Change AUTHORS File, added Nils Bender #1
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Create ARCHITECTURE.MD
fix some newly introduced warnings
## Description <!-- Please include a summary of the change and which issue is fixed here. --> ## Checklist - [ ] Make sure that you are listed in the AUTHORS file - [ ] Add relevant changes and new features to the CHANGELOG file - [ ] I have commented my code, particularly in hard-to-understand areas - [ ] New and existing unit tests pass locally with my changes - [ ] Updated or added python bindings for changed or new classes (Tick if no updates were necessary.) ### How can I get additional information on failed tests during CI <details> <summary>Click to expand</summary> If your PR is failing you can check out - The details of the action statuses at the end of the PR or the "Checks" tab. - http://cdash.seqan.de/index.php?project=OpenMS and look for your PR. Use the "Show filters" capability on the top right to search for your PR number. If you click in the column that lists the failed tests you will get detailed error messages. </details> ### Advanced commands (admins / reviewer only) <details> <summary>Click to expand</summary> - `/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. - setting the label "NoJenkins" will skip tests for this PR on jenkins (saves resources e.g., on edits that do not affect tests) - commenting with `rebuild jenkins` will retrigger Jenkins-based CI builds </details> --- :warning: Note: Once you opened a PR try to minimize the number of *pushes* to it as every push will trigger CI (automated builds and test) and is rather heavy on our infrastructure (e.g., if several pushes per day are performed).
fix: some compile warning
Fix Wrapping of `IsotopeDistribution`
* remove unstable scores * fix msgf * update test * more tests
Bumps [contrib](https://github.com/OpenMS/contrib) from `3cdef5c` to `e6fde7c`. - [Release notes](https://github.com/OpenMS/contrib/releases) - [Commits](OpenMS/contrib@3cdef5c...e6fde7c) --- updated-dependencies: - dependency-name: contrib dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* OpenMSInfo now informs about custom CXX compile flags * update changelog * use latest contrib
* pyoms fix activationmethods * add test * move enum value docs to class --------- Co-authored-by: Timo Sachsenberg <timo.sachsenberg@uni-tuebingen.de>
feature: Nucleotide-Protein search engine NuXL
* quick save * add additional level for aggregation and better export in protein quantifier * inital support for extended protein tables * fix * fix number of filenames * still some bug * better name for abundance variable * refactor. extracted a few methods * proper file+channel level output * update name * remove debug code * compile fix * make file name in output columns consistent * better separator * also sample level quant * add sample names to output
fixes bug introduced earlier
Use GitHub issue forms to encourage users to report more information and to direct questions to more appropriate venues.
* Adding support for building apache arrow/parquet integration * Reverting to original suggested changes based on feedback + docs * ArrowTest * Fixing weird git merge * get Arrow_test setup * Arrow test (compiles!) * Set Parquet flag to on, github CI changes * One liner for parquet flag * Maybe cmake cares about where the flag is? Idk just a try. * Json on? * committing to fetch! * Commit after all the cursed merges. * Fixed cmake for nlohmann * Set implicit conversion to off * using a set variable? * force * revert to normal, purge nlohmann right after install. * sleeeep * It's always the one liners * explicit conversion * from_json overload * whoops! double declaration. * Add arrow to win/mac in CI * turn external json off only for mac. Unsure of windows. * doing it right this time - mac cmake flag * try self closing tags? * warnings -> errors * external stuff * reverting some unnecessary (I THINK) changes * Unsure why it doesn't read env.WITH_PARQUET * revert to this if the next idea fails * checking if this works for the pr * Works + fixing windows' external json * learned what git revert does LOL This reverts commit a93afcf. * Revert "checking if this works for the pr" This reverts commit df44c6a. * back to normal * detailed comment * small changes as per PR * Arrow on Conda
* Update ARCHITECTURE.MD * Update ARCHITECTURE.MD
SIMD XML conversion from UTF16 to ASCII (e.g. mzML)
* Remove py2 stuff in pyopenMS so we can use Cython3.1, update building to work with new cython and autowrap * update required cython and autowrap versions * Apply suggestion from @coderabbitai[bot] Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com> * Fix failing unit tests caused by a combo of changes to our API, and missing accessor functions (plus a major PITA issue where _testMetaData was clearing the metadata on a test) * remove explicit implementation of stringpos (and test), we don't seem to need it in py3. * Update CMakeLists.txt Remove comment referring to earlier debugging efforts * add tests remove dead code * enable inequality tests --------- Co-authored-by: Julianus Pfeuffer <8102638+jpfeuffer@users.noreply.github.com> Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
* Remove py2 stuff in pyopenMS so we can use Cython3.1, update building to work with new cython and autowrap * Add fixed modification search to NASE, update parameters file. Also fix uninitialized pointer in FeatureFinderAlgorithmHelperStruts which was making G++ sad. * Update src/topp/NucleicAcidSearchEngine.cpp --------- Co-authored-by: Timo Sachsenberg <timo.sachsenberg@uni-tuebingen.de>
* proper data array comparisons * add comparison * test * introduce <=> in base classes * add ADL lookup for <=> * Update Helpers.h * revert <=> * revert helper * performance consideration * Update DataArrays_test.cpp * Update DataArrays_test.cpp
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Description
Checklist
How can I get additional information on failed tests during CI
Click to expand
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)
Click to expand
/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