Update paper reference #361
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bittremieux
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bittremieux
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* bug report template * punctuation, hardware description item * Restrict NumPy to pre-2.0 (#344) * Restrict NumPy to pre-2.0 * Update changelog * Update paper reference (#361) --------- Co-authored-by: Lilferrit <[email protected]>
Lilferrit
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* implemented integer charce to comply with mztab standard * updated changelog * updated changelog * Update paper reference (#361) * implemented jmztab validation steps * removed unecessary status code checks * tiny model checkpoints * upgrade codecove to v4 * fixed java command * codecov fix * seperated JMZtab validator command * syntax error fix * grep exit status handling * status code logic * export grep status code * syntax error * moved mzTab validation functionality to sh and bat scripts * Generate new screengrabs with rich-codex * git file permissions * Generate new screengrabs with rich-codex * platform specific validation * Generate new screengrabs with rich-codex * error condition test * fail output fix * remove test condition * eliminate redundant output * Generate new screengrabs with rich-codex * success output * Generate new screengrabs with rich-codex * remove if exists * Implemented jmzTab mzTab validation unit test * Generate new screengrabs with rich-codex * minor style change --------- Co-authored-by: Wout Bittremieux <[email protected]> Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
Lilferrit
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Aug 12, 2024
* bug report template * punctuation, hardware description item * Restrict NumPy to pre-2.0 (#344) * Restrict NumPy to pre-2.0 * Update changelog * Update paper reference (#361) --------- Co-authored-by: Lilferrit <[email protected]>
Lilferrit
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Aug 21, 2024
* prediction output in model eval mode * eliminate eval command, introduce -e flag for predict command * adapted unit test to new model runner and model functionality * updated documentation * removed log and result files * Generate new screengrabs with rich-codex * Update paper reference (#361) * Bug report template (#360) * bug report template * punctuation, hardware description item * Restrict NumPy to pre-2.0 (#344) * Restrict NumPy to pre-2.0 * Update changelog * Update paper reference (#361) --------- Co-authored-by: Lilferrit <[email protected]> * upgrade codecove to v4 (#364) * implemen eval mode at model runner level, fix unit test * CLI documentation * Generate new screengrabs with rich-codex * requested changes * Generate new screengrabs with rich-codex * evaluation test cases * file warnings, evaluation tests * fixed ubuntu specific test case bug * verify annotated mgf files * verify annotated mgf files * Generate new screengrabs with rich-codex * Save best model (#365) * save best model * save best model * updated unit tests * remove save top k config item * added save_top_k to deprecated config options * changelog entry * test case, formatting * requested changes * prediction output in model eval mode * eliminate eval command, introduce -e flag for predict command * adapted unit test to new model runner and model functionality * updated documentation * removed log and result files * implemen eval mode at model runner level, fix unit test * CLI documentation * Bug report template (#360) * bug report template * punctuation, hardware description item * Restrict NumPy to pre-2.0 (#344) * Restrict NumPy to pre-2.0 * Update changelog * Update paper reference (#361) --------- Co-authored-by: Lilferrit <[email protected]> * requested changes * evaluation test cases * file warnings, evaluation tests * fixed ubuntu specific test case bug * verify annotated mgf files * AnnotatedSpectrumIndex type error * requested changes, changelog entry --------- Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Co-authored-by: Wout Bittremieux <[email protected]>
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