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

some preps for upcoming GUI PR

f00d103293359325e18ff849043a5c15af592753 authored over 2 years ago by bielow <[email protected]>
some small changes

fa4a6e170f2a0eb477a88773d7a92f3ce6c788dd authored over 2 years ago by beschorneh32 <[email protected]>
Merge branch 'maxquant-output' of https://github.com/vrossow/OpenMS into maxquant-output

a9b0a23255ea15e0f9e00978432a9c039ab48394 authored over 2 years ago by beschorneh32 <[email protected]>
MQEvidence completely uses MQExporterHelper

2918d8a06ac709f73b15e32fb59e4dede7e55020 authored over 2 years ago by beschorneh32 <[email protected]>
Fix (EnzymaticDigestion): exact match for SPEC_FULL and no_cleavage onlyh when allow_random_asp_pro_cleavage is false

4e929a2092b0ecaed1da149648ea49294a72686f authored over 2 years ago by zhuchcn <[email protected]>
added option to remove hulls

8f6165f5f2f203acada107b32c5721a243d5202a authored over 2 years ago by Timo Sachsenberg <[email protected]>
lots of fixes

b6bec7806be31c07346a40b69636cb3a4164d87d authored over 2 years ago by bielow <[email protected]>
lots of fixes...

d586cbf770b8a7d2d8f06cdf9e202aa8b86536e1 authored over 2 years ago by bielow <[email protected]>
Test function + a few documentation needed

f9eb425b7125515e2a0ae5513513f67f63d507fa authored over 2 years ago by kyowonjeong <[email protected]>
Msms should work now.

287f947cb574349ec93703e31cd48e5fd2dee674 authored over 2 years ago by Virginia Rossow <[email protected]>
Merge branch 'maxquant-output' of https://github.com/vrossow/OpenMS into maxquant-output

dd6d4b6a8e1f5462ed40f9b92e4271df4c17fffc authored over 2 years ago by Virginia Rossow <[email protected]>
fixed the TOPP_QualityContorl_1 test, by adding the new input fasta_file

c03dade94f7a5d725b8faa5dfba2128754cd6827 authored over 2 years ago by lennykovac <[email protected]>
Test function + a few documentation needed

92b7295e739519dd32ade9b1dad2289c54f85e4d authored over 2 years ago by kyowonjeong <[email protected]>
Merge branch 'maxquant-output' of https://github.com/vrossow/OpenMS into maxquant-output

836a67a821000a6dd5117cae30591182acb5e871 authored over 2 years ago by Virginia Rossow <[email protected]>
change log updated for "no cleavage" of CometAdapter & XTandemAdapter

91691164ba3fb41d5bbb8702ec4528da7244282d authored over 2 years ago by zhuchcn <[email protected]>
[FIX] DatabaseSuitability Tests only executed when CometAdapter is found (#6134)

* additional CMake variable for finding CometAdapter

* forget 'endif()'

* reverting accide...

586fdefb965f2108d8f96803eb1e57fea7d46786 authored over 2 years ago by TomW <[email protected]>
Metavalue number of datapoints (#6128)

* initial change to get the new metavalue number_of_datapoints

* found a very stupid mistake ...

d4a5b32e04c565bc1c0d012994cea12697e2e1be authored over 2 years ago by Virginia Rossow <[email protected]>
getting 1d layers to work

0381e04bd15252f3d90a5291c2105bed4e8964e7 authored over 2 years ago by bielow <[email protected]>
Addressed Chris's comment : move file write parts to FORMAT.

9d8971f4edf6738f1f891cdd82d1d1aaa86c56a9 authored over 2 years ago by kyowonjeong <[email protected]>
Addressed Chris's comment : move file write parts to FORMAT.

