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OpenMS

Make mass spectrometry analysis accessible to anyone
Collective - Host: opensource - https://opencollective.com/openms - Website: https://openms.org - Code: https://github.com/openms

[refactoring] moving files into more appropriate folders (PR 1 of X) (#7238)

* minor refactoring

* Update HyperScore.pxd

* Update MorpheusScore.pxd

---------

Co-...

github.com/OpenMS/OpenMS - 795c19f54fecb5ea1004fb7d8de329a0ab909d37 authored 11 months ago by Timo Sachsenberg <[email protected]>
Merge pull request #7237 from OpenMS/pr-7226

[FEATURE] z* and z' ions for ExD (fixed tests)

github.com/OpenMS/OpenMS - 9604cfc0e7d5462a5e49845e5fc68158ccc5f4df authored 11 months ago by Timo Sachsenberg <[email protected]>
Merge pull request #7236 from OpenMS/feature/vcpkg

Added port file to use qt from system libraries, fixed bug in LPWrapper cmake files (thanks Juli...

github.com/OpenMS/OpenMS - 7ede0c9691e90cb371cdef76b459c52b8d9625a9 authored 11 months ago by Timo Sachsenberg <[email protected]>
Merge remote-tracking branch 'origin/pr-7226' into pr-7226

github.com/OpenMS/OpenMS - b88db9587ca1e986a41ac4a63e2742a7633b4321 authored 11 months ago by timosachsenberg <[email protected]>
fix pyopenms wrapper

github.com/OpenMS/OpenMS - f51ac071b9555e919b14eee9b7f96509c83b01c8 authored 11 months ago by timosachsenberg <[email protected]>
Update src/openms/source/ANALYSIS/OPENSWATH/TransitionTSVFile.cpp

github.com/OpenMS/OpenMS - cb1108177ebf45df6b0d8b7f0af7271f05cfaf97 authored 11 months ago by Timo Sachsenberg <[email protected]>
fix warning

github.com/OpenMS/OpenMS - 513aa808483d05bca26ae99af331bbc6f2c1d53d authored 11 months ago by timosachsenberg <[email protected]>
fix test

github.com/OpenMS/OpenMS - 7ebc2888b588a6bf2c12df33258d09a496dd629d authored 11 months ago by timosachsenberg <[email protected]>
Merge branch 'develop' into fix/fragmentIons

github.com/OpenMS/OpenMS - 30db4b6147395ec9452d87acb193eb65c1d33042 authored 11 months ago by Timo Sachsenberg <[email protected]>
Merge remote-tracking branch 'origin/develop' into feature/vcpkg

github.com/OpenMS/OpenMS - 27b296796ebe70c0c644c27133e54ddbd540f8c9 authored 11 months ago by timosachsenberg <[email protected]>
fix LPWrapper test for vcpkg

github.com/OpenMS/OpenMS - 86b5a85b7d1382839c565367a7897e4bbfedf88e authored 11 months ago by timosachsenberg <[email protected]>
FindCOIN.cmake use imported targets (#7235)

github.com/OpenMS/OpenMS - b9e04deeb783561400cede4497ff87e0e8c11c5c authored 11 months ago by Julianus Pfeuffer <[email protected]>
Merge remote-tracking branch 'origin/develop' into feature/vcpkg

github.com/OpenMS/OpenMS - 824db24b9ed81730bc9e463d4768d6cad81b52bc authored 11 months ago by timosachsenberg <[email protected]>
add overlay for qt to prefer system libraries

github.com/OpenMS/OpenMS - eacbd00fe0c583a25266af5d638a4f212b9be4ba authored 11 months ago by timosachsenberg <[email protected]>
add vcpkg as submodule

github.com/OpenMS/OpenMS - f9756b703e7d0ddb0f881fa74045ed6071f465ee authored 11 months ago by timosachsenberg <[email protected]>
Merge pull request #115 from radusuciu/update-version-badges

Update versions on release badges

github.com/OpenMS/OpenMS-website - 76cf54080e0697035ac8fa0d9fd4a5d914324461 authored 11 months ago by Samuel Wein <[email protected]>
work around Clang bug (#7230)

github.com/OpenMS/OpenMS - dfda8e2de54a75a76c16c9074aaa192057824699 authored 11 months ago by Chris Bielow <[email protected]>
always print error when MSGF+ fails (#7229)

github.com/OpenMS/OpenMS - 3c1fcb11924c74d3d7e306253ca0b6c767413d47 authored 11 months ago by Julianus Pfeuffer <[email protected]>
fix typo notes for monday

