Prepare release v4.2.0 #331
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Instead of having to specify `train_from_scratch` in the config file, training will proceed from an existing model weights file if this is given as an argument to `casanovo train`. Fixes #263.
* Add epsilon to index zero * Fix typo * Use base PyTorch for repeating along the vocabulary size * Combine masking steps * Lint with updated black version * Lint test files * Add topk unit test * Fix lint * Add fixme comment for future * Update changelog * Generate new screengrabs with rich-codex --------- Co-authored-by: Wout Bittremieux <[email protected]> Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
* Rename max_iters to cosine_schedule_period_iters * Add deprecated config option unit test * Fix missed rename * Proper linting * Remove unnecessary logging * Test that checkpoints with deprecated config options can be loaded * Minor change * Add test for fine-tuning with deprecated config options * Remove deprecated hyperparameters during model loading * Include deprecated hyperparameter warning * Test whether the warning is issued * Verify that the deprecated option is removed * Fix comments * Avoid defining deprecated options twice * Remap previous renamed config option `every_n_train_steps` * Update changelog --------- Co-authored-by: melihyilmaz <[email protected]>
* Test different beams with identical scores * Randomly break ties for beams with identical peptide score * Update changelog * Don't remove unit test
* Add 9-species model weights link to FAQ (#303) * Add model weights link * Generate new screengrabs with rich-codex * Clarify that these weights should only be used for benchmarking --------- Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Co-authored-by: Wout Bittremieux <[email protected]> * Add FAQ entry about antibody sequencing (#304) * Add FAQ entry about antibody sequencing * Generate new screengrabs with rich-codex --------- Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Co-authored-by: Melih Yilmaz <[email protected]> * Allow csv to handle all newlines The `csv` module tries to handle newlines itself. On Windows, this leads to line endings of `\r\r\n` instead of `\r\n`. Setting `newline=''` produces the intended output on both platforms. * Update CHANGELOG.md * Fix linting issue * Delete docs/images/help.svg --------- Co-authored-by: Melih Yilmaz <[email protected]> Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Co-authored-by: Wout Bittremieux <[email protected]> Co-authored-by: William Stafford Noble <[email protected]> Co-authored-by: Wout Bittremieux <[email protected]>
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #331 +/- ##
==========================================
- Coverage 89.64% 89.23% -0.41%
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Files 12 12
Lines 917 929 +12
==========================================
+ Hits 822 829 +7
- Misses 95 100 +5 ☔ View full report in Codecov by Sentry. |
melihyilmaz
approved these changes
May 14, 2024
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