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Recent Releases of phylofisher

phylofisher - v1.2.14

What's Changed

  • updates raxml tree path by @robert-ervin-jones in https://github.com/TheBrownLab/PhyloFisher/pull/104
  • Add .circleci/config.yml by @robert-ervin-jones in https://github.com/TheBrownLab/PhyloFisher/pull/115
  • fix typo matrix_constructor.smk by @giacomomutti in https://github.com/TheBrownLab/PhyloFisher/pull/114
  • Integrates nucl matrix contsructor by @robert-ervin-jones in https://github.com/TheBrownLab/PhyloFisher/pull/118
  • add leaf rename utility by @robert-ervin-jones in https://github.com/TheBrownLab/PhyloFisher/pull/117
  • Fix the bug in issue#120 "NameError: name 'metadata' is not defined" by @shuiyujinlan in https://github.com/TheBrownLab/PhyloFisher/pull/121
  • added lock by @DavidZihala in https://github.com/TheBrownLab/PhyloFisher/pull/123

New Contributors

  • @giacomomutti made their first contribution in https://github.com/TheBrownLab/PhyloFisher/pull/114
  • @shuiyujinlan made their first contribution in https://github.com/TheBrownLab/PhyloFisher/pull/121
  • @DavidZihala made their first contribution in https://github.com/TheBrownLab/PhyloFisher/pull/123

Full Changelog: https://github.com/TheBrownLab/PhyloFisher/compare/v1.2.13...v1.2.14

- Python
Published by robert-ervin-jones over 1 year ago

phylofisher - v1.2.13

What's Changed

  • Updates raxml ng by @robert-ervin-jones in https://github.com/TheBrownLab/PhyloFisher/pull/103

Full Changelog: https://github.com/TheBrownLab/PhyloFisher/compare/v1.2.12...v1.2.13

- Python
Published by robert-ervin-jones over 2 years ago

phylofisher - v1.2.12

What's Changed

  • updates forest_local to reflect change to raxml-ng by @robert-ervin-jones in https://github.com/TheBrownLab/PhyloFisher/pull/92
  • updates logic behind sanity check by @robert-ervin-jones in https://github.com/TheBrownLab/PhyloFisher/pull/94
  • updates matrixconstructorstats.tsv and adds occupancy.tsv by @robert-ervin-jones in https://github.com/TheBrownLab/PhyloFisher/pull/96
  • adds sht_include option to informant by @robert-ervin-jones in https://github.com/TheBrownLab/PhyloFisher/pull/97

Full Changelog: https://github.com/TheBrownLab/PhyloFisher/compare/v1.2.11...v1.2.12

- Python
Published by robert-ervin-jones over 2 years ago

phylofisher - v1.2.11

What's Changed

  • updates raxml command to only use one thread by @robert-ervin-jones in https://github.com/TheBrownLab/PhyloFisher/pull/90

Full Changelog: https://github.com/TheBrownLab/PhyloFisher/compare/v1.2.10...v1.2.11

- Python
Published by robert-ervin-jones over 2 years ago

phylofisher - v1.2.10

What's Changed

  • 84 forestpy produces an empty directory by @robert-ervin-jones in https://github.com/TheBrownLab/PhyloFisher/pull/85

Full Changelog: https://github.com/TheBrownLab/PhyloFisher/compare/v1.2.9...v1.2.10

- Python
Published by robert-ervin-jones over 2 years ago

phylofisher - v1.2.9

What's Changed

  • Fix select taxa chimera bug by @robert-ervin-jones in https://github.com/TheBrownLab/PhyloFisher/pull/83

Full Changelog: https://github.com/TheBrownLab/PhyloFisher/compare/v1.2.8...v1.2.9

- Python
Published by robert-ervin-jones over 2 years ago

phylofisher - v1.2.8

What's Changed

  • Nucl matrix utility by @robert-ervin-jones in https://github.com/TheBrownLab/PhyloFisher/pull/76
  • changes raxml threads by @robert-ervin-jones in https://github.com/TheBrownLab/PhyloFisher/pull/79
  • updates raxml rule to use raxml-ng by @robert-ervin-jones in https://github.com/TheBrownLab/PhyloFisher/pull/80

Full Changelog: https://github.com/TheBrownLab/PhyloFisher/compare/v1.2.7...v1.2.8

- Python
Published by robert-ervin-jones almost 3 years ago

phylofisher - v1.2.7

What's Changed

  • adds trimal gt param to matrix_constructor.py by @robert-ervin-jones in https://github.com/TheBrownLab/PhyloFisher/pull/75

Full Changelog: https://github.com/TheBrownLab/PhyloFisher/compare/v1.2.6...v1.2.7

- Python
Published by robert-ervin-jones almost 3 years ago

phylofisher - v1.2.6

What's Changed

  • fixes aa_recoder by @robert-ervin-jones in https://github.com/TheBrownLab/PhyloFisher/pull/70
  • changes sgt to homolog in informant by @robert-ervin-jones in https://github.com/TheBrownLab/PhyloFisher/pull/71
  • adds path to matrix_constructor.smk to setup.py by @robert-ervin-jones in https://github.com/TheBrownLab/PhyloFisher/pull/73
  • bumps version to 1.2.6 by @robert-ervin-jones in https://github.com/TheBrownLab/PhyloFisher/pull/74

Full Changelog: https://github.com/TheBrownLab/PhyloFisher/compare/v1.2.5...v1.2.6

