Code

Prepare release v4.0#273

Code

Merged

bittremieux merged 32 commits intomainNoble-Lab/casanovo:mainfrom releaseNoble-Lab/casanovo:releaseCopy head branch name to clipboardDec 22, 2023

+2,242-640

Commits

Commits on Apr 6, 2023

• Upgrade depthcharge (#160)

  Show description for 7ec31be
  bittremieux

  authored
  7ec31be

Commits on Apr 10, 2023

• Fix val step and add unit test (#164)

  melihyilmaz

  authored
  59974e3

Commits on Apr 11, 2023

• Add validation frequency option (#165)

  Show description for da1d16d
  melihyilmaz

  authored
  da1d16d

Commits on Apr 14, 2023

• Minor refactoring + issue fix (#166)

  Show description for 5ba0275
  bittremieux

  authored
  5ba0275

Commits on Apr 17, 2023

• Always use full file paths (#168)

  Show description for 868952e
  bittremieux

  authored
  868952e

• Only split off known extensions from output filename (#171)

  Show description for effc955
  bittremieux

  authored
  effc955

Commits on May 10, 2023

• Fix CPU bug, overhaul model runner, and update to lightning >=2.0 (#176)

  Show description for 6299bd2
  

  wfondrie

  and

  melihyilmaz

  authored
  6299bd2

Commits on Jun 23, 2023

• Only create log directory when checkpointing is enabled (#196)

  Show description for ea69360
  bittremieux

  authored
  ea69360

Commits on Jun 27, 2023

• Avoid uninformative warnings (#175)

  Show description for f74a6ff
  

  bittremieux

  and

  wfondrie

  authored
  f74a6ff

• Use a single beam by default (#195)

  Show description for b271dff
  

  bittremieux

  and

  melihyilmaz

  authored
  b271dff

• Run linting and tests for the dev branch (#197)

  Show description for 621ebdc
  bittremieux

  authored
  621ebdc

Commits on Jul 18, 2023

• CLI revamp (#184)

  Show description for ad48a09
  

  4 peopleauthored
  ad48a09

Commits on Aug 3, 2023

• Remove Pytorch Lightning logger (#220)

  Show description for 8d2593b
  bittremieux

  authored
  8d2593b

• Nicely format logged warnings (#223)

  Show description for e1e1bb0
  bittremieux

  authored
  e1e1bb0

• Fix validation and checkpointing interval (#224)

  Show description for 3ac0887
  bittremieux

  authored
  3ac0887

Commits on Aug 16, 2023

• Fix custom residues in config (#229)

  Show description for 514db80
  bittremieux

  authored
  514db80

Commits on Aug 17, 2023

• Added shuffling to trainset dataloaders, no shuffle by default for other dataloaders.

  cfmelend

  committed
  bbce330

• Merge pull request #234 from cfmelend/shuffle

  Show description for 51221f9
  cfmelend

  authored
  51221f9

Commits on Aug 18, 2023

• Force gradient calculation during inference (#231)

  Show description for d9396aa
  

  3 peopleauthored
  d9396aa

• Document batch shuffling in the changelog

  Show description for 82be5ae
  bittremieux

  committed
  82be5ae

Commits on Aug 21, 2023

• Upgrade depthcharge to v0.2.3 (#235)

  bittremieux

  authored
  727ead6

Commits on Aug 24, 2023

• Edits to config file. (#237)

  wsnoble

  authored
  86630e3

Commits on Oct 19, 2023

• Remove unused custom_encoder option (#254)

  Show description for 9a44630
  

  3 peopleauthored
  9a44630

Commits on Oct 24, 2023

• Correctly report AA precision and recall during validation (#253)

  Show description for 3a18fed
  

  bittremieux

  and

  melihyilmaz

  authored
  3a18fed

• Remove gradient calculation during inference (#258)

  Show description for 7721962
  

  melihyilmaz

  and

  bittremieux

  authored
  7721962

Commits on Nov 9, 2023

• Issue error for unrecognized/missing config file entry (#257)

  Show description for 235420f
  

  ishagokhale

  and

  Isha Gokhale

  authored
  235420f

Commits on Dec 11, 2023

• Check for invalid/missin config entries (#268)

  Show description for e073415
  bittremieux

  authored
  e073415

Commits on Dec 12, 2023

• Label smoothing in training (#261)

  Show description for 3b688e8
  

  melihyilmaz

  and

  Justin Sanders

  authored
  3b688e8

• Use config options and auto-downloaded weights (#246)

  Show description for 2aed9e5
  

  4 peopleauthored
  2aed9e5

Commits on Dec 13, 2023

• Minor fix to label smoothing (#270)

  Show description for ad9ba0f
  melihyilmaz

  authored
  ad9ba0f

Commits on Dec 22, 2023

• Merge dev into main

  bittremieux

  committed
  0486de2

• Update version number in changelog

  bittremieux

  committed
  c862bb5