github.com/OpenMS/OpenMS commits | Ecosyste.ms: OpenCollective

[FIX] move GumbelMaxLikelihoodFitter function to cpp

- remove Eigen dependency from header file

f9dba4f099933140f994c4f26836c22c37b16894 authored about 3 years ago by Hannes Roest <[email protected]>

Merge branch 'develop' into feature/header_cleanup

b102743bf6a3421233f7714d46d899b3a44136b0 authored about 3 years ago by Hannes Roest <[email protected]>

Merge pull request #5609 from cbielow/fix_doxy

Fix doxygen warnings

f99a891af86c7ee254d9cc719059bf921e6429e5 authored about 3 years ago by Chris Bielow <[email protected]>

Merge branch 'develop' into fix_doxy

d4a494adc4d8c3325dd4c0fcc7c2363fe6bbc834 authored about 3 years ago by Chris Bielow <[email protected]>

[pyopenms] use np.empty instead of np.zeros (#5607)

* [pyopenms] use np.empty instead of np.zeros

for a little bit of speed. We know we will init...

6052e35a363f70577ffcdd966615be447680306b authored about 3 years ago by Julianus Pfeuffer <[email protected]>

Feature/header cleanup inc (#5608)

* [FIX] move Qt headers

* [MOVE] split String Utils

- split into StringConversions (uses b...

92be666110942d43987e12f5639fef084229f73f authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] Windows fix

c92087a38192f6c707e93d1e28ef667380103ff7 authored about 3 years ago by Hannes Roest <[email protected]>

Merge branch 'develop' into feature/header_cleanup

b4d5ddb66e71c4643c775d14dda65bb63f8e3713 authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] missing Windows include

977a63c7fa177f19869b60013f280ddfab1559db authored about 3 years ago by Hannes Roest <[email protected]>

fix forgotten include

a51d68068c28cfc449253ddc8af669dbfcdfdb14 authored about 3 years ago by Hannes Roest <[email protected]>

fix

f0c57e93cca5c0b57919ab82ea52a9c9bb8dfb18 authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] check for self-assignemnt

cb1983a726bd1821bc1c7649d91d6ffb348809ac authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] go back to boost because of clang

7b63a863d6e350dfbc452d50653ed6d58f417469 authored about 3 years ago by Hannes Roest <[email protected]>

[PYOPNEMS] remove fxn

96c12bd8981cb886b66fc5d9d22e4fde1ef55d81 authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] Windows fix

cb2c2925847dff020c10909bc354ab59e41e9f02 authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] Windows fix

8eda721c28e8da136c9e9b92adb4162c9883f8e9 authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] compile fix

f0d95c2cbebc8966c18753e30ce35bf6bc15f23e authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] add LogStream where required

82cfede9610925bbe5b23ec3730f50f3656bf53a authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] test fix

1f7fb53a334bcf6cd3a2f40dc87d74b27bb60ed5 authored about 3 years ago by Hannes Roest <[email protected]>

fix doxygen warnings

8cb90e31e7069a5be0e5c8437c706b048dbc1df0 authored about 3 years ago by bielow <[email protected]>

Merge branch 'develop' of https://github.com/OpenMS/OpenMS into develop

fb364fa8c3ddf409f26c7c91b98915dc090ae30a authored about 3 years ago by bielow <[email protected]>

[pyopenms] fix wrapping of idXML store (#5605)

0596a671b0f41dc33fb4ede9ded9f92c58e8c248 authored about 3 years ago by Timo Sachsenberg <[email protected]>

[pyopenms] deisotoper add other (common) wrapping of optional parameters

515640d614a85015cbc3b158964c39d4008b846e authored about 3 years ago by Timo Sachsenberg <[email protected]>

Fix/comparator utils (#5601)

* add missing elements

* replace comparator with lambda expression

* refactor mapalignerba...

