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

FLASHDeconv Only decoy removed with the current version!!

b3b923f190c6892f6e45b3b5ad56cf01ae048d59 authored about 2 years ago by kyowonjeong <[email protected]>
Update DimMapper.h

01daa7d36b1d40fab1c860570070510667757ecc authored about 2 years ago by Timo Sachsenberg <[email protected]>
remove unused method parameter names

3c67d4d141608672f05872f24295fb1f534018a7 authored about 2 years ago by Timo Sachsenberg <[email protected]>
fix compile bug

d1e54885afee35f307850d5dab764ea437da874d authored about 2 years ago by Timo Sachsenberg <[email protected]>
Chris comment has been addressed 3.

5f0bbaf55ebb88a751b047ffc547800fc700c7d3 authored about 2 years ago by kyowonjeong <[email protected]>
Merge remote-tracking branch 'origin/feature/FLASHDeconv' into feature/FLASHDeconvOnly

48152adb7e037b2888b46743fa90cc2d834d6099 authored about 2 years ago by JeeH-K <[email protected]>
Chris comment has been addressed 2.

a5738bbb5b05546a0f29972c42e95b7b6db7796b authored about 2 years ago by kyowonjeong <[email protected]>
Merge pull request #6273 from jpfeuffer/nose2pytest

Switch from nose to pytest

1506bb36aede11e68a038e541b658f61d8cd8c07 authored about 2 years ago by Timo Sachsenberg <[email protected]>
fix UTILS;

add tests;
fix small bugs

9e4a67472e32d28bea69efa1e8113af640ef719d authored about 2 years ago by bielow <[email protected]>
Chris comment has been addressed.

fd9fb35a99798ee2b00712783933139a68a5dc3e authored about 2 years ago by kyowonjeong <[email protected]>
remove unused file

d47a9832d2e1138d03392c5b1f5d4b0eb7008199 authored about 2 years ago by JeeH-K <[email protected]>
add MSPGenericFile

2a6fcf7a7906c97d93362e3b18bcdd9329d34cf3 authored about 2 years ago by Timo Sachsenberg <[email protected]>
revert to the ugly hack.

6cc781903f4bff99116e10ff337e9e01212adad6 authored about 2 years ago by Julianus Pfeuffer <[email protected]>
update peakgroup_test based on the changes

2080bbe5828c5899ef86088b007e4fb7e5c8886d authored about 2 years ago by JeeH-K <[email protected]>
update peakgroup_test based on the changes

eb886bacf7edb55851339016bbac0b31b6dd98d2 authored about 2 years ago by JeeH-K <[email protected]>
Merge remote-tracking branch 'origin/feature/FLASHDeconv' into feature/FLASHDeconvOnly

# Conflicts:
# doc/doxygen/public/TOPP.doxygen
# src/openms/include/OpenMS/ANALYSIS/TOPDOWN/FLAS...

eb8fe86917418a22056da774967a152aefdbc40a authored about 2 years ago by JeeH-K <[email protected]>
fixing year number, typo and tests

8a1a30e42134e1ed039139e81db0d456de7206c8 authored about 2 years ago by JeeH-K <[email protected]>
change messages

61d85286af520e792b007d1450f54f1a29f598ef authored about 2 years ago by Julianus Pfeuffer <[email protected]>
Switch from nose to pytest

dfe38c6a6125a2aea0be754ece5568add6748e00 authored about 2 years ago by Julianus Pfeuffer <[email protected]>
coloring usage

fc632b90058d9976b0dee2e15237d478f4a66ca0 authored about 2 years ago by bielow <[email protected]>
Merge branch 'develop' into feature/flashdeconv

3b2c12d905cac4521f7bf762a348ae47baf6f2a1 authored about 2 years ago by JeeH-K <[email protected]>
more fixes

d5b5365de8eb9b754a271eb04edcc7dfd87f5e45 authored about 2 years ago by bielow <[email protected]>
Merge branch 'develop' into feature/FLASHDeconvOnly

