Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

downgrade pyteomics version in pyproject.toml #133

Closed
wants to merge 74 commits into from
Closed

downgrade pyteomics version in pyproject.toml #133

Changes from all commits
Commits
Show all changes
74 commits
Select commit Hold shift + click to select a range
50aff5e
parsing from spectrum id
ArthurDeclercq Nov 22, 2023
dcfcc00
change regex function used
ArthurDeclercq Dec 5, 2023
25aa0ea
fix unboundLocalError
ArthurDeclercq Dec 8, 2023
0e2b192
add regex patterns for im and rt parsing from spectrum id
ArthurDeclercq Jan 2, 2024
b45007f
im2deep
rodvrees Jan 9, 2024
112860c
add debug statement for im, rt parsing
ArthurDeclercq Jan 10, 2024
0330096
Merge remote-tracking branch 'origin/timsRescore' into timsRescore
rodvrees Jan 10, 2024
f6c9564
models + debug
rodvrees Jan 10, 2024
7585d51
fix
rodvrees Jan 10, 2024
a0f792f
add models
rodvrees Jan 10, 2024
b4660fd
fixes in im2deep.py
rodvrees Jan 11, 2024
1a18a42
fixes in im2deep.py
rodvrees Jan 11, 2024
b93df98
im2deep implementation
rodvrees Jan 11, 2024
8749ddf
remove peprec implementation deeplc
ArthurDeclercq Jan 11, 2024
782c7a0
CCS shift calculation fix
rodvrees Jan 12, 2024
7604153
models + plot
rodvrees Jan 12, 2024
b2d65eb
add inverse reduced ion mobility key to mzml parsing
ArthurDeclercq Jan 16, 2024
aa9cde0
Merge branch 'compomics:timsRescore' into timsRescore
ArthurDeclercq Jan 16, 2024
230753c
remove print statements
ArthurDeclercq Jan 16, 2024
d9f9feb
updated inverse reduced ion mobility
ArthurDeclercq Jan 17, 2024
6ccb429
Merge branch 'compomics:timsRescore' into timsRescore
ArthurDeclercq Jan 17, 2024
00d6704
add unused argument
ArthurDeclercq Jan 17, 2024
50a01e9
skip ms1 scans in mzml
ArthurDeclercq Jan 17, 2024
2645378
Merge branch 'compomics:timsRescore' into timsRescore
ArthurDeclercq Jan 17, 2024
a99b492
IM2Deep plot correct labels
rodvrees Jan 22, 2024
1f6e973
calibrate per charge option
rodvrees Jan 26, 2024
301d632
Merge branch 'timsRescore' of github.com:rodvrees/ms2rescore into tim…
rodvrees Jan 26, 2024
dd8bd18
new models and reference
rodvrees Jan 29, 2024
ad0f3d7
correct format reference
rodvrees Jan 29, 2024
3a5b1ab
fix model name in IM2Deep
rodvrees Jan 29, 2024
4a5ff63
change deeplc calibration
ArthurDeclercq Jan 31, 2024
3b4899a
Merge branch 'compomics:timsRescore' into timsRescore
ArthurDeclercq Jan 31, 2024
f773c90
typo
ArthurDeclercq Jan 31, 2024
fd09f88
Merge branch 'compomics:timsRescore' into timsRescore
ArthurDeclercq Jan 31, 2024
16abf78
remove automatically putting deeplc on false
ArthurDeclercq Jan 31, 2024
012e9d0
change use of reference dataset
ArthurDeclercq Jan 31, 2024
d07c3b6
Merge branch 'timsRescore' of https://github.com/rodvrees/ms2rescore …
ArthurDeclercq Jan 31, 2024
13155e6
Merge branch 'compomics:timsRescore' into timsRescore
ArthurDeclercq Jan 31, 2024
aea9d9f
IM2Deep calibrate correctly
rodvrees Jan 31, 2024
52d0761
Merge branch 'timsRescore' of github.com:rodvrees/ms2rescore into tim…
rodvrees Jan 31, 2024
de04bdd
bug fix
ArthurDeclercq Jan 31, 2024
167deb7
Merge branch 'compomics:timsRescore' into timsRescore
ArthurDeclercq Jan 31, 2024
f9cca43
bugfix
ArthurDeclercq Jan 31, 2024
337d81a
Merge branch 'compomics:timsRescore' into timsRescore
ArthurDeclercq Jan 31, 2024
f3bdb26
changes in deeplc calibration
ArthurDeclercq Feb 1, 2024
ff34fc2
Merge branch 'compomics:timsRescore' into timsRescore
ArthurDeclercq Feb 1, 2024
d8340f5
remove print statements
ArthurDeclercq Feb 1, 2024
f5ec8e5
Merge branch 'compomics:timsRescore' into timsRescore
ArthurDeclercq Feb 1, 2024
65f134c
Implement IM2Deep package
rodvrees Feb 2, 2024
e1f0ddf
Merge branch 'timsRescore' of github.com:rodvrees/ms2rescore into tim…
rodvrees Feb 2, 2024
a9fc45f
GUI changes im2deep
ArthurDeclercq Feb 5, 2024
fa97517
add im2deep to pyproject
ArthurDeclercq Feb 5, 2024
a4fd01a
change dockerfile
ArthurDeclercq Feb 5, 2024
721cd08
optimise spectrum parsing
ArthurDeclercq Feb 5, 2024
ceed348
update toml file
ArthurDeclercq Feb 6, 2024
fcd393c
added debug logging
ArthurDeclercq Feb 6, 2024
3fc994f
requested changes
ArthurDeclercq Feb 15, 2024
42debd8
change numpy version upper limit
ArthurDeclercq Feb 15, 2024
c0713ed
fix bug
ArthurDeclercq Feb 15, 2024
fcf579d
Use newer setup-python action; revert numpy upper limit
RalfG Feb 15, 2024
48fae0e
Fix numpy version for py311
RalfG Feb 17, 2024
9063a84
Update pyproject.toml
RalfG Feb 18, 2024
7ede2f8
requested changes
ArthurDeclercq Feb 20, 2024
b2a126a
Update ms2rescore/feature_generators/im2deep.py
RalfG Feb 21, 2024
667822e
Add IM2Deep feature generator (#121)
ArthurDeclercq Feb 21, 2024
ee36b09
Merge branch 'timsRescore' of https://github.com/compomics/ms2rescore…
RalfG Feb 22, 2024
e5b7b87
Remove unused code; import im2ccs from im2deep package; use im2ccs ve…
RalfG Feb 22, 2024
82e7789
Remove unused code and imports; Replace pandas apply with vectorized …
RalfG Feb 22, 2024
d158a86
Formatting
RalfG Feb 22, 2024
a4f198a
Fix config descriptions for psm_id_im_pattern and psm_id_rt_pattern
RalfG Feb 22, 2024
86363ee
Check with Ruff on test (also disallow print statements)
RalfG Feb 28, 2024
ff81bd9
Merge branch 'timsRescore' into main
ArthurDeclercq Mar 22, 2024
d6e76cf
Revert "Merge branch 'timsRescore' into main"
ArthurDeclercq Mar 22, 2024
3cde57b
downgrade pyteomics version in pyproject.toml
ArthurDeclercq Mar 22, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion pyproject.toml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,7 @@ dependencies = [
"numpy==1.24.3; python_version == '3.11'", # Incompatibility with sklearn, pygam, and TF...
"pandas>=1.0",
"rich>=12",
"pyteomics>=4.1.0",
"pyteomics>=4.1.0,<4.7.0",
"lxml>=4.5",
"ms2pip>=4.0.0-dev4",
"click>=7",
Expand Down
Loading