github.com/OpenMS/OpenMS - 13d533d1505a789c4793fc8dd79394109e9c73d8 authored 11 months ago by Samuel Wein <[email protected]>
fix o

github.com/OpenMS/OpenMS - 76cbaca6d72ab7e0859a99185f195cc6cee5eb82 authored 11 months ago by Samuel Wein <[email protected]>
Merge branch 'develop' into release/2.9.1-action

github.com/OpenMS/OpenMS - 5401d8998e1c0876e83b5255a50dfef6d090f3e3 authored 11 months ago by Samuel Wein <[email protected]>
explicitly specify API token

github.com/OpenMS/OpenMS - 7ba7cf248266400532a8118156d91fbe55039fca authored 11 months ago by Samuel Wein <[email protected]>
get rid of unnecessary ref

github.com/OpenMS/OpenMS - c7ce6fedae902da8b08620d32140ae3522cefbcc authored 11 months ago by Samuel Wein <[email protected]>
Fix resampler (#7225)

* some documentation

* Resampler: allow combination of ppm-binning without alignment (used to...

github.com/OpenMS/OpenMS - 8721438c7a237759fffb57bacc42ada60239001a authored 11 months ago by Chris Bielow <[email protected]>
fix supernumerary "

github.com/OpenMS/OpenMS - 956e3dad84a3a926a6b40a5d89328da337e52309 authored 11 months ago by Samuel Wein <[email protected]>
fix bash bs

github.com/OpenMS/OpenMS - f72d2676b7f204215e7bd2569dd0268edd79439a authored 11 months ago by Samuel Wein <[email protected]>
make tags using gh instead of javascript

github.com/OpenMS/OpenMS - bd9b43da84c9609eb06dda8a9b481e7a4de2842b authored 11 months ago by Samuel Wein <[email protected]>
Merge branch 'develop' into fix/fragmentIons

github.com/OpenMS/OpenMS - 96026197e9ca4e53806228b6e721ac5ad6b93bf8 authored 11 months ago by Timo Sachsenberg <[email protected]>
Handle coinor from brew as well (#7218)

* handle coinor from brew as well

* remove debug

* minor fixes

github.com/OpenMS/OpenMS - cd6baf09074c3baa4899db855e6a187f3dd1e76f authored 11 months ago by Julianus Pfeuffer <[email protected]>
add new stuff to mzmlhandler

github.com/OpenMS/OpenMS - e6af98644924a73b68fce54e7b785be13ec3af1b authored 11 months ago by julianuspfeuffer <[email protected]>
[FEATURE] z* and z' ions for ECD

github.com/OpenMS/OpenMS - e72c6f3d624dcac04f6479ab17d39fc2d56c89f0 authored 11 months ago by julianuspfeuffer <[email protected]>
fix latest linking

github.com/OpenMS/OpenMS - 3241201fe00cd041f456a639e5cfc5ab8ef89819 authored 11 months ago by Samuel Wein <[email protected]>
[FIX] TOPPView: fix crash when viewing certain Chromatograms (#7221)

* fix RT range update when RT range is empty

* fix: add range to all Chroms, irrespective of ...

github.com/OpenMS/OpenMS - 2051cdf54c11cdbe6fbeb39f09baed709c263654 authored 11 months ago by Chris Bielow <[email protected]>
update links to latest, merge-to-develop

github.com/OpenMS/OpenMS - 46a52422e4d3be09e0c6bba8a6d1bfd087673f01 authored 11 months ago by Samuel Wein <[email protected]>
fix envs in create_SHA

github.com/OpenMS/OpenMS - a817702289a2e501fbb25f648c78995acd04f894 authored 11 months ago by Samuel Wein <[email protected]>
fix (hopefully) getting the RUN_NAME for release.

github.com/OpenMS/OpenMS - fddb15ed0b268e2b30f8afff6a5dc316690dd63e authored 11 months ago by Samuel Wein <[email protected]>
comma delimit release paths.

github.com/OpenMS/OpenMS - 9dcf3aef4662a01aff3a3ed680c5f7b79eb7b6ab authored 11 months ago by Samuel Wein <[email protected]>
fix regex for upload path in KNIME addons

github.com/OpenMS/OpenMS - 7afea62443c22088692a674e5a20208418bac446 authored 11 months ago by Samuel Wein <[email protected]>
[FIX] TOPPAS: open files in TOPPView (#7213)

* [fix] do not allow duplicate input filenames (leads to output name issues)

* [fix] "Open fi...

