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

#1 - Update Mzlib to 1.0.547 (Omics Update) #2334

Closed nbollis closed 4 months ago

nbollis commented 5 months ago

A vast majority of the files changed is just changing using statements at the top. The rest are noted below

IndexingEngine.cs -- Default product no longer exists, instread changed to code to check for null

Tweaked TomlConfig to ignore new fields in DigestionParams, enabling old toml's to be read in and written

Changed many property names to match new Interfaces

MatchedFragmentIon constructor changed to exclude the ref on first parameter. This change was made due to the Product class changing from a struct, which is passed by value, to a class, which is automatically passed by reference.

codecov[bot] commented 5 months ago

Codecov Report

Attention: 13 lines in your changes are missing coverage. Please review.

Comparison is base (da174f0) 92.68% compared to head (cbb2956) 92.65%. Report is 1 commits behind head on master.

Additional details and impacted files [![Impacted file tree graph](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2334/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/2334?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 #2334 +/- ## ========================================== - Coverage 92.68% 92.65% -0.03% ========================================== Files 136 137 +1 Lines 21302 21274 -28 Branches 2924 2928 +4 ========================================== - Hits 19744 19712 -32 + Misses 1086 1083 -3 - Partials 472 479 +7 ``` | [Files](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2334?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc) | Coverage Δ | | |---|---|---| | [...s/EngineLayer/ClassicSearch/ClassicSearchEngine.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2334?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL0NsYXNzaWNTZWFyY2gvQ2xhc3NpY1NlYXJjaEVuZ2luZS5jcw==) | `97.84% <ø> (ø)` | | | [...gineLayer/ClassicSearch/MiniClassicSearchEngine.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2334?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL0NsYXNzaWNTZWFyY2gvTWluaUNsYXNzaWNTZWFyY2hFbmdpbmUuY3M=) | `92.14% <ø> (ø)` | | | [MetaMorpheus/EngineLayer/CommonParameters.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2334?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL0NvbW1vblBhcmFtZXRlcnMuY3M=) | `95.05% <ø> (ø)` | | | [...gineLayer/CrosslinkSearch/CrosslinkSearchEngine.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2334?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL0Nyb3NzbGlua1NlYXJjaC9Dcm9zc2xpbmtTZWFyY2hFbmdpbmUuY3M=) | `91.08% <ø> (ø)` | | | 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[...orpheus/EngineLayer/CrosslinkSearch/Crosslinker.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2334?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL0Nyb3NzbGlua1NlYXJjaC9Dcm9zc2xpbmtlci5jcw==) | `85.83% <ø> (ø)` | | | [...pheus/EngineLayer/FdrAnalysis/FdrAnalysisEngine.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2334?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL0ZkckFuYWx5c2lzL0ZkckFuYWx5c2lzRW5naW5lLmNz) | `91.42% <100.00%> (+0.04%)` | :arrow_up: | | [...EngineLayer/FdrAnalysis/PEPValueAnalysisGeneric.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2334?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL0ZkckFuYWx5c2lzL1BFUFZhbHVlQW5hbHlzaXNHZW5lcmljLmNz) | `95.96% <ø> (ø)` | | | [MetaMorpheus/EngineLayer/GlobalVariables.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2334?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL0dsb2JhbFZhcmlhYmxlcy5jcw==) | `84.83% <ø> (ø)` | | | ... and [56 more](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2334?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc) | | ... and [1 file with indirect coverage changes](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2334/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)