- Python
Published by robert-ervin-jones almost 3 years ago

phylofisher - v1.2.5

What's Changed

  • fixes conda env paths by @robert-ervin-jones in https://github.com/TheBrownLab/PhyloFisher/pull/64
  • reworks backup strategy by @robert-ervin-jones in https://github.com/TheBrownLab/PhyloFisher/pull/67
  • fixes paths by @robert-ervin-jones in https://github.com/TheBrownLab/PhyloFisher/pull/66

Full Changelog: https://github.com/TheBrownLab/PhyloFisher/compare/v1.2.4...v1.2.5

- Python
Published by robert-ervin-jones about 3 years ago

phylofisher - v1.2.4

What's Changed

  • updates update_dataframe to reflect addition of long name by @robert-ervin-jones in https://github.com/TheBrownLab/PhyloFisher/pull/61

Full Changelog: https://github.com/TheBrownLab/PhyloFisher/compare/v1.2.3...v1.2.4

- Python
Published by robert-ervin-jones about 3 years ago

phylofisher - v1.2.3

What's Changed

  • adds recoding classes by @lnk1196 in https://github.com/TheBrownLab/PhyloFisher/pull/54
  • Matrix construct to smk by @robert-ervin-jones in https://github.com/TheBrownLab/PhyloFisher/pull/56

New Contributors

  • @lnk1196 made their first contribution in https://github.com/TheBrownLab/PhyloFisher/pull/54

Full Changelog: https://github.com/TheBrownLab/PhyloFisher/compare/v1.2.2...v1.2.3

- Python
Published by robert-ervin-jones over 3 years ago

phylofisher - v1.2.2

What's Changed

  • Revert apply to db by @robert-ervin-jones in https://github.com/TheBrownLab/PhyloFisher/pull/52
  • add try excepts to plot generation by @robert-ervin-jones in https://github.com/TheBrownLab/PhyloFisher/pull/53

Full Changelog: https://github.com/TheBrownLab/PhyloFisher/compare/v1.2.1...v1.2.2

- Python
Published by robert-ervin-jones over 3 years ago

phylofisher - v1.2.1

What's Changed

  • Update astral help by @robert-ervin-jones in https://github.com/TheBrownLab/PhyloFisher/pull/44
  • Add .circleci/config.yml by @robert-ervin-jones in https://github.com/TheBrownLab/PhyloFisher/pull/46
  • removes rogue print by @robert-ervin-jones in https://github.com/TheBrownLab/PhyloFisher/pull/50
  • Bipartition cleanup by @robert-ervin-jones in https://github.com/TheBrownLab/PhyloFisher/pull/48

Full Changelog: https://github.com/TheBrownLab/PhyloFisher/compare/v1.2.0...v1.2.1

- Python
Published by robert-ervin-jones over 3 years ago

phylofisher - v1.2.0

What's Changed

  • 29 no output from fisherpy by @robert-ervin-jones in https://github.com/TheBrownLab/PhyloFisher/pull/34
  • Add gfmix utility by @robert-ervin-jones in https://github.com/TheBrownLab/PhyloFisher/pull/24
  • refactors and adds better exception handling by @robert-ervin-jones in https://github.com/TheBrownLab/PhyloFisher/pull/26
  • 27 purgepy errors when purging a collapsed taxon by @robert-ervin-jones in https://github.com/TheBrownLab/PhyloFisher/pull/37
  • 31 informantpy errors by @robert-ervin-jones in https://github.com/TheBrownLab/PhyloFisher/pull/36
  • adds long names to select_taxa output by @robert-ervin-jones in https://github.com/TheBrownLab/PhyloFisher/pull/35
  • 25 add checks to taxon collapserpy by @robert-ervin-jones in https://github.com/TheBrownLab/PhyloFisher/pull/38
  • updates readme and removes manual by @robert-ervin-jones in https://github.com/TheBrownLab/PhyloFisher/pull/39
  • Aa comp calc handle chimeras by @robert-ervin-jones in https://github.com/TheBrownLab/PhyloFisher/pull/40
  • cleans up dead code by @robert-ervin-jones in https://github.com/TheBrownLab/PhyloFisher/pull/41
  • adds checks by @robert-ervin-jones in https://github.com/TheBrownLab/PhyloFisher/pull/42
  • Mammal modeler to smk by @robert-ervin-jones in https://github.com/TheBrownLab/PhyloFisher/pull/43

Full Changelog: https://github.com/TheBrownLab/PhyloFisher/compare/v1.1.2...v1.2.0

- Python
Published by robert-ervin-jones over 3 years ago

phylofisher - v1.1.2

What's Changed

  • fixes sgt_constructor parallelization by @robert-ervin-jones in https://github.com/TheBrownLab/PhyloFisher/pull/20
  • fixes issue when not using --to_exclude arg by @robert-ervin-jones in https://github.com/TheBrownLab/PhyloFisher/pull/21

Full Changelog: https://github.com/TheBrownLab/PhyloFisher/compare/v1.1.1...v1.1.2

- Python
Published by robert-ervin-jones almost 4 years ago

phylofisher - v1.1.1

- Python
Published by robert-ervin-jones about 4 years ago

phylofisher - v1.1.0

What's Changed

  • There is now a checkpoint post length filtration in sgt_constructor.py. This is to prevent empty alignments to continue through the pipeline. Empty alignments occur when all sequences are filtered out by BMGE.
  • Minor bug fixes

Full Changelog: https://github.com/TheBrownLab/PhyloFisher/commits/v1.1.0

- Python
Published by robert-ervin-jones about 4 years ago