Auto irt #5
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Auto irt #5
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added OpenNuXL
… use it within its child Protease Digestion; expand ProteaseDigestion_test; expand ProteaseDigestion python binding test and move it from test000.py to new test_ProteaseDigestion.py
Related to OpenMS#8104.
Expanded and reworded documentation, added some input data checks and exceptions to `ProteaseDigestion.digest()` and `EnzymaticDigestion.semiSpecificDigestion_()`, added some tests.
[FIX] DIAScore slow, unprecise dotproduct. Add ASAN support for Windows
Fixed invalid (not implemented) use of SPEC_NONE with `ProteaseDigestion::digest()` by functions `DecoyGenerator::reversePeptides()` and `DecoyGenerator::shufflePeptides()`. These now use `SPEC_FULL`, which should produce identical results as before - but perhaps this was not the behaviour intended?
…omparisons in tests.
…ator `not` for negation.
…tion_; missing documentation; additional tests; fix pyOpenMS tests
…digestion Semi specific digestion
* FileInfo reports J instead of I for FASTA files * add some math convenience functions; use them in FileInfo * add tests * don't add small AAA's by accident * fix doxygen * fix tests and counting
* fix docs for annotate() * Apply suggestions from code review --------- Co-authored-by: Timo Sachsenberg <timo.sachsenberg@uni-tuebingen.de>
* merged * adapt test to account for two extra hydrogens due to charge==2 * handle negative charges * update CHANGELOG --------- Co-authored-by: Samuel Wein <sam@samwein.com> Co-authored-by: Timo Sachsenberg <timo.sachsenberg@uni-tuebingen.de>
…aware (OpenMS#7975) * modify MTD and EPD to be ion mobility aware * add static iterativeweight function. Simplify floatdataarray handling. Bug fux moving up in rt dimension * Update src/openms/include/OpenMS/FEATUREFINDER/MassTraceDetection.h Co-authored-by: Timo Sachsenberg <timo.sachsenberg@uni-tuebingen.de> * attempt to remove code duplication by unifying im and im-free logic flow * removed redundant im array check * added hard coded strings to constants.h. Must coordinate with peakpickerIM pr * improve im check readability * added getIMIndices_() private function to handle im meta array index * MassTraceExtractor was manually checking meta values -- causing test errors. * replacted MassTraceExtractor_1_output.featureXML with a new file containing fwhm_mz_avg for all traces * replaced MassTraceExtractor_2_output.featureXML. It used to have 9/101 traces annotated with fwhm_mz_avg. Now all traces are annotated * updated MassTraceExtractor json test files to include ion_mobility_tolerance parameter * regenerate test output files using test mode. Add name * regenerate MassTraceExtractor_3_expected.ini in test condition * added new MassTraceExtractor test with ion mobility data * write 0.0 as 0 cleanup * fix MTD_3 test * Sort MTD output before writing to file * faster lookup of closest im value * update test * fix uninitialized * introduce a smaller test (mtd-5). Comment out mtd-4. * add larger test (mtd-6). * reorder new mtd tests. Remove old mtd-4 test * comment cleanup * numbering fix * isolate problem trace in a separate file in an attempt to reproduce error * push files * try to change quant method for mtd-5 test to max_height. * revert back to area quant * attempt to reproduce mtd-5 error in mtd-6 * cmakelist fix * update test --------- Co-authored-by: Mohammed AlHigaylan <alhigaylan@Mohammeds-MacBook-Pro-2.local> Co-authored-by: Mohammed AlHigaylan <alhigaylan@macbookpro.home> Co-authored-by: Timo Sachsenberg <timo.sachsenberg@uni-tuebingen.de> Co-authored-by: Julianus Pfeuffer <8102638+jpfeuffer@users.noreply.github.com>
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How can I get additional information on failed tests during CI
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If your PR is failing you can check outIf you click in the column that lists the failed tests you will get detailed error messages.
Advanced commands (admins / reviewer only)
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/reformat(experimental) applies the clang-format style changes as additional commit. Note: your branch must have a different name (e.g., yourrepo:feature/XYZ) than the receiving branch (e.g., OpenMS:develop). Otherwise, reformat fails to push.rebuild jenkinswill retrigger Jenkins-based CI builds