* 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]>