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

remove duplicated code

d20daba6adb5fef9aad76d796ca60c3ed22a002d authored about 4 years ago by Chris Bielow <[email protected]>
remove unused parameters; make parsing more efficient

c8ab4aee2b1718e758e33b692c0dc248e36d9972 authored about 4 years ago by Chris Bielow <[email protected]>
signal rename

56cf588f749409c0accbe82f8ff53ea96330fbe5 authored about 4 years ago by Chris Bielow <[email protected]>
better docs

a4f62bcd2208867ccc855bb066f3b37acbf84598 authored about 4 years ago by Chris Bielow <[email protected]>
[API, TEST] calculateMDV(..) : changing calculation routines and adding test cases

5a95c69704ddffd36c9162c183a1bd8533708464 authored about 4 years ago by Ahmed Khalil <[email protected]>
update THIRDPARTY

5dfa4e9d80e602c86ebef419c9aa938750d1ca82 authored about 4 years ago by Timo Sachsenberg <[email protected]>
Update rebase.yml

d6c8f3a74cf5e7cdc433a94adc843e011801dcdb authored about 4 years ago by Timo Sachsenberg <[email protected]>
Update rebase.yml

9f9c04b2d72ee45ebe5657775d2aaee4f3afd42b authored about 4 years ago by Timo Sachsenberg <[email protected]>
fix: made strict_ param in MRMFeatureFinderScoring an optional parameter

92c6566974d5211c3183895486c4f3fdfb8575cb authored about 4 years ago by Douglas McCloskey <[email protected]>
Merge pull request #4894 from jpfeuffer/fix/MzTabSearchEngines

Only export main SE to mzTab. Correct scoretype. Keep scores and localization as Metavals in PLFQ.

d0dbeb6f7d141094e2c1d3c99de8b0a662e01568 authored about 4 years ago by jpfeuffer <[email protected]>
Update src/openms/source/FORMAT/MzTab.cpp

86a8ba6820ca3eb6c501ed1c033eb0328666de5d authored about 4 years ago by jpfeuffer <[email protected]>
Fix tests

3f1cb873337d36995f335d9e50d7f864cf43143f authored about 4 years ago by Julianus Pfeuffer <[email protected]>
[LOG] improved log output of FeatureFinderIdentification

c913cbd3f8057486c0b4a421b546778b9262f7d0 authored about 4 years ago by Hendrik Weisser <[email protected]>
Only export main SE to mzTab. Correct scoretype. Keep scores and localilzation as Metavals in PLFQ.

d5695fa53f9b049f394d3756d64e4a56cad0de7b authored about 4 years ago by Julianus Pfeuffer <[email protected]>
refactor menu and Recent files submenu into separate classes

4aa59508bee0375a6d4bc5440dc92ccc9eb7027c authored about 4 years ago by Chris Bielow <[email protected]>
no warning if rerank_percentile to high, (1-rerank_percentile) to just rerank_percentile

2a3d46ab0173e34f0eff39ce13c8aec2be20cf8a authored about 4 years ago by Tom Waschischeck <[email protected]>
Merge branch 'develop' of https://github.com/OpenMS/OpenMS into idfile-integration

74fd88e440ea54587a4270542ae883457fe6297a authored about 4 years ago by Hendrik Weisser <[email protected]>
switching QCBase to FlagSet

de1837f04406ba53f4e50fac27d2658edeb42189 authored about 4 years ago by Chris Bielow <[email protected]>
[FIX] FeatureFinderIdentification: fix m/z values of mass traces for adducted molecules

01ecf822a0bde7c8391776e85d958f540250fa05 authored about 4 years ago by Hendrik Weisser <[email protected]>
[FIX] take electrons into account when calculating mass shifts caused by adducts

cf06fa782852e1a5d9835fe7e2809bdd72b529ee authored about 4 years ago by Hendrik Weisser <[email protected]>
[FEATURE,PARAM] support for adducts in MapAlignerIdentification; new parameter 'algorithm:use_adducts'