39acc2e27cb3fb41f0001100308e6e7f3d7e3845 authored over 2 years ago by kyowonjeong <[email protected]>
fixed some errors with MQExporterHelper

b84a6b93003cf729acc3d539123565b5ac77ab01 authored over 2 years ago by beschorneh32 <[email protected]>
Merge pull request #6091 from jpfeuffer/feat/specAnnotationSirius

[FEATURE] Export annotated spectra from Sirius as mzml

9b5a8e0de00c1a257d84c0cd9a01a42b6ef1fa2b authored over 2 years ago by Julianus Pfeuffer <[email protected]>
Merge branch 'develop' into feat/specAnnotationSirius

b4ba11b797e3773449b6e799a22720c0e091ca11 authored over 2 years ago by Julianus Pfeuffer <[email protected]>
fix: added precursor mz comparison for annotateSpectra

3b9eb35e6b90ab34431d39a84fd65a5ef4aba85b authored over 2 years ago by dmccloskey <[email protected]>
Merge remote-tracking branch 'upstream/develop' into uclacds-develop

3f8466d0f6a2b0690e46b4af793abbe5f1059340 authored over 2 years ago by zhuchcn <[email protected]>
pyopenms

e8aad846b74b6b998288725329b640c82937ca72 authored over 2 years ago by Julianus Pfeuffer <[email protected]>
add 1DChromLayer

57192a0fe83df487e34edd94c2a2a7507ba542ff authored over 2 years ago by bielow <[email protected]>
Addressed Chris's comment : move file write parts to FORMAT.

3cb7cf591e9f09c1050389a17774aa880e8cc2c1 authored over 2 years ago by kyowonjeong <[email protected]>
Merge branch 'maxquant-output' of https://github.com/vrossow/OpenMS into maxquant-output

69e554fbb8ec105eea8b3d4e42e5bd83100fc3a4 authored over 2 years ago by Virginia Rossow <[email protected]>
Disable indeterministic tests on other platforms.

14c6c6be0537ad82407865a1573164377497e26b authored over 2 years ago by Julianus Pfeuffer <[email protected]>
some work on helpers and started using the helper in MQEvidenceExporter

ab94d434e8aacd5ce05bc20ead586591d28be3f7 authored over 2 years ago by beschorneh32 <[email protected]>
changed msms further

85e57b86664a90320114a90da540170052b860c4 authored over 2 years ago by Virginia Rossow <[email protected]>
Add tests and refactor user param names

181e36f14fe9ec11aff9531b71bd4aacc414361f authored over 2 years ago by Julianus Pfeuffer <[email protected]>
rename

fc8b7c061ab5f06e02981cfba962500187eb6242 authored over 2 years ago by bielow <[email protected]>
move code for projections into Layer

12735be2cd10ce7a80aa6f5d21d02f67d9923bf3 authored over 2 years ago by bielow <[email protected]>
working evidence & quality controll, need to addapt the tests

47e7137df5d7190eed3501a00d1e11c7369682c1 authored over 2 years ago by lennykovac <[email protected]>
Merge remote-tracking branch 'origin/feature/FLASHDeconv' into feature/FLASHDeconv

# Conflicts:
# src/openms/include/OpenMS/FORMAT/sources.cmake

acc2f1f8ad064c6dafbc20080f8303d2b350328a authored over 2 years ago by kyowonjeong <[email protected]>
SpectraMerger: recover lost codes from FLASHDeconv branch during merge

201e842f86443780c26e14f907611bdc405a3bda authored over 2 years ago by JeeH-K <[email protected]>
Move FLASHDeconv file outputs under FORMAT

7a709caed8c79c4bd4fa5d050192aecf2d2f819d authored over 2 years ago by kyowonjeong <[email protected]>
Merge remote-tracking branch 'upstream/develop' into feature/FLASHDeconv

03e9b7ae12e22179521d772cfdc7fff06d055065 authored over 2 years ago by JeeH-K <[email protected]>
Merge pull request #6122 from bernt-matthias/sirius-workdir

