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

Merge pull request #5169 from Waschi97/feature/FMEInterface

Second Compute Function for FragmentMassError

cc53479aceb6f0adebe2178913a24b86fbe538f8 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Merge branch 'feature/FMEInterface' of https://github.com/Waschi97/OpenMS into feature/FMEInterface

merging because of rebase

37234f67834cb5970628e44a96b9e55d64e5534c authored over 3 years ago by Tom Waschischeck <[email protected]>

update QC test files

a9933614b353a6a907cad275efd07b2690751d41 authored over 3 years ago by Tom Waschischeck <[email protected]>

merging develop

3828d7855627b637644715f77181afba70444b4b authored over 3 years ago by Tom Waschischeck <[email protected]>

Merge pull request #5213 from Waschi97/feature/QC/PSMCorrectness

New QC Metric "PSMCorrectness"

541a8af26e0988e07b5179171392436b71a8d629 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

remove const from move ctor of unique_xerces_ptr

#5253

9239bf4d74fc9888b5ea81865ad29f88ebbafa22 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

removed unneeded include & fwd declaration

040b143cbab805812c0837eb159f6f18da6c5a29 authored over 3 years ago by Tom Waschischeck <[email protected]>

amend (#5254)

be4559b3ca07032c6b315fe0b1f8633ce5d4e430 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Update src/openms/source/FORMAT/QcMLFile.cpp

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

d505a3ed58165352007b021262212324f66ba370 authored over 3 years ago by axelwalter <[email protected]>

Update src/utils/QCCalculator.cpp

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

c453eacd453fec8ecf8ae505ecb33bc542f6edf5 authored over 3 years ago by axelwalter <[email protected]>

Update src/openms/source/FORMAT/QcMLFile.cpp

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

19735854116a9bb1a0d0ed5c75c837e2db3a4c0a authored over 3 years ago by axelwalter <[email protected]>

Update MzQCFile.cpp

622e841c2e4de3d543b3d8e11f98fe9fd6b0551a authored over 3 years ago by Timo Sachsenberg <[email protected]>

mass global target rt added

d67113fdd59ff4529e4add8fb46df55ddf700479 authored over 3 years ago by kyowonjeong <[email protected]>

Merge remote-tracking branch 'upstream/develop' into feature/FMEInterface

794aa87fe46c6877849a995d39ac51b17bb2958d authored over 3 years ago by Timo Sachsenberg <[email protected]>

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

07cf39716cf367e5c0bfd1ec93fca5fd0ce57d04 authored over 3 years ago by oliveralka <[email protected]>

add TIC quality metrics

b21eda23d3e5dcf1ae9d91d4b9bded004d9a602c authored over 3 years ago by axelwalter <[email protected]>

Update FeatureFindingMetabo.cpp (#5250)

a6b58bc11539aa52fa686089cf0617a8529b478b authored over 3 years ago by Timo Sachsenberg <[email protected]>

fixed QC topp tests

812389c1d8e22a6b2e0519b850e47e167f482c1a authored over 3 years ago by Tom Waschischeck <[email protected]>

Merge pull request #5248 from OpenMS/timosachsenberg-patch-1

[NOP] Simplify condition in thread check

3ca26ef972757b49248e82b1192a9db15f77eda5 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Update openms-ci.yml

8488430b9689f29820b41e65ff5948c4f692b450 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Merge pull request #5242 from OpenMS/fix/github_actions

Fix/GitHub actions

4752edbd0e10c383f7130735855a852822c08788 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Update PercolatorAdapter.cpp

e3b169d7bc8feb683b46b92fd6822f4b5a483f33 authored over 3 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #5249 from jpfeuffer/fix/mzidParserMem

