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ChangeLog.md

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0.17.3 [2022-01-11]

  • Export type annotations

0.17.2 [2022-01-05]

  • Fix bugs in older Python versions caused by MyPy
  • Drop support for Python 3.6 and prior versions - this is unfortunate, is MyPy worth it?

0.17.1 [2021-12-28]

  • Add MyPy type annotations
  • Migrate from Travis to GitHub Actions CI

0.17.0 [2021-11-15]

  • Change the --scale=r parameter in sample para and sample mono to represent n^(1/r) instead of n^r. With this parameterization, r ranges from 1 to infinity and thus does not conflict with the --proportion term (which ranges from 0 to 1). They do overlap at --scale=1 and --proportion=1, but these are equivalent, both sampling everything.

0.16.0 [2021-10-21]

  • Setup smot module interface
  • Add color push and color pull commands

0.15.0 [2021-08-08]

  • Add stat subcommand
  • Replace sample prop with sample mono. This contrasts with para.
  • Add -v/--version option

0.14.2 [2021-09-14]

  • Fix several issues found my flake8
  • Fix --factor-by-table option and documentation
  • Keep tip colors after tipsed

0.14.1 [2021-07-19]

  • More robust color map parsing

0.14.0 [2021-06-07]

  • Add -n NUM option to samplers to select NUM elements from each group
  • Fix bug in sampling from root - the two sides under root were always sampled independently. With -n option, this led to twice too many selections when no factoring was done. With proportional options, the bug would only cause problems in the corner case where one side under root had fewer than minTips tips.

0.13.1 [2021-05-19]

  • Add filter subcommand

0.12.1 [2021-05-06]

  • Fix KeyError raised when a factor is not in the color table, resolve by simply not coloring the element

  • Fix tree formatting when using color maps (trim whitespace)

0.12.0 [2021-04-23]

  • Add color rm to remove all coloring annotations, with the --newick option, this also clears all metadata (e.g., FigTree annotations)

  • Fixed bugs in regex captures and para coloring

0.11.0 [2021-04-21]

  • Add monophyletic and paraphyletic branch coloring

[FYI - due to ghosts in pyp, v0.10.0 is gone]

0.9.0 [2021-04-20]

  • Add color command

    smot color -p "swine" "#FFA500" -p "2020-" "#00FF00" my.tre > color.tre

  • Print to nexus by default, preserving figtree colors and settings, with --newick option for printing raw newick trees.

  • Remove plot, convert, and random commands and the the biopython dependency. These commands were not well-supported and their dependency was very heavy. Use phylomander or dedicated plotting packages instead.

  • Remove clean function - I may bring this back in the future, but at the moment there isn't an obvious use-case for clean.

  • Add support for parsing metadata from and writing Nexus - the main need for this is to properly handle tip colors and preserve metadata.

0.8.2 [2021-04-13]

  • Add test for unicode support (e.g., Chinese characters or emoticons)

  • Add parser support for escaping characters. Any character following a '' is kept, so quotes within strings and backslashes can be escaped. Special characters are not supported (e.g., substituting '\t' for a TAB character).

  • Add parser support for FigTree's weird single-quote escape convention. They replace within-string single-quotes with a pair of single-quotes.

0.8.1 [2021-04-09]

  • add --keep-regex option for sample prop

0.8.0 [2021-04-08]

  • add --keep-regex option

0.7.1 [2021-03-26]

  • remove debugging crap

0.7.0 [2021-03-26]

  • allow factor imputation through patristic distance

0.6.0 [2021-03-26]

  • add power scaling option to samplers
  • add grep

0.5.0 [2020-08-09]

  • remove midpoint command - it was too slow to be useful, there are better CLI tools for this job
  • Fix bug preventing STDIN

0.4.0 [2020-08-06]

  • update CLI interface
    • subcommand documentation
    • documentation for each field
    • cleaner argument checking

0.3.0 [2019-12-04]

  • allow automatic reading of NEXUS
  • remove '--format' option (infer input format and write newick)
  • add BioPython-based convert function
  • let factors be appended or prepended to tip labels
  • merge sampling commands
  • ladderize tree before plotting
  • clean command also ladderizes the tree

0.2.0 [2019-11-20]

  • add factor imputing
  • add --seed argument to smot random
  • mix bug in proportional sampler
  • add tests of the command line utility
  • fix bug in unfactored proportional sample
  • allow the default factor

0.1.0 [2019-11-19]

  • initial release