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Refactoring #245

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@ArthurDeclercq ArthurDeclercq commented Jan 9, 2026 •
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ArthurDeclercq and others added 30 commits February 24, 2024 15:48
@ArthurDeclercq
initial commit
fdceeba
@ArthurDeclercq
finalize ms2 feature generation
5374ed8
@ArthurDeclercq
add rustyms
60207a3
@ArthurDeclercq
remove exit statement fixed IM required value
ae39844
@ArthurDeclercq
change logger.info to debug
9b98c4d
@ArthurDeclercq
added profile decorator to get timings for functions
5e45756
@ArthurDeclercq
removed profile as standard rescore debug statement
304777c
@ArthurDeclercq
added new basic features
95ee475
@ArthurDeclercq
fixes for ms2 feature generator, removed multiprocessing
73f4573
@ArthurDeclercq
return empty list on parsing error with rustyms, removed multiprocessing
947233e
@ArthurDeclercq
add deeplc_calibration psm set
24ce565
@ArthurDeclercq
Merge branch 'timsRescore' of https://github.com/compomics/ms2rescore …
114b006 
…into spectrum-feature-generator
@ArthurDeclercq
remove unused import
33c38b0
@ArthurDeclercq
Merge branch 'timsRescore' of https://github.com/compomics/ms2rescore …
40425c7 
…into spectrum-feature-generator
@ArthurDeclercq
Merge branch 'timsRescore' of https://github.com/compomics/ms2rescore …
b810b8c 
…into spectrum-feature-generator
@ArthurDeclercq
Merge tag 'main' of https://github.com/compomics/ms2rescore into spec…
69b5d1a 
…trum-feature-generator
@ArthurDeclercq
Merge pull request #177 from compomics/main
6e2d102 
pull main in spectrum-feature-generator
@ArthurDeclercq
integrate mumble into ms2branch
11fdc51
@ArthurDeclercq
Merge remote-tracking branch 'origin/main' into spectrum-feature-gene…
3140c44 
…rator
@ArthurDeclercq
temp removal of sage features before rescoring
883169a
@ArthurDeclercq
Merge branch 'main' of https://github.com/compomics/ms2rescore into s…
97865e7 
…pectrum-feature-generator
@ArthurDeclercq
remove psm_file features when rescoring with mumble
da39ae8
@SamvPy
linting
37fff28
@SamvPy
add hyperscore calculation
e8b59f3
@ArthurDeclercq
calibration fixes
c51cd34
@ArthurDeclercq
changes for mumble implementation
295e37f
@SamvPy
change openms peptide formatting
909860d
@ArthurDeclercq
add mumble psm filtering functionality
c5902c2
@ArthurDeclercq
Merge branch 'spectrum-feature-generator' of https://github.com/compo…
6eaceb2 
…mics/ms2rescore into spectrum-feature-generator
@SamvPy
remove pyopenms dependency for hyperscore calculation
5ce55f5
paretje and others added 30 commits January 17, 2025 13:34
@paretje
drop rustyms requirement to 0.8.3
21cafc7 
rustyms 0.9.0a3 requires python 3.11, while we support 3.9.
@ArthurDeclercq
mumble related changes
ca9da7d
@paretje
add mumble
c5b6eb0 
As mumble hasn't been published on pypi yet, use a git dependency for
now.
@paretje
update mumble to use user cache dir
aee8ec7
@paretje
bump im2deep dependency
7ce56c2 
im2deep.utils was introduced in 0.3.0.
CompOmics/IM2Deep@0a4bc9d
@ArthurDeclercq
make mumble and rustyms optional dependancy
106ad8f
@ArthurDeclercq
Merge branch 'main' of https://github.com/compomics/ms2rescore into s…
72e2b71 
…pectrum-feature-generator
@ArthurDeclercq
set defaults in mumble config
29aac8a
@SamvPy
fix rustyms 0.8.0 -> 0.10.0
487f661
@ArthurDeclercq
Merge remote-tracking branch 'origin/main' into refactoring
9a97ed1
@ArthurDeclercq
moved maxquant features to ms2
05078cd
@ArthurDeclercq
im2deep refactoring
2011241
@ArthurDeclercq
ms2pip refactoring
36750b4
@ArthurDeclercq
parsing spectra once and storing spectra objects
3091b0f
@ArthurDeclercq
directly operate on spectra objects instead of reacquiring them
5b3d4c4
@ArthurDeclercq
updated profiling
a3cbb1b
@ArthurDeclercq
removed maxquant generator from fg
a1df72d
@ArthurDeclercq
changes to column names
2c7a09b
@ArthurDeclercq
changes to avoid out of memory error due to multiprocessing
e855abf
@ArthurDeclercq
replace list with set to reduce lookup time to O(1)
577df19
@ArthurDeclercq
remove unused imports
a80238b
@ArthurDeclercq
migrate ms2 and ms2pip features to ms2rescore-rs
abf66b4
@ArthurDeclercq
reimplement deeplc feature calculation
a9108b9
@ArthurDeclercq
change logging
698dd5e
@ArthurDeclercq
fix im2deep fg
862f9be
@ArthurDeclercq
add support for continue runs and writing intermediate file on error …
889b42d 
…to continue from
@ArthurDeclercq
changes to default features sets instead of based on charge
ba930b8
@ArthurDeclercq
minor changes
a3875da
@ArthurDeclercq
conditional import of mumble
8e793a0
@ArthurDeclercq
add tracking to spectrum file reading
07b96e7
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4 participants

@ArthurDeclercq @SamvPy @paretje