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

[DOC] minor doc improvement

[NOOP] minor code improvements

bd5e8d0160ea62c12ad70d72505ee34e0de67c20 authored about 6 years ago by Chris Bielow <[email protected]>

refactor: avoid pointers and arrays

156a4dfe4c6482230a15090b55140dee1cc6f6fd authored about 6 years ago by Pasquale Domenico Colaianni <[email protected]>

Fix wrong macro names

97a8d1a61ad3a42581919a7ca420ef331e4d768a authored about 6 years ago by michalsta <[email protected]>

[nop] documentation for NASequence

81d17aa8fdbd274eaaca400e30262efc30795f58 authored about 6 years ago by poshul <[email protected]>

Updated maintainer

d7467c204cd685f6deb2c12b20ca2d6040cec83d authored about 6 years ago by Julianus Pfeuffer <[email protected]>

Added small multithreading test to see if OMP is correctly active.

e0056851bc9bf9820c2231530b9c6912aa827cc9 authored about 6 years ago by Julianus Pfeuffer <[email protected]>

test: use correct macros according to types involved

0f1eb08c31091346fe213020bcf482566ffbe9c1 authored about 6 years ago by Pasquale Domenico Colaianni <[email protected]>

pragma once

890d08f124a54b99ecd9d521d19a0b182231775f authored about 6 years ago by Pasquale Domenico Colaianni <[email protected]>

Merge branch 'develop' into feature/MRMFeatureSelector

e5ad96f3553de81276b89ceace61feed69d9dc97 authored about 6 years ago by Pasquale Domenico Colaianni <[email protected]>

style: C++11

dd15666be59275c92a30162cab09c209e1c052c6 authored about 6 years ago by Svetlana <[email protected]>

feat: output filtered features

1813d88cdd5dd71999fd01278f51ca4ffa93fa09 authored about 6 years ago by Svetlana <[email protected]>

feat: score optimize function

8519cea1d3bc0cf326b2742ff8b89582ec1e7615 authored about 6 years ago by Svetlana <[email protected]>

feat: optimize score, correct objective

22d5e67cfab83816719a703076756c4a0dcbe8ef authored about 6 years ago by Svetlana <[email protected]>

feat: coin-or solver - get solution

afd51d04fec1919062cfeafb1de57d675e660c81 authored about 6 years ago by Svetlana <[email protected]>

feat: coin-or solver

860b867f3f9e65923ac42e5e458a5f41ccfda623 authored about 6 years ago by Svetlana <[email protected]>

feat: fix MILP problem

aa2ead392a7627aea926d0dd85ecf3fb102bf147 authored about 6 years ago by Svetlana <[email protected]>

feat: MRMFeatureSelector, start

b66bc73881871d2fe8596062e20efb943f8b7f88 authored about 6 years ago by Svetlana <[email protected]>

[FIX] enum -> enum class; Type CopyOptions

3430029cdb922ffa3effec97febbe7c6536d7184 authored about 6 years ago by oliveralka <[email protected]>

Merge branch 'fix/SiriusAdapterWorkspaceOutput' of https://github.com/oliveralka/OpenMS into fix/SiriusAdapterWorkspaceOutput

Conflicts:
src/openms/include/OpenMS/SYSTEM/File.h
src/openms/source/SYSTEM/File.cpp

f94144a6a670c85292bbfda772d59c383610e071 authored about 6 years ago by oliveralka <[email protected]>

[ADD] enum copy_options, boolean, switch,case, further tests

84b6a314e2dcb5992712b4789736268d10e00864 authored about 6 years ago by oliveralka <[email protected]>

Pull in IsoSpec v1.9.0alpha3

60a993a1092ed6faaf5c80a5ad10dfb446a1fcda authored about 6 years ago by michalsta <[email protected]>

Merge branch 'develop' of https://github.com/michalsta/OpenMS into develop

6877500762734e422744320eafd99ed120963e4d authored about 6 years ago by michalsta <[email protected]>

Delete mman.c

f4e2e239a44503cf405c034540f262cd880bff3c authored about 6 years ago by Hannes Roest <[email protected]>

Delete mman.h

177e13c738aab0b8930836870e93d9b1a1bfa7ab authored about 6 years ago by Hannes Roest <[email protected]>

Bring IsoSpec implementation up to d41e5f89924d12518e0c96904baa88edac37c667

250a78a0661d3115975d4a2aba34584e5df612c7 authored about 6 years ago by michalsta <[email protected]>

Rename IsoSpec class to IsoSpecWrapper to avoid name clashes with IsoSpec namespace

070d7671dfc7bfd14215da6e83283df006a69b16 authored about 6 years ago by michalsta <[email protected]>