32942281e0c707ddbbd7ecd3f9ae5cb187dec9ed authored about 3 years ago by JangJang3 <[email protected]>

[FIX] move MaxLikeliFitter1D to cpp

b933787a7b8c49c050d672c6e685cc991758b631 authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] several boost header fixes

3e96a2eacd0f7568c0e85ea4e9c7a157a18cbb48 authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] fix STL headers

- remove STL dependencies
- remove <algorithm> headers where appropriate

052cbd455bb8b7d78cd8f8e76faf624e839163ce authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] move TargetedSpectraExtractor to cpp (I/O)

d986426db6bb6a5eb84401d03f8f86d79268cad2 authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] move XMLHandler to cpp

- remove STL dependencies

f862ba9eb8336dba910f33ceefc70c9c16323ccb authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] move FastLowessSmoothing function to cpp

- remove STL dependencies

de8039ec5b22fffa9b4af4d88c79ecc0bcd121f8 authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] fix iostream headers

- remove STL dependencies

fa5214a5bf033b0f214e1f4c1a963dc4978f1081 authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] move GaussFilter to cpp (I/O)

- remove LogStream dependencies

48cd6c49357adf44bf2aa88861da0238f55041a0 authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] fix LogStream headers

11544ae89756e211d6bc95c9763c51516e69a088 authored about 3 years ago by Hannes Roest <[email protected]>

[MOVE] extract StringView

- remove STL dependencies
- extract StringView.h into its own header file
- otherwise String.h p...

e333f629867be464bc2ef31ccc4eb67bfa0a9f05 authored about 3 years ago by Hannes Roest <[email protected]>

[MOVE] move BinnedSpectrum

b05a16e9b42a589ddafc7cbaf04a734e772c010e authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] move ConsensusMap to cpp (I/O)

26468d04f01d0d81c2004b62573a54cdb125b5bc authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] replace boost::unordered

- remove boost dependencies

2fb468d3efa6def32495c259034623bc950cae72 authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] remove boost::lexical_cast where possible

- remove boost dependencies

e153e912730a821ad2e88100b75f2167fd3dfe80 authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] move TwoDOptimization to cpp

- remove Eigen dependency from header file

410f8f6a008a16a5736c00f51ec4aed30203b9a5 authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] move LevMarqFitter1D to cpp

- remove Eigen dependency from header file

afc5d31609ecb215ee349c9fed289ee2b25a2294 authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] move GumbelMaxLikelihoodFitter function to cpp

- remove Eigen dependency from header file

8015c70d99156642b97f065ac3baf088265feaed authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] move Eigen to cpp

d1bbbdfb58d1ed3691a9f710f19c9d11f36e8064 authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] move Eigen dependencies to cpp

a206bf1be8c1d0facae5e10ec97b8ffa02de76b1 authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] move ConfidenceScoring to cpp (boost)

144a5367b30163629508a9ebdbcb6c92bfa4f4f6 authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] move boost includes

- replaced boost::math::cyl_bessel_i with std::cyl_bessel_i function

36a0ef96105feff092552e1861134256f9d788e2 authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] move boost includes

1f8c860fd4058c1d0c3bfe8748ace6d787c4fff5 authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] remove unused fxn

940f24ccc25add550e1734340c50660d6ba65b29 authored about 3 years ago by Hannes Roest <[email protected]>

[MOVE] split String Utils

- split into StringConversions (uses boost::spirit)
- split into StringUtilsSimple (no Qt, no bo...

2c930cb8613f2a53f945fe458ab9ad7d790f7e14 authored about 3 years ago by Hannes Roest <[email protected]>

[FIX] move Qt headers

a2614a87dee88f8bf32e07cb86cdfc9ccde48af4 authored about 3 years ago by Hannes Roest <[email protected]>

FLASHDeconv peak count limit = 20k per spectrum.

