Ecosyste.ms: OpenCollective

An open API service for software projects hosted on Open Collective.

github.com/OpenMS/OpenMS

The codebase of the OpenMS project
https://github.com/OpenMS/OpenMS

[TEST] disable Python memory leak test

3f0ab02347c3453f64b9e05eb0cf8d4c7c0ad133 authored about 5 years ago by Hannes Roest <[email protected]>
[TEST] add test

8fe65e9c5c9cb79ae3668525ad7bbe0ed7b3f450 authored about 5 years ago by Hannes Roest <[email protected]>
[FIX] allow spectra access as well

8b8e885f2a9f5b55f81d5bc1b93a82835d5a25a5 authored about 5 years ago by Hannes Roest <[email protected]>
[FIX] pyOpenMS fix

9a91ceac3384b33eed0144e05d6b8f01deee4f83 authored about 5 years ago by Hannes Roest <[email protected]>
[DOC] small improvements to IDFileConverter parameter documentation

9b2aafe18b473a615673e9cb86b8a632ee805c7e authored about 5 years ago by Hendrik Weisser <[email protected]>
[FORMAT] registered '.oms' as a file format

2dbe7fe2866a71f151c209575427b710e2453884 authored about 5 years ago by Hendrik Weisser <[email protected]>
Merge pull request #4317 from hendrikweisser/fix-id-coverage

Fix issues with (missing) protein coverage in IdentificationData

5d961be216823625676053b6782fc385ec413c2c authored about 5 years ago by hendrikweisser <[email protected]>
[FIX] fix OnDiscMSExperiment

cf06dde0f02d4679e6a6dbaa686ba343b7805b39 authored about 5 years ago by Hannes Roest <[email protected]>
[FEATURE] get chromatogram by id

d2714626610395bd223116d33bd5158b8ab80260 authored about 5 years ago by Hannes Roest <[email protected]>
[TEST] add test

2738570611233446a5e3f8752d9b4572657b85d3 authored about 5 years ago by Hannes Roest <[email protected]>
[FIX] get spectrum by native id

ae67ef540f26123835bf97be3731d42f91c6849c authored about 5 years ago by Hannes Roest <[email protected]>
[FIX] set native id of spec/chrom

6023e36ece3ec55ca5122aedcbca6389466a1a9d authored about 5 years ago by Hannes Roest <[email protected]>
[FEATURE] SQLite file format for ID data (OMSFile): support for storing and loading molecule-query matches

dda68de7dda0785abb9da75cee2b0c2c12b927cc authored about 5 years ago by Hendrik Weisser <[email protected]>
[INTERNAL] SQLite file format for ID data (OMSFile): store all id'd molecules in one table to simplify referencing

dabc0c007c15b2e4845af7b95cd6b3657ddc26fd authored about 5 years ago by Hendrik Weisser <[email protected]>
disable broken code for now

1680fb5df1e74c17a396ea130b5617d06257c26e authored about 5 years ago by Chris Bielow <[email protected]>
temp workaround; please check if this is really what should happen. It avoids the PRECONDITION in mrmscore_.initializeXCorrMatrix(aligned_mobilograms); for now...

41536f11cad5b0db65fc7a2667d9be9837c72677 authored about 5 years ago by Chris Bielow <[email protected]>
remove pointless checks

7366a11ad52d486ba58f97f95416ce987cff3517 authored about 5 years ago by Chris Bielow <[email protected]>
fix differently sized arrays

485d85e98da119e1bd752050a097ece8645141ad authored about 5 years ago by Chris Bielow <[email protected]>
[FEATURE] SQLite file format for ID data (OMSFile): support for storing and loading id'd compounds

e08c1de672136368293717a98a4447df065a3a67 authored about 5 years ago by Hendrik Weisser <[email protected]>
Merge pull request #4321 from oliveralka/fix/AccurateMassSearch_mztabIsotope

[FIX] AMS mzTab output

9d92d1863dc8cb7c0c8590a54d62da92245ab0d5 authored about 5 years ago by Timo Sachsenberg <[email protected]>
[FEATURE] SQLite file format for ID data (OMSFile): support for loading id'd sequences and their parent matches

75f53ad214197a6cfbaf5019c403233a1da1f535 authored about 5 years ago by Hendrik Weisser <[email protected]>
[feature] Replaced all 0 isotope matrix for TMTtenplex. New values are the mean of all existing (as of Oct 2019) lots.

