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

Update pyopenms-wheels.yml

6d0ab3e36b44cda9d258c1ea37cb9f4fa579f4b0 authored almost 3 years ago by Julianus Pfeuffer <[email protected]>
[PERFORMANCE] add index for peakannotations (#5753)

* [PERFORMANCE] add index for peakannotations

* add primary key to metainfo

07b841aabf7ef92ea1ee6eda6c90b7de453ccdb4 authored almost 3 years ago by Timo Sachsenberg <[email protected]>
Fixup both Qt*.framework/Versions/$V and Current

seems like people change at will which one gets symlinked

1d0ffd9ce224000eb60a7c1c20c8a59a7fe92f7c authored almost 3 years ago by Julianus Pfeuffer <[email protected]>
Update CMakeLists.txt

9c8ac62523dc57a6dd011c1fd73bd9dd2f86f066 authored almost 3 years ago by Julianus Pfeuffer <[email protected]>
Minor fixes + computeRank test fix

6f275ac6a69e74ba7e9f39d7b26afc608b02434f authored almost 3 years ago by khue.nm <[email protected]>
[ADD] MzTabM support for AccurateMassSearch (based on IdentificationData) (#5744)

* Prototyping of novel ID datastructure in accurate mass search

* cleanup and todos

* add ...

aa03c7f187069d9e7aaeca78a3ac453ec4c7c6d6 authored almost 3 years ago by Oliver Alka <[email protected]>
Merge pull request #5751 from jpfeuffer/fix/pymacdeps

[FIX] pyopenms mac fix dependency order

af9cf0dd3d5dd44956700e0465f64c2afdf962f8 authored almost 3 years ago by Julianus Pfeuffer <[email protected]>
Reduce warnings (#5750)

d7c7f7f30aacee1a5d85896a5380f5508a0ecf40 authored almost 3 years ago by Julianus Pfeuffer <[email protected]>
[FIX] pyopenms mac fix dependency order

7d5da7a8dc3be67807f482ce6a3d20ac77d66de1 authored almost 3 years ago by Julianus Pfeuffer <[email protected]>
Merge branch 'develop' of https://github.com/OpenMS/OpenMS into develop

f47b19daa2119c41bc66821a21225e0f5869a0c3 authored almost 3 years ago by bielow <[email protected]>
Merge pull request #5749 from tillenglert/fix/MSFraggerAdapter

Bugfix MSFraggerAdapter

0828c7e836cbab3357cbb11690609431fa28c3e2 authored almost 3 years ago by Julianus Pfeuffer <[email protected]>
Fixed the options of isotope error to match the ones of MSFragger

be6bda8b3918bb7b613e3134b83c45365e289f8a authored almost 3 years ago by tillenglert <[email protected]>
Bugfix of depracated MSFragger parameter

max_modifications_per_mod changed to max_modifications_per_peptide

e770528157d415c44f1c05e63f4be7bd247350c5 authored almost 3 years ago by tillenglert <[email protected]>
[FIX?] pyopenms nightlies. Wrong deps after CMake restructure?

d6c0c72cefc33f92ce729a1b5f6af8c602ebdb8f authored almost 3 years ago by Julianus Pfeuffer <[email protected]>
reduce boost math usage (#5742)

* reduce boost math usage

* removed extra include

* add missing cmath

* add sstream inc...

8c4c988be7339e3332f921e411edada64df8ca61 authored almost 3 years ago by Timo Sachsenberg <[email protected]>
use std::optional (#5723)

* use std::optional

* merge

7671b74fd9ff5bbc66b7f341c5c8bbcc948e19f8 authored almost 3 years ago by Timo Sachsenberg <[email protected]>
Update CMakeLists.txt

890662aa7e9c844c1d92dba2605bb8a525827e8a authored almost 3 years ago by Timo Sachsenberg <[email protected]>
move GNPSExport to lib (#5638)

* move GNPSExport to lib

* rebase

* add documentation

* Update GNPSMGFFile.pxd

* mis...

b8f8567f05e87e70c4fdc833f4c6ab24c9fe7077 authored almost 3 years ago by Timo Sachsenberg <[email protected]>
FLASHIda.cpp and FLASHIda.c PR comments have been addressed

