Malariagen-data

Highlights
* `Ag3`: Add site filter columns to dataframes returned by `snp_effects()` and `snp_allele_frequencies()`.



What's Changed
* Add site filter columns to SNP dataframes by alimanfoo in https://github.com/malariagen/malariagen-data-python/pull/48


**Full Changelog**: https://github.com/malariagen/malariagen-data-python/compare/v0.7.0...v0.8.0

Highlights

* `Ag3`: Rename parameter "populations" to "cohorts" to be consistent with sgkit terminology.

What's Changed
* Rename populations to cohorts by alimanfoo in https://github.com/malariagen/malariagen-data-python/pull/47


**Full Changelog**: https://github.com/malariagen/malariagen-data-python/compare/v0.6.0...v0.7.0

Highlights
* `Ag3`: Add `gene_cnv()` and `gene_cnv_frequencies()`.
* `Ag3`: Improvements and maintenance to `snp_effects()` and `snp_allele_frequencies()`.


What's Changed
* Maintenance on SNP effects and allele frequencies functions by alimanfoo in https://github.com/malariagen/malariagen-data-python/pull/45
* Add methods for computing copy number variation by gene by alimanfoo in https://github.com/malariagen/malariagen-data-python/pull/38


**Full Changelog**: https://github.com/malariagen/malariagen-data-python/compare/v0.5.0...v0.6.0

Highlights
* `Ag3`: Add `snp_allele_frequencies()`.

* `Ag3`: Add `snp_effects()`.

* `Ag3`: Add `cnv_hmm()`, `cnv_coverage_calls()` and
`cnv_discordant_read_calls()`.

* Speed up test suite via caching.

* Add configuration for pre-commit hooks.


What's Changed
* Variant effects prototyping by alimanfoo in https://github.com/malariagen/malariagen-data-python/pull/6
* Ag3 snp effects updates by cclarkson in https://github.com/malariagen/malariagen-data-python/pull/26
* ag3.snp_allele_frequencies() by cclarkson in https://github.com/malariagen/malariagen-data-python/pull/28
* Setup pre-commit by alimanfoo in https://github.com/malariagen/malariagen-data-python/pull/29
* Ag3 CNV methods by alimanfoo in https://github.com/malariagen/malariagen-data-python/pull/31
* Optimise snp effects by cclarkson in https://github.com/malariagen/malariagen-data-python/pull/32
* Prep v0.5.0 release by alimanfoo in https://github.com/malariagen/malariagen-data-python/pull/34


**Full Changelog**: https://github.com/malariagen/malariagen-data-python/compare/v0.4.3...v0.5.0

Highlights
* `Ag3`: Make public the `open_genome()`, `open_snp_sites()`, `open_site_filters()` and `open_snp_genotypes()` methods.

* `Ag3`: Add the `cross_metadata()` method.

* `Ag3`: Add `site_annotations()` and `open_site_annotations()` methods.

* `Ag3`: Add the `snp_calls()` method.

* Improve unit tests.

* Improve memory usage.



What's Changed
* Ag3 by alimanfoo in https://github.com/malariagen/malariagen-data-python/pull/1
* s/cohort/sample_sets/ by alimanfoo in https://github.com/malariagen/malariagen-data-python/pull/2
* Rename seq_id to contig by alimanfoo in https://github.com/malariagen/malariagen-data-python/pull/3
* Fix path for fsspec changes by alimanfoo in https://github.com/malariagen/malariagen-data-python/pull/7
* Misc enhancements by alimanfoo in https://github.com/malariagen/malariagen-data-python/pull/11
* Add CI via github action by alimanfoo in https://github.com/malariagen/malariagen-data-python/pull/18
* Ag3 SNP xarray dataset enhancements by alimanfoo in https://github.com/malariagen/malariagen-data-python/pull/17
* Improve memory; support inline_array by alimanfoo in https://github.com/malariagen/malariagen-data-python/pull/20


**Full Changelog**: https://github.com/malariagen/malariagen-data-python/commits/v0.4.0