Code

Numpy performance improvements#37

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Merged

JLSteenwyk merged 16 commits intomasterJLSteenwyk/ClipKIT:masterfrom np-refactorJLSteenwyk/ClipKIT:np-refactorCopy head branch name to clipboardSep 24, 2023

+7,395-8,957

Commits

Commits on Sep 11, 2023

• used numpy accelerate for smart gap determination

  Show description for bd24d59
  JLSteenwyk

  committed
  bd24d59

Commits on Sep 12, 2023

• start msa refactor with gappy and kpi modes

  JLSteenwyk

  committed
  12a08e6

Commits on Sep 13, 2023

• finished writing logic of trimming modes

  JLSteenwyk

  committed
  7c0dee8

Commits on Sep 17, 2023

• Start refactor of trim run and stats to use new MSA class

  TJBIII

  committed
  6d28849

Commits on Sep 18, 2023

• Harden MSA trimming

  TJBIII

  committed
  4a2a799

• Fix integration tests for kpi_smart_gap_mode due to new gap chars logic

  TJBIII

  committed
  1ef9d9b

Commits on Sep 23, 2023

• Implement is_any_entry_sequence_only_gaps and clean up unit tests for warnings

  TJBIII

  committed
  4804516

Commits on Sep 24, 2023

• Move SiteClassificationType enum out of modes module and organize MSA methods

  TJBIII

  committed
  fda1408

• Factor out site_classification_types and column_character_frequencies

  Show description for 9ca1741
  

  TJBIII

  and

  JLSteenwyk

  committed
  9ca1741

• Implement debug log file

  TJBIII

  committed
  1c08ccc

• Fix to_bio_msa to preserve full sequence descriptions

  TJBIII

  committed
  90e1dc7

• Remove old unit tests that are no longer relevant

  TJBIII

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  8442f43

• Fix case for trimmed property when no positions to trim

  TJBIII

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  905e560

• Remove unused helpers

  TJBIII

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  59200e3

• Bump version and update changelog

  TJBIII

  committed
  3dbae1d

• Run black formatter

  TJBIII

  committed
  6eabe7b