search

smith-chem-wisc / MetaMorpheus

Proteomics search software with integrated calibration, PTM discovery, bottom-up, top-down and LFQ capabilities
MIT License
90 stars 45 forks source link

Mzlib Update to 1.0.542 - Averaging crash fix+ #2318

Closed nbollis closed 7 months ago

nbollis commented 7 months ago

Update to most recent version of mzlib which fixes a crash in SpectralAveraging.

Mzlib PR is found at https://github.com/smith-chem-wisc/mzLib/pull/739

Cleaned up GUI switch cases. Eliminated AverageDdaScansWithOverlap and updated toml format to automaticaly convert old toml's with AverageDdaScansWithOverlap to load in as AverageDdaScans

codecov[bot] commented 7 months ago

Codecov Report

Merging #2318 (3fe2eaa) into master (6676503) will decrease coverage by 0.01%. The diff coverage is 95.45%.

Additional details and impacted files [![Impacted file tree graph](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2318/graphs/tree.svg?width=650&height=150&src=pr&token=m0HXyK8tFy&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc)](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2318?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc) ```diff @@ Coverage Diff @@ ## master #2318 +/- ## ========================================== - Coverage 92.67% 92.67% -0.01% ========================================== Files 135 135 Lines 20987 20995 +8 Branches 2880 2880 ========================================== + Hits 19450 19457 +7 Misses 1063 1063 - Partials 474 475 +1 ``` | [Files](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2318?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc) | Coverage Δ | | |---|---|---| | [...etaMorpheus/GuiFunctions/MetaDraw/MetaDrawLogic.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2318?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0d1aUZ1bmN0aW9ucy9NZXRhRHJhdy9NZXRhRHJhd0xvZ2ljLmNz) | `95.70% <100.00%> (+<0.01%)` | :arrow_up: | | [...ViewModels/SpectralAveragingParametersViewModel.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2318?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0d1aUZ1bmN0aW9ucy9WaWV3TW9kZWxzL1NwZWN0cmFsQXZlcmFnaW5nUGFyYW1ldGVyc1ZpZXdNb2RlbC5jcw==) | `97.24% <100.00%> (ø)` | | | [...s/TaskLayer/AveragingTask/SpectralAveragingTask.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2318?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL1Rhc2tMYXllci9BdmVyYWdpbmdUYXNrL1NwZWN0cmFsQXZlcmFnaW5nVGFzay5jcw==) | `93.75% <100.00%> (+0.96%)` | :arrow_up: | | [MetaMorpheus/TaskLayer/MetaMorpheusTask.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2318?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL1Rhc2tMYXllci9NZXRhTW9ycGhldXNUYXNrLmNz) | `87.30% <88.88%> (+<0.01%)` | :arrow_up: | ... and [1 file with indirect coverage changes](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2318/indirect-changes?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc)
trishorts commented 7 months ago

I feel like we better fix the empty toml thing

nbollis commented 7 months ago

When I ran the averaging task, it wrote a blank .toml file in the Task1-AveragingTask folder. Other than that, everything works great

I feel like we better fix the empty toml thing

Took care of this. It will now only spit out the toml if file specific parameters (most likely from a preceeding calibration task) are present for the averaged spectra file