8a583377a0d6982667d80de8875a9dc9f16a1e3c authored about 4 years ago by Hendrik Weisser <[email protected]>
add FlagSet class to model combinations of enum values

a6e1245ad3c18101712910699a17ba6aa77afcb1 authored about 4 years ago by Chris Bielow <[email protected]>
[FEATURE,PARAM] support for adducts in FeatureFinderIdentification; new parameter 'extract:max_isotopes'

526c0982d02f554f01595ccb7e484c68ee341a0e authored about 4 years ago by Hendrik Weisser <[email protected]>
[INTERNAL] simplified implementation of 'CoarseIsotopePatternGenerator' c'tors using default values

802d16b06c5603fa9affb5558733619dcc5c8e5b authored about 4 years ago by Hendrik Weisser <[email protected]>
Merge pull request #4874 from jpfeuffer/fix/AASeqProteinNTerm

[FIX] Protein terminal mods in AASequence

8062249e8558a9f355a178e1b91fde06265eb930 authored about 4 years ago by jpfeuffer <[email protected]>
Last cleanup.

150295f98e8deb694eedbc230f40ca53992f0d15 authored about 4 years ago by Julianus Pfeuffer <[email protected]>
...

e10646357c648de030f1da1fc2ea996c6b5b71d1 authored about 4 years ago by Julianus Pfeuffer <[email protected]>
forgot whitelist in test

9b873b7057cd3ca0e03520a5219b30082c52e321 authored about 4 years ago by Julianus Pfeuffer <[email protected]>
small percentile now tested in class test, also some phrasing

b78b81f3a440009bc45b3abdea38e21b602e6aa5 authored about 4 years ago by Tom Waschischeck <[email protected]>
returning smallest diff instead of throwing error when index out of bounce

aa38301ab6b06d50795e2715ca4367e3c553b3d6 authored about 4 years ago by Tom Waschischeck <[email protected]>
Improve enzyme handling in pepXML

4bc93c05e7f63a3d1424c473abf535eaf5fb4546 authored about 4 years ago by Julianus Pfeuffer <[email protected]>
Revert "Update function names in addons/ConvexHull2D.pyx"

This reverts commit 633b977f33ff5699e087adae6089cf3c8c4ea0b7.

d533744dfa31834411ac14b94ccfd784f149f2a5 authored about 4 years ago by Shekhar Shukla <[email protected]>
Revert "Updated name of align in addons/MapAlignmentAlgorithmIdentification.pyx"

This reverts commit b2f2937c178eb989055855ba267b40a9c32110b7.

db6a11e051966919edff9ae77e84df91ff241f46 authored about 4 years ago by Shekhar Shukla <[email protected]>
changed rerank_cutoff_percentile default to 0.99

9085b38d74cd4bfabcebca1eb105269fbd69587a authored about 4 years ago by Tom Waschischeck <[email protected]>
Updated name of align in addons/MapAlignmentAlgorithmIdentification.pyx

b2f2937c178eb989055855ba267b40a9c32110b7 authored about 4 years ago by Shekhar Shukla <[email protected]>
Update function names in addons/ConvexHull2D.pyx

633b977f33ff5699e087adae6089cf3c8c4ea0b7 authored about 4 years ago by Shekhar Shukla <[email protected]>
[API] calculateMDV(..) : removing unnecessary assignments

ff3dbc95d6fa8c6675b59b164d5336ac5262606f authored about 4 years ago by Ahmed Khalil <[email protected]>
[API] Moving calculateMDV(..) to IsotopeLabelingMDVs class

cd9888e800d5172acdedb20df0af5c6970ac0f17 authored about 4 years ago by Ahmed Khalil <[email protected]>
Merge branch 'develop' into fix/AASeqProteinNTerm

ed74f83e87bb0a9632819b37b99d5f2d1ee9b445 authored about 4 years ago by jpfeuffer <[email protected]>
revert debug mode of test

cd24de61927ee4a7e858a0143a524225500b6a01 authored about 4 years ago by Julianus Pfeuffer <[email protected]>
Enabled MSFraggerAdapter and adapt tests. At the same time upgraded our "private" Thirdparties for testing to MSFragger 3.0.

