Ecosyste.ms: OpenCollective

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

github.com/OpenMS/OpenMS-1

The codebase of the OpenMS project
https://github.com/OpenMS/OpenMS-1

FLASHDeconv ver 2.0 beta -

42d33122af0d0380a43d70184becc4bdef05440b authored over 3 years ago by kyowonjeong <[email protected]>
FLASHDeconv ver 2.0 beta -

d82725b3296ef6d895b0a729cd23e17ae0e35aca authored over 3 years ago by kyowonjeong <[email protected]>
Merge pull request #5185 from Waschi97/develop

Updated Contrib Submodule Commit

25cd676614a44910ca06b91bdb2afd589f49409e authored over 3 years ago by Julianus Pfeuffer <[email protected]>
[FIX] FeatureFinderIdentification: fixed counting of internal/seed-based IDs (for summary statistics)

740c60daa0fa30e4825146df00c0f037f021987b authored over 3 years ago by Hendrik Weisser <[email protected]>
TOPPic output structure added

2cab324a139d6e449064a8669b8f5905222fb817 authored over 3 years ago by kyowonjeong <[email protected]>
updated contrib submodule commit

5bd5b571423f62152e1fda36b8354c15a28a84fb authored over 3 years ago by Tom Waschischeck <[email protected]>
Merge pull request #4922 from OpenMS/pyopenms3

Some tries to build pyopenms with language_level=3

492c5bd05923a68c2aa8d57ea8068977a912ba08 authored over 3 years ago by Julianus Pfeuffer <[email protected]>
FLASHIdaBridgeFunctions.cpp modified so it outputs color, intensities.

7d3214e0ec7df56653c7e21278ecc849ac100090 authored over 3 years ago by kyowonjeong <[email protected]>
Update ADD_TO_ALL_OTHER.pyx

8e27d0b8d0f0a884863bfbc99a8c1bb600ea5382 authored over 3 years ago by Julianus Pfeuffer <[email protected]>
Update setup.py

ab343f6c3e4aa79636529469173073c64dd5cb12 authored over 3 years ago by Julianus Pfeuffer <[email protected]>
Remove include die from cython

6b167bf84272ad8c0a484829ca4cdabe9417cfee authored over 3 years ago by Julianus Pfeuffer <[email protected]>
Adapt include does?

99ff5123fc2158febb4adbed92270e0c1fc1b59a authored over 3 years ago by Julianus Pfeuffer <[email protected]>
Add new autowrap flag for relative imports

0263c574c84e6d3d6e78300006b03e216703fecd authored over 3 years ago by Julianus Pfeuffer <[email protected]>
FLASH Ida bug (overlapping nominal mass results in incorrect colors) fixed.. print out color requency..

85e763e57f1f8a3f4c1c26a4a8153cd0a3cdec4d authored over 3 years ago by kyowonjeong <[email protected]>
[FEATURE] converted FeatureFinderIdentification to use new IdentificationData members in Feature[Map] (work in progress)

37714c5855733ec539a686919b46eaf43a0c269d authored over 3 years ago by Hendrik Weisser <[email protected]>
[FEATURE] IdentificationData: improved 'RefTranslator' subclass

6f3bd83feb8eed783a52d50f271011bfb4db8b71 authored over 3 years ago by Hendrik Weisser <[email protected]>
docu & FME test

03a6798833cdd1b2e61ff3a1890e850f7b4c2710 authored over 3 years ago by Tom Waschischeck <[email protected]>
Merge pull request #5179 from cbielow/mgf_spec_annotation

NOVORAdapter fixes

c30f370bc5913a09765247682fec976147a5c3ec authored over 3 years ago by Chris Bielow <[email protected]>
update link to new macos contrib

85cf0791cc736691e1855e6392682807d168fd15 authored over 3 years ago by Julianus Pfeuffer <[email protected]>
move avg calc, metavalue name in Constants, FMEStatistics renamed