068d4ec0e9b95b23501d478d1979cd0c5187f950 authored about 5 years ago by poshul <[email protected]>
[FIX] SQLite file format for ID data (OMSFile): preserve score priority and ordering of applied processing steps

6041d10385d664e0e7125637702ff71a2de16fbd authored about 5 years ago by Hendrik Weisser <[email protected]>
Merge pull request #4320 from OpenMS/feature/IDFilter_output

IDFilter output

1796d2e2900bb8be238b870f42aad9ec9e9b41a7 authored about 5 years ago by jpfeuffer <[email protected]>
[feature] updated default isotope distribution matrix. As of late 2019, all the different lots of TMTpro have the exact same isotope correction values, so these are included instead of the previous defaults of all 0.0s

6ea6aa7e503e61777174455fe6565861a2de5401 authored about 5 years ago by poshul <[email protected]>
[FIX] style

b715f318bf6eafc7c4bc292f662da902d22cdf20 authored about 5 years ago by oliveralka <[email protected]>
[FIX] AMS mzTab output; classtest, [Test] add additional test for mzTab/fxml output

69d11f7fb50fe9e33377212a2807c84f30da2d1a authored about 5 years ago by oliveralka <[email protected]>
Merge pull request #4315 from OpenMS/hroest-patch-1

[DOC] small fix

8784e89ba3b7d331eaab6c22ddb7355e796bb50b authored about 5 years ago by Timo Sachsenberg <[email protected]>
IDFilter output

5a5e0ca11fac1998b3010b3431a8127fdaf87305 authored about 5 years ago by Timo Sachsenberg <[email protected]>
Merge pull request #4316 from hendrikweisser/id-score-name

Remove redundant field from IdentificationData::ScoreType

bfb69f61fa6bb877d9e03da7717d4035d7a34c93 authored about 5 years ago by Hannes Roest <[email protected]>
[FEATURE] SQLite file format for ID data (OMSFile): support for storing id'd sequences and their parent matches

dd3051477c9645b37999e5df5fdf7a5165a8485f authored about 5 years ago by Hendrik Weisser <[email protected]>
[NOP] whitespace/style fixes

fa41efdd7464dc71bbebe52b03c38fe704497434 authored about 5 years ago by Hendrik Weisser <[email protected]>
[NOP] whitespace/style fixes

0083f226fc73c2e0876e9f21e753902006231ebb authored about 5 years ago by Hendrik Weisser <[email protected]>
[API] remove redundant 'name' field from class 'IdentificationData::ScoreType' (already has a name in the CV term)

cafc549c369bd090dbb5f0e777d8ba0833238c55 authored about 5 years ago by Hendrik Weisser <[email protected]>
[TEST] updated NucleicAcidSearchEngine tests

b344f8c83906d98aba286957df0f8ed16fd23fa9 authored about 5 years ago by Hendrik Weisser <[email protected]>
[DOC] small fix

ff757bbc658b7131bb67e614d7776f1c76a4369c authored about 5 years ago by Hannes Roest <[email protected]>
Merge pull request #4312 from cbielow/sim_docs

[DOC] documentation update for MSSimulator

d58c4a88bda04563c028e3e26f7a64a008e13135 authored about 5 years ago by Hannes Roest <[email protected]>
[FIX] ID data conversion: fixed handling of unknown protein coverage

e43778ff1f89e1326aa8d1741ac99249cee2a1f0 authored about 5 years ago by Hendrik Weisser <[email protected]>
[FEATURE] added constraints check for coverage to 'IdentificationData::registerParentMolecule'

d0615c2e712da5d18bf40a15da651cd07057a45e authored about 5 years ago by Hendrik Weisser <[email protected]>
[FIX,TEST] ID data conversion: fixed handling of unknown protein coverage (addendum), updated test

ff93cb0396789624a2722d616fcebc19e3d0cf75 authored about 5 years ago by Hendrik Weisser <[email protected]>
Merge branch 'develop' into feature/TDdeconv