github.com/OpenMS/OpenMS - dd93684fd10a6c759f0a23c395e2297f28aa8711 authored 11 months ago by Chris Bielow <[email protected]>
fixed locking problem using changes to authorized_keys on archive host. Revert attempts to do so in here

github.com/OpenMS/OpenMS - 569ab4dbaebf5c08b87ae2e8b05dd7b4fc1262db authored 11 months ago by Samuel Wein <[email protected]>
fix regex for uploadpath, mark release as Draft

github.com/OpenMS/OpenMS - acc5acf5b5e45df67975c4f1bf07cdc4ab9f70ae authored 11 months ago by Samuel Wein <[email protected]>
Update spectrum_normalization.rst (#424)

This commit enhances the 'Spectrum Normalization' section of the documentation. The changes incl...

github.com/OpenMS/pyopenms-docs - 5fc350318f8c54b62eb0f479caf01ec40de643b8 authored 11 months ago by Ayesha-Feroz <[email protected]>
try with a static tag

github.com/OpenMS/OpenMS - 0e194eb735c967b658015f5d02d42c82e01bf6c0 authored 11 months ago by Samuel Wein <[email protected]>
replace release action

github.com/OpenMS/OpenMS - a84ed245579d70fd9f1f84c0d8f53299633b6deb authored 11 months ago by Samuel Wein <[email protected]>
create a tag first, because the release action doesn't do so.

github.com/OpenMS/OpenMS - 154d4abfea87e1ced7a0d45864ed5b797b2f353c authored 11 months ago by Samuel Wein <[email protected]>
fix release syntax, fix bash stuff.

github.com/OpenMS/OpenMS - 693e84a82d9a741677829931e60e6bb8c9c90e1e authored 11 months ago by Samuel Wein <[email protected]>
bash indent bs

github.com/OpenMS/OpenMS - cf0d91e10fb2c307400d4c6de526f2516cccbbc5 authored 11 months ago by Samuel Wein <[email protected]>
fix other path

github.com/OpenMS/OpenMS - e4a00ef90cde0623ee4ee9caf12f231c91645c89 authored 11 months ago by Samuel Wein <[email protected]>
Add files via upload

github.com/OpenMS/pyopenms-docs - cae748a47938f4cf87967fc001874b78bb7f1b77 authored 11 months ago by Ayesha-Feroz <[email protected]>
handle rrsync competition for lock.

github.com/OpenMS/OpenMS - 13639945c71e2b19971d1c1fce4e52429d0cebf5 authored 11 months ago by Samuel Wein <[email protected]>
fix path

github.com/OpenMS/OpenMS - 2b0a64e019d7b686a1942d314d7daa220f6271db authored 11 months ago by Samuel Wein <[email protected]>
re-enable slow OS'

github.com/OpenMS/OpenMS - 55a4ae9939fcf591d7ad7adba3f781ab717a65a2 authored 11 months ago by Samuel Wein <[email protected]>
fix changelog name in releasetext

github.com/OpenMS/OpenMS - bbdfbf89d18305d2689c1b62f930858cc8c88c64 authored 11 months ago by Samuel Wein <[email protected]>
comment out windows and mac builds to speed debugging

github.com/OpenMS/OpenMS - 0ddacf9a2cd2522af1ba0bdf29ded70a48c07645 authored 11 months ago by Samuel Wein <[email protected]>
Update build_from_source.rst

github.com/OpenMS/pyopenms-docs - 0a3ad66daeef4db1aac2586d73824cdcdb4534ff authored 11 months ago by Julianus Pfeuffer <[email protected]>
fix name of changelog artifact

github.com/OpenMS/OpenMS - b65215b06d9fd5adb178af2512623e1dfd80b628 authored 11 months ago by Samuel Wein <[email protected]>
fix path for changelog

github.com/OpenMS/OpenMS - f1ba8a11ac72dfc04c0bf411fb230ca2e4aaa61e authored 11 months ago by Samuel Wein <[email protected]>
more regex

github.com/OpenMS/OpenMS - d9a0aec36126532ec6b6c8b8981c9de687536af7 authored 11 months ago by Samuel Wein <[email protected]>
regex

github.com/OpenMS/OpenMS - ca4ef9cd288fce8d659df73984458026add2bb81 authored 11 months ago by Samuel Wein <[email protected]>
comment out inprogress code

github.com/OpenMS/OpenMS - 21216eb6fbd551fe306a2cca47ffe4b9f5aaf70d authored 11 months ago by Samuel Wein <[email protected]>
Merge branch 'develop' into release/2.9.1-action

github.com/OpenMS/OpenMS - af92927ea316c81b6cd430b863e73b0385fd7b0a authored 11 months ago by Samuel Wein <[email protected]>
Further work on release