[Fix] Memory leaks

51945f82ae190e647068a220d016813d678fbd1f authored over 3 years ago by Julianus Pfeuffer <[email protected]>

remove boost dependency in QcMLFile

38aa0e6627ed58e41cf38e1d8b603d5b687da90b authored over 3 years ago by axelwalter <[email protected]>

address issues pointed out by reviewer

3732d7406c423eb3f4fb7eb01dbe5302fe5ea101 authored over 3 years ago by axelwalter <[email protected]>

update thirdparty

fe1ec4774f4f19867ee52700ede1b0db12297295 authored over 3 years ago by Timo Sachsenberg <[email protected]>

add tests for QCCalculator

4e06d464ed0738571370df3c8bd82a053f9b6887 authored over 3 years ago by axelwalter <[email protected]>

Dllapi?

f16e3379e3ae97e762b29921fff2aa44238fbb01 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

mass global target rt added

eae5fde4e1cbd53efe2668d16828321df4a22ab7 authored over 3 years ago by kyowonjeong <[email protected]>

mass global target rt added

7c6d0b20b78ebcc4adf8ae3532e56a181079288a authored over 3 years ago by kyowonjeong <[email protected]>

gcc includes and tests

ba8f79d74c9a22608e816e5acdacf54c863e7cd7 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

gcc

80f2d6bb406147ad7b541faf46aa162f4fdf3c25 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

include?

acd59caa0e47f84b21f08067a7439d7c3bd5c3e9 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

fix

ca5dd4cb4a9c31393ad43e701f8bd49f547d451e authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Merge pull request #5238 from jpfeuffer/feature/mzTabExportAllPsms

[FEATURE] Allow exporting all PSMs to mzTab (ID-only for now)

204aa3e85b09ef8bef98fc4da1277968bc223e08 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

TP............

caf2e6162f6ebf3ad2caae059050c5d74974d9b6 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

fix

585b9598e7e0a327da6409e26a085b4d08099308 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

comment

4706e23bd15ebc3f943154e17caaa2be8dfdb748 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

[FIX] Some fixes an unique_ptr introductions

e51efa231ae09eee739fb2bc6e232fdef480f770 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Var

b73e1761ad3383e1d68cb5c605d859a5280d0e4b authored over 3 years ago by Julianus Pfeuffer <[email protected]>

merge

c57349d7184dd7b9ea12adf36b50b4fbe523d375 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

[FIX] Memory Leaks

733d2dfd609527310c178d6d69206fb65415e04f authored over 3 years ago by Julianus Pfeuffer <[email protected]>

[FIX] Make ProgressLogger destructor virtual (#5247)

d68d651236227f036fbb0c4bda9816f66bc1cd33 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

[FEATURE] Allow exporting all PSMs to mzTab (ID-only for now)

0ed740fc394f54fc9b49a3ec26c343925546275a authored over 3 years ago by Julianus Pfeuffer <[email protected]>

[FEATURE] Add OpenMSDatabasesInfo Util to list supported Enzymes and Mods in tsv.

909ba588d093c0d8b0335062ed7f1d5b39a1b1aa authored over 3 years ago by Julianus Pfeuffer <[email protected]>

forgot commit CMakelists

7aa12e73e4d5c10eedb80dab6515794d1b57fa6e authored over 3 years ago by Julianus Pfeuffer <[email protected]>

allow consensusXML with all psms and doc fixes

a54d827db0d05fdca3caddd5bbe9167d8dd8561f authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Fix and make safer?

2c7b52eaf16fd9a7584f99cacfcfda75b553b643 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Update PercolatorAdapter.cpp version number (merge after THIRDPARTY update) (#5246)

* Update PercolatorAdapter.cpp

* pass threads parameter

* Update PercolatorAdapter.cpp

...

