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spectrumAI into py-pgatk #77

Merged
merged 59 commits into from
Apr 19, 2024
Merged

spectrumAI into py-pgatk #77

merged 59 commits into from
Apr 19, 2024

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ypriverol
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@ypriverol ypriverol commented Apr 19, 2024 •
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This PR includes:

  • spectrumAI algorithm added.
  • remove of dependencies version in the requirements and other files.
  • fix small bug in cbioportal downloader
  • remove ms2rescore and deeplc from the code until we get better results

DongdongdongW and others added 30 commits August 23, 2022 20:08
@DongdongdongW
add spectrumAI
aee99d5
@DongdongdongW
fix and add test files
c1cad6c
@DongdongdongW
ci test
6523368
@DongdongdongW
fix matplotlib version
a47425b
@DongdongdongW
fix pyopenms version
9d70914
@DongdongdongW
fix
364e1e0
@DongdongdongW
Revert "fix"
b4b722c 
This reverts commit 364e1e0.
@DongdongdongW
update
b019874
@DongdongdongW
Update requirements.txt
78e6bf7
@DongdongdongW
Create __init__.py
f7efc8f
@DongdongdongW
Update setup.py
3535a23
@DongdongdongW
add mztab class-fdr
302c7f3 
add mztab class-fdr and modified the code that validates peptides
@DongdongdongW
Update mzTab_class_fdr.py
8ac96b5
@DongdongdongW
update test
a65d584
@DongdongdongW
fix Codacy Static Code Analysis
a366907
@DongdongdongW
fix
88e6036
@DongdongdongW
fix
739e741
@DongdongdongW
fix
3231d32
@DongdongdongW
add blast
3484c48
@DongdongdongW
update biopython version
94262ef
@DongdongdongW
add test file
e1d697f
@DongdongdongW
Update pypgatk_tests.py
c4a2b57
@ypriverol
Merge pull request #70 from DongdongdongW/spectrumAI
b60cef1 
add spectrumAI
@DongdongdongW
Fix the bug of class-fdr, adjust the blast to multi-process running t…
f63af96 
…o speed up the running speed
@DongdongdongW
update pathos version
ecc653b
@DongdongdongW
update test command
572b94e
@DongdongdongW
Update pythonpackage.yml
b1e860f
@DongdongdongW
Update pythonapp.yml
7b3d843
@DongdongdongW
Update mzTab_class_fdr.py
0be2b1c
@ypriverol
Merge pull request #71 from DongdongdongW/spectrumAI
8369615 
Fix the bug of class-fdr, adjust the blast to multi-process running t…
ypriverol and others added 22 commits October 31, 2022 15:21
@ypriverol
minor refinements in the code.
65f54b8
@DongdongdongW
update blast
6501ad7
@DongdongdongW
update spectrumAI
2383256
@DongdongdongW
Merge branch 'spectrumAI' of https://github.com/DongdongdongW/py-pgatk …
fd717a0 
…into spectrumAI
@DongdongdongW
update info
2c51161
@DongdongdongW
update
7ee34b3
@DongdongdongW
update
9a0a9b4
@ypriverol
removing versions of dependencies
5064b82
@ypriverol
changes on cbioportal download system.
e46bffe
@ypriverol
Merge branch 'spectrumAI' of https://github.com/DongdongdongW/py-pgatk …
8fe67f1 
…into spectrumAI

# Conflicts:
#	requirements.txt
#	setup.py
@ypriverol
Merge branch 'master' of https://github.com/bigbio/py-pgatk into spec…
77886ad 
…trumAI
@ypriverol
remove unnecesary code
397edca
@ypriverol
remove unnecesary code
a40265e
@ypriverol
skip to tests not working with pytests pooling.
40c022f
@ypriverol
skip to tests not working with pytests pooling.
f8009b6
@ypriverol
skip to tests not working with pytests pooling.
69002b8
@ypriverol
skip to tests not working with pytests pooling.
a5a8937
@ypriverol
skip to tests not working with pytests pooling.
805c592
@ypriverol
skip to tests not working with pytests pooling.
0f3f7fe
@ypriverol
skip to tests not working with pytests pooling.
1c38d7b
@ypriverol
skip to tests not working with pytests pooling.
4b4c8ab
@ypriverol
skip to tests not working with pytests pooling.
040c291
@ypriverol ypriverol mentioned this pull request Apr 19, 2024
Closed
@ypriverol ypriverol merged commit 6faf53c into master Apr 19, 2024
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@ypriverol @DongdongdongW