544388a4ef44d3f59ee6ad63e02ddfe8ed3b21e9 authored almost 3 years ago by KyowonJeong <[email protected]>
Merge pull request #5352 from hendrikweisser/idfile-integration

IdentificationData updates, integration with tools, and SQLite-based file format

7f5009cfbabe74c126eece86f86cb9b7a5e4af62 authored almost 3 years ago by Timo Sachsenberg <[email protected]>
Merge pull request #5739 from OpenMS/jpfeuffer-patch-5

[FIX] Major error in pyopenms addon MSSpectrum

523b806bd47f11ef67ad86eb0a112142c1d21bbf authored almost 3 years ago by Julianus Pfeuffer <[email protected]>
add dll export (#5738)

d7b2b44494ad59ce4f9ae225853b8fdb69e1d89d authored almost 3 years ago by Timo Sachsenberg <[email protected]>
[FIX] Major error in pyopenms addon MSSpectrum

3d158d7245b1e10985962305a4f991c2f7c750ef authored almost 3 years ago by Julianus Pfeuffer <[email protected]>
Merge pull request #5730 from jpfeuffer/feat/betterPyOmsBuild

[FEATURE] Make pyopenms cmake better. And log output better.

738747e5279dd2600c565f6e7bb71f6e827aa585 authored almost 3 years ago by Julianus Pfeuffer <[email protected]>
update autowrap and other ifcases

ed63d87e97130a0c50d17ae527dabe645c1f01d2 authored almost 3 years ago by Julianus Pfeuffer <[email protected]>
[FIX] included MetaInfoInterface in IdentificationData copy c'tor and 'swap' method

d7b6cb79d9e2abefc570122671298ffd91f76aa9 authored almost 3 years ago by Hendrik Weisser <[email protected]>
[FIX] fixed ambiguities when using 'swap' methods (due to multiple inheritance)

e5fce43e520fba2cbf9a1d97a1ccd824f2972ce8 authored almost 3 years ago by Hendrik Weisser <[email protected]>
[API,TEST] added 'swap' method to MetaInfoInterface

a503602cb03274ee4cecf178de8e154ee30dcd8d authored almost 3 years ago by Hendrik Weisser <[email protected]>
Allow overlapping elution profiles in elution peak detection (#5734)

* allow overlaps of neighbors in elution peak detection

* add test

* update tests

* rev...

88f1ebf490d5e4b21bc36bbf8362dc754dcff3d0 authored almost 3 years ago by Timo Sachsenberg <[email protected]>
Normalize intensity before calculating cross correllation

bef4bf8e19831c93c09d8f3667b10906d3e89e00 authored almost 3 years ago by khue.nm <[email protected]>
[FIX] Add MassTrace ctor (#5737)

688c40748f09e191996105d98e983598c98ab0e3 authored almost 3 years ago by Julianus Pfeuffer <[email protected]>
Merge branch 'develop' into idfile-integration

a4b7e8594f458a64dc598c9ee916a33444b41c14 authored almost 3 years ago by Julianus Pfeuffer <[email protected]>
Merge pull request #5720 from OpenMS/dhanmoni_gsoc21_toppview

Dhanmoni gsoc21 toppview

88689f58eb50c807b4e82717feb5b6e461f607ca authored almost 3 years ago by Julianus Pfeuffer <[email protected]>
Review comments and fix exit code.

bea90eb2c75e00708844466d1e0fb67e93131e0d authored almost 3 years ago by Julianus Pfeuffer <[email protected]>
Layer refactor (#5733)

* rename function to better describe its purpose

* [DOC, PARAM] improvements for TSGs paramet...

ee6ddd73c548e2c0271c7092fe5652fbc5ec82fb authored almost 3 years ago by Chris Bielow <[email protected]>
Fix overload

700ef15ae60556b75997b8dd65724bddcb4cfd2b authored almost 3 years ago by Julianus Pfeuffer <[email protected]>
[DOC, PARAM] improvements for TSGs parameters

d6424cdeb5951680d95c82a89f63b689647a749e authored almost 3 years ago by bielow <[email protected]>
rename function to better describe its purpose