5441ac80a7dda65167e64945816474bc4c173d81 authored about 2 years ago by Timo Sachsenberg <[email protected]>
Merge pull request #6271 from axelwalter/feature/GNPSMetaValues-index

[Feature] Index column for GNPS meta value file

c93665ba0f9cfe42c1e33dbcdf3ff914ae16ac6d authored about 2 years ago by Timo Sachsenberg <[email protected]>
Merge branch 'develop' of https://github.com/OpenMS/OpenMS into ConsoleFun

cedf36f0d30f66a95762be64a62456308c4df4b3 authored about 2 years ago by bielow <[email protected]>
fix log functions

9aeaa89e93da11b10bc36cb04affc4a3cbe0bc51 authored about 2 years ago by bielow <[email protected]>
[FIX] CorrectMZ support for PASEF data

Change CorrectMZ function to be similar to correctIM() such that in
PASEF data, precursors are e...

7a6b444b4f2fc88976a7eaddc207fa1f758706f8 authored about 2 years ago by Joshua <[email protected]>
a first version ...

e4980a0fcd2f5dee09408395094fb49cc320ed1f authored about 2 years ago by bielow <[email protected]>
[NOP] fix spacing

72b68966855e26d0f1ef1cdbfe2b2ad8776565e1 authored about 2 years ago by Joshua <[email protected]>
Merge branch 'develop' into feature/OswImCalibOutput

5f63055c84ccba7bacd5b4fa3246723fc8dec8ba authored about 2 years ago by Timo Sachsenberg <[email protected]>
indent in header row

815d71fc4564bde675eb4c62ea92d4ac63cb2b30 authored about 2 years ago by axelwalter <[email protected]>
update GNPSExport test

1fc0d7407578a1b9624df5b749ed25a6bd0412c8 authored about 2 years ago by axelwalter <[email protected]>
add index column for meta value file

163eaed41e2fa2c0a538949e3b6d2fc0ddc37598 authored about 2 years ago by axelwalter <[email protected]>
[FIX] OpenSwathDecoy exclude too many peptides bug

Previously I added a function to ensure OpenSwathDecoy generator does
not add decoys that are al...

b5658824c8182a0490e2844623bd633edc1c1c24 authored about 2 years ago by Joshua <[email protected]>
[TEST] OpenSwathDecoyTest_5

add to test to ensure decoys of different charge states and same
sequence are not excluded.

b06a19d18d9afb75c2a68e79ea8809e46d19e5e0 authored about 2 years ago by Joshua <[email protected]>
[TEST] add test for PASEF IM irt calibration

Append to OpenSwathWorkflow_23 test to also test that pasef windows can be
correctly assigned in...

5c8402a1f388027563910a5b62e7f6e78d3b4375 authored about 2 years ago by Joshua <[email protected]>
[NOP] format changes for PR

5a66d1356c20a00d0127f721fe366bf73d3779f2 authored about 2 years ago by Joshua <[email protected]>
log sirius stdout for SiriusAdapter tests

2b367eb0c93130fd32fc82dba61d802e9fc33c3c authored about 2 years ago by axelwalter <[email protected]>
merged develop and resolved conflict in SiriusAdapterAlgorithm.cpp

5bd65a4cc36f30af22a6b2719cdd6d4a0705c5aa authored about 2 years ago by axelwalter <[email protected]>
update changelog

54be3454b6c382f52ae300bfdf8df8c716db7487 authored about 2 years ago by Joshua <[email protected]>
[TEST] fix tests with new output

replace output files for tests which now include the new delta_im
parameters

ebff85461cadd75b181e68a6d6ac2ae88b59e639 authored about 2 years ago by Joshua <[email protected]>
Add extra IM output to OSW

add output of delta im (both MS1 and MS2 level) and add IM for both MS1
and MS2

10475cc620935614e25d040cab48627c1af09ede authored about 2 years ago by Joshua <[email protected]>
[FIX] fix swath tests for calibrate IM