9a9dfc6bda43c65632141a84ff0d3d80f1bddc3d authored over 3 years ago by Tom Waschischeck <[email protected]>
[FIX] NOVORAdapter: also write MS2 spectra even if their metadata type is not annotated

[FIX] NOVORAdapter: error if no MS2 spectra were passed to NOVOR
[FEATURE] NOVORAdapter: report M...

e0d1dd3f4cb6b12481091d0ee99cdc05823e5a33 authored over 3 years ago by bielow <[email protected]>
fix warning

8cb40db5acd4cbef7b2330efd41707e3c5591639 authored over 3 years ago by bielow <[email protected]>
fix NOVOR DOi

50c136c9556c3c6e66b280265e04bf30c65928f0 authored over 3 years ago by bielow <[email protected]>
Merge branch 'develop' into pyopenms3

dde4be2101ab8625a83d85ee01308ed3f30b882e authored over 3 years ago by Julianus Pfeuffer <[email protected]>
Merge pull request #5140 from jpfeuffer/fix/clangwarnings

[FEATURE] switch to C++17

77af895cca1dd05360f5ebe8aba4f36415a3f3a3 authored over 3 years ago by Chris Bielow <[email protected]>
Merge pull request #5053 from OpenMS/fix/paths_actions

[FIX] pyopenms_wheel actions - env_var changes

432e7c5b9062be698af354d281274f7c78ba191b authored over 3 years ago by Julianus Pfeuffer <[email protected]>
Create .clang-format (#5155)

a3f89c7a726fa5e5f83f73782bc14a52a3f25f3c authored over 3 years ago by Timo Sachsenberg <[email protected]>
Merge pull request #5177 from cbielow/mgf_spec_annotation

[FIX] SearchEngineBase

882b3e1bccaf548280eeffb4e49fecd9af9e74d8 authored over 3 years ago by Chris Bielow <[email protected]>
[API] store references to matches (e.g. PSMs) instead of observations (e.g. spectra) in features

219a1bef9ea5b1be36197e28d6273ec2cc88f709 authored over 3 years ago by Hendrik Weisser <[email protected]>
Merge branch 'develop' into pyopenms3

07841159d447f94c9167364d323caacb088e8eb7 authored over 3 years ago by Julianus Pfeuffer <[email protected]>
little fix

0f22f2d81b9e6b70bf0dc59abd25e61e0627fefd authored over 3 years ago by Julianus Pfeuffer <[email protected]>
add header

72dbc65ca62f9cc388333a95d4d6000fba6a2318 authored over 3 years ago by bielow <[email protected]>
[FIX] SearchEngineBase: inspect spectra's data if metainfo not available

[FIX] annotate MGF data as centroided

5a5bc8ab3e3048195df410e15694bd1a2c436ef0 authored over 3 years ago by bielow <[email protected]>
rm PATH reset

85b0e069184d0ac9706da4a1458bdf52a4c72aad authored over 3 years ago by oliveralka <[email protected]>
Merge pull request #5176 from cbielow/mgf_spec_annotation

[FIX] TOPPAS crash when double clicking disconnected output node

0510f1bd34fdc2c22018510b2d15d1430e656c05 authored over 3 years ago by Chris Bielow <[email protected]>
test reset path - works without reset paths

8e3bdcb95560bdfc3a367e3694937136ea2e42ac authored over 3 years ago by oliveralka <[email protected]>
[FIX] IdentificationData: add adducts to move c'tor and 'swap'

6d4d1dca85eff87fd5bffa64d4e90ec3fc737007 authored over 3 years ago by Hendrik Weisser <[email protected]>
minor

ae0166a47c93e5a340a40454375127669092bbe3 authored over 3 years ago by bielow <[email protected]>
fix compile error

ec3363283ebea96bdf454bd18ab818a031702b67 authored over 3 years ago by bielow <[email protected]>
Merge branch 'develop' of https://github.com/OpenMS/OpenMS into mgf_spec_annotation