842d6d5315e7e2532d50f32a6737a31c74167f60 authored almost 3 years ago by bielow <[email protected]>
restructure call to defaultsToParam_

696ff79f85a6871cd91b78e49abaa84e85a1a0ac authored almost 3 years ago by bielow <[email protected]>
- replace TheoSpecGen parameter UI with a more generic ParamEditor and make use of automatic parameter copying

- support spectra alignment using PPM instead of Dalton

d4ac008df09cd5890cef6d55b81ce6128a18dad5 authored almost 3 years ago by bielow <[email protected]>
allow to retrieve validStrings for a Param

12e52c9e16bdba3a6eaacc156cbc9bcb9876f51f authored almost 3 years ago by bielow <[email protected]>
[FIX] Resolve compatibility issues between IDRipper and IDMerger (#4957)

* [FIX] Resolve compatibility issues between IDRipper and IDMerger

* compile fix

Co-author...

1cbde3999d5279d357eca8536bf7cde572a242e0 authored almost 3 years ago by Leon Kuchenbecker <[email protected]>
initial implementation of output prefix parameters (#4527)

* initial implementation of output prefix parameters

as discussed in https://github.com/OpenM...

31228f1d0bd3180b65530988105dcc1b7710d4cf authored almost 3 years ago by M Bernt <[email protected]>
rebuild

be29996ca5858580870374b674138e8fbf06c253 authored almost 3 years ago by Timo Sachsenberg <[email protected]>
Cleanup of Qt warnings. Better table col sizes. Better fallback in JS.

f7c4d3b57d39bf14b46fe2308befdad1216da319 authored almost 3 years ago by Julianus Pfeuffer <[email protected]>
Remove more comments

c6a112f64c7c31e03b16c1ba58eab130f17767b1 authored almost 3 years ago by khue.nm <[email protected]>
Add author name

38862f1bbfe4f717c9a667313abd2bf0a82139b9 authored almost 3 years ago by khue.nm <[email protected]>
[FEATURE] Make pyopenms cmake better. And log output better.

6ec780c02bae4b25e7d8ac2118dceecc5e235636 authored almost 3 years ago by Julianus Pfeuffer <[email protected]>
Merge branch 'develop' of https://github.com/khuenm/OpenMS into swath_merge2

66832364f4a05bdece495a84ca4a203c1e91bd5d authored almost 3 years ago by khue.nm <[email protected]>
Fix seg fault and clean up code

cce5deb2aa84368864de6d2049a58db6c37d34e2 authored almost 3 years ago by khue.nm <[email protected]>
Update GNPSExport.cpp (#5594)

* Update GNPSExport.cpp

I added a few more details on the proposed workflow (command examples...

3c38f4887b5dce2638be08a1e56a7ed4305bfcc0 authored almost 3 years ago by Efi Kontou <[email protected]>
Calculating a Corrected Database Suitability (#4905)

* function in DefaultParamHandler

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

fc5e2d4af3de16c275058c816d7a59beaff25feb authored almost 3 years ago by TomW <[email protected]>
Merge branch 'develop' into idfile-integration

37dd83b0881cf1b434279730ce45740c39e4d6b8 authored almost 3 years ago by Hendrik Weisser <[email protected]>
[TEST] updated FFId and ProteomicsLFQ tests after revert

92517d070a4ea3de40e4bb9858166874d91a2d91 authored almost 3 years ago by Hendrik Weisser <[email protected]>
[API,IO] revert adaptation of FeatureFinderIdentifiation to new ID data structures (incl. ProteomicsLFQ)

a9990f0cf9ef7643fb4229be78ceecb21449a32a authored almost 3 years ago by Hendrik Weisser <[email protected]>
Merge pull request #5729 from cbielow/layer_refactor

Layer refactor

8eb6bdf92def92a50809d1b732c9cec722bf859b authored almost 3 years ago by Chris Bielow <[email protected]>
Apply suggestions from code review

