github.com/OpenMS/OpenMS-1 commits | Ecosyste.ms: OpenCollective

Allow missing score types in IDDData conversion (#6097)

* warning

* conversion works

* Apply suggestions from code review

Co-authored-by: Chris...

f3f35c9c9e7face3c5194b453ed2b1d9a48e8360 authored over 2 years ago by Timo Sachsenberg <[email protected]>

more columns filled and some removed again

ddda072e51d03ac713a7057d3bda45a930a8f1d7 authored over 2 years ago by vrossow <[email protected]>

working on AnnotationItems

729a9f6e62c0d9c45b6cecaa8b7448f098b37efb authored over 2 years ago by bielow <[email protected]>

[FIX] Suppress -Wunused-private-field warnings (#6046)

* Suppress unused sonar_ in osw writer

* (fix) remove unused private field

Remove pos_min_...

c289655514e3a4d46cb2984a53d37eb924008c31 authored over 2 years ago by Matchy <[email protected]>

Merge branch 'develop' of https://github.com/OpenMS/OpenMS into maxquant-output

600c7047bb9dc060a5bec452b8ace151c0c95279 authored over 2 years ago by vrossow <[email protected]>

Merge pull request #6095 from OpenMS/timosachsenberg-patch-1

Update stale.yml

360dd58a3d47062400de79a245870c5f64ab5d77 authored over 2 years ago by Samuel Wein <[email protected]>

Update stale.yml

let's reduce times gradually

aaa74797186d46bee146bdf73cf775fe2f2e6d58 authored over 2 years ago by Timo Sachsenberg <[email protected]>

Update stale.yml

e1d64bde6dd9362cc574167858641871a9780ede authored over 2 years ago by Timo Sachsenberg <[email protected]>

All missing column names added and started filling them with the correct info. And test file changed.

50258b67d01351ddb1398263d8dfe9adbd6c0732 authored over 2 years ago by vrossow <[email protected]>

[FEATURE] std::move to spectra merger (#6063)

* [FEATURE] MicroOptimazations: auto in some for-loops, got rid of unnecessary allocations & if ...

f58bfb93d6ebefcaef66ca707b37039bb6213b80 authored over 2 years ago by Lenny Kovac <[email protected]>

Add the native_id identifier to the list of spectrum references (#6078)

Co-authored-by: Timo Sachsenberg <[email protected]>

c59e7fab3d33ce23c45c4672871d03672ecc2e67 authored over 2 years ago by tillenglert <[email protected]>

Season of Docs application - My edits (#6064)

* test edit of QuickStart.doxygen

* minor edits to QuickStart.doxygen file

* added a short...

cbf1a2921ed66a14edf2c1bddcabfc6596ba085e authored over 2 years ago by greengypsy <[email protected]>

[FIX]: deprecated Qprocess::execute(const Qstring& command) (#6086)

* [FIX]: deprecated Qprocess::execute(const Qstring& command)

* [FIX]: deprecated Qprocess::e...

15ffe52a06365756ccc8d702f978774cc256996a authored over 2 years ago by AMIT KUMAR MISHRA <[email protected]>

[FIX]: suppressed deprecated QRegion::rects() (#6089)

6a9a000d6fcc5c9f192f5d44de5abab0753212f3 authored over 2 years ago by AMIT KUMAR MISHRA <[email protected]>

[FIX]: suppressed deprecated QWheelEvent::x() const (#6088)

* [FIX]: suppressed deprecated QWheelEvent::x() const

* update contrib

Co-authored-by: Tap...

5c93b16bcca2bc9dd7ab755d84783e66ad6d6df3 authored over 2 years ago by AMIT KUMAR MISHRA <[email protected]>

[FIX]: deprecated addRoundRect (#6085)

* [FIX]: deprecated addRoundRect

* update contrib

4306b58b27ffe3ffe606e2de9aad9d77598bd01f authored over 2 years ago by AMIT KUMAR MISHRA <[email protected]>

[FIX]: deprecated setBackgroundColor (#6084)

* [FIX]: deprecated setBackgroundColor

* update contrib

Co-authored-by: Timo Sachsenberg <...

