Add 9-species model weights link to FAQ #303
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #303 +/- ##
=======================================
Coverage 89.64% 89.64%
=======================================
Files 12 12
Lines 917 917
=======================================
Hits 822 822
Misses 95 95 ☔ View full report in Codecov by Sentry. |
bittremieux
approved these changes
Feb 23, 2024
bittremieux
added a commit
that referenced
this pull request
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 <wout@bittremieux.be> * 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 <32707537+melihyilmaz@users.noreply.github.com> * 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 <32707537+melihyilmaz@users.noreply.github.com> Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Co-authored-by: Wout Bittremieux <wout@bittremieux.be> Co-authored-by: William Stafford Noble <wnoble@uw.edu> Co-authored-by: Wout Bittremieux <bittremieux@users.noreply.github.com>
bittremieux
added a commit
that referenced
this pull request
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 <wout@bittremieux.be> 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 <yilmazmelih97@gmail.com> * 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 <wout@bittremieux.be> * 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 <32707537+melihyilmaz@users.noreply.github.com> * 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 <32707537+melihyilmaz@users.noreply.github.com> Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Co-authored-by: Wout Bittremieux <wout@bittremieux.be> Co-authored-by: William Stafford Noble <wnoble@uw.edu> Co-authored-by: Wout Bittremieux <bittremieux@users.noreply.github.com> * Don't test on macOS versions with MPS (#327) * Prepare for release v4.2.0 * Update CHANGELOG.md (#332) --------- Co-authored-by: Melih Yilmaz <32707537+melihyilmaz@users.noreply.github.com> Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Co-authored-by: melihyilmaz <yilmazmelih97@gmail.com> Co-authored-by: wsnoble <wnoble@uw.edu> Co-authored-by: Joshua Klein <mobiusklein@gmail.com>
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
No description provided.