github.com/OpenMS/OpenMS - 4288921f4e8cc7a65b881da68a4e800197ad5971 authored 11 months ago by Samuel Wein <[email protected]>
remove debug

github.com/OpenMS/OpenMS - 41ff7fcb3c739e0d29ee2db9e62b1dd1462f373d authored 11 months ago by julianuspfeuffer <[email protected]>
Update build_from_source.rst

github.com/OpenMS/pyopenms-docs - 7a092ec5d343a111718470fbc19b261ee8049991 authored 11 months ago by Timo Sachsenberg <[email protected]>
Fix SpectrumAnnotator small metadata issue (#7216)

github.com/OpenMS/OpenMS - 59ee60e0652adf027a9f96de5c7fbac8b0760ce7 authored 11 months ago by Julianus Pfeuffer <[email protected]>
Added logic to update SHAs

github.com/OpenMS/OpenMS - 2cbd3257d234c49dcec8e96f6ed411adabbfdf59 authored 11 months ago by Samuel Wein <[email protected]>
Merge branch 'develop' into release/2.9.1-action

github.com/OpenMS/OpenMS - 736b4fc709e17f9a83dba6a7d1a8d467a73eb43c authored 11 months ago by Samuel Wein <[email protected]>
Fix typo

github.com/OpenMS/OpenMS - 4eb649242e9dd219cd9a7225756034eed87914e2 authored 11 months ago by Samuel Wein <[email protected]>
Merge branch 'develop' into release/2.9.1-action

github.com/OpenMS/OpenMS - 63b04a5e163b82e482051d97003a7a6c6e19b18d authored 11 months ago by Samuel Wein <[email protected]>
Merge pull request #7193 from OpenMS/GHA-full-fixes

Update openms_ci_matrix_full.yml

github.com/OpenMS/OpenMS - a2636857d40be03279a32944f36c6e7fed33779e authored 11 months ago by Samuel Wein <[email protected]>
Merge branch 'develop' into GHA-full-fixes

github.com/OpenMS/OpenMS - 3b315755d87d085fc84727ca893156ee7d74252d authored 11 months ago by Samuel Wein <[email protected]>
Update openms_ci_matrix_full.yml

Renable docs for Mac when building package, disable building docs when no package.

github.com/OpenMS/OpenMS - 8c0838af8a5549c61c1fa070b71779c14608de74 authored 11 months ago by Samuel Wein <[email protected]>
Merge pull request #7212 from OpenMS/fix-MacOs-runner-overwrite-issues

Update openms_ci_matrix_full.yml

github.com/OpenMS/OpenMS - 41fae7641addae1f1bb1c5234660952d3184c4c5 authored 11 months ago by Samuel Wein <[email protected]>
Update openms_ci_matrix_full.yml

github.com/OpenMS/OpenMS - b85716e6b65516b932dad42f2e57ee7746eae4b0 authored 11 months ago by Samuel Wein <[email protected]>
Update openms_ci_matrix_full.yml

Add breadcrumbs to end of file for planned work

github.com/OpenMS/OpenMS - 76271f3f44a0c3ec53196d7305f6572ed1e5a53c authored 11 months ago by Samuel Wein <[email protected]>
Update openms_ci_matrix_full.yml

github.com/OpenMS/OpenMS - c561bc7aa5b923ffeae0fe74023cf2b076410d91 authored 11 months ago by Samuel Wein <[email protected]>
Update openms_ci_matrix_full.yml

github.com/OpenMS/OpenMS - ea2520ade9ca4e3ef49521dfe51e534b4c6df0e1 authored 11 months ago by Samuel Wein <[email protected]>
Update openms_ci_matrix_full.yml

github.com/OpenMS/OpenMS - ea566da04272777d98975300b8e83b917007a063 authored 11 months ago by Samuel Wein <[email protected]>
Update openms_ci_matrix_full.yml

github.com/OpenMS/OpenMS - b669c61f849aa1e0f5b8aa70a46813154820c3c7 authored 11 months ago by Samuel Wein <[email protected]>
Update openms_ci_matrix_full.yml

