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v4.0.0 #201

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@RalfG RalfG commented Jun 25, 2023 •
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Fully refactored and drastically more user-friendly version of MS²PIP:

  • More modular Python API
  • One consolidated command-line interface with subcommands
  • Support for all file formats readable by psm_utils
  • Support for both MGF and mzML spectrum files
  • Support for ProForma 2.0 peptide notation (no modification configuration required anymore)
  • Support for multiple peptides/PSMs per spectrum
  • Detailed documentation on ms2pip.readthedocs.io
  • ...

RalfG and others added 30 commits February 2, 2023 22:33
@RalfG
Import exceptions module completely
b603fc0
@RalfG
Refactor process_peptides and process_spectra to avoid code duplicati…
bc471fe 
…on and to allow multiple PSMs per peptide.
@RalfG
Remove obsolete tests for SinglePrediction
ea0936c
@RalfG
Remove old feature_names code (should still be reimplemented)
ba7d1ee
@RalfG
Merge branch 'releases' of https://github.com/compomics/ms2pip_c into…
075e172 
… more-refactoring
@ArthurDeclercq
psm_id in peprec/pred_emp
2ff4e5c
@RalfG
Restructured Python API and CLI (WIP)
dcc5279
@RalfG
Merge branch 'more-refactoring' of https://github.com/compomics/ms2pip_c
7dd257b 
 into more-refactoring-rg
@RalfG
Reorder psm_id
f56c967
@RalfG
Move package metadata to pyproject.tom
afac375
@ArthurDeclercq
change return_results to MSPIP obj
7dfd636
@RalfG
Restructure package; remove obsolete and unused code
5ace6c8
@RalfG
Merge branch 'more-refactoring' of https://github.com/compomics/ms2pip_c
de89bc5 
 into more-refactoring
@RalfG
More restructuring (WIP)
5945ab8
@RalfG
Implement ProcessingResult
19ed993
@RalfG
Update pyproject, setup.py, manifest
876b5b1
@RalfG
Add psm_id before filtering input; do not use yield in batch_processing
dc200fe
@RalfG
Implement psm_list throughout MS²PIP, removing peprec dataframe usage
2f2b82e
@ArthurDeclercq
logging for modification handling
0c2c1e4
@ArthurDeclercq
Merge branch 'more-refactoring' of https://github.com/compomics/ms2pip …
ff17054 
…into more-refactoring
@ArthurDeclercq
put warning for modificaiton on invalid aa
9150dc5
@ArthurDeclercq
import change
559a3d4
@RalfG
Further refactoring for 4.0:
6642566 
- Reimplement encoder to fully support ProForma without PEPREC intermediate.
- Reimplement multiprocessing chunking approach to improve handling of very large PSM files.
- Add psm_index to output.
- Move batch_processing back into core.
- Move encoder out of _utils
@RalfG
Merge branch 'more-refactoring' of https://github.com/compomics/ms2pip_c
b2fe5a6 
 into more-refactoring
@ArthurDeclercq
bug fix invalid modification
d6e18b2
@RalfG
Fix invalid modification bug in encoder
70a161d
@RalfG
Merge branch 'more-refactoring' of https://github.com/compomics/ms2pip_c
36ba316 
 into more-refactoring
@RalfG
Remove typing of optional spectrum_utils import
f824356
@RalfG
Temporarily disable tests (outdated)
36724ae
@RalfG
Remove match_spectra functionality
8e044d8 
(Could be re-added and implemented if ever needed)
RalfG and others added 29 commits May 3, 2024 16:14
@RalfG
Initial restructuring of fasta2speclib for predict-library
683d52d
@rodvrees
working predict_library and csv output
4cf2fde
@rodvrees
Functional .msp output
c6073e1
@rodvrees
unset normalization defaults
b89b0fb
@RalfG
Continue predict-library implementation; add tests
8bf8641
@RalfG
search_space: Add docs, better define api; restructure
dfceb3d
@RalfG
Merge branch 'reimplement-predict-library' of https://github.com/comp…
7916326 
…omics/ms2pip_c into reimplement-predict-library
@RalfG
Merge branch 'v4.0.0' of https://github.com/compomics/ms2pip_c into s…
2ee2340 
…pectrum-output
@RalfG
Reimplement most of spectrum_output for v4.0.0
59ad47d
@RalfG
Remove unused imports
5afa835
@RalfG
Finish DLIB; add general write_spectra function...
375ea07
@RalfG
Clip negative predicted intensities; Allow psm_list with multiple run…
cdb8ca1 
…s/collections for prediction
@RalfG
Implement spectrum output for CLI functions
bc65c93
@RalfG
Fix linting errors
8a91a57
@RalfG
Merge pull request #220 from compomics/spectrum-output
bd66087 
Reimplement spectrum_output module for v4
@RalfG
Merge branch 'v4.0.0' of https://github.com/compomics/ms2pip_c into r…
a959f75 
…eimplement-predict-library
@RalfG
Implement spectrum-output for predict-library
a879808
@RalfG
Avoid memory issues by converting to Peptidoforms lazily
66c5c2a
@RalfG
Remove obsolete tests; fix search space test imports
345ccd8
@RalfG
CI: Reinstate tests
b09f4e9
@RalfG
Remove unused import; clean up test imports
92088fa
@RalfG
Fix test workflow
7ac939c
@RalfG
Fix search_space_test
5d1f11a
@RalfG
Merge pull request #219 from compomics/reimplement-predict-library
e595c9d 
Reimplement predict library
@RalfG
Update docs
ab81ad4
@RalfG
Doc updates; version bump
a335bf2
@RalfG
predict-library: Allow fasta file to be missing from config file if p…
1ad181b 
…rovided in CLI
@RalfG
Fix build artifact upload
2275a97
@RalfG
Revert fasta assignment
fd34319
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5 participants
@RalfG @ArthurDeclercq @jaspervdh @Cajac102 @rodvrees