Rename the IsoSpec.cpp/.h files to IsoSpecWrapper.cpp/.h to match the name of classes inside

01c12d8ee0d3e371c3f41004402c7ef767c79aa7 authored about 6 years ago by michalsta <[email protected]>

Comment out Ordered and Layered for now; remove tabulators

64c02ec3c29fbce7a5c78357b2ffbf3ee25a46ae authored about 6 years ago by michalsta <[email protected]>

FIX

b7530656b825ebf27ab0960ead0caf65de9931a6 authored about 6 years ago by Hannes Roest <[email protected]>

Update isoMath.cpp

7831d2065ce025d50469d108af07ab9f067e8abf authored about 6 years ago by Hannes Roest <[email protected]>

Update IsoSpecWrapper.cpp

b6047f33f8f0b984cd13f4da4a8d0a9f789f0550 authored about 6 years ago by Hannes Roest <[email protected]>

[fix] tolled back IdentificationData move constructor default, which didn't work with CLang

d00387ffdf6ddecb7e6afbf049c3f0330ec56ce1 authored about 6 years ago by poshul <[email protected]>

[FIX] Fix issue mentioned in comment https://github.com/OpenMS/OpenMS/pull/3780#discussion_r223198483

74a050cd044d8ba15f98708ff5cd1ee89395e580 authored about 6 years ago by michalsta <[email protected]>

Avoid some memory copies by having IsoSpec generate right into a vector<Peak1D>

b1f4b6da6c964346be5156a079fb2abc7a807d41 authored about 6 years ago by michalsta <[email protected]>

Pull a bugfix from main IsoSpec repo

ce29e4589fa6b5f47895f70f09871dfa0c11939a authored about 6 years ago by michalsta <[email protected]>

[FIX] fix memleak

7d5e824572cf05dfc9bc9906b90e060277643a6e authored about 6 years ago by Hannes Roest <[email protected]>

[TEST] fix test

565cde463aa4dddb9252370783c8386e31cd543a authored about 6 years ago by Hannes Roest <[email protected]>

[nop] clarified doxygen comments

f17f6454e95fdc3c34303dfef315f91424f847f7 authored about 6 years ago by poshul <[email protected]>

Merge branch 'poshul/hendrikweisser-rna-ms2-id' of ssh://github.com/poshul/OpenMS into poshul/hendrikweisser-rna-ms2-id

d5dc4c3a3de95d255ef1602e799ac6c49bc8f138 authored about 6 years ago by poshul <[email protected]>

[nop] fixed more documentation strings

af717602cd1ccaf95e0323eaab061074c0b6c4ca authored about 6 years ago by poshul <[email protected]>

[nop] fixed some documentation strings

8c366d36eb40eac8b31be158f23c5d944b5a7a45 authored about 6 years ago by poshul <[email protected]>

Merge branch 'develop' into poshul/hendrikweisser-rna-ms2-id

f4837f7dd3dbb12b2a6af184fe733ae489e74ae8 authored about 6 years ago by Samuel W <[email protected]>

Merge pull request #39 from hendrikweisser/rna-ms2-id

Addressed reviewer comments in OpenMS PR #3746

8284d36331cee3905f12717ba88a38ca1ad47a97 authored about 6 years ago by Samuel W <[email protected]>

Merge branch 'poshul/hendrikweisser-rna-ms2-id' into rna-ms2-id

ca53fa1dcc56e896d9714ac3b18e8536d38b0180 authored about 6 years ago by Samuel W <[email protected]>

Merge remote-tracking branch 'origin' into refactor/AssayGeneratorMetabo

a23f0074f6dafec3573e4a3a2e98d39c86dcef4b authored about 6 years ago by oliveralka <[email protected]>

[Test] remove concatenate for adducts

23fc5b661ceea921062827d83b46e6f311d04153 authored about 6 years ago by oliveralka <[email protected]>

[FIX,TEST] fixed copy-paste errors in test signatures in 'IdentificationData_test'

902f39d624911e99c933cc317d6459a1a587f2b9 authored about 6 years ago by Hendrik Weisser <[email protected]>

Merge remote-tracking branch 'origin/develop' into fix/SiriusAdapterWorkspaceOutput

9bf5d7c4b98468d7e66a36ec0317cd9a70a02696 authored about 6 years ago by oliveralka <[email protected]>

[INTERNAL] simplify code by using range-based for loop in 'IdentificationDataConverter::exportIDs'

f86e33621ac460728a86294b87c5674d1b26415b authored about 6 years ago by Hendrik Weisser <[email protected]>

Merge pull request #3797 from oliveralka/update/SiriusAdapter_4.0.1

[UPDATE] SiriusAdapter (with SIRIUS 4.0.1)

