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Migration to depthcharge v0.4.8#350

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andradesalazar wants to merge 51 commits intoNoble-Lab:devNoble-Lab/casanovo:devfrom andradesalazar:dev_latest_depthchargeandradesalazar/casanovo:dev_latest_depthchargeCopy head branch name to clipboard

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Commits

Commits on Nov 19, 2024

• migration to depthcharge v0.4.8

  

  Daniela Klaproth-Andrade

  authored and

  Lilferrit

  committed
  6826a1c

• shuffling training set by default

  

  Daniela Klaproth-Andrade

  authored and

  Lilferrit

  committed
  8c8dc61

• Reformat with Black

  

  wfondrie

  authored and

  Lilferrit

  committed
  70cdea6

• Fix formatting again after merge

  

  wfondrie

  authored and

  Lilferrit

  committed
  8771d78

• Resolve requested changes

  

  Daniela Klaproth-Andrade

  authored and

  Lilferrit

  committed
  7984bdc

• Reformat with Black

  

  wfondrie

  authored and

  Lilferrit

  committed
  f4b6ec6

• removed invalid imports

  Lilferrit

  committed
  4ec36b3

• removed to be added functionality (for now)

  Lilferrit

  committed
  355edc6

• tensorboard logger

  Lilferrit

  committed
  d224011

• circular import bug

  Lilferrit

  committed
  e6ac94e

• removed tensorboard unit tests

  Lilferrit

  committed
  39de098

• beam search decode unit tests (IP)

  Lilferrit

  committed
  97b8de7

• teast_beam_search decode test update

  Lilferrit

  committed
  2ee2845

• test_eval_metrics test update

  Lilferrit

  committed
  9b9349d

• unit tests updates

  Lilferrit

  committed
  0295493

• spectrum id unit tests

  Lilferrit

  committed
  3d1c20f

• integration test fix

  Lilferrit

  committed
  3ec8d7c

• model prediction io flow fixes

  Lilferrit

  committed
  9b8efea

• PyLightning logging refactor

  Lilferrit

  committed
  47df27e

• mgf file reader title field formatting

  Lilferrit

  committed
  45b3e26

• integration tests fix

  Lilferrit

  committed
  a1b42af

• integration tests

  Lilferrit

  committed
  261f63c

• test_initialize_model fix

  Lilferrit

  committed
  e3e8456

• test_save_and_load_weights fix

  Lilferrit

  committed
  0fb6692

• test_save_and_load_weights_deprecated fix

  Lilferrit

  committed
  5594bf8

• test_evaluate fix, evaluate unnanotated peak file error handling

  Lilferrit

  committed
  7bd2b5e

• test_evaluate fix, evaluate unnanotated peak file error handling

  Lilferrit

  committed
  d178860

• test_eval_metrics fix

  Lilferrit

  committed
  340695a

• test_spectrum_id tests fix

  Lilferrit

  committed
  e4d93f9

• unit tests fixes

  Lilferrit

  committed
  eb4af71

• teast_beam_search_decode fix

  Lilferrit

  committed
  2a946c2

• negative residue work around

  Lilferrit

  committed
  17bc3a2

• depthcharge upgrade - all unit tests pass

  Lilferrit

  committed
  7d789a7

• pylance depthcharge compatability fix

  Lilferrit

  committed
  c1ca436

• removed scans field from dataloaders

  Lilferrit

  committed
  2d539fd

Commits on Nov 21, 2024

• non db functionality working

  Lilferrit

  committed
  6ab3397

Commits on Nov 26, 2024

• import orders, CasanovoDB psm batching

  Lilferrit

  committed
  9dc293f

• CasanovoDB unit tests

  Lilferrit

  committed
  051a82a

• no batch made edge case

  Lilferrit

  committed
  8ebb55a

• mass caclulation

  Lilferrit

  committed
  a6a2db8

Commits on Nov 27, 2024

• CasanovoDB mass mod fixes

  Lilferrit

  committed
  d3cd392

• remove unsqueeze batch method

  Lilferrit

  committed
  113c879

Commits on Nov 28, 2024

• reduced test epochs from 20 to 15

  Lilferrit

  committed
  54366a5

Commits on Dec 2, 2024

• integration test fix

  Lilferrit

  committed
  3028cd2

• integration test fix

  Lilferrit

  committed
  ec20013

• psm batch generator unit test

  Lilferrit

  committed
  2233839

• cleanup debug code

  Lilferrit

  committed
  c612785

Commits on Dec 6, 2024

• disable multi threading on linux

  Lilferrit

  committed
  c43c515

• skip n_threads unit test

  Lilferrit

  committed
  2123894

Commits on Dec 19, 2024

• fixed double batching bug

  Lilferrit

  committed
  a49fc5c

Commits on Dec 24, 2024

• use tokens to compare peptides

  

  Gwen Straub

  authored and

  Gwen Straub

  committed
  759c02e