2bd0dc66f2f28304359ea3cceb06bfacb93d2e74 authored about 2 years ago by Joshua <[email protected]>
[FIX] IM calibration with PASEF data

Previously IM calibration not working with PASEF data, code thought it
was sonar data. Added fun...

e51f1eb5fbfd58fc5efaaa322e670d34df91850f authored about 2 years ago by Joshua <[email protected]>
[FEATURE] PASEF picking for iRT calibration

Allow iRT peptides to be picked from the SWATH which they are most
centered around with their io...

e5ab3cc16c1d7ad3b63d2846365c561a30cfaf06 authored about 2 years ago by Joshua <[email protected]>
Merge pull request #6265 from tillenglert/fix/MSFragger_PEPmodel_Support

Fix/MSFragger_PEPModel_Support

031a36f3790a8a2fcd9818a2f9414e58bfe720c9 authored about 2 years ago by Julianus Pfeuffer <[email protected]>
Added myself to the Author list

204bb9e25dadd83bd9b4b2ec0459180444390a24 authored about 2 years ago by tillenglert <[email protected]>
fixed downstream support for MSFragger idXML, when using the PEP tool

edb2006aacd33d6c1fff3d72a834812ddefc045f authored about 2 years ago by tillenglert <[email protected]>
Merge branch 'OpenMS:develop' into maxquant-output

ce1a004456f20ed359c944d633ec5a22d413ca88 authored about 2 years ago by Virginia Rossow <[email protected]>
Build version

08e532cb86d443db5153ec9ee7f8265dcc299eac authored about 2 years ago by kyowonjeong <[email protected]>
Bugs in decoy scannumber fixed. Reintroduced charge score threshold of 0.7. Should make a parameter for this

cfde822a6d3846346947ae19885c8390ffc8e35d authored about 2 years ago by kyowonjeong <[email protected]>
small fixes

789ee0c23947708851950d2c279ec6fe167f6dbb authored about 2 years ago by bielow <[email protected]>
fix tutorial

9683e4b1df0956d1ef089f8df7e2a1c4338851d6 authored about 2 years ago by bielow <[email protected]>
Merge branch 'develop' of https://github.com/OpenMS/OpenMS into refact_toppview

# Conflicts:
# contrib
# src/openms/include/OpenMS/KERNEL/DimMapper.h
# src/openms/include/OpenM...

712c663f9d557f7f82e49c31483e4cef337dd551 authored about 2 years ago by bielow <[email protected]>
Update binaries_lnx.ini

re-remove myrimatch binary

2a9ca82b1f043bd930865ea0ee0bf010fb752f73 authored over 2 years ago by Samuel Wein <[email protected]>
Update binaries_win.ini

re-remove myrimatch

e44038a5f8d630e230b9ef35279cde25689d65c8 authored over 2 years ago by Samuel Wein <[email protected]>
Merge pull request #6230 from OpenMS/remove_crux

Crux related parts have been removed. Tested in M1 arm64 machine.

1744153f0ce0faf816ab7760a4c8d96384a932a8 authored over 2 years ago by Samuel Wein <[email protected]>
Merge remote-tracking branch 'upstream/develop' into HEAD

309183a8ff0f3db9ca4fb17dcd54ec11abfc7334 authored over 2 years ago by Samuel Wein <[email protected]>
Merge pull request #6257 from cbielow/prepTV

More preparations for TOPPView refactor

be9861f50ac9c3c68a399bbf83d8d5bc771a8128 authored over 2 years ago by Timo Sachsenberg <[email protected]>
Also expose peptide identification meta values (first one) attached to consensus/feature (#6256)

* add methods to extract peptide id meta values

* export consensus feature meta values of fir...

