…ppfast

This reverts commit 94e59bd.

… alignwork

Made align function work on const data

* add test run

* push on dev

* create contrib folder

* Delete .github/workflows/test_contrib.yml

* disable openmp for arm wheels

* set rpath

* try fix from abibuilder

* switch linking

* fix typo

* add print for libraries

* fix openmp build flags

* fix rpath in workflow

* dont remove source

* install wheels

* run unit test separately

* Revert "install wheels"

This reverts commit 7c159d2.

* Revert "run unit test separately"

This reverts commit 5b854cb.

* Reapply "install wheels"

This reverts commit 0f1ff8d.

* Revert "dont remove source"

This reverts commit 227b3a9.

* is brew libomp the issue?

* update rpath

* rpath to lib

* update cmake args

* remove lib

* move test files to tests

* move test files

* dont uninstall brew

* cleanup

* fix typo

* clean up libs

* cleanup

…Values (OpenMS#7981)

* move basename member out of PeptideIdentification into MetaValues

* fix tests and simplify them

* remove base name (not needed)

* strange character fix

* improve doc, add type alias

* Add deprecation notice for PeptideHit class

* Deprecate PeptideIdentification in favor of SpectrumIdentification

* Add ubuntu arm to matrix

* Update thirdparty with new percolator and some arm64 stuff

* Update thirdparty, update Percolator version

* Update percolator test for 3.07 (NB the actual Percolator 3.07 release still uses 3.06 in their executable)

* Add logic to copy the correct THIRDPARTY executables for the current arch

* Update Comet versions in all OSs update comet test files for the new version.

* add status of copy

* cp issues for macZZ

* Update openms_ci_matrix_full.yml

Comment out the actual ARM run for now so we can merge the updated THIRDPARTY

* third

* reserve a type alias

* small additions to architecture file

* Documents manual Python extension capabilities

Adds a detailed section on using manual PYX files to extend Python bindings, covering advanced functionality such as handling complex C++ features, Python-specific enhancements, performance optimizations, and integration with Python libraries. Clarifies the role of PYX files in enabling features beyond automatic wrapping.

* Update ARCHITECTURE.MD

…ber in PeptideIdentifications to a meta value as it is often unused (OpenMS#7985)

* improve doc, add type alias

* move pepxmlanalysis results into meta values to simplify datastructure

* move significant threshold to metavalue

* some fixes

* Merge remote-tracking branch 'origin' into openms-pr-5547

* more test updates

* more fixes

* don't write it twice

* tests works

* fix tests

* more test fixes

* nop