Prepare release v4.0 #273
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Prepare release v4.0 #273
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* Upgrade depthcharge * Update CHANGELOG.md
* Fix logging and checkpointing bug * Add option to validate every n steps
Fixes minor issues in #165.
* Always use full file paths Fixes #167. * Update changelog * Formatting fix
* Only split off extension if it's mzTab * Also check for .log extension * Update output format in help message
* Overhaul runner * Update linting to only happen once * Fix linting error * Specify utf-8 encoding * Specify utf-8 encoding only for default config * Skip weights tests for now * Update skipping API test * Revert accidental max_epochs change * msg -> reason for pytest.mark.skip * Wout's suggestions and more tests * Remove encoding * Specify device type when weight loading * Fix lint * Capture init params and figure out device automagically * Add runner tests * Fix bug and limit saved models * Support old weights too * Remove every_n_train_steps from checkpoint --------- Co-authored-by: melihyilmaz <yilmazmelih97@gmail.com>
Checkpointing during training can be enabled using the `logger` config option. If this is not specified, or during inference, don't create the `lightning_logs/` directory. Fixes #187.
* Avoid detailed fsspec logging * Replace deprecated `auto_select_gpus` * Show nice dataloader workers log message Capture the Pytorch Lightning warning as per https://lightning.ai/docs/pytorch/stable/advanced/speed.html#dataloaders * Overhaul runner * Update linting to only happen once * Fix linting error * Specify utf-8 encoding * Specify utf-8 encoding only for default config * Skip weights tests for now * Update skipping API test * Revert accidental max_epochs change * msg -> reason for pytest.mark.skip * Remove obsolete imports * Fix type hints * Wout's suggestions and more tests * Remove encoding * Ignore irrelevant PyTorch warnings * Update changelog * Remove unused imports * Undo unnecessary whitespace change --------- Co-authored-by: William Fondrie <fondriew@gmail.com>
* Run linting and tests for dev branch * Fix tests Limit DepthCharge to v0.2. * No DepthCharge v0.3
* Overhaul runner * Update linting to only happen once * Fix linting error * Specify utf-8 encoding * Specify utf-8 encoding only for default config * Skip weights tests for now * Update skipping API test * Revert accidental max_epochs change * msg -> reason for pytest.mark.skip * Wout's suggestions and more tests * Remove encoding * Specify device type when weight loading * Fix lint * Capture init params and figure out device automagically * Add runner tests * Fix bug and limit saved models * WIP * Support old weights too * Remove every_n_train_steps from checkpoint * Implementation done. Need to update tests * Update tests * add -h * Add auto screenshot generation * Add screenshots workflow [screenshots] * Add manual dispatch * Added image * Updated instructions [screenshots] * Update screenshot workflow * Fix bug and screenshot uploads * Restirct workflow * fix ref * Generate new screengrabs with rich-codex * increase timeout * bump changelog and increase timeout * Generate new screengrabs with rich-codex * Add more tests * Add option for calculating precision during training * Restrict depthcharge version * Log scalars instead of tensors * Fix typo * Fix issue Wout found * Write to stdout instead of stderr * Minor refactoring * Separate logger and model initialization * Generate new screengrabs with rich-codex * Generate new screengrabs with rich-codex * Fix test formatting * Fix edge case --------- Co-authored-by: melihyilmaz <yilmazmelih97@gmail.com> Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Co-authored-by: Wout Bittremieux <wout@bittremieux.be>
* Remove Pytorch Lightning logger Fixes #219. * Update changelog * Clarify tb_summarywriter
* Format how warnings are logged Fixes #222. * Update changelog * Fix linting
* Rename every_n_train_steps to val_check_interval * Disable check_val_every_n_epochs * Update changelog
* Fix specifying custom residues * Update changelog
Added shuffling to train dataloader
* Add lines to force gradient calculation. During inference only. * Add comments in the code to document the temporary workaround * Update changelog --------- Co-authored-by: Varun Ananth <vananth3@nexus2.gs.washington.edu> Co-authored-by: Wout Bittremieux <wout@bittremieux.be> Co-authored-by: Wout Bittremieux <bittremieux@users.noreply.github.com>
And fix duplicate changelog organization.
* resolves issue #238: remove custom_encoder option * fixed lint issue * fixed lint issue * Revert "fixed lint issue" This reverts commit bd1366c. * lint * lint issue * Consistently format changelog. --------- Co-authored-by: Isha Gokhale <igokhale@tyrosine.gs.washington.edu> Co-authored-by: Wout Bittremieux <wout@bittremieux.be>
Fixes #252. Co-authored-by: Melih Yilmaz <32707537+melihyilmaz@users.noreply.github.com>
* Remove force_grad in inference * Upgrade required PyTorch version * Update CHANGELOG.md * Update CHANGELOG.md * Fix typo in torch version * Specify correct Pytorch version change --------- Co-authored-by: Wout Bittremieux <bittremieux@users.noreply.github.com>
* added unit tests to raise exceptions when unrecognized/missing file entry * fixed lint issue * fix lint issue * fixed failing unit test * lint issue * lint * lint issue --------- Co-authored-by: Isha Gokhale <igokhale@tyrosine.gs.washington.edu>
* Refactor config checking - More efficient checking for unknown and missing config entries (no needless conversions/creations of sets and lists). - Avoid creating temporary files in root directories during unit testing. - Update outdated test. * Add unit test fix
* Add option to change learning rate scheduler and made it easier to add a new one. * docs * tests and formatting * Add label smoothing * Modify config file * Minor fix config.yaml * Run black * Lint casanovo.py * Revert "Merge branch 'add_lr_schedule_options' into label-smoothing" This reverts commit 5716c7a, reversing changes made to b044bc6. * Add unit test * Fix config test and add changelog --------- Co-authored-by: Justin Sanders <jsander1@n033.grid.gs.washington.edu>
* Use auto-downloaded weights * Use config options in model init * Fix linting * Fix missing return value * Override mismatching params with ckpt * Handle corrupt ckpt * Add test case for parameter mismatch * Add Python version to screenshot action * Generate new screengrabs with rich-codex * Fix import order * Minor reformatting --------- Co-authored-by: William Fondrie <fondriew@gmail.com> Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Co-authored-by: Wout Bittremieux <wout@bittremieux.be>
Add option to change label smoothing for model initialization from a checkpoint file.
Codecov ReportAttention:
Additional details and impacted files@@ Coverage Diff @@
## main #273 +/- ##
==========================================
+ Coverage 81.41% 89.54% +8.12%
==========================================
Files 11 12 +1
Lines 807 918 +111
==========================================
+ Hits 657 822 +165
+ Misses 150 96 -54 ☔ View full report in Codecov by Sentry. |
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Merge
devintomain, resolve version conflicts, and update version numbers in the changelog.