Code

TIMS²Rescore#142

Code

Merged

ArthurDeclercq merged 129 commits intomaincompomics/ms2rescore:mainfrom timsRescorecompomics/ms2rescore:timsRescoreCopy head branch name to clipboardJul 17, 2024

+1,023-287

Commits

Commits on Nov 22, 2023

• parsing from spectrum id

  ArthurDeclercq

  committed
  50aff5e

Commits on Dec 5, 2023

• change regex function used

  ArthurDeclercq

  committed
  dcfcc00

Commits on Dec 8, 2023

• fix unboundLocalError

  ArthurDeclercq

  committed
  25aa0ea

Commits on Jan 2, 2024

• add regex patterns for im and rt parsing from spectrum id

  ArthurDeclercq

  committed
  0e2b192

Commits on Jan 9, 2024

• im2deep

  rodvrees

  committed
  b45007f

Commits on Jan 10, 2024

• add debug statement for im, rt parsing

  ArthurDeclercq

  committed
  112860c

• Merge remote-tracking branch 'origin/timsRescore' into timsRescore

  rodvrees

  committed
  0330096

• models + debug

  rodvrees

  committed
  f6c9564

• fix

  rodvrees

  committed
  7585d51

• add models

  rodvrees

  committed
  a0f792f

Commits on Jan 11, 2024

• fixes in im2deep.py

  rodvrees

  committed
  b4660fd

• fixes in im2deep.py

  rodvrees

  committed
  1a18a42

• im2deep implementation

  rodvrees

  committed
  b93df98

• remove peprec implementation deeplc

  ArthurDeclercq

  committed
  8749ddf

Commits on Jan 12, 2024

• CCS shift calculation fix

  rodvrees

  committed
  782c7a0

• models + plot

  rodvrees

  committed
  7604153

Commits on Jan 16, 2024

• add inverse reduced ion mobility key to mzml parsing

  ArthurDeclercq

  committed
  b2d65eb

• Merge branch 'compomics:timsRescore' into timsRescore

  ArthurDeclercq

  authored
  aa9cde0

• remove print statements

  ArthurDeclercq

  committed
  230753c

Commits on Jan 17, 2024

• updated inverse reduced ion mobility

  ArthurDeclercq

  committed
  d9f9feb

• Merge branch 'compomics:timsRescore' into timsRescore

  ArthurDeclercq

  authored
  6ccb429

• add unused argument

  ArthurDeclercq

  committed
  00d6704

• skip ms1 scans in mzml

  ArthurDeclercq

  committed
  50a01e9

• Merge branch 'compomics:timsRescore' into timsRescore

  ArthurDeclercq

  authored
  2645378

Commits on Jan 22, 2024

• IM2Deep plot correct labels

  rodvrees

  authored
  a99b492

Commits on Jan 26, 2024

• calibrate per charge option

  rodvrees

  committed
  1f6e973

• Merge branch 'timsRescore' of github.com:rodvrees/ms2rescore into timsRescore

  rodvrees

  committed
  301d632

Commits on Jan 29, 2024

• new models and reference

  rodvrees

  committed
  dd8bd18

• correct format reference

  rodvrees

  committed
  ad0f3d7

• fix model name in IM2Deep

  rodvrees

  committed
  3a5b1ab

Commits on Jan 31, 2024

• change deeplc calibration

  ArthurDeclercq

  committed
  4a5ff63

• Merge branch 'compomics:timsRescore' into timsRescore

  ArthurDeclercq

  authored
  3b4899a

• typo

  ArthurDeclercq

  committed
  f773c90

• Merge branch 'compomics:timsRescore' into timsRescore

  ArthurDeclercq

  authored
  fd09f88

• remove automatically putting deeplc on false

  ArthurDeclercq

  committed
  16abf78

• change use of reference dataset

  ArthurDeclercq

  committed
  012e9d0

• Merge branch 'timsRescore' of https://github.com/rodvrees/ms2rescore into timsRescore