Co-authored-by: Timo Sachsenberg <[email protected]>

2862f290a5698c7fd257de118ad43babffc31058 authored almost 3 years ago by Chris Bielow <[email protected]>
remove switching based on layer type

8ae673b68d1ff44634ebc0853ac84198fbe51f38 authored almost 3 years ago by bielow <[email protected]>
improve compilation time by removing includes

4d2403569fc298a90dc9c5927033af173d718791 authored almost 3 years ago by bielow <[email protected]>
minor code duplication removed

0531023ab1d8c411d67fab2cedda4b4cbea2de53 authored almost 3 years ago by bielow <[email protected]>
Merge branch 'layer_refactor' of https://github.com/cbielow/OpenMS into layer_refactor

75822449391916597aa35d4f74d0cb5c8a6ecdf2 authored almost 3 years ago by bielow <[email protected]>
some minor fixes

4f5e7c0a2e6a545b797616ae4f75c615fc42cf11 authored almost 3 years ago by bielow <[email protected]>
Fix/activation modes (#4918)

* [FIX] adopt activation modes to new obo

* [FIX] copy-paste error

* Update MzMLHandler.cp...

9b22a2955b45808a148793bd5ceb62df840978fe authored almost 3 years ago by Timo Sachsenberg <[email protected]>
Merge pull request #5722 from axelwalter/feature/massql-export

[Feature] export MSExperiment to data frames for MassQL

beeda3b07f317bdadba2e2089ea18ab54c1468c3 authored almost 3 years ago by axelwalter <[email protected]>
smaller test file

fc68a0592687ff6d4821ca55d3a28800b1a2afe8 authored almost 3 years ago by axelwalter <[email protected]>
fix relative path

cd83df9caa015c346d1ae4f5faa3893a54b89cac authored almost 3 years ago by axelwalter <[email protected]>
add massql test file

76d3387c211f12e4d65362fdc57b17e4c8f4f589 authored almost 3 years ago by axelwalter <[email protected]>
[REFACTOR] function to copy spectrum meta data / settings (#3913)

* [FIX] extract function

* [FIX] also copy unit

* Apply suggestions from code review

* ...

3103eb878971eee038395dfdc88b34f1c25f3c53 authored almost 3 years ago by Hannes Roest <[email protected]>
add fallback if no precursor

14e1887e2ecd2eeec2afb1bef9ec52cb7525884c authored almost 3 years ago by axelwalter <[email protected]>
test of cppcheck action (#5727)

* test of cppcheck action

* Update cppcheck.yml

* Update cppcheck.yml

* Update cppcheck...

c68aec83c212d6151cad6215644510a12911a14b authored almost 3 years ago by Timo Sachsenberg <[email protected]>
performance improvements

3f3879758c1bc263345177be81d87f7a0be65c11 authored almost 3 years ago by axelwalter <[email protected]>
update get_massql_df

f1fb96b6ae9f95c100a170862daff011a39cf493 authored almost 3 years ago by axelwalter <[email protected]>
Merge pull request #5721 from cbielow/layer_refactor

Extend LayerStatistics

fceec07d7ef2b9da225e8d70f05a1631d30d4ae2 authored almost 3 years ago by Chris Bielow <[email protected]>
Merge branch 'develop' into layer_refactor

6c074484e17c3d4eed335d0ed394dff111c67753 authored almost 3 years ago by Timo Sachsenberg <[email protected]>
add massql dataframe export for MSExperiment

63ec9f87764953eafb2503588b0b3379898a9bc9 authored almost 3 years ago by axelwalter <[email protected]>
add rvalue reference (#5685)

* add rvalue reference setter to PId

* Update src/openms/source/METADATA/PeptideIdentificatio...

d7218c71b18f90f96e603da269b81ee1023afbb3 authored almost 3 years ago by Timo Sachsenberg <[email protected]>
Merge pull request #4425 from bernt-matthias/topic/CVInspector-mapping-is-mandatory

CVInspector: the mapping_file argument is mandatory

ab1b8ef254f47a9a43b9c7138fafac3b41249726 authored almost 3 years ago by Timo Sachsenberg <[email protected]>
minor fix

