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Unify naming#120

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jamesli124 merged 47 commits intodevelopepifluidlab/FinaleToolkit:developfrom unify-namingepifluidlab/FinaleToolkit:unify-namingCopy head branch name to clipboardDec 10, 2024

+837-166

Commits

Commits on Dec 7, 2024

• fix some typehints

  jamesli124

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  9e32a14

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• added internal _typing module

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  17cf743

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• moved typing to utils

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• added finaletoolkit.utils._deprecation module containing decorators for deprecated or moved functions/methods

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• formatting

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Commits on Dec 8, 2024

• rename cli test module

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• added test to check for missing args in CLI

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  6ed0636

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• rename fraction_high and fraction_low to min_length

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• add some missing args to CLI

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  01d71e5

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• update docstring

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  370f9e5

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• fix typo

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• change default for both_strands to True of end_motifs to match behavior of original scripts

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• update changelog

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Commits on Dec 10, 2024

• add --no-both-strands option to end-motifs

  jamesli124

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  9051b92

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• rename fraction_low and fraction_high to min_length and max_length for interval_end_motifs

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  833701b

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• add missing args to interval-end-motifs

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  5e9b66e

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• add missing args

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  ec771a9

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• add header option

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  1998483

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• remove restriction for numpy<2

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  5da9941

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• formatting

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  c13b0b5

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• added test files

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• add test files

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• test file

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  ddc1339

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• update docstring

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  3ac4511

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• Merge branch 'unify-naming' of github.com:epifluidlab/FinaleTools into unify-naming

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  a3fc9e8

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• change to hg19

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• add 2bit test file

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  6298db1

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• Merge branch 'unify-naming' of github.com:epifluidlab/FinaleTools into unify-naming

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• Merge branch 'unify-naming' of github.com:epifluidlab/FinaleTools into unify-naming

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• test file

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• Merge branch 'unify-naming' of github.com:epifluidlab/FinaleTools into unify-naming

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  95a2f7a

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• test for delfi

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• Merge branch 'unify-naming' of github.com:epifluidlab/FinaleTools into unify-naming

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  06ce2a3

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• test file

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  b847f60

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• formatting

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  77238e1

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• update test

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• Merge branch 'unify-naming' of github.com:epifluidlab/FinaleTools into unify-naming

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  bf98845

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• fixed delfi API function

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  809125f

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• fixed delfi test

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  fcdd88e

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• remove unused cli_hist module

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  fa75747

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• remove strand_location and simply use 5th column every time

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  126ba92

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• except deprecated args from test

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  4ca46eb

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• Merge branch 'unify-naming' of github.com:epifluidlab/FinaleTools into unify-naming

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  689db32

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• update changelog

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  b22687c

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• change some type annotations

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  d2a71bc

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• change some type annotations

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  0c66d85

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• fix interval mds CLI command

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