e1bd67c71643e974841847f2a3214e75e34cc9eb authored over 2 years ago by Timo Sachsenberg <[email protected]>
Crux related parts have been removed. Tested in M1 arm64 machine. Jihyung's comments have beend addressed : revoke pepXML_v122.xsd and just edit "new" for OpenMS 3.0 in CHANGELOG

6b5f08de100ecaf6116a04c7ab8e98972981460f authored over 2 years ago by kyowonjeong <[email protected]>
minor variable name fix

102cc66972faa2688c8b39b68cddffa7d3e1927c authored over 2 years ago by bielow <[email protected]>
fix gcc compile error

5c45589c09c65c050f85f2b5d0c62b43107ffe49 authored over 2 years ago by bielow <[email protected]>
Merge branch 'develop' into feature/FLASHDeconv

6947bc453343724effbe5b0642f6db2ee9ef1dd0 authored over 2 years ago by JeeH-K <[email protected]>
fix include (#6259)

3d9b1cc6c70caaffa12d9bdbd77a2e9aa5326c94 authored over 2 years ago by Samuel Wein <[email protected]>
Codefactor fixes

c02c2a67aa5c151a5d18159c1f8e686b2363dcc2 authored over 2 years ago by bielow <[email protected]>
fix initialization of members

601af94b149dc767a645af654102fa0a228da8ef authored over 2 years ago by bielow <[email protected]>
fix compile errors

1332df94d996bf53d80264231bffcc025ef3a9dd authored over 2 years ago by bielow <[email protected]>
Several sirius fixes (#6255)

* several sirius fixes

* remove obsolete processor parameter

a98ddd68a410e11eefd077d95f01340538a0ba06 authored over 2 years ago by Julianus Pfeuffer <[email protected]>
fix tests

ec0f97110452df1c3c02fec3b3bc1ed9ba53e218 authored over 2 years ago by bielow <[email protected]>
Feature/awesome css (#6243)

* [feature] switched doxygen to use the "Doxygen Awesome" theme

* Change accent color to matc...

ea0316ed72842ff3918dfd393eda323879f7d554 authored over 2 years ago by Samuel Wein <[email protected]>
Two qvalues = w/ w/o isotope errors taking into account have been implemented.

2734c4a4656f123b63f13a2d06040934f2ee6556 authored over 2 years ago by kyowonjeong <[email protected]>
added MobilityPeakTest; made sure Peak2D is trivially copyable/movable

fb1ed96bb9b8a60ca4c7a3a99e91d55ffc24c8e9 authored over 2 years ago by bielow <[email protected]>
extend test for MSExperiment

6f65869bbf0ba2d9358be2c573c810493d85f90a authored over 2 years ago by bielow <[email protected]>
extend DTA2D test

10fcd81305a74004fefbd7635d2ed1ceada7167e authored over 2 years ago by bielow <[email protected]>
augment areaiterator test

6427077f4222f54e4c6a958ab1cff4c06917f39a authored over 2 years ago by bielow <[email protected]>
minor

c41eeadb18ad228e00e14b61962335862680c36c authored over 2 years ago by bielow <[email protected]>
lib files from refact_toppview

6f8b258d6fd757499aabb589459ca73d2a2761ec authored over 2 years ago by bielow <[email protected]>
undo

5f475956adee33e6e21d20e2baad13cd6534c692 authored over 2 years ago by bielow <[email protected]>
Merge branch 'refact_toppview' of https://github.com/cbielow/OpenMS into refact_toppview

e2b27cd9b5df990d099763a8246c369b7474be28 authored over 2 years ago by bielow <[email protected]>
Merge branch 'refact_toppview' of https://github.com/cbielow/OpenMS into refact_toppview

# Conflicts:
# src/openms/include/OpenMS/CHEMISTRY/EnzymaticDigestion.h
# src/openms/include/Ope...

b4222a0000aa54dabefd775dd464ec79f06e06cc authored over 2 years ago by bielow <[email protected]>
Merge branch 'develop' of https://github.com/OpenMS/OpenMS into refact_toppview

