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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

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  committed
  6826a1c

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• shuffling training set by default

  

  Daniela Klaproth-Andrade

  authored and

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  committed
  8c8dc61

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• Reformat with Black

  

  wfondrie

  authored and

  Lilferrit

  committed
  70cdea6

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• Fix formatting again after merge

  

  wfondrie

  authored and

  Lilferrit

  committed
  8771d78

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• Resolve requested changes

  

  Daniela Klaproth-Andrade

  authored and

  Lilferrit

  committed
  7984bdc

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• Reformat with Black

  

  wfondrie

  authored and

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  f4b6ec6

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• removed invalid imports

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  4ec36b3

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• removed to be added functionality (for now)

  Lilferrit

  committed
  355edc6

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• tensorboard logger

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  d224011

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• circular import bug

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  e6ac94e

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• removed tensorboard unit tests

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  39de098

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• beam search decode unit tests (IP)

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  committed
  97b8de7

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• teast_beam_search decode test update

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  committed
  2ee2845

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• test_eval_metrics test update

  Lilferrit

  committed
  9b9349d

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• unit tests updates

  Lilferrit

  committed
  0295493

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• spectrum id unit tests

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  committed
  3d1c20f

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• integration test fix

  Lilferrit

  committed
  3ec8d7c

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• model prediction io flow fixes

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  committed
  9b8efea

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• PyLightning logging refactor

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  committed
  47df27e

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• mgf file reader title field formatting

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  committed
  45b3e26

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• integration tests fix

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  committed
  a1b42af

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• integration tests

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  committed
  261f63c

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• test_initialize_model fix

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  committed
  e3e8456

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• test_save_and_load_weights fix

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  0fb6692

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• test_save_and_load_weights_deprecated fix

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  5594bf8

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• test_evaluate fix, evaluate unnanotated peak file error handling

  Lilferrit

  committed
  7bd2b5e

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• test_evaluate fix, evaluate unnanotated peak file error handling

  Lilferrit

  committed
  d178860

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• test_eval_metrics fix

  Lilferrit

  committed
  340695a

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• test_spectrum_id tests fix

  Lilferrit

  committed
  e4d93f9

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• unit tests fixes

  Lilferrit

  committed
  eb4af71

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• teast_beam_search_decode fix

  Lilferrit

  committed
  2a946c2

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• negative residue work around

  Lilferrit

  committed
  17bc3a2

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• depthcharge upgrade - all unit tests pass

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  committed
  7d789a7

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• pylance depthcharge compatability fix

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  committed
  c1ca436

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• removed scans field from dataloaders

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  2d539fd

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Commits on Nov 21, 2024

• non db functionality working

  Lilferrit

  committed
  6ab3397

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Commits on Nov 26, 2024

• import orders, CasanovoDB psm batching

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  committed
  9dc293f

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• CasanovoDB unit tests

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  committed
  051a82a

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• no batch made edge case

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  committed
  8ebb55a

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• mass caclulation

  Lilferrit

  committed
  a6a2db8

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Commits on Nov 27, 2024

• CasanovoDB mass mod fixes

  Lilferrit

  committed
  d3cd392

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• remove unsqueeze batch method

  Lilferrit

  committed
  113c879

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Commits on Nov 28, 2024

• reduced test epochs from 20 to 15

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  committed
  54366a5

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Commits on Dec 2, 2024

• integration test fix

  Lilferrit

  committed
  3028cd2

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• integration test fix

  Lilferrit

  committed
  ec20013

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• psm batch generator unit test

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  committed
  2233839

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• cleanup debug code

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  committed
  c612785

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Commits on Dec 6, 2024

• disable multi threading on linux

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  committed
  c43c515

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• skip n_threads unit test

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  committed
  2123894

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Commits on Dec 19, 2024

• fixed double batching bug

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  committed
  a49fc5c

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Commits on Dec 24, 2024

• use tokens to compare peptides

  

  Gwen Straub

  authored and

  Gwen Straub

  committed
  759c02e

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