254d260d242cf47f369e53d853cf9dcce1add840 authored about 6 years ago by jpfeuffer <[email protected]>

[FIX] check before accessing elements in a potentially empty string (in 'IdentificationDataConverter::exportIDs')

cdfd0b37910596c0819d6b2db2149e816439d412 authored about 6 years ago by Hendrik Weisser <[email protected]>

[INTERNAL] use default move c'tor for class 'IdentificationData' (removed implementation)

e17af90ce3a8bae6da5fb6f8ded66cd0050301e2 authored about 6 years ago by Hendrik Weisser <[email protected]>

[fix] updated Software.h and Software.cpp

d4c969bc90fa93a5de005755b74aab29002cd738 authored about 6 years ago by poshul <[email protected]>

[FEATURE] Updated OpenMP inclusion to modern target based CMake to simplify macOS support for OMP

7307544a5a60e1ec267b7114cb562a5601fdc2b0 authored about 6 years ago by Julianus Pfeuffer <[email protected]>

Merge pull request #3795 from jpfeuffer/fix/knime_linux_package

[Fix] knime linux package

5d0557dcb7a074c41df660002f6375db07aeabd8 authored about 6 years ago by jpfeuffer <[email protected]>

[ADD] updated THIRDPARTY

a77e6ae96a4d9660667587a7ab947012ddf908b3 authored about 6 years ago by oliveralka <[email protected]>

[TEST] fix tests for SIRIUS 4.0.1

0942f7f5f85634f24eac45b9193034726e5a2c5c authored about 6 years ago by oliveralka <[email protected]>

[FIX] removed unnecessary includes in 'IdentificationData' header file

d84750c34571b6f963f3639a36a0300375931994 authored about 6 years ago by Hendrik Weisser <[email protected]>

[INTERNAL] declared static member variables in class 'MoleculeParentMatch' as 'constexpr' to eventually allow odr-use (C++17)

b18259df7f4b3a59db28910d67945ee1f8d76cc4 authored about 6 years ago by Hendrik Weisser <[email protected]>

update contrib

45966221506166a36296e9308099a40ed38fc1ff authored about 6 years ago by timosachsenberg <[email protected]>

Merge pull request #38 from hendrikweisser/rna-ms2-id

Added tests for the remaining public methods of 'IdentificationData'

160d3f5b4f14b79810f1060df7b4e5bcdf28b403 authored about 6 years ago by Samuel W <[email protected]>

[UPDATE] VersionNumber

6836e7d2742151e8744a2e746d76aa954b11dc71 authored about 6 years ago by oliveralka <[email protected]>

Merge branch 'fix/knime_linux_package' of https://github.com/jpfeuffer/OpenMS into fix/knime_linux_package

6b1f05e34a0afb0852fbd958d7644a418be9620a authored about 6 years ago by jpfeuffer <[email protected]>

Also added libz and libbz

21fd4f8978b60af039122825f24ef1abc09ab9e6 authored about 6 years ago by jpfeuffer <[email protected]>

[TEST] completed tests for class 'IdentificationData'

b925f8a27baab95b3c1ceb125c5c26e244d06fdc authored about 6 years ago by Hendrik Weisser <[email protected]>

[INTERNAL] initialize static member variables of class 'MoleculeParentMatch' in the header file

0201eac693c6bb3d9d3f1d3fac8857b0039211a5 authored about 6 years ago by Hendrik Weisser <[email protected]>

[DOC] extended documentation for 'IdentificationData::cleanup'

f3899f60f1a8ce0e2330cd6520955ced3cacd250 authored about 6 years ago by Hendrik Weisser <[email protected]>

copy paste error

2ef126165af06b037ded155c4776a175a4762397 authored about 6 years ago by jpfeuffer <[email protected]>

Fixes for KNIME packaging. Shipping every non-system lib now.

a53dbf9f1acb3abadcfbe726fffe349a3ab05de2 authored about 6 years ago by jpfeuffer <[email protected]>

Merge pull request #3794 from hendrikweisser/ffid-debug-log

Small logging improvement in FeatureFinderIdentification

2e4bcee0a16204b872621441c51b13f424e218ff authored about 6 years ago by Hannes Roest <[email protected]>

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

b33b93a3a87c8206896f10f3c20ec5a9fbb2a1ea authored about 6 years ago by enetz <[email protected]>

[LOG] FeatureFinderIdentification: show output from OpenSWATH feature detection when in debug mode

ee0f67d47f1de0e4844b1220136ac852314886c2 authored about 6 years ago by Hendrik Weisser <[email protected]>

Moved file into correct subfolder

c6e62f793cbf893267d33981d0ff84ffe1496800 authored about 6 years ago by jpfeuffer <[email protected]>