94e39d3c0de23fde356b409b72783d5ba18be13d authored over 3 years ago by Timo Sachsenberg <[email protected]>

FME test updated

fab4eb0ba8d4b4d720575a202ea9c56fe22ccb12 authored over 3 years ago by Tom Waschischeck <[email protected]>

matching spec not ms2 error message changed

770c835d381332a3741a877975ead38aa5aafddc authored over 3 years ago by Tom Waschischeck <[email protected]>

rename metavalue variable in Constants, docu

844935e3cf03bb8d338beda09e4e2bd24812d3e0 authored over 3 years ago by Tom Waschischeck <[email protected]>

private functions, potential seq fault prevented

86fb136278b8032001dcd5a8f9efec47e1c75d2d authored over 3 years ago by Tom Waschischeck <[email protected]>

typo

3590fcf18d7841e424b73b34b12c51708e16cdbe authored over 3 years ago by Tom Waschischeck <[email protected]>

QC test files with new metavalue name

a027ea9fbee5209417265dcffa68053b8bce1af3 authored over 3 years ago by Tom Waschischeck <[email protected]>

TSG: precursor charge set to 2 if 0 is given

e33d06442bbbcb2b0bc75d1c004d919da99eff0a authored over 3 years ago by Tom Waschischeck <[email protected]>

private function to annotate PSMEIC, metavalue rename, docu

3fe417f5a7b6117cc64ff96d750fe1ee193c1e54 authored over 3 years ago by Tom Waschischeck <[email protected]>

add additional peakfiletypes in TOPPView (#5240)

* add additional file types to TOPPView

* fix compile error

* add some doc and MSP support...

3b91dfe897e794546e1a0c984c4d6e36317c0c1f authored over 3 years ago by Timo Sachsenberg <[email protected]>

[nop] added a short description to Enzymes_RNA.xml

ba8918f7c076921b856d9f744734fb7cf4f48273 authored over 3 years ago by Samuel Wein <[email protected]>

Forgot to consider labels for labelled designs. Added tests.

97413fb5f43e5df7e0c8e163e3e755feefe503cb authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Update THIRDPARTY

0b5820dfc9b5b5dc467900ccf03a3257597a9e1d authored over 3 years ago by oliveralka <[email protected]>

Update openms-ci.yml

112432325162eccf7922770ee836b434958a5a77 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Update cibuild.cmake

bf556080f1e11600fa742fc9fbd77d650809c3a3 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Update cibuild.cmake

4f0f9a440b95712e7767014d2782d22d6a1a71f8 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

[HOTFIX] Array OOB

1468c9c3514448e60e51a06ae0986c5e8878713c authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Merge branch 'idfile-integration' into fix/hendrik_idfile_integration

e5a553c8a6029c3d29fd54d7e7a5e7717b4409e0 authored over 3 years ago by hendrikweisser <[email protected]>

[FIX,TEST] fixed 'FFIdAlgo::extractTargetID_' for ref. strings with '#' (multiple RT regions); added test

f06ba216da1f30ff239212609f25499dd7ebaa44 authored over 3 years ago by Hendrik Weisser <[email protected]>

[fix] Added missing virtual deconstructor to SiriusAdapterAlgorithm (#5244)

213daa4b6ca61d0eb0a0e02eb19c5a594a588c95 authored over 3 years ago by David Voigt <[email protected]>

Update cibuild.cmake

cf3e0df199c542cd1faa7004e1c1e0b0871f682c authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Update cibuild.cmake

637469ea086b6acc00bb928778601f507561bd80 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

cleanup

d3c7f41835a6bf35d087e8460f89e0582281bedb authored over 3 years ago by oliveralka <[email protected]>

use add_compile_options

1c29d9efce24f7a83ca07433411d40c9703f350e authored over 3 years ago by Julianus Pfeuffer <[email protected]>

disable optimization

2cdd0c5a6b795380a65887cd6647b21ee8b03ddd authored over 3 years ago by Julianus Pfeuffer <[email protected]>

revert to release on win

d1f44e935fcee2bccfd36c0a4678b18034983da6 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Detailed summary too slow

43188e2e6c75540ceb6dc39dc0dd2fe4636af225 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

[Fix] plfq cornercases and exp. design checks (#5243)

* [FIX] check experimental design more thoroughly and avoid unnecessary work in plfq for single ...