45bf823ec40dfd2f398bfff5d44892b84bdc616a authored about 5 years ago by JeeK <[email protected]>
Merge pull request #4310 from oliveralka/fix/fractions_ISO

[FIX] MSstatsConverter MSstatTMT fractions

ecf1a5d4b7a0b56d158b0c4032ae54b766137a5d authored about 5 years ago by Timo Sachsenberg <[email protected]>
fix test

385df3d3781ae8c918927a1d6cbbd9fbc2f15325 authored about 5 years ago by Chris Bielow <[email protected]>
[DOC] add QC tool to docs

b7a30d98e3418686fa1d07480dca42fa9acc025f authored about 5 years ago by Chris Bielow <[email protected]>
[DOC] documentation update for MSSimulator

ef4c05ebc5b16891f80099a8d69ba76da4ee7010 authored about 5 years ago by Chris Bielow <[email protected]>
[TEST] one fraction ISO

df5ad9460cfee588bee7d977bc33d27edfefe98c authored about 5 years ago by oliveralka <[email protected]>
Merge pull request #4309 from oliveralka/fix/error_message_LuciPhorAdapter

[ADD] LuciphorAdapter FileNotFound

51686a3c48e212f87e6d54a2b644857395fd6877 authored about 5 years ago by jpfeuffer <[email protected]>
[FIX] copy/paste; win fail java mem 1024

8bf9f7cf3e7cff2fbd0f8fad41e89f0b6a32e50e authored about 5 years ago by oliveralka <[email protected]>
[TEST] add LuciphorAdapter test

6b499fc30facf0bde30bd3a34ca1fea3cac6d6a9 authored about 5 years ago by oliveralka <[email protected]>
[FIX] space

44fe0d814b6883a0bd30e3138e1abe0010214d3d authored about 5 years ago by oliveralka <[email protected]>
[FIX] Always report fractions for MSstatsTMT

ad69cb70aaf261031b8895d2831fe396c908b778 authored about 5 years ago by oliveralka <[email protected]>
[fix] Removed all boost::list_of uses and replaced with C++11 list syntax

f4c34616f06a2e5f2334c1067fe4e6d691121855 authored about 5 years ago by poshul <[email protected]>
[ADD] FileNotFound Exception for LuciPhor2; [FIX] runExternalProcess_ debug number

02ca3365ff9d3621dde592ae03b580a2b36d63fd authored about 5 years ago by oliveralka <[email protected]>
Merge pull request #4305 from cbielow/sqlite-connector

[FIX] Sqlite connector improvements

1fd89f2ef4532ff4ab3f15d48a23f4ff4abc98d0 authored about 5 years ago by Chris Bielow <[email protected]>
[Fix] Moved default destructor to header files for TMT

89dafc384847bd157cdc3a4a218e11ed4f2e2197 authored about 5 years ago by poshul <[email protected]>
[Fix] C++11ified TMT destructors

c14407861e464c7f227abfed8eec97ad1b1f3edf authored about 5 years ago by poshul <[email protected]>
[feature] removed boost lib dependecy for TMT*QuantitationMethod

b93880bacb25dd27b59607a83e0316abfe6896b6 authored about 5 years ago by poshul <[email protected]>
Merge pull request #4307 from cbielow/fix_TOPPView

[FIX] TOPPView error when running TOPP tool from TMP path with spaces

2ef9cf006d9231c99fd669b22d5be60e328ab91d authored about 5 years ago by Chris Bielow <[email protected]>
Merge branch 'sqlite-connector' of https://github.com/cbielow/OpenMS into sqlite-connector

6e6b05b306ba2113324146e75754f57adca98e5b authored about 5 years ago by Chris Bielow <[email protected]>
strcmp include fix