SiriusAdapter: do not change in the executable dir

89dd3df90df49d5374c4920b28210de125e2154c authored over 2 years ago by Julianus Pfeuffer <[email protected]>
reverse changes to findHit and some changes to MQExporterHelper

44dcff30d8a801abb88eaf102d94d44e43d69b3f authored over 2 years ago by beschorneh32 <[email protected]>
Merge branch 'develop' into feature/searchSpectrum_extended

69c9d5a2460acf64b043d5a3a4e01d695523cfe2 authored over 2 years ago by bertrandboudaud <[email protected]>
FLASHIda beta+, Sean's comments

00d888c64306f5e83140133bca3acf7c6f9e1c45 authored over 2 years ago by kyowonjeong <[email protected]>
Merge pull request #6127 from axelwalter/feature/FFMID-num-masstraces

[Feature] Add num_of_masstraces meta value to FFMID

23a774211f662341e15882c0c85722e8e330d5e0 authored over 2 years ago by axelwalter <[email protected]>
add num_of_masstraces to constants

beff1c8f768ca28e906e05b6858550a56fddee42 authored over 2 years ago by axelwalter <[email protected]>
first implementation of helper class for MQ Exporter

a496352f20042607bdbde91b5fe725e964009c46 authored over 2 years ago by beschorneh32 <[email protected]>
update test output file

37638923d1ce5aac3de61db31ad4c8a90cf7f925 authored over 2 years ago by axelwalter <[email protected]>
correct mv name

907e43138a8b373cc55cb113190a416d87735062 authored over 2 years ago by axelwalter <[email protected]>
add num_mass_traces to FFMID

fb7c0272731f099516ed0ee0e13874137cfd5c64 authored over 2 years ago by axelwalter <[email protected]>
cleanup includes

merge void Plot1DCanvas::saveCurrentLayer(bool visible)

0aec74c469dad5c11e76040507ee68f911dcceeb authored over 2 years ago by bielow <[email protected]>
Merge pull request #6125 from OpenMS/jpfeuffer-patch-1

[FIX/PYOPENMS] update min. req. autowrap version

0a2f20cb6f3c92ff19a1cb758e3c5957e2e3a363 authored over 2 years ago by Julianus Pfeuffer <[email protected]>
Merge branch 'develop' into feat/specAnnotationSirius

0d16b7b855af8a562bfbedc22784f2c8775155b6 authored over 2 years ago by Julianus Pfeuffer <[email protected]>
Add tests

a2527a51b47ac4c2d1e6a2e22fc74413e923f73c authored over 2 years ago by Julianus Pfeuffer <[email protected]>
[FIX/PYOPENMS] update min. req. autowrap version

fixes #6124

7c1f1f32e5f8a13fca2491de749acc99e6deee0c authored over 2 years ago by Julianus Pfeuffer <[email protected]>
[Feature] dynamic tool load (#5877)

* add executable function

* add possibility to search for executables in folder

* Rebase o...

764cb04ff5bf9cfab9e1346b0db004b6f25c11ed authored over 2 years ago by Ruben Grünberg <[email protected]>
Merge pull request #6123 from bertrandboudaud/fix/log_thread_issue

Fix/log thread issue

a66d710d5ba77c329d1fb9d5bc0100b324a51bab authored over 2 years ago by Julianus Pfeuffer <[email protected]>
a visitor for saving layer data

396aae31f2134afd78e2711710b8b03288d3a075 authored over 2 years ago by bielow <[email protected]>
Merge branch 'maxquant-output' of https://github.com/vrossow/OpenMS into maxquant-output

aee16ddec3844b564660f55b5c4f8b0477d1f636 authored over 2 years ago by lennykovac <[email protected]>
redesigned the annotation, TODO the MQeveidencetest and some minor refining

0f19f4cb04d28e4785a00cedc75c3d36c4914b1e authored over 2 years ago by lennykovac <[email protected]>
Merge branch 'develop' into sirius-workdir