311083646c4fab15654b3fc1655a4accfd434a39 authored about 4 years ago by Julianus Pfeuffer <[email protected]>
Merge pull request #2 from jpfeuffer/patch-1

[FIX] Add new DBsearchDeconvMass util to list of executables to be built (and documented)

cbe6794e25f08d2bfc376500741eb75a944bce2c authored about 4 years ago by JihyungKim <[email protected]>
[FIX] Add new DBsearchDeconvMass util to list of executables to be built (and documented)

7a473ca6788f21536ada202693d7bebfd702685e authored about 4 years ago by jpfeuffer <[email protected]>
Adapter Parameters Written as MetaValues to SearchParameters (#4887)

* function in DefaultParamHandler

* meta values written in comet- & msgf+ adapter, test missi...

62899d6211aedc666ba8d4f31c65dbc958afdc24 authored about 4 years ago by TomW <[email protected]>
section for algorithm parameters in TOPP tool, some renaming

c2557323c6c9b26c533718055f6047aa86984276 authored about 4 years ago by Tom Waschischeck <[email protected]>
Always remove zips for notarization. Otherwise they stay in the dmg when it fails.

7c93e22e9cc8430614a5989531471c36111ef528 authored about 4 years ago by jpfeuffer <[email protected]>
remove version from autowrap to always have the latest

52ab750b1e6d6ec3609e22b87dfc05ff5a0c0a68 authored about 4 years ago by jpfeuffer <[email protected]>
LogWindow cleanup

60d8db26acadd828ddeb999a6ea042d4e4670295 authored about 4 years ago by Chris Bielow <[email protected]>
use signal/slot instead of pointer (unsafe due to order of destruction)

5978d02f396d9d73ea7fe8687a6b16a5a1c46112 authored about 4 years ago by Chris Bielow <[email protected]>
Merge pull request #4889 from OpenMS/feature/combineSEsettingsConsID

[FEATURE] combine SE settings during ConsensusID (instead of taking 1st)

309c0a856306ae149421c719499171c70d1ffb78 authored about 4 years ago by jpfeuffer <[email protected]>
Last style fixes.

f4feec6c4dbf9c449083c2bb3513ee1339d813e2 authored about 4 years ago by Julianus Pfeuffer <[email protected]>
exclude loop

2896bc8c21ac554740c34ba989f26f3a9498948d authored about 4 years ago by jpfeuffer <[email protected]>
[CI] rebase using /rebase (#4890)

* [CI] rebase using /rebase

writing /rebase in a comment will automatically attempt to rebase...

018d479e8fb8aa09a7168a2094031e04659f4413 authored about 4 years ago by Timo Sachsenberg <[email protected]>
Added check for db basename and consider unknown_enzyme. Add a force flag to IDMerger to be safe.

101bf0121460010b929c47a370ec841c9707d2c8 authored about 4 years ago by jpfeuffer <[email protected]>
Consider units and disagreeing enzymes.

0515131768a03dd9093c749accdd55c5383ccae0 authored about 4 years ago by jpfeuffer <[email protected]>
[API] Adding calculateMDV to AbsoluteQuantitation class

84c084a995788b6169dd81751d69d7cdd4838395 authored about 4 years ago by Ahmed Khalil <[email protected]>
phrasing changes

2b7cc223373c35d8b8142e0818e1d70eedc155d7 authored about 4 years ago by Tom Waschischeck <[email protected]>
refactor log to separate class

8b5064cd07755898f3d0005e877163f5d58b8ca0 authored about 4 years ago by Chris Bielow <[email protected]>
add doc