956d5ceb57ff2bf9f7b9cbce10372fed3c74d4fa authored about 5 years ago by Chris Bielow <[email protected]>
[FIX] fixes bug when running TOPP tool from TOPPView when TEMP path contains spaces on Windows

5f0ededb4506727e6f3de4681642b8efd882a9c0 authored about 5 years ago by Chris Bielow <[email protected]>
[FEATURE] using decreasing Deisotoper model in OPXL

941700347db9f42f7c43ec4ce26870afc2eec9c2 authored about 5 years ago by enetz <[email protected]>
[FIX] corrected Deisotoper parameters in OPXL

f5d452e36e750c9285dfe58d715ceff9c38f9493 authored about 5 years ago by enetz <[email protected]>
Update src/openms/source/ANALYSIS/OPENSWATH/TransitionPQPFile.cpp

Co-Authored-By: Hannes Roest <[email protected]>

c6c16fd60363f43e581e83320fd7e381c9d4ac71 authored about 5 years ago by Chris Bielow <[email protected]>
amend #4280 (undo unsigned char* ctor for OpenMS::String)

e81d4c7472aaa0217c723828583453089b1d81f8 authored about 5 years ago by Chris Bielow <[email protected]>
peak group seg fault for MS2 fixed

b472a7e94c4ec0517abb897a3945f2c2936b4773 authored about 5 years ago by kyowonjeong <[email protected]>
[TEST] adapted SwathQC test

86860378194822d5471cda0d6f777d347bb0ccd1 authored about 5 years ago by enetz <[email protected]>
Merge pull request #4304 from cbielow/develop

Add citation to FF-ID

ab0d9636b89e4ba1d1d7683f27e9bbb321384b0f authored about 5 years ago by Timo Sachsenberg <[email protected]>
follow up on #4296

fb21d030d8fefeb85ee8f54875ea27621534ccb6 authored about 5 years ago by Chris Bielow <[email protected]>
Merge pull request #4302 from jpfeuffer/fix/minorEpifanyFixes

[FIX] Minor fixes for Epifany

27a5b7a3d5967688ea7ff4e21f949b9c5e38f622 authored about 5 years ago by Timo Sachsenberg <[email protected]>
Remove unreferenced proteins. Fix FDR difference calculation for

corner case. Add more tests. Update parameter defaults.
Add debug ifdefs.

Signed-off-by: Julianu...

d2fe1546c1d6819cf72f9123f4bfff6a45283584 authored about 5 years ago by Julianus Pfeuffer <[email protected]>
[fix] added SPW to authors of TMTSixteenPlexQuantitationMethod. Created test for TMTSixteenPlexQuantitationMethod.

0826a8cfdc4461ee19ae76f0313f7968a8b838a8 authored about 5 years ago by poshul <[email protected]>
Merge pull request #4300 from jpfeuffer/feat/notarizeScript

[BUILD] Put notarization into script and wait until approved.

51851d4e6eeca92ae2942ddcb63e95aefe0ceff8 authored about 5 years ago by jpfeuffer <[email protected]>
Merge pull request #4298 from nateglasser/vs2019

Minor changes to allow compiling with Visual Studio 2019

c6a92da763893555eb634d20a5caf596209e178e authored about 5 years ago by Timo Sachsenberg <[email protected]>
Merge pull request #4297 from hroest/feature/msvs_fix

[FIX] fix tests for MSVS after move semantics were added

88b41ff978d97a9a61945f6cf2e3b5833784faae authored about 5 years ago by Hannes Roest <[email protected]>
Put notarization into script and wait until approved.

