* 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 <[email protected]>

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 <[email protected]>

* Ensure correct output with n_beams=1

Fixes #185.

* Use a single beam by default

Fixes #193.

* Add unit test for single beam

---------

Co-authored-by: melihyilmaz <[email protected]>

* 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 <[email protected]>
Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
Co-authored-by: Wout Bittremieux <[email protected]>

* 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

…her dataloaders.

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 <[email protected]>
Co-authored-by: Wout Bittremieux <[email protected]>
Co-authored-by: Wout Bittremieux <[email protected]>

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 <[email protected]>
Co-authored-by: Wout Bittremieux <[email protected]>

Fixes #252.

Co-authored-by: Melih Yilmaz <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>
Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
Co-authored-by: Wout Bittremieux <[email protected]>

Add option to change label smoothing for model initialization from a checkpoint file.