22949783291e8ea15d9061fa7da94361679a1dd8 authored about 4 years ago by Chris Bielow <[email protected]>
add free function

dbc5c151f83312b7083baad49dfea8976631d290 authored about 4 years ago by Chris Bielow <[email protected]>
add member function hasPeptideIds

fd84b105aebfde9892c5b0c5b1f67b10b0514b9a authored about 4 years ago by Chris Bielow <[email protected]>
Merge branch 'develop' of https://github.com/OpenMS/OpenMS into toppview_refactor

cf1184a46f1d70bee12fbf23007d01e2ea5e54af authored about 4 years ago by Chris Bielow <[email protected]>
Some refactoring and errors/warnings/todos

48dd1f4c4f379ed21474a81e754163ab154d5d7b authored about 4 years ago by Julianus Pfeuffer <[email protected]>
fix compile error

fea07fae7b695b30f4a07312c524a90747574a5c authored about 4 years ago by Chris Bielow <[email protected]>
refactor LayerView into own class

097654eacd94bf5390fed7cb4d35b241e9a0a7ca authored about 4 years ago by Chris Bielow <[email protected]>
? forgot to commit output?

510bdd21f2c11de457275cd4e71760f87b158a48 authored about 4 years ago by Julianus Pfeuffer <[email protected]>
merging origin changes

95abfb9db585819b2f195f3a610660be340e261d authored about 4 years ago by Tom Waschischeck <[email protected]>
more class docu, instances novo_fract in docu replaced with new name

5b8cfb98a572e25342ac4dc87e784869946b6528 authored about 4 years ago by Tom Waschischeck <[email protected]>
Fixed some TODOs, a small copypaste error. Added more tolerant lookups which added another Modification that was found.

4ffcdf9012e09ad36d2bfcb41875957748585c27 authored about 4 years ago by Julianus Pfeuffer <[email protected]>
remove unused method

f622512ca55f47bfb97a262efdccfee037c92e3a authored about 4 years ago by Chris Bielow <[email protected]>
fix CI

1e588d802b2c31267414059113bd61ebeec0e71b authored about 4 years ago by Chris Bielow <[email protected]>
use set for specs

06ae91d2001d7e66542528e7a79bb411153f8d0f authored about 4 years ago by jpfeuffer <[email protected]>
another small fix

0d33e5898ccab1ff0f68452c41ba08b5302d1300 authored about 4 years ago by Julianus Pfeuffer <[email protected]>
Do not use direct initialization

b2b81046dabca612a2c9e4f90e89225b7cb00d67 authored about 4 years ago by Julianus Pfeuffer <[email protected]>
small error

4c9c1e0550df2c0af67a25f90a940786368c5aca authored about 4 years ago by Julianus Pfeuffer <[email protected]>
Feature/pyopenms acquisitioninfo access (#4329)

* [FIX][pyOpenMS] Enable access to AcquisitionInfo items, ..

.. enable access to metainfointe...

548abfaa87a7ef345fcd051e10ee93e240bc3ff8 authored about 4 years ago by Mathias Walzer <[email protected]>
[FEATURE] combine SE settings during ConsensusID (instead of taking 1st)

2e11d9365a7ef6e3f46f142129072f8ab4d9f54b authored about 4 years ago by jpfeuffer <[email protected]>
Raised tolerance

3685c8aef089945a8139e8c590cead5e322f810d authored about 4 years ago by Julianus Pfeuffer <[email protected]>
Remove unused variable.

91ba516ab5916b96755c8364896f3047adb7f1c4 authored about 4 years ago by Julianus Pfeuffer <[email protected]>
Improved tolerance to match pepXML precision.

Cleanup.

7a103123784ece3b9f6d4c43d317cb6a0cfbc3a6 authored about 4 years ago by Julianus Pfeuffer <[email protected]>
Complete rewrite of mod-parsing in pepXML. Fixes huge bugs:

- fixed modifications were not considered if not explicitly annotated at the sequence (Mascot)
- ...

c17c3a21f738aefbc7451eb41aee967714480000 authored about 4 years ago by Julianus Pfeuffer <[email protected]>
[FEATURE] correct return value for operator[] (#4536)

* [FEATURE] correct return value for operator[]

* Update AcquisitionInfo.pxd

Co-authored-b...

