dependencies: - dependency-name: actions/upload-pages-artifact dependency-version: '5' dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com>
…tions/upload-pages-artifact-5 Bump actions/upload-pages-artifact from 4 to 5
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