Forgot to add mini script

28c0a4a82159533cf7bc01ad613585228e1cfb3e authored about 6 years ago by jpfeuffer <[email protected]>

Update File.h

more doc

271836f0b2c8c5e8a20429970f5d368966a63db3 authored about 6 years ago by Chris Bielow <[email protected]>

Update File.cpp

92ee5a3755d11cf58a7cb3274fa16218e91fb24d authored about 6 years ago by Chris Bielow <[email protected]>

Update File.h

fix doc

bbc778ec94d6623984e6bb87c857a403eabbbb99 authored about 6 years ago by Chris Bielow <[email protected]>

[FIX] naming, review

22f8bba434a2ee5f1b90bc959c0c5b7500c56c83 authored about 6 years ago by oliveralka <[email protected]>

Delete mman.h

25010f22b55a93180ee622b9bf1135e44b07484c authored about 6 years ago by Hannes Roest <[email protected]>

Delete mman.c

2f2a0def080abd2d9fa3584378a3fca674532cd1 authored about 6 years ago by Hannes Roest <[email protected]>

FIX

bf6bb70357f4acd9cb8d0b0fccf78c7c0839821f authored about 6 years ago by Hannes Roest <[email protected]>

[fix] Fixed error in IdentificationData_test

1a83be4071ab1d232960b037e6897be932b6db9e authored about 6 years ago by poshul <[email protected]>

Merge pull request #37 from hendrikweisser/rna-ms2-id

Documentation for class IdentificationData

06af421a1b64be76fbd2113a2011333493050bef authored about 6 years ago by Samuel W <[email protected]>

[FEATURE] new model with balanced XL/non-XL training set

2c8523e477149eedf23109177b3b88ecc870c54f authored about 6 years ago by timosachsenberg <[email protected]>

[DOC] finished (?) documentation of class 'IdentificationData'

4d66c51c462f500152657f19857110e43c209c47 authored about 6 years ago by Hendrik Weisser <[email protected]>

Update MacrosTest.h

e0928c950fef0801595552b438dc33d30c15aacb authored about 6 years ago by Hannes Roest <[email protected]>

Comment out Ordered and Layered for now; remove tabulators

6615c6492d81b33696d2643c243780085b3ec3b2 authored about 6 years ago by michalsta <[email protected]>

[DOC] more documentation for class 'IdentificationData' (work in progress)

6f53a3d59a5d8933c0af2eb2d39929f75fa0b4b9 authored about 6 years ago by Hendrik Weisser <[email protected]>

Update MetaboliteSpectralMatching.pxd

4c4b530ba94e02cd493f34f57b6fe6dbf54576b3 authored about 6 years ago by Hannes Roest <[email protected]>

Merge branch 'poshul/hendrikweisser-rna-ms2-id' of ssh://github.com/poshul/OpenMS into poshul/hendrikweisser-rna-ms2-id

8dfc539fc65698cc382a90e7a451655b714b009f authored about 6 years ago by poshul <[email protected]>

[fix] reverted changes which did not fix windows compile problem

29396b67ae52c5a47a5f5d606c70acf50200ebcc authored about 6 years ago by poshul <[email protected]>

Update IsoSpecWrapper.cpp

c985e2e6fbdf362e20678e71f3e5ff102f384dfa authored about 6 years ago by Hannes Roest <[email protected]>

Update isoMath.cpp

a470c900569ebff2cbe3d217eb6dd12c9496a873 authored about 6 years ago by Hannes Roest <[email protected]>

Merge pull request #3776 from jpfeuffer/fix/linux_package

[Fix/Rework] debian linux package

f6e0426b3dfd8c41b71a8c1feca6e4b00bce809f authored about 6 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #3786 from cbielow/JSON

[FEATURE] add json library as third-party include

86ec1ed77529d4094b4320d316803b53e7803ab8 authored about 6 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #3790 from hroest/feature/TDDescription

Feature/td description

4c5e4f50108349d7b4bc94ca1f76f961ec8c0c74 authored about 6 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #3768 from lars20070/fix/FFM_performance

performance improvements for FeatureFinderMultiplex

2ba75c3f8f71c8c828003325e98539490e26568e authored about 6 years ago by Lars Nilse <[email protected]>

Merge pull request #3784 from jpfeuffer/update/contrib

Updated contrib to head of master.

664534c59898750f43deaf7f8e97ac1c40c069ab authored about 6 years ago by Hannes Roest <[email protected]>

Update MetaboliteSpectralMatching.pxd

71b5ea6234511ef5dbc14e475f0609f1b93c258a authored about 6 years ago by Hannes Roest <[email protected]>

expose method

628e61c93124d59bddc9bcdde4d883eba7901aa2 authored about 6 years ago by Hannes Roest <[email protected]>