  ArthurDeclercq

  committed
  d07c3b6

• Merge branch 'compomics:timsRescore' into timsRescore

  ArthurDeclercq

  authored
  13155e6

• IM2Deep calibrate correctly

  rodvrees

  committed
  aea9d9f

• Merge branch 'timsRescore' of github.com:rodvrees/ms2rescore into timsRescore

  rodvrees

  committed
  52d0761

• bug fix

  ArthurDeclercq

  committed
  de04bdd

• Merge branch 'compomics:timsRescore' into timsRescore

  ArthurDeclercq

  authored
  167deb7

• bugfix

  ArthurDeclercq

  committed
  f9cca43

• Merge branch 'compomics:timsRescore' into timsRescore

  ArthurDeclercq

  authored
  337d81a

Commits on Feb 1, 2024

• changes in deeplc calibration

  ArthurDeclercq

  committed
  f3bdb26

• Merge branch 'compomics:timsRescore' into timsRescore

  ArthurDeclercq

  authored
  ff34fc2

• remove print statements

  ArthurDeclercq

  committed
  d8340f5

• Merge branch 'compomics:timsRescore' into timsRescore

  ArthurDeclercq

  authored
  f5ec8e5

Commits on Feb 2, 2024

• Implement IM2Deep package

  rodvrees

  committed
  65f134c

• Merge branch 'timsRescore' of github.com:rodvrees/ms2rescore into timsRescore

  rodvrees

  committed
  e1f0ddf

Commits on Feb 5, 2024

• GUI changes im2deep

  ArthurDeclercq

  committed
  a9fc45f

• add im2deep to pyproject

  ArthurDeclercq

  committed
  fa97517

• change dockerfile

  ArthurDeclercq

  committed
  a4fd01a

• optimise spectrum parsing

  ArthurDeclercq

  committed
  721cd08

Commits on Feb 6, 2024

• update toml file

  ArthurDeclercq

  committed
  ceed348

• added debug logging

  ArthurDeclercq

  committed
  fcd393c

Commits on Feb 15, 2024

• requested changes

  ArthurDeclercq

  committed
  3fc994f

• change numpy version upper limit

  ArthurDeclercq

  committed
  42debd8

• fix bug

  ArthurDeclercq

  committed
  c0713ed

• Use newer setup-python action; revert numpy upper limit

  RalfG

  committed
  fcf579d

Commits on Feb 17, 2024

• Fix numpy version for py311

  RalfG

  authored
  48fae0e

Commits on Feb 18, 2024

• Update pyproject.toml

  Show description for 9063a84
  RalfG

  authored
  9063a84

Commits on Feb 20, 2024

• requested changes

  ArthurDeclercq

  committed
  7ede2f8

Commits on Feb 21, 2024

• Update ms2rescore/feature_generators/im2deep.py

  RalfG

  authored
  b2a126a

• Add IM2Deep feature generator (#121)

  Show description for 667822e
  

  3 peopleauthored
  667822e

Commits on Feb 22, 2024

• Merge branch 'timsRescore' of https://github.com/compomics/ms2rescore into timsRescore

  RalfG

  committed
  ee36b09

• Remove unused code; import im2ccs from im2deep package; use im2ccs vectorized

  RalfG

  committed
  e5b7b87

• Remove unused code and imports; Replace pandas apply with vectorized usage;

  RalfG

  committed
  82e7789

• Formatting

  RalfG

  committed
  d158a86

• Fix config descriptions for psm_id_im_pattern and psm_id_rt_pattern

  RalfG

  committed
  a4f198a

Commits on Feb 28, 2024

• Check with Ruff on test (also disallow print statements)

  RalfG

  committed
  86363ee

Commits on Mar 25, 2024

• Merge branch 'main' of https://github.com/compomics/ms2rescore into timsRescore

  RalfG

  committed
  1e8cbfc

Commits on Mar 28, 2024

• Tweaks in inferring spectrum path for Bruker raw .d directories (handle as 'file')

  RalfG

  committed
  9e1528d

• MS2PIPFeatureGenerator: Ensure spectrum path is string (temp fix for timsrust_pyo3, until fixed in ms2pip).

  RalfG

  committed
  3a8b361

Commits on Mar 29, 2024

• set peptide as column for set instead of index to see overlap

  ArthurDeclercq

  committed
  65d4e2e

Commits on Apr 5, 2024

• Add file support for Bruker miniTDF

  RalfG

  committed
  17a4e12

Commits on Apr 8, 2024

• Merge branch 'main' of https://github.com/compomics/ms2rescore into timsRescore

  RalfG

  committed
  86ba7b6

Commits on Apr 9, 2024

• Merge branch 'main' of https://github.com/compomics/ms2rescore into peptide-num-fix

  ArthurDeclercq

  committed
  43334de

• Add new tims2rescore entrypoint with tims-specific config defaults; update and sort dependencies

  RalfG

  committed
  901c27e

• Fix bug in parsing spectrum path if config spectrum_path is None

  RalfG

  committed
  fe8f301

• Fix bug that always set im_required to True, even if no IM fgens were configured.

  RalfG

  committed
  088e24a

• Raise exception if missing precursor info was not found in PSM and spectrum files.

