Add FAQ entry about antibody sequencing #304
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## main #304 +/- ##
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Coverage 89.64% 89.64%
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Lines 917 917
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melihyilmaz
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Feb 24, 2024
bittremieux
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Mar 25, 2024
* 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]>
bittremieux
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May 14, 2024
* Remove `train_from_scratch` config option (#275) 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. * Stabilize torch.topk() behavior (#290) * 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 (#300) * 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]> * Add FAQ entry about antibody sequencing * Don't crash when multiple beams have identical peptide scores (#306) * Test different beams with identical scores * Randomly break ties for beams with identical peptide score * Update changelog * Don't remove unit test * Allow csv to handle all newlines (#316) * 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]> * Don't test on macOS versions with MPS (#327) * Prepare for release v4.2.0 * Update CHANGELOG.md (#332) --------- Co-authored-by: Melih Yilmaz <[email protected]> Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Co-authored-by: melihyilmaz <[email protected]> Co-authored-by: wsnoble <[email protected]> Co-authored-by: Joshua Klein <[email protected]>
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