190dd7504a4434fd7823e3cb32c1ffb893fc0462 authored over 2 years ago by Julianus Pfeuffer <[email protected]>
Update PULL_REQUEST_TEMPLATE.md

d66eaa6e4bd87ad8f174a8bb8386e26ce77dd422 authored over 2 years ago by Julianus Pfeuffer <[email protected]>
Added change log entry to describe fix

e9169b89cf7824b71517dd64413bc466851faaa6 authored over 2 years ago by bertrandboudaud <[email protected]>
Using same name for omp critical sections

7aa133547a97c1bd274667f44d9884a7cbc183db authored over 2 years ago by bertrandboudaud <[email protected]>
SiriusAdapter: do not change in the executable dir

hopefully fixes https://github.com/OpenMS/OpenMS/issues/6068

386870dbed0ff1030fa62dc4bf18133aa1d7d843 authored over 2 years ago by Matthias Bernt <[email protected]>
Merge branch 'develop' into idfile-json-export

f1bfa32eeeecd37210ee725dd3963396f232bbeb authored over 2 years ago by Timo Sachsenberg <[email protected]>
Merge pull request #6119 from OpenMS/fix/mzML_dpForDAs

[FIX] mzml: Dont write empty DataProcessing for DataArrays

14f7c887a79730c12ad46a26b12b516d5aa6204d authored over 2 years ago by Julianus Pfeuffer <[email protected]>
[FIX] class test

eb429fa6d1a5141939097dd3211b3557f7673fa6 authored over 2 years ago by jpfeuffer <[email protected]>
[FIX] tool tests

b1722f1f87cbbdfbecbb8aaeb17f3d97c9f46763 authored over 2 years ago by jpfeuffer <[email protected]>
[FEATURE, TEST] added test mode flag to xQuest spec.xml output format (#6117)

* [TEST] commented out OpenPepXLS's spec.xml tests

These tests are unstable due to difference...

a039f216a0ab8ea8592bcad155284e0af1a41bbb authored over 2 years ago by Eugen Netz <[email protected]>
progress..

16e91178f9c42029e0f5eee04dddad386e6b01b4 authored over 2 years ago by bielow <[email protected]>
[FIX] mzml: Dont write empty DataProcessing for DataArrays

cca2f1dd4ca2c008a1fc6e68cd56ae3f0c5f7bb5 authored over 2 years ago by Julianus Pfeuffer <[email protected]>
revert last commit. should be on branch

5859883114b6f13160331341d7a52dfbb0b3bed7 authored over 2 years ago by Julianus Pfeuffer <[email protected]>
[FIX] Do not write empty DataProcessing for DataArrays

7aaab598d031d9991fdc8c37139c8caf214b669a authored over 2 years ago by Julianus Pfeuffer <[email protected]>
use OpenMS string split method to handle synonyms in MSPGenericFile::store

f200aad7460b72f6964a78efbdd637f4bc5d9634 authored over 2 years ago by bertrandboudaud <[email protected]>
Factorized code in organizeMapWithSameIdentifier using a lambda

1820cd8ef7596db3bd04417c697daf94d3df5568 authored over 2 years ago by bertrandboudaud <[email protected]>
Factorized code for annotateSpectra using lambda

54c733e5e9636fed71ff213c4bf54b5a0323002e authored over 2 years ago by bertrandboudaud <[email protected]>
Started to prepare MQMsmsExporter a little for the addition of MQExportHelper. But not complete yet!

6a3a6c80ecdc5f1476ca87390980e99367604a40 authored over 2 years ago by Virginia Rossow <[email protected]>
[TEST] commented out OpenPepXLS's spec.xml tests (#6116)

These tests are unstable due to differences in number to string conversions between versions of ...

