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Release 0.5.0 #88

Merged
merged 55 commits into from
Jan 17, 2025
Merged

Release 0.5.0 #88

merged 55 commits into from
Jan 17, 2025

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khoroshevskyi
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@khoroshevskyi khoroshevskyi commented Jan 6, 2025 •
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Changes

  • Important speed improvements.
  • Added open_chromatin plot back into processing.
  • Added gtrs dependency, that calculates gc content.
  • Added skipper that automatically skips samples in pep that were already processed.
  • Added lite functionality to main functions that allows to run uploading without using any heavy processing.
  • Added function that will reprocess files, if they were unprocessed in the bedbase.
  • Added function that predicts genome if genome wasn't provided

@khoroshevskyi
updated regions number
55680c2
@khoroshevskyi
added qdrant label colection uploader
e127a24
@khoroshevskyi
removed one plot from stats and updated tss dist
2da625b
@khoroshevskyi
added gc content and isort
4bfef80
@khoroshevskyi
added skipper to run-pep
4f638ae
@khoroshevskyi
few tweaks
6116916
@khoroshevskyi
added bedset annotation from pep
ad4d6e4
@khoroshevskyi
updated bbconf requirements
272f17a
@khoroshevskyi
added reference genome predictor
4b5ceaf
@khoroshevskyi
some more improvements on skipper
2fff1b4
@khoroshevskyi
updated version
37e863e
@khoroshevskyi
for debugging
dc86e56
@khoroshevskyi
for debugging2
3657166
@khoroshevskyi
updated cli, requirements and R script
70006e6
@khoroshevskyi
remove debugger lines
7080c2d
@khoroshevskyi
Work on new reindexing
ac7877f
@khoroshevskyi
fixed r stats bug, and improved genome predictor
76ecb0e
@khoroshevskyi
fix of not recreation of bedset in geo uploader
f76b179
@khoroshevskyi
fixed bedqc messaging error
86ba98b
@khoroshevskyi
added mouse standard genome name
c0a54f5
@khoroshevskyi
Work on bbuploader:
f674080 
1) added better overwritten arguments.
2) added preload option, that preloads bedfiles before uploading.
@khoroshevskyi
increased length of genome standardization, updated bbuploader cli
6f69bdf
@khoroshevskyi
optimization of bbuploader
2631cbd
@khoroshevskyi
work on partial processing and lint
809bca7
@khoroshevskyi
Added cli light
1d57cfb
@khoroshevskyi
strict versions
15821dd
@khoroshevskyi
added light mode to bedmaker
3726bd1
@khoroshevskyi
Added light mode to bedbuncher and cli
97d4570
@khoroshevskyi
Added run unprocessed files
60563bd
@khoroshevskyi
added reprocess functions for bed and bedsets and cli options
5ce2d6d
khoroshevskyi and others added 24 commits December 18, 2024 16:27
@khoroshevskyi
Merge pull request #85 from databio/speed_improvements
6f0d977 
Speed improvements
@khoroshevskyi
changed light -> lite
a4f4cea
@khoroshevskyi
Merge pull request #87 from databio/partial_processing
a75b987 
Added partial processing
@khoroshevskyi
updated requirements
fa4f5fe
@khoroshevskyi
updated version
63e6129
@khoroshevskyi
updated tests
2015082
@khoroshevskyi
updated python version in test
6710811
@khoroshevskyi
updated python version in test - reverting
bfa1c42
@khoroshevskyi
error fix
7447966
@khoroshevskyi
updated bedmaker logger
a0ba1a3
@khoroshevskyi
updated search limit
8b67bd4
@khoroshevskyi
updated docstring in cli
8230cec
@khoroshevskyi
added logging provided parameters
f3e9856
@khoroshevskyi
updated logger in bedmaker
1a49462
@khoroshevskyi
updated exceptions in geo uploader
7414e1e
@khoroshevskyi
updated reprocessing of the files
db77732
@khoroshevskyi
lint
36927d1
@khoroshevskyi
updated geo bed file uploader
a52a57f
@khoroshevskyi
fixed #81
502aa63
@khoroshevskyi
updated docs
2cb8568
@khoroshevskyi
updated requirements
fc9152e
@khoroshevskyi
fixed #23
b34c486
@khoroshevskyi
Release updates
828ed89
@khoroshevskyi
Release updates
de9cc36
donaldcampbelljr
donaldcampbelljr approved these changes Jan 16, 2025
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@donaldcampbelljr donaldcampbelljr left a comment

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I did a very quick review, but it makes sense and looks good to me.

bedboss/skipper.py Show resolved Hide resolved
@khoroshevskyi khoroshevskyi merged commit ad184bf into main Jan 17, 2025
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@donaldcampbelljr donaldcampbelljr donaldcampbelljr approved these changes

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@khoroshevskyi @donaldcampbelljr