824be54f5739ba22ef6222f9d5c2de31bd3ece57 authored about 5 years ago by Builder <[email protected]>
[FIX] test fix for MSVS

a9591b53f56944b27fcdc4d146f964be9133ce79 authored about 5 years ago by Hannes Roest <[email protected]>
Minor changes to allow compiling with Visual Studio 2019

d306aca9fe14ff4ada25d94308d5ae3eb9455966 authored about 5 years ago by Nate Glasser <[email protected]>
[fix] removed residue from earlier branch

2d32afe414c299fb63bf3fc37e25a3435de4f226 authored about 5 years ago by poshul <[email protected]>
[fix] fixed CodeFactor whitespace complaint

078517878d04e270a083b193e798985450754558 authored about 5 years ago by poshul <[email protected]>
[feature] Initial TMT 16 plex support

834fd346e8de1bbdc037dd223b4b9b0111ae381d authored about 5 years ago by poshul <[email protected]>
[feature] added correct contents to TMTSixteenPlexQuantitationMethod

f13780d7985c47b29b415b24db15700801750b1a authored about 5 years ago by poshul <[email protected]>
Added new files for TMTpro

d1518ce32a9dae2b6efbc31a60e55ef8f592f9cb authored about 5 years ago by poshul <[email protected]>
Merge pull request #51 from OpenMS/develop

Update from head

94fb87e11307b7f316eb6e4139ec93f591fa33fe authored about 5 years ago by Samuel Wein <[email protected]>
[FEATURE] SQLite file format for ID data (OMSFile): support for loading/storing data queries

e38c2263ced708cc233b3a9bb0767d80645e1c38 authored about 5 years ago by Hendrik Weisser <[email protected]>
[FEATURE] SQLite file format for ID data (OMSFile): support for loading applied processing steps

b9249e41006b81e6f4aad55b71ddf1e397df8e4f authored about 5 years ago by Hendrik Weisser <[email protected]>
memory leak, speed optimized.

aef95b7a50f4b336e88f2ec46d630999ceefba4e authored about 5 years ago by kyowonjeong <[email protected]>
deconv mass trace bug fixed

4091c5eb81de0b7fc511f25cc1d4bc0de648ab19 authored about 5 years ago by kyowonjeong <[email protected]>
[FEATURE] SQLite file format for ID data (OMSFile): support for storing/loading database search parameters

28d7142134a571799e68cee2629460549f6f9cf5 authored about 5 years ago by Hendrik Weisser <[email protected]>
Scoring part separated

931152e7629ca856bbdac7126786b46135812767 authored about 5 years ago by kyowonjeong <[email protected]>
[INTERNAL] SQLite file format for ID data (OMSFile): generalised storing of parent class data via templates

d6eb9c42530ff0e2c925024a438612863121a896 authored about 5 years ago by Hendrik Weisser <[email protected]>
Merge pull request #4286 from OpenMS/hroest-patch-1

Update OpenSwathOSWWriter.cpp

63b88731c8f1553f3cbb11c8024524393f2cb532 authored about 5 years ago by Timo Sachsenberg <[email protected]>
Bug fixed

e4ace68ff254c644fa7a4dc8dc67bc56a594588e authored about 5 years ago by kyowonjeong <[email protected]>
[DOCU] Win req. tools versions

3fc53799771457690d917989179a8f0075a18bc8 authored about 5 years ago by jpfeuffer <[email protected]>
[API] declared String c'tor from 'unsigned char*' as explicit

ddf369dc5df97d70226ce426543919af55999f87 authored about 5 years ago by Hendrik Weisser <[email protected]>
Update add_mac_bundle.cmake

a111aa975c37a21c2e297420df2feacbd827ea30 authored about 5 years ago by jpfeuffer <[email protected]>
Update CMakeLists.txt

04bf420a42f9c55aa67f4e9dd849a68299bf28b7 authored about 5 years ago by jpfeuffer <[email protected]>
[INTERNAL] two more applications of new String c'tor

659752036b6087f011e5f23e3abfdd1da27435b4 authored about 5 years ago by Hendrik Weisser <[email protected]>
[FEATURE] SQLite file format for ID data (OMSFile): support for storing applied steps and scores

6787a709507680c5c8fdc9761e8f222a06b241b2 authored about 5 years ago by Hendrik Weisser <[email protected]>
Merge pull request #4273 from jpfeuffer/fix/gcc48

[Fix] Epifany and gcc4.8

4d8a3ccccbe230160f41f6a50b3dabfa998fa870 authored about 5 years ago by Timo Sachsenberg <[email protected]>