921d3dae57d9bf52c5777c4fad0869cfcabfe32e authored over 2 years ago by Eugen Netz <[email protected]>
update -- trying to abstract away MSSpectrum from Canvas1D

162ae186793b3983c946abec5b18928376acd17b authored over 2 years ago by bielow <[email protected]>
Merge branch 'maxquant-output' of https://github.com/vrossow/OpenMS into maxquant-output

274f65e0ccbc9551590171d3eb7af3bab8bc6ae1 authored over 2 years ago by beschorneh32 <[email protected]>
const verload for findHit, get gene name from description

b82126204d23ec14b480e8800b111b22d4d1e4d7 authored over 2 years ago by beschorneh32 <[email protected]>
annotated preoteindescription to featuremap instead of consensus....

4959f597aea8c6b19b8ae1a1c3d5c3442079ab16 authored over 2 years ago by lennykovac <[email protected]>
Removing commented lines from RT Transition list construction

26cec5a9b0bf937925428c20828d9cde2efa9ea8 authored over 2 years ago by bertrandboudaud <[email protected]>
fix: missing RT in transition list

1addd55730f7cde5747eb7ca9b347a9b1134201e authored over 2 years ago by dmccloskey <[email protected]>
MQEvidenceexporter now fixed -> working quality control, mapping from feature to protein name / gene name

589efd278ecee5bf1abe9559a58b3ce9c24d20ba authored over 2 years ago by beschorneh32 <[email protected]>
Using OpenMS::String's prefix method

ad0987c9ccfe8330a6caf6a261d7815182c9bda6 authored over 2 years ago by bertrandboudaud <[email protected]>
Merge branch 'develop' of https://github.com/OpenMS/OpenMS into idfile-json-export

073eec2ab6034c77affecdf0c9b5321ee2c3fff6 authored over 2 years ago by Hendrik Weisser <[email protected]>
[TEST] added tool tests for JSONExporter (incl. test files)

cb3f70480891269a78d321bff361c6ba42c9d3aa authored over 2 years ago by Hendrik Weisser <[email protected]>
Added comment on how we extract adduct

1cf9c432ee8aa2d23302ac5ebaafd4cbdd93e934 authored over 2 years ago by bertrandboudaud <[email protected]>
fix: missing RT in transition list

f4078fd68b085935563496780f1e41886c8ed036 authored over 2 years ago by dmccloskey <[email protected]>
Changed API of extractSpectra, removed the compute_features flag

8b3ff0c7717f4a63693c10cdfc4ac569433c659a authored over 2 years ago by bertrandboudaud <[email protected]>
Update stale.yml

b7f296d361c43c1e922fe4fc83ce4308b3206c61 authored over 2 years ago by Timo Sachsenberg <[email protected]>
cleaned up a bit, not final ...

ac73f4ed407ad50b9e6d08439df6ce02a013b7af authored over 2 years ago by lennykovac <[email protected]>
[FEATURE] JSON export of OMS (SQLite) files: peak annotations, meta info, applied processing steps

587f128933540f671fdb777befbf8784b5933d21 authored over 2 years ago by Hendrik Weisser <[email protected]>
[FORMAT] OMS (SQLite) file format: added unique constraint for labels of parent group sets

4b6551a5f5edfed9b2aa33cebb7bdeb452a5d808 authored over 2 years ago by Hendrik Weisser <[email protected]>
[FIX] removed unneeded variable

75d520f7f57f51ce910834bf3cc8727159fe78a9 authored over 2 years ago by Hendrik Weisser <[email protected]>
Fasta Indexing done, functionality seems correct. QualityControl still crashing.

06866f333b69f17c423d0b4b8555bf492cccb47b authored over 2 years ago by lennykovac <[email protected]>
add_unknown_features renamed add_unidentified_features

d2207bf2979bc871794b1a5f03ea056b21f629d8 authored over 2 years ago by berbou <[email protected]>
Removed constexpr for std::array that is init with std::string (non literal)

780b843c1f2469b778a29e3455f281bc0c20e06c authored over 2 years ago by berbou <[email protected]>