7ca9af8083c8a662334b5d14177bd6aae451badd authored over 3 years ago by bielow <[email protected]>
switch to last 3 python versions

e36563be22c79903678d3f5a078f75c9f5d151b0 authored over 3 years ago by oliveralka <[email protected]>
fix TOPPAS crash when double clicking disconnected output node

3c37e01428f6c3eb6d9505fd214214849fada294 authored over 3 years ago by bielow <[email protected]>
fix seed for internalcalibration tests

239760c590fded89afc3571f956f735f8956a9f1 authored over 3 years ago by Julianus Pfeuffer <[email protected]>
use only 3.9 to see if it is a specific issue; print path windows

578b3495b2d78ec91aadb5f03d5bb72cad011242 authored over 3 years ago by oliveralka <[email protected]>
TextExporter output filetype(s) (#5121)

* add out_type option to TextExporter with tsv, csv support

* adjusted .ini files

* remove...

7b267436d473a1ba35c2955d6e20fa7265d2fd63 authored over 3 years ago by RobertDeibel <[email protected]>
update travis script (#5171)

b3915b88214f9abeb20fe994b3c937537e423b9e authored over 3 years ago by Julianus Pfeuffer <[email protected]>
Extends precondition check bounds to equality (#5170)

85924bf475c4e4cd2ea585d21b91371918357fc3 authored over 3 years ago by bertrandboudaud <[email protected]>
mascot batch processing (#5162)

* batch processing

* fix

* fix

* fix

* online edits ftw

* fix

* fix

* fix
...

fe8f3082d434ef04fd3a475eba32a4b9ed81b1c0 authored over 3 years ago by Timo Sachsenberg <[email protected]>
[API,TEST] IdentificationData: added convenience function 'getMatchesForObservation'

c19b489180052465cad8fc9c92cf5ce142916a2d authored over 3 years ago by Hendrik Weisser <[email protected]>
[FEATURE] IdentificationData: remove unused adducts in 'cleanup' function

126fff960bc0c8b90b05255e1c18d7b32571e0e2 authored over 3 years ago by Hendrik Weisser <[email protected]>
[TEST] test loading of IDs on feature maps from SQLite file

4d2e7712f5f7d619427e155f6bbc0e4059781f98 authored over 3 years ago by Hendrik Weisser <[email protected]>
[FEATURE] SQLite file format for feature maps: support meta infos on 'DataProcessing' items

cac3e3d50cbdbf43656f8272a3c64c1580288b98 authored over 3 years ago by Hendrik Weisser <[email protected]>
[INTERNAL] IdentificationData: renamed 'InputItem' -> 'Observation', 'InputMatch' -> 'ObservationMatch'

08cbe98371e4233086252e76a2e00a38b0aedd7b authored over 3 years ago by Hendrik Weisser <[email protected]>
[TEST] test for reading/writing of feature maps from/to SQLite

15939f8822bd5ec258f224abaa72f46b45ed9c6a authored over 3 years ago by Hendrik Weisser <[email protected]>
[TEST] test for conversion of ID data in feature maps

ceb6366dd657d4de3a6a6ff2f3e1d453faec27d2 authored over 3 years ago by Hendrik Weisser <[email protected]>
[API] added conversion functions for ID results stored in feature maps ('Peptide-'/'ProteinIdentification' <-> 'IdentificationData')

335873539a57caee117c773b8f4be0c0ec60da56 authored over 3 years ago by Hendrik Weisser <[email protected]>
[FIX] fixes for reading/writing of feature maps to/from SQLite

5de205b5875e9e545fd8bfc0c0be34ed827bcee5 authored over 3 years ago by Hendrik Weisser <[email protected]>
[NOP] slight formatting change

0b089ed0f21bfbe0201f4c99117c23c3f4c8940f authored over 3 years ago by Hendrik Weisser <[email protected]>
[API] IdentificationData: added 'setMetaValue' overloads

c23979ab5965f0952175d16eea9479021d3b3368 authored over 3 years ago by Hendrik Weisser <[email protected]>
testing second compute function

