Malariagen-data

What's Changed
* Tweak Ag3 repr - add "client" by alimanfoo in https://github.com/malariagen/malariagen-data-python/pull/230
* Fix broken igv notebook by alimanfoo in https://github.com/malariagen/malariagen-data-python/pull/238
* Use blank DataFrame when cohorts metadata are missing by leehart in https://github.com/malariagen/malariagen-data-python/pull/235
* Prep v4.3.1 by alimanfoo in https://github.com/malariagen/malariagen-data-python/pull/239


**Full Changelog**: https://github.com/malariagen/malariagen-data-python/compare/v4.3.0...v4.3.1

**Full Changelog**: https://github.com/malariagen/malariagen-data-python/compare/v4.2.0...v4.3.0

Highlights
* Add progress bars for longer-running computations using tqdm
([GH217](https://github.com/malariagen/malariagen-data-python/issues/217)).
* Add SNP genotypes to `Ag3.view_alignments()`
([GH216](https://github.com/malariagen/malariagen-data-python/issues/216)).


What's Changed
* Add SNP genotypes to Ag3.view_alignments by alimanfoo in https://github.com/malariagen/malariagen-data-python/pull/219
* Use tqdm to show progress during longer-running computations by alimanfoo in https://github.com/malariagen/malariagen-data-python/pull/218
* IGV tweaks by alimanfoo in https://github.com/malariagen/malariagen-data-python/pull/220
* Simplify allele frequencies implementations vis-a-vis handling sample queries by alimanfoo in https://github.com/malariagen/malariagen-data-python/pull/221
* Use debug logging by alimanfoo in https://github.com/malariagen/malariagen-data-python/pull/222
* Prep v4.2.0 by alimanfoo in https://github.com/malariagen/malariagen-data-python/pull/223


**Full Changelog**: https://github.com/malariagen/malariagen-data-python/compare/v4.1.0...v4.2.0

Highlights
* Use pypi for igv-notebook dependency
([GH209](https://github.com/malariagen/malariagen-data-python/issues/209)).
* Add `sample_query` parameter to `Ag3.haplotypes()`
([GH210](https://github.com/malariagen/malariagen-data-python/issues/210)).
* Add `sample_query` and `max_coverage_variance` parameters to
`Ag3.cnv_hmm()` and `Ag3.gene_cnv()`
([GH213](https://github.com/malariagen/malariagen-data-python/issues/213)).


What's Changed
* Depend on igv-notebook by alimanfoo in https://github.com/malariagen/malariagen-data-python/pull/212
* Add parameters to Ag3.haplotypes() and Ag3.cnv_hmm() by alimanfoo in https://github.com/malariagen/malariagen-data-python/pull/214
* Prep v4.1.0 release by alimanfoo in https://github.com/malariagen/malariagen-data-python/pull/215


**Full Changelog**: https://github.com/malariagen/malariagen-data-python/compare/v4.0.1...v4.1.0

What's Changed
* igv-notebook as optional dependency by alimanfoo in https://github.com/malariagen/malariagen-data-python/pull/207


**Full Changelog**: https://github.com/malariagen/malariagen-data-python/compare/v4.0.0...v4.0.1

Highlights
* `Ag3`: A new `pca()` function has been added for performing
principal components analysis
([GH187](https://github.com/malariagen/malariagen-data-python/issues/187)).
* `Ag3`: Functions `plot_pca_variance()` and `plot_pca_coords()` have
been added for plotting PCA results
([GH197](https://github.com/malariagen/malariagen-data-python/issues/197)).
* `Ag3`: A new `snp_allele_counts()` function has been added for
computing SNP allele counts, which is required for various analyses
such as PCA (locating segregating variants).
* `Ag3`: A new `view_alignments()` function has been added which
creates an IGV browser in the notebook and adds a track with the
sequence read alignments from a given sample
([GH202](https://github.com/malariagen/malariagen-data-python/issues/202)). There
is also an `igv()` function for initialising an IGV browser with
just reference genome and gene tracks.
* `Ag3`: The way that analysis version parameters like
`cohorts_analysis`, `species_analysis` and `site_filters_analysis`
are exposed in the API has been simplified
([GH203](https://github.com/malariagen/malariagen-data-python/issues/203)). Now
these parameters are set when the `Ag3` class is instantiated,
rather than at each method.
* `Ag3`: A check has been added for the location of the machine from
which requests are being made, and in particular to raise a warning
in the case where colab allocates a VM outside the US region, which
results in poor data retrieval performance
([GH201](https://github.com/malariagen/malariagen-data-python/issues/201)).
* `Ag3`: By default, bokeh is now automatically configured to output
plots to the notebook
([GH193](https://github.com/malariagen/malariagen-data-python/issues/193)).


What's Changed
* PCA functions by alimanfoo in https://github.com/malariagen/malariagen-data-python/pull/198
* Adds IGV viewer for sequence read alignments by alimanfoo in https://github.com/malariagen/malariagen-data-python/pull/204
* Add client location check by alimanfoo in https://github.com/malariagen/malariagen-data-python/pull/205
* prep v4.0.0 by alimanfoo in https://github.com/malariagen/malariagen-data-python/pull/206


**Full Changelog**: https://github.com/malariagen/malariagen-data-python/compare/v3.1.0...v4.0.0