b486f77a3bdfc4d5d1f1efc528c47b687acd6f07 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Update openms-ci.yml

2b7f39621a91e2d79fddb475f309881d3d30072e authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Add detailed summary and Multiproject compilation on win

fd858ec4b3d70c1b7c746c818d865c4cd6205908 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

mass global target rt added

466c0dbbf35fc51b239ed87a32013449120cf10d authored over 3 years ago by kyowonjeong <[email protected]>

Merge pull request #5239 from jpfeuffer/feature/OpenMSModEnzInfo

[FEATURE] Add OpenMSDatabasesInfo Util to list supported Enzymes and Mods in tsv

ee508d9cc033c9ca2c4372967fac4d7cd7c8d78f authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Use the nr threads from the official GH actions docu

6b820de7823d0c2bae943d4decac916368551123 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

[FIX] Remove unnecessary CMAKE_FIND_LIBRARY_SUFFIXES

The suffixes we set were the default anyway and with BigSur, macOS switched to dylib stubs (.tbd...

045f51610423cce93da3a151da3f44912dd922da authored over 3 years ago by Julianus Pfeuffer <[email protected]>

mass global target rt added

dd06a665d2009f2064930ef2fa1371e8d00749f4 authored over 3 years ago by kyowonjeong <[email protected]>

return val

39d6370e1c3230a1448fd3b756c9257f073ba486 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

mass global target rt added

f1495e372a2ffd0b9ee875a3f4bb0f4ce4770dde authored over 3 years ago by kyowonjeong <[email protected]>

mass overlap bug (no log binnumber) fixed.

25ed76e8a0f8a1e75f277ca19cd3c74aea8f96c1 authored over 3 years ago by kyowonjeong <[email protected]>

Update src/openms/include/OpenMS/CHEMISTRY/ModificationsDB.h

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

43e780fb3378d8964c7c5818b5a3b2af9971eb4c authored over 3 years ago by Julianus Pfeuffer <[email protected]>

tsv changes

071ad797074829a245abf61ddd0d10851363d213 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

mass overlap bug (no log binnumber) fixed.

2a3f16b742682c16ebebeb4dcb71ac6e4b2be86a authored over 3 years ago by kyowonjeong <[email protected]>

use cmake action since everything else is crap

7f4c52ce1c9e1e943782c34517c592632831c97a authored over 3 years ago by Julianus Pfeuffer <[email protected]>

mass overlap bug (no log binnumber) fixed.

4c1d83fda204cf17c0d7851f532f0bbfebb1d89a authored over 3 years ago by kyowonjeong <[email protected]>

Update openms-ci.yml

02d4c0a34e833ce20c4d2602adef4d7e794e79c9 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

CMAKE_DIR

7a8f11cdb2523e7967598678fd5c6d808a1d61c9 authored over 3 years ago by Leon Bichmann <[email protected]>

CMAKE_DIR

9f35ca6dfeb96df2f2be99607dbb40166b276c6a authored over 3 years ago by Leon Bichmann <[email protected]>

chocolatey already installed + bash syntax

c398c95969022dcf362b75fbba8813000706b25d authored over 3 years ago by Leon Bichmann <[email protected]>

FLASHIda global target

8dc8e89049fe17dec907dbccf16a193d577479b3 authored over 3 years ago by kyowonjeong <[email protected]>

FLASHIda global target

be775fb52cf8229c4a08588072a3a4c94a2c60b2 authored over 3 years ago by kyowonjeong <[email protected]>

FLASHIda global target

4e74f9c7e12874baa1f0c84258c8383852ea8d8f authored over 3 years ago by kyowonjeong <[email protected]>

FLASHIda global target

a3eefb51b9508fec4cebff0de8711838b1250f51 authored over 3 years ago by kyowonjeong <[email protected]>

FLASHIda global target

738056c832b8672469db09b17dbcbb22b72ada4f authored over 3 years ago by kyowonjeong <[email protected]>