32c85f38bf19c8b556122169cec7e78555e32a3e authored over 3 years ago by Tom Waschischeck <[email protected]>
catching ppms = 0

6147ab64cfff41ca10a59f0d33c1341385df3fed authored over 3 years ago by Tom Waschischeck <[email protected]>
docu

fef2056391d67eba626cad87acc292e202608f57 authored over 3 years ago by Tom Waschischeck <[email protected]>
Merge pull request #5167 from Waschi97/feature/SpecRefInNovorAdapter

Writting Spectrum Reference in NovorAdapter

a7e8b05472fd7f0407ca1bf881bd00bd3564d412 authored over 3 years ago by Chris Bielow <[email protected]>
avoid copy

fb2ba71b2eefa2ec659b10a71f01d6af3aae02ce authored over 3 years ago by Chris Bielow <[email protected]>
MetadataOnly and MSLevel 2 while loading MzML

72391d48297c02fff2bb8f566a6099a23b1f86d1 authored over 3 years ago by TomW <[email protected]>
FLASH Ida log file is now read by FLASHDeconv!!

5aa41c2bdf8dd566942305e3db770dc29dcf4453 authored over 3 years ago by kyowonjeong <[email protected]>
SpectrumLookup used for SpecRef, test file changed accordingly

b5cac288cc6c9ac2e01d1519e0949304adead530 authored over 3 years ago by Tom Waschischeck <[email protected]>
forward declaring

511addbafb271c57b70923cd998bb5210382fe88 authored over 3 years ago by Tom Waschischeck <[email protected]>
second compute for vector<PepID> input

457067a0cc8e632d98579ea181b050803791fad8 authored over 3 years ago by Tom Waschischeck <[email protected]>
Merge pull request #5166 from OpenMS/doc/FFMID

[DOC] FFMetaboIdent supports raw&centroided

b68a89c2e352df6568b9cb2bf0b300bbc84ea392 authored over 3 years ago by Chris Bielow <[email protected]>
[DOC] FFMetaboIdent

1b16076793d730d1a8d869d5968fce9b6d9385c6 authored over 3 years ago by Timo Sachsenberg <[email protected]>
FLASH Ida log file is now read by FLASHDeconv!!

02a9a83b46b1c2a407e08c489409b7453513a4fe authored over 3 years ago by kyowonjeong <[email protected]>
QScore bug (feature vector has only 0 elements) fixed!!

d2734fd439fe65aa02f342a50725ae111455aec0 authored over 3 years ago by kyowonjeong <[email protected]>
A searchengine base (#5157)

* a first go at a searchengine base

* fix codefactor

* add tests

* lb

* change to si...

3aa2f4f2ac2f98c9aa5f279bec10ed05067ab106 authored over 3 years ago by Chris Bielow <[email protected]>
IDMapper map ids by native_id (#5120)

* IDMapper map ids by native_id

* Apply suggestions from code review

Co-authored-by: Julia...

3a2f985d966b962b99fdc39d61ffe625972fa2b6 authored over 3 years ago by RobertDeibel <[email protected]>
[FEATURE] Allow skipping MS2 isotope scores in SWATH and disable it in FFID. (#5161)

* [FEATURE] Allow skipping MS2 isotope scores in SWATH And disable it in FFID.

* reverted ord...

f30d5cd28a6ffab278137a7422dca4cd4a7f8ccd authored over 3 years ago by Julianus Pfeuffer <[email protected]>
Negative mode charge resolved. Still need test functions...

