CHANGELOG.md

2024-10-29

Patch release pgscatalog-utils-1.4.2

• Bump core dependency

Patch release pgscatalog-core-0.3.3

• Remove rsID format check from CatalogScoreVariant model

2024-10-08

Patch release pgscatalog-utils-1.4.1

• Fix missing imports
• Bump dependencies

Patch release pgscatalog-match-0.3.3

• Migrate classes deleted in pgscatalog.core to pgscatalog.match
• Add missing test data

Patch release pgscatalog-utils-1.4.0

• Bump dependencies

2024-10-07

Patch release pgscatalog-match-0.3.2

• Bumps pgscatalog.core dependency

Minor release pgscatalog-calc-0.3.0

• Add --verify_variants CLI option to pgscatalog-aggregate to confirm that scoring file variants (input) match the scored variants perfectly during score calculation

Patch release pgscatalog-core-0.3.1

• Convert all relative imports to absolute to fix broken autoapi documentation

Minor release pgscatalog-core-0.3.0

• Implements unified PGS Catalog data models with pydantic (used in pgscatalog-combine)
• Rate limits pgscatalog-download to prevent throttling

2024-08-05

Patch release pgscatalog-utils-1.3.1

• Bump dependencies to latest

Patch release pgscatalog-match-0.3.1

• Fix splitting but revert implementation to original function. v0.3.0 would trigger ValueErrors consistently on larger datasets
• Fix variant match information getting dropped from the log if an accession was filtered from output scoring files

2024-08-02

Minor release pgscatalog-utils-1.3.0

• Bump dependencies to latest

Minor release pgscatalog-match-0.3.0

• Important Fix splitting duplicate variant IDs across different scoring files #38
• Fix --keep_ambiguous PGScatalog/pgsc_calc#346
• Fix --ignore_strand_flips

2024-07-29

Minor release pgscatalog-utils-1.2.0

• Bump dependencies to latest

Patch release pgscatalog-match-0.2.3

• Update pgscatalog-intersect PCA_ELIGIBLE filters #33

Patch release pgscatalog-calc-0.2.2

• Sample IDs now use FIDs if available #31

Patch release pgscatalog-core-0.2.2

• Fixes support for missing other_allele column in custom scoring files #30

2024-06-19

Patch release pgscatalog-match-0.2.2

• Fixes pgscatalog-intersect with bim target input #25

2024-06-14

Patch releases to downgrade minimum Python version to 3.10:

• pgscatalog-utils-1.1.1
• pgscatalog-match-0.2.1
• pgscatalog-calc-0.2.1
• pgscatalog-core-0.2.1

2024-06-13

Minor release pgscatalog-utils-1.1.0

• Bump dependencies to latest

Minor release pgscatalog-match-0.2.0

• Improve performance when reading target genomes and scoring files #20
• Fix raising MatchRateError when one or more scores fails matching but at least one score passes #21
• Fix warnings about map_element dtypes during labelling

Minor release pgscatalog-calc-0.2.0

• Improve aggregation to have clearer logic and logging #23
  • Fix aggregating scores with different numbers of columns
• Fix adjusting averages during ancestry adjustment #19

2024-06-12

Minor release pgscatalog-core-0.2.0

• Drop pyarrow support when reading target genomes or scoring files
• Add natural sorting functions to sort scoring file paths by effect type or chromosome
• Remove pyarrow dependency

2024-05-23

Patch release pgscatalog-core-0.1.2 and pgscatalog.calc-0.1.1:

• Bug fixes for PGS Catalog Calculator integration

Patch release pgscatalog.match-0.1.1:

• Bug fixes for PGS Catalog Calculator integration
• New pgscatalog-intersect CLI application

Bump pgscatalog-utils to use patched dependencies

2024-04-09

Patch release pgscatalog-core-0.1.1:

• Add NCBI35 to GenomeBuild
• Disable concurrency in pgscatalog-combine to prevent memory usage explosion (will be fixed and re-enabled later)
• Fix handling scoring file cases when only one optional effect type column is present
• Fix reading pvar files with complex headers (like ones made from a VCF)

Bump pgscatalog-utils to use patched core

2024-03-22

Initial release of new python packages:

• pgscatalog.core-0.1.0
• pgscatalog.match-0.1.0
• pgscatalog.calc-0.1.0

Also pgscatalog-utils migrated to using these tools on the backend (v1.0.0)