Testpatch #165
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Testpatch #165
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* correctly forward TOPP's log_type to FileHandler calls * augment CHANGELOG
… some helping functions to class StringManager
…ved performance inside the compress64 function. Edited the the XMLHandler_test to work with new implemantation and got rid of new/delete:
… Added a for loop to prevent this method from crossing page Boundaries
…onversion from a size_t to an int which led to an overflow
* add missing kernel doc * more doc
…separate class. (OpenMS#8016) * start separating external id stuff * move svm code into externid class * moved more * simplify a bit more * nop * removed unused functions * Adds private method suffix for consistency Renames private methods in FFIDAlgoExternalIDHandler with a trailing underscore to follow naming conventions and improve code readability. No functional changes introduced. * Namespaces FFIDAlgoExternalIDHandler for clarity Encapsulates FFIDAlgoExternalIDHandler within the Internal namespace to improve code organization and clarify its intended scope of use. Updates relevant references and adds the required namespace import. Improves code modularity and maintainability. * Fix namespace closure for FFIDAlgoExternalIDHandler * Update src/openms/source/FEATUREFINDER/FFIDAlgoExternalIDHandler.cpp Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com> --------- Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
* Update openms_ci_matrix_full.yml Fix destination paths for KNIME artifact downloads. * Update package_mac_productbuild.cmake Change logo scaling for installer to "tofit" * Update FLASHDeconvWizardBase.cpp (OpenMS#8034) updated link to flashdeconv web site * Replace neckarfront with logo * Update package_mac_productbuild.cmake Disable mac installer logo * Fix debian installer (OpenMS#8035) * add libyaml dependency * proper fix * Update openms_ci_matrix_full.yml fix download-artifact issue * rework tag creation to be less cryptic, add action to publish draft release * fix knime makr latest target * Update openms_ci_matrix_full.yml --------- Co-authored-by: Tjeerd Dijkstra <tjeerd.dijkstra@uni-tuebingen.de> Co-authored-by: Tom David Müller <57191390+t0mdavid-m@users.noreply.github.com> Co-authored-by: Timo Sachsenberg <timo.sachsenberg@uni-tuebingen.de>
…sion of strLength to generate a SEGFAULT and the new version to pass the test. Error was caused because when given a nullptr the the input_ptr didnt check if the input is a nullptr before dereferencing it and immediatlely attempted to perform pointer operations. Patched it with an if statement. Also changed some int datatypes to size_t datatypes to prevent potential errors with overflow and to improve concistency
…ections) (OpenMS#8047) * avoid "unknown pragma" warnings on MSVC * fix TV error message box when right-clicking on a 2D mobilogram (which has no RT information) * avoid error in TV when activating 2D projections (for any type of data) * fix: allow projections for IM frames from MS2 data (would otherwise be empty)
* added update ranges to other file formats * explorative attempt Introduces dual-range management for spectra and chromatograms Replaces the single RangeManager with separate SpectrumRangeManager and ChromatogramRangeManager, enabling independent handling of ranges for MS spectra and chromatograms. Maintains backward compatibility using a combined range manager. Adds extensive tests to validate the new dual-range system and its integration with existing functionality. This change aims to improve modularity and clarity in range handling, while preserving legacy behavior for seamless integration. * some progress * fix * more fixes * Adds detailed range reporting for MSExperiment data Introduces specialized templates for human-readable and machine-readable range reporting in MSExperiment, covering retention time, mass-to-charge, ion mobility, and intensity across combined, spectrum-specific, and chromatogram ranges. Enhances the clarity and granularity of data outputs. * more fixes * more fixes * some fixes * compiles again * fix tests * add file * add cos * add python bindings * make private * simplify interface * simplify a bit more * update test * address reviewer comments * remove non const access * don't treat chromatograms as metadata * exclude precursors from range calculation
* [CI] Extract the version update code into its own script * [Docker] Use the correct THIRDPARTY directory name --------- Co-authored-by: Samuel Wein <sam@samwein.com>
r^2 is zero because it is not computed. Causes downstream OpenSwath to fail. Ensure goodness of fit is set to true so r^2 is computed
* patch: rename ENABLE_CWL to ENABLE_CWL_GENERATION * feat: add ENABLE_TDL option to enable/disable TDL dependency
* Add AnnotatedMSRawData and integrate it instead of MSExperiment where identification is needed * Various refactorings in order to integrate the new class "AnnotatedMSRawData" Build target "OpenMS" is successfully compiling now. * some fixes to tests * remove remnantsof protein identification at spectra * Apply suggestions from code review Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com> * minor * fix test * class and tool tests pass * more fixes * rename * removed commented out code * Update src/openms_gui/source/VISUAL/PlotCanvas.cpp * Update src/openms/source/ANALYSIS/ID/IDMapper.cpp * nop * simplified interface a bit more * moved file out of kernel * remove mzML from IDSplitter * forgot one file * removed unused mapping class * compiles again * some TV fixes * More identification view fixes * peak annotations work again * more safety checks * more imp to cpp * mend * Comment out unused variable declarations * fix idfilter * fix doxygen * reverted ignored setting file * nop * merge * fix warning --------- Co-authored-by: dvdvgt <david.voigt1998@gmail.com> Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
* some pyopenms fixes * fix * still error in pyx * more fixes * last fix * add to ci * add ci * Update src/pyOpenMS/pxds/ConsensusMap.pxd Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com> --------- Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
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Description
I patched the strLength method. Now it's passing every test. Added test case to XMLHandler_test that caused the error in the old version. Changed some internal datatypes from int to size_t to prevent overflow errors and improve consistency.
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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