1b8b82d9460bbde94a75737bac29097f44e5f35d authored over 3 years ago by kyowonjeong <[email protected]>
Merge pull request #5150 from jpfeuffer/feature/ExposeFFMSettingsPLFQ

[FEATURE] Expose a few FFM settings in PLFQ for finetuning.

dd584853c8e9ac1236c7f77948745e149814bf78 authored over 3 years ago by Julianus Pfeuffer <[email protected]>
Negative mode charge resolved. Still need test functions...

d3dc37ce299361e1845b366034c9fd63602d2cc3 authored over 3 years ago by kyowonjeong <[email protected]>
Merge remote-tracking branch 'origin/feature/ExposeFFMSettingsPLFQ' into feature/ExposeFFMSettingsPLFQ

# Conflicts:
# src/openms/source/DATASTRUCTURES/QTCluster.cpp

722fe3a5bea6d8774fc175a4d9a1f09216dfd823 authored over 3 years ago by Julianus Pfeuffer <[email protected]>
cleanup and style

09e53ee990882a5128e82dc65aa5686005c07f33 authored over 3 years ago by Julianus Pfeuffer <[email protected]>
New Qscore weights..

ef23ad9551fe540718f8f3c832f53c87faeaa76a authored over 3 years ago by kyowonjeong <[email protected]>
Update QTCluster.cpp

589c843f209a5afacd2b912e1c80ea8b1d1a35d3 authored over 3 years ago by Timo Sachsenberg <[email protected]>
tests

e8c742011e405d5239c958b5ea1ae189be0e510c authored over 3 years ago by Julianus Pfeuffer <[email protected]>
More comments and try to pop at beginning since it is safer

be7566bc637b658fc2e3b0d0ff660c54050bd5e4 authored over 3 years ago by Julianus Pfeuffer <[email protected]>
fixes to QtClusterFinder

c20e9fad52b2e8dd0323f1d6f9c89b03be542c3e authored over 3 years ago by Julianus Pfeuffer <[email protected]>
fix percolator URL (#5159)

ba426a2c8395536937ad00b24f72c8bcb2353b02 authored over 3 years ago by M Bernt <[email protected]>
Low mass coverage succeeded!! only need to remove min_charge_ for MSn

3aaa7908bb824b52a2e81dbc4a608076c8af3c8f authored over 3 years ago by kyowonjeong <[email protected]>
Low mass coverage succeeded!! only need to remove min_charge_ for MSn

2510f67cb38bfd0aa4fde791a3ff91a94db84750 authored over 3 years ago by kyowonjeong <[email protected]>
trigerred peaks are now included for deconvolution ...

702da254f91ec206842ca7da0af8fd7ee7f56f25 authored over 3 years ago by kyowonjeong <[email protected]>
trigerred peaks are now included for deconvolution ...

beacb07d2743b997a41dc39e9b1bc02878cd4afe authored over 3 years ago by kyowonjeong <[email protected]>
Fatal bug in MS2 deconvolution fixed

87526cd4f6240845b11a713122124c50120ad19a authored over 3 years ago by kyowonjeong <[email protected]>
avoid errors through register keyword in seqan

2188f933e7ed44a724bd0cf99f5491877e78400f authored over 3 years ago by Julianus Pfeuffer <[email protected]>
revert

86d2d05c1cea1a225dbf330ffc155a812bc02b24 authored over 3 years ago by Timo Sachsenberg <[email protected]>
Update .travis.yml

2971924319e241849e1357d0fab5959518b72f5f authored over 3 years ago by Timo Sachsenberg <[email protected]>
Expose a few FFM settings in PLFQ for finetuning

9e60a4664468068f58a3ce20a6181c71dbe6e966 authored over 3 years ago by Julianus Pfeuffer <[email protected]>
allow reading in a mod as protein-nterm in mzIdentML (#5143)

* allow reading in a mod as protein-nterm in mzIdentML

* adding a test ...

* check all mod...

91bead89d1810f9c1511234060008dee73c32cda authored over 3 years ago by Chris Bielow <[email protected]>
FLASHIda part updated new color 'g' introduced

0cbe15ddc07c10adcb338c12726fa47b23c15a85 authored over 3 years ago by kyowonjeong <[email protected]>
Update python, cython and autowrap on travis

812919e8df851b4ce1ed5041dca7721721ff8e11 authored over 3 years ago by Julianus Pfeuffer <[email protected]>
FLASHIda update

ede5688afe462919f0dfafb25e3279001ebac65f authored over 3 years ago by KyowonJeong <[email protected]>