4b5401991b46ce4aa132111318e8ffe724e7b320 authored over 2 years ago by AMIT KUMAR MISHRA <[email protected]>

Merge remote-tracking branch 'origin/feature/FLASHDeconv' into feature/FLASHDeconvOnly

3537731d3958df1b5dcb6f0ae0251372de74c989 authored over 2 years ago by JeeH-K <[email protected]>

Change printProgress to OpenMS ProgressLogger

283a579c9e50e9542bbaaf383a1db56f029fb33e authored over 2 years ago by JeeH-K <[email protected]>

revert to "mass_error_da_" version to avoid test errors from other tools

cd78291fbe3ec4b460ad6d9c881a6c6e53f264bf authored over 2 years ago by JeeH-K <[email protected]>

debug error while merging

683c4d02ed7ad7170bee7be32b4ffa205b3a5407 authored over 2 years ago by JeeH-K <[email protected]>

Merge remote-tracking branch 'origin/feature/FLASHDeconv' into feature/FLASHDeconvOnly

bf374bffa4a136c2557342dda31b2789a7bb44c8 authored over 2 years ago by JeeH-K <[email protected]>

Addressing Chris' comments - FLASHIda sort bug fixed3

63b6fd6c3aab023c7159f9f5cd0af584749e73e7 authored over 2 years ago by kyowonjeong <[email protected]>

Merge branch 'develop' into feat/specAnnotationSirius

12c207110a16aced1968aa9e39d62becf0943b8e authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Merge pull request #6090 from poshul/add_sponsor

added funding.yml

19013e5841c7fe2f32e12cfd688b0dc0e05cb8a3 authored over 2 years ago by Samuel Wein <[email protected]>

smaller headers in PR template

c0917f20d957127f49d09ed451aa09eef1056a45 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

added funding.yml

4bbf66be85ec05602887fe95287b692f645dfefc authored over 2 years ago by Samuel Wein <[email protected]>

Merge branch 'develop' into develop

65cef8bfc1137f21d69975944b550dbf6f088b9c authored over 2 years ago by greengypsy <[email protected]>

Ordered the header of evidence.txt and started to add missing column names/data

da7970abd9612e60b3caf4147dc02a59fb20eb42 authored over 2 years ago by vrossow <[email protected]>

remove indent from QuickStart.doxygen and add approved text from pull request

ff34b143fb84a1d2ece9434c255031fb9e19181e authored over 2 years ago by greengypsy <[email protected]>

Rename pyopenms-extra to pyopenms-docs (#6087)

* Update CHANGELOG

* Add Tapasweni Pathak in AUTHORS

* Rename submodule pyopenms-extra to ...

5fc379a455dac3d66b7ee58c935706bad422fbd9 authored over 2 years ago by Tapasweni Pathak <[email protected]>

Merge pull request #5915 from OpenMS/jpfeuffer-patch-7

Uncomment wrapping of other operators in Empirical Formula

09c7143ba919840569d7b54ab76e0b495475339c authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Comment mul since autowrap requires same type

21031fb9ff546f696a3aa4a4b1b562c76ecfa8e7 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Update PULL_REQUEST_TEMPLATE.md with information on reformat (#6076)

* Update PULL_REQUEST_TEMPLATE.md

Co-authored-by: Julian...

fdb295b65a5dc695a0f20ef321a7477655864e74 authored over 2 years ago by Timo Sachsenberg <[email protected]>

Merge branch 'develop' into develop

77c8207e33ec5f32783488b8d9d500bc6c30baeb authored over 2 years ago by Timo Sachsenberg <[email protected]>

[CI] Rename tools/travis to tools/ci (#6075)

* Rename travis folder

* Fix GHA yml config

c046c222850041069f55fe9f3423f61bfdbfac86 authored over 2 years ago by Matchy <[email protected]>

backup

ed710d1b4d1e770fb99c114e890721864212f092 authored over 2 years ago by bielow <[email protected]>

Merge pull request #6065 from bernt-matthias/topic/redundant-wd

SiriusAdapter: remove redundant setting of working dir

95a938c152f78bdb0a5941a09625c82d5b6bc137 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Update doc/doxygen/public/QuickStart.doxygen

Co-authored-by: Timo Sachsenberg <[email protected]>

25fdf91d603220c4ed84d0ad14ac2d93648932e6 authored over 2 years ago by greengypsy <[email protected]>

Merge pull request #6069 from cbielow/fix_trafo

Fix trafoXML parsing

216ab3e1e5fc9ae232e52a6a52d1542669c2d8ce authored over 2 years ago by Chris Bielow <[email protected]>

minor opt

a155f1c74cb3aaee90c4f4510737f8cb3ad7335b authored over 2 years ago by bielow <[email protected]>

make old TrafoXML's backwards compatible again

8177a506c9e658caa8d20c7db8693a9d739d9faa authored over 2 years ago by bielow <[email protected]>

Uncomment imul

b56138f4c0d22832f535dd50897135f351aefc67 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

remove redundant setting of working dir

7aa15a545ecaa6dc23fb504eb6041f7c2f39569a authored over 2 years ago by Matthias Bernt <[email protected]>

add imul

5ce7e93a44881bc8935b86962d43bb14af06754d authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Uncomment wrapping of other operators in Empirical Formula

Fixes #5914 if it runs through. I have no idea why it was uncommented.

