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CHANGELOG.md

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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

Unreleased

v0.6.0 - 2024-11-06

Changed

  • Make better-exceptions an optional dependency.

Fixed

  • Discrepancy with OrthoANI values for high similarity genomes (#2).
  • Remaining files of temporary BLAST databases not being removed.

Removed

  • Support for Python 3.5.

v0.5.0 - 2021-05-28

Fixed

  • Exception messages not properly rendering with --traceback enabled.
  • Use os.cpu_count instead of multiprocessing.cpu_count where applicable.
  • Make BlockIterator zero-copy using indices instead of slices.

Changed

  • Use seqidlist to reduce number of blocks compared in backward search.
  • Switch to use BLASTdb v5 (instead of v4 previously).
  • Prefix temporary files with orthoani prefix.
  • Skip blocks containing more than 80% unknown nucleotides like in original implementation.
  • Average ANI values based on HSPs instead of reciprocical blocks like in original implementation.

v0.4.0 - 2020-06-26

Changed

  • Entire sequences smaller than the given blocksize will be padded with N.
  • biopython requirement was relaxed to v1.73.

Fixed

  • Code using builtin API not available in Python3.5.

v0.3.2 - 2020-06-24

Fixed

  • orthoani CLI ignoring the value of the --jobs flag.

v0.3.1 - 2020-06-24

Fixed

  • blastn and makeblastdb being called with shell=True, causing issues if shell cannot be forked.
  • Traceback not being displayed even with --traceback flag.

Changed

  • ANI values are collected using decimal.Decimal instead of float.

v0.3.0 - 2020-06-22

Added

  • Support for genomes segmented in multiple contigs.

v0.2.1 - 2020-06-19

Fixed

  • Temporary files with chopped FASTA not being deleted.

v0.2.0 - 2020-06-16

Added

  • threads argument controlling BLASTn thread count to orthoani and orthoani_pairwise.
  • -j / --jobs flag controlling BLASTn thread count to CLI.
  • Proper documentation and error codes to CLI.
  • orthoani console script to call the CLI without python -m invocation.

v0.1.0-post1 - 2020-06-15

Fixed

  • Travis-CI badge not rendering on README.md.

Changed

  • Made development status Beta instead of Alpha in setup.cfg.

v0.1.0 - 2020-06-15

Initial release.