3cf74f7c124f4646437dbb0314d1fb6e5a276eba authored almost 3 years ago by Timo Sachsenberg <[email protected]>
rewrite of layerstatistics

enable creation of distributions from LayerStatistics -- remove a lot of duplicate code in Canvas'

b7e62e8b14d717529acc71453516bee4ec6b5bcf authored almost 3 years ago by bielow <[email protected]>
missing rename

d2892621d29aab0539e77142ef75c900a427390b authored almost 3 years ago by Timo Sachsenberg <[email protected]>
reviewer comments

731eb4ea06324475f09e684032f0b46609095cd2 authored almost 3 years ago by Timo Sachsenberg <[email protected]>
Merge pull request #5719 from timosachsenberg/fix/compile_warnings

fix compile warnings

23c3063a49644403cb852f932a7bcf633c45d7f4 authored almost 3 years ago by Timo Sachsenberg <[email protected]>
allow for horizontal and vertical layout

14789e2d91bf718b3414ae232275eb941ee77543 authored almost 3 years ago by timosachsenberg <[email protected]>
Use newest version of action

fae01cb874a1de111ec47a75e070f0430dc713e0 authored almost 3 years ago by Julianus Pfeuffer <[email protected]>
Do not use minus in step IDs??

20bc0b7a83b2765a9bc01847b80aa08a831d8110 authored almost 3 years ago by Julianus Pfeuffer <[email protected]>
fix compile warnings

c792d3928031877f27b9cb1232f0d5217a63a74a authored almost 3 years ago by timosachsenberg <[email protected]>
add missing type

6dd17ce7f24d50ff69a0f904bd9f2c55d0fe97bb authored almost 3 years ago by Timo Sachsenberg <[email protected]>
wrong output in clang-format GH action

12656aa640abfdd0efb3611f6c42d09b0d72e239 authored almost 3 years ago by Julianus Pfeuffer <[email protected]>
merge develop

261cfd6774692f9ac3be58bea7e1fc95e594f910 authored almost 3 years ago by Timo Sachsenberg <[email protected]>
Merge pull request #5718 from OpenMS/jpfeuffer-patch-5

Only run clang-format if sth was changed

6eadea1e3ecf1df77e6eb432d46446687e3cff52 authored almost 3 years ago by Timo Sachsenberg <[email protected]>
add docs

565ea9b20e40fa97557953d3831824e1499b5e5b authored almost 3 years ago by bielow <[email protected]>
Only run clang-format if sth was changed

8f3dc5ebe7b76396078f39dc049fc971b4c08cbe authored almost 3 years ago by Julianus Pfeuffer <[email protected]>
set column limit to high value

5caaa89e3f1e7c13909899fb536940c0233a1e55 authored almost 3 years ago by Timo Sachsenberg <[email protected]>
Merge pull request #5716 from OpenMS/feature/update_automatic_rebase

Update rebase.yml

60da4736f4f317393f1d91a571ac65b1ef225311 authored almost 3 years ago by Timo Sachsenberg <[email protected]>
Update rebase.yml

d5d245fff3a19fc930fc11a06e1d28e911720e9b authored almost 3 years ago by Timo Sachsenberg <[email protected]>
Merge pull request #5715 from OpenMS/feature/update_clang_format

clang-format version 13

bca0a861ca176d9e551667caffc6fdcae02f6bf0 authored almost 3 years ago by Timo Sachsenberg <[email protected]>
Update openms_clang_format_add_and_commit.yml

faa16d4b6df2f417cdd19df07a7a1378fcb88e26 authored almost 3 years ago by Timo Sachsenberg <[email protected]>
clang-format version 13

b978546713634b7b1a2e2acb3f6bb34c9be5fe95 authored almost 3 years ago by Timo Sachsenberg <[email protected]>
Merge pull request #5713 from cbielow/layer_refactor

Layer refactor: StatisticsDialog

d11477e182ca63c34b3f0a314ffd465541c0d65d authored almost 3 years ago by Timo Sachsenberg <[email protected]>
explicitly add `containsDIM()` functions

c1e1ca9c70af4f3ff6e38849d6b67046639d75e5 authored almost 3 years ago by bielow <[email protected]>