d5d8340866b4576cf02ec56b7010b2220c7d51a4 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

edited NeedlemanWunsch.h

bb915b381f625dd0f0bd43fad4e0a37ded581534 authored over 2 years ago by greengypsy <[email protected]>

added an example description of the tutorial AA sequence as none previously existed

4191650bb3f6a611f759d6adb055dc3a08a2db51 authored over 2 years ago by greengypsy <[email protected]>

minor edit of TOPP_concepts.doxygen

8e46073c2804772db79a0a89c92525a064da8361 authored over 2 years ago by greengypsy <[email protected]>

added a short intro and background to quick start guide

c94673d7eebe54133b068a5c51d2012227bacdb5 authored over 2 years ago by greengypsy <[email protected]>

minor edits to QuickStart.doxygen file

3b9503293af3c857fbec6bd6e614014265d8829a authored over 2 years ago by greengypsy <[email protected]>

test edit of QuickStart.doxygen

ad2304d03cf24671d556e7274f6ed7dd9170c810 authored over 2 years ago by greengypsy <[email protected]>

Merge pull request #6060 from matchy233/fix/boost-linking-error

[FIX] Add FASTAContainer_test to Boost_dependent_tests

cacde2a4dc6d34ef44ab36e2c0df6691f39a4222 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Add FASTAContainer_test to Boost_dependent_tests

5dbb636ac745ccd3787a583686675da8296f6914 authored over 2 years ago by matchy233 <[email protected]>

fix: small updated to library intensity in construct transition list

b36e3c62d53062bef0000e3b0db988e80ab9374a authored over 2 years ago by dmccloskey <[email protected]>

fix: major modifications to DDA related code to allow for transition list construction and spectral export

58787e0d4f9edefc42ffc1b330049bdf096e49e8 authored over 2 years ago by dmccloskey <[email protected]>

fix: added check for unannotated spectra in

3ea0967e332eb9147d4a71d16a6ae1e255eea714 authored over 2 years ago by dmccloskey <[email protected]>

Merge pull request #6053 from hbeschorner/detect_decoys

[FIX] DecoyDatabase detects already decoy'd DBs

301882072d307d45d882890abe9bfa155a456719 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Addressing Chris' comments - FLASHIda sort bug fixed2

536717405aa8262ec6bf2d8e05196e3d9d5a57e3 authored over 2 years ago by kyowonjeong <[email protected]>

Addressing Chris' comments - FLASHIda sort bug fixed2

4319caba9518434ce33742b5f4213a078e1a0282 authored over 2 years ago by kyowonjeong <[email protected]>

Added force flag to allow all custom decoy strings

f451cc65f6fb9e7b342f97168a273d2ae0d04a17 authored over 2 years ago by vrossow <[email protected]>

Added class test for findDecoyString and countDecoys

d1d2019b37628d757468579c364a18d4e84ddade authored over 2 years ago by vrossow <[email protected]>

some minor fixes

197e42e4d4fd577b4ffddc4d5f5a3fdf677f4745 authored over 2 years ago by beschorneh32 <[email protected]>

Merge remote-tracking branch 'upstream/develop' into uclacds-develop

49512c044979c94ae57decd621022d1b4db8fff4 authored over 2 years ago by zhuchcn <[email protected]>

[TEST] for Range and Dim mapper classes

1ed72435d2146493247f031039bed111e7d8d4e9 authored over 2 years ago by bielow <[email protected]>

[FIX,BUILD,PYOMS,TYPING] add import as second line?

c5f5cec1ef27a24e221d49f63d59e2ddeaa52683 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Merge pull request #6043 from Amit0617/docsday1

[DOC] fix links on github readme and doxygen tutorial

aee47e7defe032bdd9067a0f115ae324e5798607 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

link addresses

1c5e2abed5cd9be933b4f74b7efa930792aba139 authored over 2 years ago by amit0617 <[email protected]>

[Gitpod] update clangd in dockerfile to 14

49baa3bf729834201dc46482c7b34dc1671910b0 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

removed our new exception, wasn't necessary anymore

003d6d6fdacf224f1c82f4e31fb4dbc9bd1924fd authored over 2 years ago by beschorneh32 <[email protected]>

some (minor) changes and revisions

f28b4a3c17cf0c6d2564ff98564f5dcae94609df authored over 2 years ago by beschorneh32 <[email protected]>

Merge pull request #6041 from OpenMS/fix/pyoms_typing_imports

[FIX,PYOMS,TYPING] add global imports to every pyi

b0f43dc8c06c3281f7b218734f80c0aacc63725a authored over 2 years ago by Julianus Pfeuffer <[email protected]>

no bup suffix and add newline

58dc7451230ee224c8df4cc2fe0b8c9045fb4d0b authored over 2 years ago by Julianus Pfeuffer <[email protected]>

[FIX,PYOMS,TYPING] add global imports to every pyi

3c57db653bbb1bc00accbf92dcf924e3c36bc8b3 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Merge pull request #6026 from enetz/fix/OpenPepXL_test_files

[FIX] update OpenPepXL test files that fail in nightly

df8d8f5bff67340bf7b26d091e56f9c205e591d1 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

[FIX] update OpenPepXL test files that fail in nightly

Probably related to updated contrib libs (zlib)

ecb45a7fbf680d94bf5e969f064f820c74244cf6 authored over 2 years ago by Eugen Netz <[email protected]>

[FIX] make Base64 encoded xquest.spec.xml spectra more robust

slight differences in rounding can cause the Base64 encoding to change, which is difficult compa...