Regex bs

github.com/OpenMS/OpenMS - f70f76405e4cc6c1cf59bb621c794a548b19c81e authored 11 months ago by Samuel Wein <[email protected]>
Update openms_ci_matrix_full.yml

github.com/OpenMS/OpenMS - c64687447b642a26fcb475c9e22b5a02ceb312dc authored 11 months ago by Samuel Wein <[email protected]>
Update openms_ci_matrix_full.yml

github.com/OpenMS/OpenMS - 949f4310d0eeafd6d2cb2e22f0f4f8d1781cb70c authored 11 months ago by Samuel Wein <[email protected]>
Update openms_ci_matrix_full.yml

github.com/OpenMS/OpenMS - 19dbd1aa0f7fcb2f341b8611adf6bc3184339d63 authored 11 months ago by Samuel Wein <[email protected]>
Start adding the Release action Jenkins stuff to GHA

github.com/OpenMS/OpenMS - d217514055610e7bfdffd37f8dacf365b43ccb72 authored 11 months ago by Samuel Wein <[email protected]>
Update openms_ci_matrix_full.yml

Fix trailing slash

github.com/OpenMS/OpenMS - 840fe63eed156202bffab420c3c5da53740cdf6a authored 11 months ago by Samuel Wein <[email protected]>
Update openms_ci_matrix_full.yml

Fix base directory for Rsync

github.com/OpenMS/OpenMS - d96686adae346ea98e0a1a839be99e67a5c6549e authored 11 months ago by Samuel Wein <[email protected]>
Update openms_ci_matrix_full.yml

Exclude non-html stuff

github.com/OpenMS/OpenMS - dd823180e9af7de33572533f845623f35d90644b authored 11 months ago by Samuel Wein <[email protected]>
Update openms_ci_matrix_full.yml

use directory instead of path on zip action

github.com/OpenMS/OpenMS - 2d8bf58a4fdc28cbd947306d12ab8ceb08888d70 authored 11 months ago by Samuel Wein <[email protected]>
Update openms_ci_matrix_full.yml

github.com/OpenMS/OpenMS - 99aa90a888b74ca7ca6e5938f42851c299538ccc authored 11 months ago by Samuel Wein <[email protected]>
[TEST] added comment lines to test file to test CsvFile comment feature

github.com/OpenMS/OpenMS - 4688a90a53e2b86465644e8a7008be79985cc37a authored 11 months ago by Eugen Netz <[email protected]>
[TEST] added rowCount test to CsvFile class test

Also added comment lines to an input test file to test new comment feature.

github.com/OpenMS/OpenMS - d7d579d58b1ab70f9bd766a99e1759635b209c96 authored 11 months ago by Eugen Netz <[email protected]>
[FEATURE] support for comment lines in CsvFile

A '#' at the beginning of a line will be ignored by CsvFile for both the rowCount and getRow fun...

github.com/OpenMS/OpenMS - 1d79a1ed6e25906c6aacc8572170c03fcbd95c57 authored 11 months ago by Eugen Netz <[email protected]>
Update openms_ci_matrix_full.yml

github.com/OpenMS/OpenMS - 855c4ea9232ab3fdd6a3589f6cc5ea93ef4bebba authored 11 months ago by Samuel Wein <[email protected]>
Update openms_ci_matrix_full.yml

Zip documentation before uploading as artifact.

github.com/OpenMS/OpenMS - fae1c4db9e0a2ca9fc2752bee7dddee60df2a0f7 authored 11 months ago by Samuel Wein <[email protected]>
Update openms_ci_matrix_full.yml

Reenable docs on windows

github.com/OpenMS/OpenMS - d283c5267ead87c5a4b5a24b019bbbe66678192e authored 11 months ago by Samuel Wein <[email protected]>
Update .github/workflows/openms_ci_matrix_full.yml

Co-authored-by: Julianus Pfeuffer <[email protected]>

github.com/OpenMS/OpenMS - 137285afb60abddbf900fc720dcd572b5da8ef89 authored 11 months ago by Samuel Wein <[email protected]>
Merge pull request #12 from OpenMS/dependabot/submodules/nuxl-app-c85f1b9

Bump nuxl-app from `9038a47` to `c85f1b9`

github.com/OpenMS/streamlit-deployment - 9bc5883221c7cd57dea3bb078c658b438ca9b92c authored 11 months ago by axelwalter <[email protected]>
Merge branch 'develop' into GHA-full-fixes

github.com/OpenMS/OpenMS - debb3b2015c6f28520b8795e099d5f9c949853fb authored 11 months ago by Samuel Wein <[email protected]>
LICENSE -> LICENSES

github.com/OpenMS/OpenMS - d313ff5c77c101c091b383971381576d312447b4 authored 11 months ago by Samuel Wein <[email protected]>
Merge pull request #13 from OpenMS/dependabot/submodules/umetaflow-gui-6cc740f

Bump umetaflow-gui from `9e84685` to `6cc740f`

github.com/OpenMS/streamlit-deployment - de0869a41c7e81a9467b25ab9f4e4fd11d03661b authored 11 months ago by axelwalter <[email protected]>