91355b37619100f044b6572ee9b85fe8e9228172 authored over 2 years ago by bielow <[email protected]>
Merge pull request #6238 from OpenMS/mztab2stream

MzTab more switches to stream reader/writer

2903ede04322dc4ef94f871cc0c863bcf9f02f5a authored over 2 years ago by Timo Sachsenberg <[email protected]>
Merge branch 'develop' of https://github.com/OpenMS/OpenMS into refact_toppview

fedbfdd879c4b2d45047d799448d0778864a997b authored over 2 years ago by bielow <[email protected]>
Merge branch 'develop' into mztab2stream

59f6110bdcf178933e07504a160ac9518f7bb8b0 authored over 2 years ago by Timo Sachsenberg <[email protected]>
Decoy implmentation done + unionbins removed. + GetCosine bug fixed.

ef8b46d36b29d65ae83ee8a0f9806d03a2c87b86 authored over 2 years ago by kyowonjeong <[email protected]>
merge

8684dfa58e7e49911494c22b1d1bf7d6f348939e authored over 2 years ago by bielow <[email protected]>
Merge branch 'develop' of https://github.com/OpenMS/OpenMS into refact_toppview

# Conflicts:
# contrib
# src/openms/include/OpenMS/DATASTRUCTURES/DPosition.h
# src/openms/inclu...

7259b33eedaf32bef99fcfae28b857246133664e authored over 2 years ago by bielow <[email protected]>
Merge pull request #6254 from OpenMS/fix/GNPSMetaValueFile-pyopenms-test

[Fix] GNPSMetaValueFile pyopenms test

4466c8473a7f3b15467710dbdae03442c0973050 authored over 2 years ago by axelwalter <[email protected]>
ChromLayer, IonMobilityLayer and Painter2D

7f478ab759b11f508413032e9d4bc54a8e599971 authored over 2 years ago by bielow <[email protected]>
Merge branch 'develop' into mztab2stream

62d0170ddeb7ef95ecb187230beb4ad180477e36 authored over 2 years ago by Timo Sachsenberg <[email protected]>
forgot plfq tests

0cf965d8ec4320f8f2955490e19d874353709071 authored over 2 years ago by Timo Sachsenberg <[email protected]>
Update src/pyOpenMS/tests/unittests/test000.py

460c47ed49d5381533da5c9a492cdf656ef46608 authored over 2 years ago by Timo Sachsenberg <[email protected]>
update GNPSMetaValueFile pyopenms test

Added file descriptions with file names to the ConsensusMap. Required for the GNPS meta value file.

98edf66201168fbf0020f33b0b8495b50c2235c8 authored over 2 years ago by axelwalter <[email protected]>
update sirius jar file location for Linux

800ce3e7020178398a0a209f366bcfd254cbdbc5 authored over 2 years ago by axelwalter <[email protected]>
remove PeptideId level meta values from PEP columns

2ff2f30327867e9fe35b13b57e4b6f2c17d1caa0 authored over 2 years ago by Timo Sachsenberg <[email protected]>
Merge pull request #6248 from OpenMS/fix6081

pyopenms test - don't modify existing element (leads to side effects …

9c05ab5c4b451a423e43ca3aa54d9ad66a8c6a10 authored over 2 years ago by Timo Sachsenberg <[email protected]>
Update test000.py

3d5175a972010dfa12100896a2584c797abd162e authored over 2 years ago by Timo Sachsenberg <[email protected]>
Update src/pyOpenMS/tests/unittests/test000.py

b872104c47110c11681fa3cdfa2f6b58d966b287 authored over 2 years ago by Timo Sachsenberg <[email protected]>
Update test000.py

00ba21fa83fb6794561369b85bf68e28f0ef1756 authored over 2 years ago by Timo Sachsenberg <[email protected]>