0bb70f97637405beb132c6caf97e41f190025af9 authored over 2 years ago by Eugen Netz <[email protected]>

Merge pull request #6036 from OpenMS/jpfeuffer-patch-5

[BUILD] Use Cmake exports from boost

1e3f8b3534dce57c717b4ce912f2e766ae7296c3 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

try to build with header only math stuff

d78c426924e05b68bfe735530bd121a2e9a6b250 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

converting from old visible_range to newer more flexible structure

f5f63ae2b8e05da32a65914c9dd3216d7b47bd0d authored over 2 years ago by bielow <[email protected]>

more Mappings

3590f4d0c1afd73a77049eab795fa95da61858d4 authored over 2 years ago by bielow <[email protected]>

more convenience functions for Ranges

ffb442115989cbdc29149b8e9626eac07392f364 authored over 2 years ago by bielow <[email protected]>

add operator

7b1973c71dda869a9ced54b1fad526b34f520f35 authored over 2 years ago by bielow <[email protected]>

fix typo

860c0bfc42b9d7e2ebc23fc1b1e9127120598895 authored over 2 years ago by bielow <[email protected]>

expose constant begin/end

d6e7076fc94c8c2fdada39edb52539b39f6b52c6 authored over 2 years ago by bielow <[email protected]>

Use static boost in Actions CI

Not sure why it ever worked.

218f8178f2b13b23391ba73a3c318363c182f416 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Require the libs in the first place

c159ac297a9706f92d0676079d0f3d82ded82d2a authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Use Cmake exports from boost

c909b8f2828a2e053faa54bbe7e88a1200fd97d1 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Merge pull request #6024 from axelwalter/feature/wrap-IIMN

[Feature] Wrap IonIdentityMolecularNetworking

963e3a5a9ae67028247e3bc7c1421df201519fe0 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

added us to the AUTHORS file

36c3671c6456eb71dc29ebfec1814213bf6d610b authored over 2 years ago by beschorneh32 <[email protected]>

added tests for new function of DecoyDatabase.cpp and changed other tests slightly to fit the new limitations of DecoyDatabase.cpp

bab4ed8d402e7beb4cdaf6f865a6029243cb8903 authored over 2 years ago by beschorneh32 <[email protected]>

added check for already decoy'd inputs to DecoyDatabase.cpp and added some limitations for the allowed decoy_strings, so the decoy_strings are recognised by the check

5c1a48b1e4d582fe5dabf5dd8a09db32cea0b40d authored over 2 years ago by beschorneh32 <[email protected]>

changed interface of FASTAContainer.h so individual parts are accessible

3e4ef060ded5e0b267fc17354475978b0545d674 authored over 2 years ago by beschorneh32 <[email protected]>

added InvalidInput exception

60ad711529e4daf477094da30a8ba4074ac0b635 authored over 2 years ago by beschorneh32 <[email protected]>

Addressing Chris' comments - FLASHIda sort bug fixed.

c7cc12eef4ca917ac65576e9df5ee9a3876ba5d0 authored over 2 years ago by kyowonjeong <[email protected]>

Addressing Chris' comments - FLASHIda sort bug fixed.

7e02b5c89d0d004d1013aa70f6de6ab08f305c5e authored over 2 years ago by kyowonjeong <[email protected]>

Addressing Chris' comments - FLASHIda sort bug fixed.

5e682be0232e2595c22b16a0b8466b6115a9c8a7 authored over 2 years ago by kyowonjeong <[email protected]>

Addressing Chris' comments - charge score bug fixed

4bd95897905f8bb0492d13284a1dba2c17286ab9 authored over 2 years ago by kyowonjeong <[email protected]>

fix for error: enum constant in boolean context [-Werror=int-in-bool-context] (#6035)

5d49de09c8b7d03fa9ef1e7b2efbae05a23f616f authored over 2 years ago by Timo Sachsenberg <[email protected]>

Addressing Chris' comments - charge score bug fixed

51b7a000f3acd21acc9b0d9aa38d1d5865f19c5b authored over 2 years ago by kyowonjeong <[email protected]>