Automatically download model weights (#68) #88
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
* Download model weights from GitHub release * Include dependencies * Update model usage documentation * Reformat with black * Download weights to the OS-specific app dir * Don't download weights if already in cache dir * Update model file instructions * Remove release notes from the README We have this information on the Releases page now. * Remove explicit model specification from example commands * Harmonize default parameters and config values As per discussion on Slack (https://noblelab.slack.com/archives/C01MXN4NWMP/p1659803053573279). * No need to specify config file by default This simplifies the examples that most users will want to use. * Simplify version matching regex * Remove depthcharge related tests The transformer tests only deal with depthcharge functionality and just seem copied from its repository. * Make sure that package data is included I.e. the config YAML file. * Remove obsolote (ppx) tests * Update integration test * Add MacOS support and support for Apple's MPS chips * Fail test but print version * Added n_worker fn and tests * Create split_version fn and add unit tests * Fix debugging unit test * Explicitly set version * Monkeypatch loaded version * Add device selector, so that on CPU-only runs the devices > 0 * Add windows patch * Fix typo * Revert * Use main process for data loading on Windows * Fix typo * Fix unit test * Fix devices for when num_workers == 0 * Fix devices for when num_workers == 0 * Minor README updates * Import reordering * Minor code and docstring reformatting * Test model weights retrieval * Fix getting the number of devices * Disable excessive Tensorboard deprecation warnings * Don't use worker threads on MacOS It crashes the DataLoader: pytorch/pytorch#70344 * Warnings need to be ignored before import * Additional weights tests - Non-matching version - GitHub rate limit exceeded * Disable tests on MacOS * Include Python 3.10 as supported version Co-authored-by: William Fondrie <[email protected]>
bittremieux
added a commit
that referenced
this pull request
Nov 18, 2022
* Add beam search * Delete print statements * Automatically download model weights (#68) (#88) * Download model weights from GitHub release * Include dependencies * Update model usage documentation * Reformat with black * Download weights to the OS-specific app dir * Don't download weights if already in cache dir * Update model file instructions * Remove release notes from the README We have this information on the Releases page now. * Remove explicit model specification from example commands * Harmonize default parameters and config values As per discussion on Slack (https://noblelab.slack.com/archives/C01MXN4NWMP/p1659803053573279). * No need to specify config file by default This simplifies the examples that most users will want to use. * Simplify version matching regex * Remove depthcharge related tests The transformer tests only deal with depthcharge functionality and just seem copied from its repository. * Make sure that package data is included I.e. the config YAML file. * Remove obsolote (ppx) tests * Update integration test * Add MacOS support and support for Apple's MPS chips * Fail test but print version * Added n_worker fn and tests * Create split_version fn and add unit tests * Fix debugging unit test * Explicitly set version * Monkeypatch loaded version * Add device selector, so that on CPU-only runs the devices > 0 * Add windows patch * Fix typo * Revert * Use main process for data loading on Windows * Fix typo * Fix unit test * Fix devices for when num_workers == 0 * Fix devices for when num_workers == 0 * Minor README updates * Import reordering * Minor code and docstring reformatting * Test model weights retrieval * Fix getting the number of devices * Disable excessive Tensorboard deprecation warnings * Don't use worker threads on MacOS It crashes the DataLoader: pytorch/pytorch#70344 * Warnings need to be ignored before import * Additional weights tests - Non-matching version - GitHub rate limit exceeded * Disable tests on MacOS * Include Python 3.10 as supported version Co-authored-by: William Fondrie <[email protected]> Co-authored-by: Wout Bittremieux <[email protected]> Co-authored-by: William Fondrie <[email protected]> * Automatically download model weights (#68) (#89) * Download model weights from GitHub release * Include dependencies * Update model usage documentation * Reformat with black * Download weights to the OS-specific app dir * Don't download weights if already in cache dir * Update model file instructions * Remove release notes from the README We have this information on the Releases page now. * Remove explicit model specification from example commands * Harmonize default parameters and config values As per discussion on Slack (https://noblelab.slack.com/archives/C01MXN4NWMP/p1659803053573279). * No need to specify config file by default This simplifies the examples that most users will want to use. * Simplify version matching regex * Remove depthcharge related tests The transformer tests only deal with depthcharge functionality and just seem copied from its repository. * Make sure that package data is included I.e. the config YAML file. * Remove obsolote (ppx) tests * Update integration test * Add MacOS support and support for Apple's MPS chips * Fail test but print version * Added n_worker fn and tests * Create split_version fn and add unit tests * Fix debugging unit test * Explicitly set version * Monkeypatch loaded version * Add device selector, so that on CPU-only runs the devices > 0 * Add windows patch * Fix typo * Revert * Use main process for data loading on Windows * Fix typo * Fix unit test * Fix devices for when num_workers == 0 * Fix devices for when num_workers == 0 * Minor README updates * Import reordering * Minor code and docstring reformatting * Test model weights retrieval * Fix getting the number of devices * Disable excessive Tensorboard deprecation warnings * Don't use worker threads on MacOS It crashes the DataLoader: pytorch/pytorch#70344 * Warnings need to be ignored before import * Additional weights tests - Non-matching version - GitHub rate limit exceeded * Disable tests on MacOS * Include Python 3.10 as supported version Co-authored-by: William Fondrie <[email protected]> Co-authored-by: Wout Bittremieux <[email protected]> Co-authored-by: William Fondrie <[email protected]> * Break beam search to testable subfunctions * Fix precursor m/z termination and filtering * Add unit testing for beam search * Add beamsearch comments and fix formatting * Address requested changes and minor fixes * Add more unit tests for beam search * Check NH3 loss for early stopping * Consistent parameter order * Update docstrings * Remove unused precursors parameter * Update beam matching mask in a level higher * Minor refactoring to avoid code duplication * Update imports * Simplification refactoring * Fix unit tests * Simplify predicted peptide caching * Simplify predicted peptide caching * Simplify predicted peptide caching * Unify predicted peptide caching * Restrict tensor reshape to subfunction and minor fixes * Finish beams when all isotopes exceed the precursor m/z tolerance * Generalize look-ahead for tokens with negative mass * Remove greedy decoding functionality * Handle case with unfinished beams and add test * Upgrade required depthcharge version * Use detokenize function * Add test for negative mass-aware termination * Fix egative mass-aware beam termination * Minor refactoring * Add test for dummy output at max length * Fixed and refactored peptide and scocre mzTab outputs * Add tests for peptide and score output formatting * Small fixes * Update changelog * Fix changelog update Co-authored-by: Wout Bittremieux <[email protected]> Co-authored-by: William Fondrie <[email protected]> Co-authored-by: Wout Bittremieux <[email protected]>
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.
Download model weights from GitHub release
Include dependencies
Update model usage documentation
Reformat with black
Download weights to the OS-specific app dir
Don't download weights if already in cache dir
Update model file instructions
Remove release notes from the README
We have this information on the Releases page now.
Remove explicit model specification from example commands
Harmonize default parameters and config values
As per discussion on Slack (https://noblelab.slack.com/archives/C01MXN4NWMP/p1659803053573279).
This simplifies the examples that most users will want to use.
Simplify version matching regex
Remove depthcharge related tests
The transformer tests only deal with depthcharge functionality and just seem copied from its repository.
I.e. the config YAML file.
Remove obsolote (ppx) tests
Update integration test
Add MacOS support and support for Apple's MPS chips
Fail test but print version
Added n_worker fn and tests
Create split_version fn and add unit tests
Fix debugging unit test
Explicitly set version
Monkeypatch loaded version
Add device selector, so that on CPU-only runs the devices > 0
Add windows patch
Fix typo
Revert
Use main process for data loading on Windows
Fix typo
Fix unit test
Fix devices for when num_workers == 0
Fix devices for when num_workers == 0
Minor README updates
Import reordering
Minor code and docstring reformatting
Test model weights retrieval
Fix getting the number of devices
Disable excessive Tensorboard deprecation warnings
Don't use worker threads on MacOS
It crashes the DataLoader: pytorch/pytorch#70344
Warnings need to be ignored before import
Additional weights tests
Disable tests on MacOS
Include Python 3.10 as supported version
Co-authored-by: William Fondrie [email protected]