  RalfG

  committed
  a8a609b

• Add maxquant fgen to timsrescore_default config

  RalfG

  committed
  88e1cd3

• Update dockerfile to use Python 3.11

  RalfG

  committed
  eb43eb2

• Version bump

  RalfG

  committed
  126c255

• fix percolator issue with report

  ArthurDeclercq

  committed
  e873e73

• ionmob fix

  ArthurDeclercq

  committed
  dec5950

• set logging of numba

  ArthurDeclercq

  committed
  09fbbfb

• Merge branch 'timsRescore' of https://github.com/compomics/ms2rescore into peptide-num-fix

  ArthurDeclercq

  committed
  5c821c9

• Merge branch 'main' of https://github.com/compomics/ms2rescore into timsRescore

  RalfG

  committed
  fad30de

• Merge branch 'timsRescore' of https://github.com/compomics/ms2rescore into peptide-num-fix

  ArthurDeclercq

  committed
  cc93d51

• remove unused import

  ArthurDeclercq

  committed
  6efddff

Commits on Apr 10, 2024

• add default random num generator seed

  ArthurDeclercq

  committed
  d1c6388

• changes to report

  ArthurDeclercq

  committed
  1e11b4b

• fix _fill_missing_precursor_info check

  ArthurDeclercq

  committed
  b144d5f

• Apply suggestions from code review ♻️

  Show description for 1999039
  

  ArthurDeclercq

  and

  RalfG

  authored
  1999039

• fixed Ralfs suggestions

  ArthurDeclercq

  committed
  162f719

• Merge pull request #144 from compomics/peptide-num-fix

  Show description for 2c55cc2
  ArthurDeclercq

  authored
  2c55cc2

• update verison number

  ArthurDeclercq

  committed
  21195c4

Commits on Apr 12, 2024

• add ms2rescore profiler

  ArthurDeclercq

  committed
  eea9500

Commits on Apr 14, 2024

• removed unused import

  ArthurDeclercq

  committed
  144610b

Commits on Apr 17, 2024

• Slightly simplify cProfile sections

  RalfG

  committed
  2bb0607

• Mokapot: Add peptide-level score, q-value, and PEP to PSM list after rescoring

  RalfG

  committed
  b65dc6e

• Remove unused import

  RalfG

  committed
  9fc2d61

• Version bump

  RalfG

  committed
  bc9532c

• Mokapot: Also consider run for merging peptide level info

  RalfG

  committed
  bc51050

Commits on Apr 18, 2024

• Mokapot: Fix merging peptide level info if run is None

  RalfG

  committed
  dcb5515

• Report: Move some loggings from info to debug

  RalfG

  committed
  9a0514e

• Version bump

  RalfG

  committed
  9409d68

Commits on Apr 19, 2024

• peptide level bug fix

  ArthurDeclercq

  committed
  5d804ea

Commits on Apr 25, 2024

• Version bump

  RalfG

  committed
  37ba9db

Commits on May 2, 2024

• Upgrade to psm_utils v0.9, which now uses Pydantic v2

  RalfG

  committed
  2a947ee

Commits on Jul 4, 2024

• Added:

  Show description for 3047f28
  RalfG

  committed
  3047f28

• Split removing invalid AAs from reading PSM files step. Now also works when passed an in-memory PSMList.

  RalfG

  committed
  02f775b

• Upgrade to Pyteomics 4.7.2 (contains caching of resolved modifications)

  RalfG

  committed
  54f0fe5

• Relax numpy version requirement

  RalfG

  committed
  d483615

• Explicitly add scikit-learn 1.5.1 to dependencies

  RalfG

  committed
  6b46fda

• Version bump

  RalfG

  committed
  a0b9ce4

Commits on Jul 8, 2024

• Add options max_psm_rank_input and max_psm_rank_output to control multi-rank rescoring.

  RalfG

  committed
  bc6c314

• Version bump

  RalfG

  committed
  1f0915c

• only install binary distributions

  Show description for 7744391
  paretje

  committed
  7744391

Commits on Jul 9, 2024

• Explicitly pass scores to 'assign_confidence' to avoid 'no psms under eval_fdr' error when calculating q-values and PEPs.

  RalfG

  committed
  e3f723d

• Version bump

  RalfG

  committed
  ee381e8

• Docs: More documentation on input files and rescoring engine configuration.

  RalfG

  committed
  684c874

• Apply only-binary fix also in publish workflow (see commit 7744391)

  RalfG

  committed
  9acaf0b

Commits on Jul 10, 2024

• tims2rescore documentation

  ArthurDeclercq

  committed
  d7935e5

Commits on Jul 12, 2024

• updated tims2rescore docs

  ArthurDeclercq

  committed
  794ac45

• changes in default config

  ArthurDeclercq

  committed
  0d2fb2e

Commits on Jul 15, 2024

• minor bugfixes

  ArthurDeclercq

  committed
  77e7c1b