v15.3.0

What's Changed

• Handle ZeroDivisionError in plot_pairwise_average_fst by @jonbrenas in #769
• Readme updates and new dev setup video by @alimanfoo in #774
• Fix Windows path compatibility in cloud storage URLs by @mohamed-laarej in #786
• Feat: Add functions to access insecticide resistance phenotype data by @mohamed-laarej in #792
• Add "taxon_by" param to *_frequencies_advanced() functions and allow the "period_by" param to specify a column name by @leehart in #694

New Contributors

• @mohamed-laarej made their first contribution in #786

Full Changelog: v15.2.2...v15.3.0

v15.2.2

What's Changed

• Amend URL for An. funestus resources #764 by @jonbrenas in #764

Full Changelog: v15.2.1...v15.2.2

v15.2.1

What's Changed

• Updates pf8 default url to s3 by @eselimnl in #761

Full Changelog: v15.2.0...v15.2.1

v15.2.0

What's Changed

• add citation information to dipclust docstring by @sanjaynagi in #736
• Linting errors connected to numpy 2.2 by @jonbrenas in #758
• IGV access after authentication requirement for master by @jonbrenas in #752
• Include package-wide citation notes by @ahernank in #762

Full Changelog: v15.1.0...v15.2.0

v15.1.0

What's Changed

• Moving karyotype to anoph by @jonbrenas in #702
• Move shared code to frq_base.py by @jonbrenas in #690
• Allow multiple SNP transcripts in plot_diplotype_clustering_advanced() by @jonbrenas in #703
• Update switcher.json up to v15.0.1 by @alimanfoo in #729
• Resolve CI linting failures by @leehart in #740
• Fix switcher.json by @leehart in #731
• Pin Bokeh <3.7.0 by @leehart in #748
• Fix URLs in switcher.json by @leehart in #747
• Pin numcodecs < 0.16 by @leehart in #754

Full Changelog: v15.0.1...v15.1.0

v15.0.1

What's Changed

• Add GitHub workflow to add the triage label to opened, reopened issues by @leehart in #713
• Update plot_njt() in distance.py - render_mode="svg" by @cclarkson in #718

Full Changelog: v15.0.0...v15.0.1

v15.0.0

What's Changed

• Add support for writing Anopheles SNP data to the plink binary file format (shadow PR) by @alimanfoo in #584
• Add support for writing Anopheles SNP data to the plink binary file format by @tristanpwdennis in #515
• Replicate anjl params to avoid global import causing delays by @leehart in #673
• Add Pf8 by @eselimnl in #659
• Add gene_labels and labels to plot_genes() by @leehart in #653
• Ensure that missing CNVs are shown in a different colour in plot_diplotype_clustering_advanced by @jonbrenas in #670
• Haplotype frequency analysis methods by @jonbrenas in #630
• Refactor CNV frequencies functions to their own module by @jonbrenas in #665
• Changed figures into optional_figures and def_figures into figures by @jonbrenas in #676
• Expansion of the documentation by @jonbrenas in #592
• Refactor unit and integration tests and corresponding github actions by @alimanfoo in #686
• Palette option in plot_cnv_hmm_heatmap by @jonbrenas in #688
• Add @jonbrenas to the list of authors by @jonbrenas in #696
• Add karyotype to the docs by @jonbrenas in #701
• fix zarr-python to v2 by @sanjaynagi in #709
• Update pyproject.toml by @cclarkson in #711

New Contributors

• @tristanpwdennis made their first contribution in #515
• @eselimnl made their first contribution in #659

Full Changelog: v14.0.0...v15.0.0

v14.0.0

What's Changed

• Sort gene annotations by contig and start coordinate in genome_features() by @sanjaynagi in #649
• Add sample_query_options to more functions by @leehart in #645
• Remove transient warning during pytests by @jonbrenas in #650
• Colors in GWSS plots by @jonbrenas in #591
• Gene CNV optimisation by @alimanfoo in #655
• Sort discovered_releases numerically by @leehart in #666
• Better error message for gene_cnv_frequencies() by @jonbrenas in #668
• Add taxa and areas params to plot_frequencies_time_series() by @leehart in #657

Full Changelog: v13.5.0...v14.0.0

v13.5.0

What's Changed

• Add support for dynamic neighbour-joining by @alimanfoo in #647
• Plot H12 GWSS traces for multiple cohorts together in a single figure by @jonbrenas in #595

Full Changelog: v13.4.0...v13.5.0

v13.4.0

What's Changed

• Replace np.in1d with np.isin in g123.py by @leehart in #637
• Add cross_metadata to sample metadata section of Ag3 docs by @leehart in #638
• Add Ag inversion karyotyping support by @sanjaynagi in #608
• Add sample location scatter maps by @leehart in #639
• Use optional env var for show_progress in Ag3, Af1 by @leehart in #640
• Improve neighbour-joining tree performance by @alimanfoo in #641
• Small simplification to progress monitoring within plot_njt by @alimanfoo in #643

Full Changelog: v13.3.0...v13.4.0