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Develop #121

Merged
merged 63 commits into from
Dec 10, 2024
Merged

Develop #121

merged 63 commits into from
Dec 10, 2024

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jamesli124
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Removed

  • strand_location arg from agg_bigwig
  • cli_hist module

Fixed

  • fixed bug involving tqdm progress bar in frag_length_intervals
  • some code formatting
  • fixed bug involving arg names in filter-bam
  • add some missing args to CLI

Changed

  • change default of arg both_strands of end_motifs to True to match
    behavior of original scripts
  • rename fraction_high and fraction_low to min_length and max_length
    for all features, deprecating old args as aliases if needed.
  • numpy 2 compatible

Added

  • internal utils._typing and utils._deprecation modules
  • test for delfi

jamesli124 and others added 30 commits December 6, 2024 16:24
@jamesli124
fixed issue
4a198b4 
    - fixed frag_length_intervals bug
    - CLI prints AttributeError details if handled.
@jamesli124
removed histogram option for frag_length_bins
de3061a
@jamesli124
update dependency groups
57c2e45
@jamesli124
updated docs
f9956f0
@jamesli124
update verbose messages
2f8458c
@jamesli124
simplify tqdm import
95948bf
@jamesli124
removed duplicate function declarations
874922d
@jamesli124
formatting and typing
fd618be
@jamesli124
fix error in changelog
03143b5
@jamesli124
formatting
2665ea5
@jamesli124
update changelog
fc26b40
@jamesli124
fix filter-bam
37ed2d1
@jamesli124
update changelog
0c55514
@jamesli124
fix some typehints
9e32a14
@jamesli124
added internal _typing module
17cf743
@jamesli124
moved typing to utils
b9978d2
@jamesli124
added finaletoolkit.utils._deprecation module containing decorators…
702a84a 
… for deprecated or moved functions/methods
@jamesli124
formatting
1a8ae62
@jamesli124
rename cli test module
ccd9553
@jamesli124
added test to check for missing args in CLI
6ed0636
@jamesli124
rename fraction_high and fraction_low to min_length
37d817c 
 and `max_length`
@jamesli124
add some missing args to CLI
01d71e5
@jamesli124
update docstring
370f9e5
@jamesli124
fix typo
1997bf3
@jamesli124
change default for both_strands to True of end_motifs to match be…
2aee0f7 
…havior of original scripts
@jamesli124
update changelog
1a1515d
@jamesli124
add --no-both-strands option to end-motifs
9051b92
@jamesli124
rename fraction_low and fraction_high to min_length and `max_le…
833701b 
…ngth` for `interval_end_motifs`

    - keep old arg names as deprecated aliases
@jamesli124
add missing args to interval-end-motifs
5e9b66e
@jamesli124
add missing args
ec771a9
jamesli124 and others added 28 commits December 9, 2024 23:05
@jamesli124
test file
ddc1339
@jamesli124
update docstring
3ac4511
@jamesli124
Merge branch 'unify-naming' of github.com:epifluidlab/FinaleTools int…
a3fc9e8 
…o unify-naming
@jamesli124
change to hg19
3342c81
@jamesli124
add 2bit test file
6298db1
@jamesli124
Merge branch 'unify-naming' of github.com:epifluidlab/FinaleTools int…
607bfb0 
…o unify-naming
@jamesli124
Merge branch 'unify-naming' of github.com:epifluidlab/FinaleTools int…
eb1c0d0 
…o unify-naming
@jamesli124
test file
b82e263
@jamesli124
Merge branch 'unify-naming' of github.com:epifluidlab/FinaleTools int…
95a2f7a 
…o unify-naming
@jamesli124
test for delfi
2113caa
@jamesli124
Merge branch 'unify-naming' of github.com:epifluidlab/FinaleTools int…
06ce2a3 
…o unify-naming
@jamesli124
test file
b847f60
@jamesli124
formatting
77238e1
@jamesli124
update test
14dcf3e
@jamesli124
Merge branch 'unify-naming' of github.com:epifluidlab/FinaleTools int…
bf98845 
…o unify-naming
@jamesli124
fixed delfi API function
809125f
@jamesli124
fixed delfi test
fcdd88e
@jamesli124
remove unused cli_hist module
fa75747
@jamesli124
remove strand_location and simply use 5th column every time
126ba92
@jamesli124
except deprecated args from test
4ca46eb
@jamesli124
Merge branch 'unify-naming' of github.com:epifluidlab/FinaleTools int…
689db32 
…o unify-naming
@jamesli124
update changelog
b22687c
@jamesli124
change some type annotations
d2a71bc
@jamesli124
change some type annotations
0c66d85
@jamesli124
fix interval mds CLI command
baac549
@jamesli124
Merge pull request #120 from epifluidlab/unify-naming
a8d1c38 
Unify naming
@jamesli124
increment version
f7409ef
@jamesli124
update changelog
69cd7b9
ravibandaru-lab
ravibandaru-lab approved these changes Dec 10, 2024
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Thanks!

@ravibandaru-lab ravibandaru-lab merged commit 3e5ba4e into main Dec 10, 2024
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@jamesli124 @ravibandaru-lab