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Remove custom_encoder from the config file #238

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wsnoble opened this issue Aug 28, 2023 · 0 comments · Fixed by #254
Closed

Remove custom_encoder from the config file #238

wsnoble opened this issue Aug 28, 2023 · 0 comments · Fixed by #254
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@melihyilmaz
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enhancement New feature or request good first issue Good for newcomers

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@wsnoble
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wsnoble commented Aug 28, 2023

The title says it all.
@wsnoble wsnoble added the enhancement New feature or request label Aug 28, 2023
@wsnoble wsnoble added the good first issue Good for newcomers label Sep 21, 2023
@ishagokhale ishagokhale mentioned this issue Oct 10, 2023
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ishagokhale pushed a commit that referenced this issue Oct 17, 2023
resolves issue #238: remove custom_encoder option
b7c2ff8
@bittremieux bittremieux linked a pull request Oct 18, 2023 that will close this issue
resolves issue #238: remove custom_encoder option #254
Merged
bittremieux added a commit that referenced this issue Oct 19, 2023
@ishagokhale @bittremieux
Remove unused custom_encoder option (#254)
9a44630 
* 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]>
melihyilmaz added a commit that referenced this issue Nov 2, 2023
@melihyilmaz @ishagokhale @bittremieux
Add label smoothing to learning rate scheduler branch (#262)
7358564 
* Remove unused custom_encoder option (#254)

* 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]>

* Correctly report AA precision and recall during validation (#253)

Fixes #252.

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

* Remove gradient calculation during inference  (#258)

* 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]>

* Add label smoothing

* Modify config file

* Minor fix config.yaml

* Run black

* Lint casanovo.py

---------

Co-authored-by: ishagokhale <[email protected]>
Co-authored-by: Isha Gokhale <[email protected]>
Co-authored-by: Wout Bittremieux <[email protected]>
Co-authored-by: Wout Bittremieux <[email protected]>
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resolves issue #238: remove custom_encoder option Noble-Lab/casanovo
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@bittremieux @wsnoble @melihyilmaz