v15.7.0

What's Changed

• Update doc switcher & readme doc by @leehart in #844
• Stabilize CI matrix and pin NumPy baseline to 1.26.4 by @adilraza99 in #855
• Document error bars behavior in ag3.plot_frequencies_time_series by @adilraza99 in #851
• Fix broken documentation URL for Anopheles gambiae surveillance project by @adilraza99 in #862
• Poetry locked by @jonbrenas in #865
• Move tests using non-simulated data on merge to master by @ahernank in #866
• Fix DOI citation link formatting in README by @adilraza99 in #858
• fix: replace mutable default arguments with None in CNV plot functions by @PaulaYaniz in #884
• Add comprehensive CONTRIBUTING.md guide for new contributors by @adilraza99 in #860
• replacing old '%' with newer f-string by @blankirigaya in #891
• fix: use _gff_gene_name_attribute in _transcript_to_parent_name (#883) by @31puneet in #887
• Fix hardcoded gene type and name attribute in test_plot_genes_with_ge… by @31puneet in #875
• Fix g123 test failures on Adir1/Amin1 by falling back to segregating sites when no phasing analysis is available by @blankirigaya in #870
• Ag3.plot frequencies time series by @blankirigaya in #906
• Add AI-use policy by @jonbrenas in #872
• Fix lstrip column corruption in plot_frequencies_heatmap() by @31puneet in #898
• Update contact details in pyproject.toml by @jonbrenas in #871
• Fix deprecated Plotly API calls in anoph (Mapbox and Trace methods) by @NgangaKamau3 in #889
• Fix path joining for Windows compatibility in PlasmodiumDataResource by @muien5080 in #909
• fix(tests): handle missing sex_call in diplotype clustering tests for Amin1/Adir1 by @adilraza99 in #888
• Add describe_api() method for API introspection (#903) by @mandeepsingh2007 in #904
• Pin pandas to 2.3.2 by @jwgarber in #943
• fix: use min_clip parameter for y-axis lower bound in plot_fst_gwss_track by @Tanisha127 in #910
• ci: upgrade latest_docs.yml to use Node.js 20 by @Tanisha127 in #931
• Improve transparency by warning when max_cohort_size triggers downsampling by @adilraza99 in #930
• fix: validate aims param early in plot_aim_heatmap for clearer error message by @Tanisha127 in #961
• feat: add consistent aim_species colors in plot_pca_coords by @Tanisha127 in #962
• Fix Fst Z-score calculation when standard error is zero by @adilraza99 in #948
• Fix duplicate intermediate node generation in _mjn_graph by @31puneet in #924
• fix: dedent empty-data check in cnv_discordant_read_calls (#777) by @AswaniSahoo in #895
• Normalize site_mask in g123_gwss cache parameters and bump cache version by @adilraza99 in #966
• Fix unbounded _cache_locate_site_class growth and instance retention via class-level lru_cache by @suhr25 in #967
• Add github action for installing python and poetry consistently by @jwgarber in #958
• Guard against invalid jackknife block sizing when n_jack exceeds site count by @adilraza99 in #911
• feat: add "lower triangle" annotation option to plot_pairwise_average_fst (#820) by @AswaniSahoo in #969
• Add SYNONYMOUS_STOP and SYNONYMOUS_START effect classifications (fixes #953) by @ZiadXI in #954
• Fix CI warnings and restore test coverage for PR #817 by @adilraza99 in #942
• add advanced haplotype clustering by @sanjaynagi in #817
• Return NaN for empty windows in G123 and H12 statistics by @adilraza99 in #977
• fix: guard against free basemap providers going out of service (#446) by @blankirigaya in #952
• refactor: replace manual cache pattern with cached_property for _snp_effect_annotator (#469) by @Tanisha127 in #972
• Add filter_unassigned parameter to _prep_samples_for_cohort_grouping by @shauryam2807 in #983
• Fix: remove stray f in ValueError messages by @suhr25 in #980
• Fix wrong type annotation for sample_query_options in average_fst by @rehanxt5 in #988
• Fix: Replace TODO Strings With Proper Variant Effect Values in veff.py by @blankirigaya in #917
• fix: add guard for empty array in g123 when window_size exceeds avail by @31puneet in #937
• Fix: Implement Abstract Cache Name Properties in All Subclasses by @blankirigaya in #901
• refactor: standardise biallelic diplotypes and handling of missing calls by @Tanisha127 in #975
• Fix simplecache storage location being ignored for chained GCS URLs by @blankirigaya in #935
• Fix raw string in cohort_diversity_stats error message by @suhr25 in #1007
• Fix wrong denominator in max_missing_an fraction filter (closes #998) by @rehanxt5 in #1000
• Fix contig variable shadowing in H12 overlay plot by @adilraza99 in #994
• Make random anoph testing data reproducible by @jwgarber in #1008
• Fix handling of missing terms-of-use metadata in sample set manifest (#766) by @adilraza99 in #990
• ci: configure codecov patch coverage threshold by @Sharon-codes in #1013
• Fix/h12 multi panel param forwarding by @shauryam2807 in #1001
• Fix TypeError for single-exon transcripts in veff.Annotator.get_children by @Vedag812 in #873
• Fix stray f in error message f-strings (closes #985) by @rehanxt5 in #986
• ci: verify tests against locked and latest supported NumPy versions by @Sharon-codes in #1023
• Forward sample_query_options in pairwise_average_fst (closes #995) by @rehanxt5 in #996
• Add Grantham and Sneath amino acid distance metrics to SNP effects (closes #115) by @ZiadXI in #922
• Adding limited support for Adar by @jonbrenas in #1032
• build: allow bokeh >=3.7 and restore mypy compatibility by @Sharon-codes in #1012
• CNV: rename cnv_discordant_read_calls parameter from contig to contigs by @Sharon-codes in #1021
• fix: return NaN confidence intervals when cohort size is zero by @adilraza99 in #1011
• fix: use per-sample denominator for CNV frequencies when nobs_mode="fixed" by @adilraza99 in #1006
• fix: replace bare asserts in veff.py with explicit ValueError exceptions by @suhaan-24 in #1034
• refactor: extract AnophelesHetAnalysis into anoph/heterozygosity.py by @31puneet in #944
• feat: add results caching to cohort_diversity_stats by @Sharon-codes in #1014
• Issue 435 cohort group metadata...

v15.6.0

What's Changed

• Update switcher.json by @leehart in #834
• Prefix undocumented functions with an underscore to indicate that they're private by @leehart in #833
• Clean Amin1.0 branch from master by @tristanpwdennis in #839

Full Changelog: v15.5.0...v15.6.0

v15.5.0

What's Changed

• docs: remove usage examples and register phenotype methods in Ag3.rst by @mohamed-laarej in #810
• fix(phenotypes): Correct GCS path construction by @mohamed-laarej in #816
• Add unrestricted_use_only and surveillance_use_only constructor params by @leehart in #724
• Adir1.x by @tristanpwdennis in #795
• Update poetry.lock by @jonbrenas in #832

Full Changelog: v15.4.0...v15.5.0

v15.4.0

What's Changed

• Update contact address in latest docs by @leehart in #801
• Fix color parameter validation in plot_haplotype_network function - Shadow PR by @jonbrenas in #755
• Fix color parameter validation in plot_haplotype_network function (issue #738) by @mohamed-laarej in #742
• Update poetry.lock by @leehart in #813
• Update pf8.py documentation by @eselimnl in #811

Full Changelog: v15.3.0...v15.4.0

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