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CHANGELOG.md

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Changelog for yhaplo

Format based on Keep a Changelog

2.1.13 - 2024-11-07

Changed

  • Removed NumPy pin and indicated Python 3.13 support

2.1.11 - 2024-05-03

Added

  • Tree.generate_tree_table method

2.1.10 - 2024-04-25

Added

  • List associated SNPs in --haplogroup_query output

2.1.9 - 2024-03-19

Fixed

  • Node.hg_snp values of SNP-less intermediate branches now stable upon repeated Tree instantiation

2.1.8 - 2024-03-12

Added

  • --haplogroup_query option

2.1.7 - 2024-02-23

Added

  • SNP.info property, called from Tree.query_snp_path

2.1.6 - 2024-02-07

Added

  • Python 3.12 support
  • __str__ and __repr__ methods
  • SNP-based haplogroup in MRCA output

Changed

  • Newick representation is now unrotated by default

Removed

  • setuptools_scm-generated version file

Fixed

  • When generating Newick representation, recalculate maximum depth to support pruned trees

2.1.4 - 2024-01-29

Added

  • Support for querying multiple SNPs from the command line
  • Support for generating aligned-tip Newick representations of subtrees
  • Support for node lookup by SNP-based haplogroup label
  • Node methods:
    • Node.iter_depth_first
    • Node.iter_breath_first
    • Node.remove_children
  • tree.get_bounded_subtree function

Changed

  • Tree constructor's Config parameter is now optional
  • Node.is_root and Node.is_leaf are now properties

Fixed

  • Output format of --snp_query option

2.1.0 - 2024-01-12

This release improves haplogroup calling by identifying and correcting various errors in the ISOGG variant metadata and, internally, by pruning poorly performing v5 SNPs.

Changed

  • Identify and correct name, position, and mutation errors in ISOGG variant metadata

2.0.2 - 2023-09-15

This is a major clean-up and refactoring release. Core logic has not changed, and output should be equivalent to prior versions. The key changes from an end-user perspective are BCF support, a cleaner API, and faster processing of most input types.

Added

  • BCF support
  • Automated tests
  • Optional dependencies
  • Sample subclasses: TextSample, VCFSample
  • CHANGELOG.md

Changed

  • Lint code
  • Update pre-commit hooks
  • Update Makefile and configuration files
  • Refactor for PEP-8 compliance (snake case, etc.)
  • Update directory structure
  • Modernize packaging and infer version dynamically
  • Namespace command-line entry points: yhaplo, yhaplo_convert_to_genos, yhaplo_plot_tree
  • Replace static methods
  • Clean up logging and use file handlers
  • Use f-strings
  • Reformat docstrings
  • Add type annotations
  • Use importlib.resources to load metadata files
  • Move example input from package to tests/fixtures/
  • Update README.md, README.23andMe.md, and yhaplo_manual.pdf
  • Speed up sample-major file processing
  • Use Pysam to process VCF/BCF input

Removed

  • Support for Python 2 and Python 3.8