0af37e2de11d6589d0b5735e03f001eb2e9920fa authored about 4 years ago by Hannes Roest <[email protected]>
bump autowrap in travis CI (#4888)

71c0d01f4d7da9939ccd66cc9cfbc31b7d165570 authored about 4 years ago by Timo Sachsenberg <[email protected]>
PercolatorAdapter and CruxAdapter: use underscore in arguments (#4529)

* PercolatorAdapter: use underscore in arguments

instead of dashes. makes it consistent and a...

97fbc6bbed05c9abf44801d9ab67fc5699265226 authored about 4 years ago by M Bernt <[email protected]>
subsitute vector<double> for map<PeakType, double> in SignalToNoiseEstimator (#4884)

* subsitute vector<double> for map<PeakType, double> in SignalToNoiseEstimator

* new version
...

e75a3616ba4ef48040909f180a7c15a6c7e0d317 authored about 4 years ago by Chris Bielow <[email protected]>
Merge branch 'develop' of https://github.com/OpenMS/OpenMS into toppview_refactor

# Conflicts:
# src/openms_gui/source/VISUAL/APPLICATIONS/TOPPViewBase.cpp

3fa90133092d4b9d08c56bdd7a27ce29ff2da468 authored about 4 years ago by Chris Bielow <[email protected]>
Merge pull request #4443 from bernt-matthias/topic/OpenSwathDIAPreScoring-out-fix

OpenSwathDIAPreScoring: fix outputs

5b1fda0e85418655e4d6c439261c23b144ea48d7 authored about 4 years ago by Hannes Roest <[email protected]>
[FEATURE] support adducts in FeatureFinderIdentification (work in progress)

52b639b6008b2576e0d7839b004aeb27be419d79 authored about 4 years ago by Hendrik Weisser <[email protected]>
DBSuitability.cpp change

b8bab8dc5560e110da2716f44f7f1c413fa4b03b authored about 4 years ago by TomW <[email protected]>
DBSuitability.h change

c2f967f9607a2831825eb6d492e2d25e1c6edbb9 authored about 4 years ago by TomW <[email protected]>
[FIX] IdentificationDataConverter: re-enabled output of adducts in mzTab

b2885fc413a09c4f0805bad0fbffa596ee5359bb authored about 4 years ago by Hendrik Weisser <[email protected]>
review

3ef2a9991888dd82dacb88fe59417f571cdeb072 authored about 4 years ago by Julianus Pfeuffer <[email protected]>
clean up TabBar handling

a292fe5dc3ddf5026929b8c3c1f17689032c5119 authored about 4 years ago by Chris Bielow <[email protected]>
more docu and Suitability to DBSuitability

94937efc46924797d684509b1329cbccbb75a07d authored about 4 years ago by Tom Waschischeck <[email protected]>
Labeling support (#4832)

* remove redundant code

* make interface safer (avoid memory leaks and dangling pointers)

...

4514827e20e18246cefa02e84fb0023110a246f0 authored about 4 years ago by Chris Bielow <[email protected]>
Add comments and bogus tests

3237d261e72ff5f50ddb5be8aa500742eaadcc16 authored about 4 years ago by Julianus Pfeuffer <[email protected]>
some invariants for DataFilters

31d3cb31a75efe86aebcb3421b98fde593af12de authored about 4 years ago by Chris Bielow <[email protected]>
Better pepXML support with still a lot of TODOs

f3fb2334890a96132e53a38741756c7691c0e0f1 authored about 4 years ago by Julianus Pfeuffer <[email protected]>
Merge branch 'develop' into feature/FLASHDeconv

7b3c87e28bdcf9c0d49721ad20014dd4129cb17a authored about 4 years ago by JeeK <[email protected]>
fixing error: FLASHDeconv test

e37dc923c26cd1a3dfbb7871db1b6930d521d79f authored about 4 years ago by JeeK <[email protected]>