v7.10.0

What's Changed

• Use webgl for bokeh genome plots by @alimanfoo in #406
• Relax ipyleaflet pinning by @alimanfoo in #408

Full Changelog: v7.9.0...v7.10.0

v7.9.0

What's Changed

• Anopheles refactor part 6 - haplotype data by @alimanfoo in #401
• Fix for API breakage in numpydoc_decorator by @alimanfoo in #403

Full Changelog: v7.8.0...v7.9.0

v7.8.0

What's Changed

• Add Python 3.11 support by @alimanfoo in #397
• Work around slow pomegranate install by @alimanfoo in #398
• Refactor Anopheles tests on genome sequence, genome features and sample metadata by @alimanfoo in #399
• Upgrade bokeh to 3.1 by @alimanfoo in #400

Full Changelog: v7.7.0...v7.8.0

v7.7.0

Please note that this release includes stricter type checking of parameters passed into functions in the public API. If you experience TypeError exceptions and are unclear about the cause, please go ahead and raise an issue.

What's Changed

• Anopheles refactor part 5 - AnophelesSnpData by @alimanfoo in #393

Full Changelog: v7.6.0...v7.7.0

v7.6.0

What's Changed

• Anopheles refactor part 4 - AnophelesSampleMetadata by @alimanfoo in #386
• Faster xarray concatenation by @alimanfoo in #395

Full Changelog: v7.5.0...v7.6.0

v7.5.0

What's Changed

• Drop support for Python 3.7 by @alimanfoo in #377
• Add min and max cohort size options to haplotypes, and add support in h12, h1x and fst functions by @sanjaynagi in #379
• Anopheles refactor part 1 - AnophelesBase by @alimanfoo in #380
• Anopheles refactor part 2 - AnophelesGenomeSequenceData by @alimanfoo in #381
• Anopheles refactor part 3 - AnophelesGenomeFeaturesData by @alimanfoo in #382
• Move _prep_sample_sets_param by @alimanfoo in #383
• Add quarter cohorts in read_cohort_metadata() exceptions by @ahernank in #385

New Contributors

• @ahernank made their first contribution in #385

Full Changelog: v7.4.0...v7.5.0

v7.4.0

What's Changed

• Ag3.genome_sequence() - add support for joined arms by @alimanfoo in #346
• ag3.genome_features() - add support for joined arms by @sanjaynagi in #347
• Add quarter derived from month to sample metadata. Add tests. by @leehart in #349
• Ag3 snp_genotypes(), snp_sites(), snp_variants(), snp_calls() - support for joined arms by @sanjaynagi in #352
• Add years, sample_sets, contributors to plot_samples_interactive_map marker titles by @leehart in #356
• ag3.haplotypes() - add support for joined arms by @sanjaynagi in #355
• plot_haplotype_clustering() fix - append extra metadata to hover data if specified by @sanjaynagi in #354
• Add Af1 site filters track for view_alignments() by @leehart in #357
• implement iHS GWSS by @sanjaynagi in #360
• Raise error when _snp_df() transcript is not found by @leehart in #364
• Support basemap str for plot_samples_interactive_map by @leehart in #372
• Implement G123 gwss method by @sanjaynagi in #369
• Type annotations and numpydoc_decorator applied to AnophelesDataResource by @alimanfoo in #353

Full Changelog: v7.3.1...v7.4.0

v7.3.1

What's Changed

• Fix bug with multiple regions in PCA and snp_allele_counts by @alimanfoo in #338

Full Changelog: v7.3.0...v7.3.1

v7.3.0

What's Changed

• Add extra sample metadata by @alimanfoo in #327
• Migrate release notes to github by @alimanfoo in #328
• Pin bokeh below 3.0 by @alimanfoo in #329
• Docstrings for Anopheles extra metadata methods by @alimanfoo in #330
• Refactor haplotypes functions to support Af1 by @leehart in #331

Full Changelog: v7.2.0...v7.3.0

v7.2.0

What's Changed

• Add cohort_size param to plot_snps() by @alimanfoo in #312
• Try to fix CI hanging on running notebooks by @alimanfoo in #314
• Fix param that should be optional by @alimanfoo in #311
• Add support for cohorts metadata in Af1 by @leehart in #318
• Ensure xarray has zarr backend by @alimanfoo in #322
• Bokeh fixes 2023-01-27 by @alimanfoo in #324

Full Changelog: v7.1.3...v7.2.0