848f08d779160f444675f6b831fe25582e122198 authored about 3 years ago by kyowonjeong <[email protected]>

Spectra are not stored if only meta data is read. (#5600)

5cb7abbf28a04ce698eb10953e0a511f691e3add authored about 3 years ago by Timo Sachsenberg <[email protected]>

Merge branch 'develop' of https://github.com/OpenMS/OpenMS into idfile-integration

dc07a82bc50cac2cdeac2600f5138bcb71cb73d1 authored about 3 years ago by Hendrik Weisser <[email protected]>

[FIX] FeatureFinderIdentificationAlgorithm: small fixes after last merge

5a681d21b787f4e04798dd7f94100f63db429646 authored about 3 years ago by Hendrik Weisser <[email protected]>

[FIX] IDFilter: small fix after variable rename; removed unused variables

1609eb6a7a6a24f04edb726469bde17665fdf676 authored about 3 years ago by Hendrik Weisser <[email protected]>

[TEST] added missing include in OMSFile test

93a6ce81b7844e1fae86dbdc1f89e78d359aa97e authored about 3 years ago by Hendrik Weisser <[email protected]>

[PARAM] IDMerger: ignore 'annotate_file_origin' (now on by default) for .oms inputs

d94980afd5920a6a1f3a441b01a3f03786804d27 authored about 3 years ago by Hendrik Weisser <[email protected]>

Feature/im calibration bugfix (#5595)

* [FIX] bugfix (actually use MS1 map)

* [FIX] use ms1 and ms2 for variable names

* [DOC] p...

e66b2c45ae29fab5fb97e4c4d0e69e75e1849b91 authored about 3 years ago by Hannes Roest <[email protected]>

Merge branch 'develop' of https://github.com/OpenMS/OpenMS into idfile-integration

5cd2dfde99375df740c7575a4d633ff6b30c177a authored about 3 years ago by Hendrik Weisser <[email protected]>

fixed unused variable warnings (#5597)

* fixed unused variable warnings

* Update IDFilter.cpp

Co-authored-by: timosachsenberg <sa...

0531793f20f0f3b1537955a08479fe76a0e3f1a0 authored about 3 years ago by Timo Sachsenberg <[email protected]>

[TEST] extended test of IdentificationData copy c'tor

83f48d5caea8c500d390ff9961cd91813ac271fd authored about 3 years ago by Hendrik Weisser <[email protected]>

[FEATURE,IO] FileConverter: convert between .featureXML and .oms (SQLite format) - thanks to Oliver Alka

1f7d3956896cf1f50e94cb27343b6d22f0c555ae authored about 3 years ago by Hendrik Weisser <[email protected]>

ParseMsAlign bug in windows fixed

ea822271206bc6334d0c3b8cb67f7ecdd9e59878 authored about 3 years ago by KyowonJeong <[email protected]>

SpectraMerger modified so precursor mass filter can be used.

d80455f61e91cbe4f5770ea9c050c10864b47ec7 authored about 3 years ago by kyowonjeong <[email protected]>

SpectraMerger modified so precursor mass filter can be used.

a251584ad0fc050551b9595d581f976c9afff2a3 authored about 3 years ago by kyowonjeong <[email protected]>

Merge pull request #5584 from OpenMS/feat/setModByMass

[Feature] make modifications better for pyopenms

cef7d2efb34c594ffe55a55029b8d3374675b16d authored about 3 years ago by Julianus Pfeuffer <[email protected]>

[FIX] forgot py binding for new methods

8dae186ea52365f855b4e44264ea607d08628847 authored about 3 years ago by jpfeuffer <[email protected]>

ms align parser added

4574cd991a579dad6eaf9303269f0a74082a475b authored about 3 years ago by kyowonjeong <[email protected]>

[FIX] add missing include (#5588)

4983800a82ff90e5033ab8e6ba66fdc1a9297462 authored about 3 years ago by Hannes Roest <[email protected]>

[FEATURE] add all the changes to the AAsequence interface as well

a0b48d5855b69b830d9d46c08b23efef2f8bdb54 authored about 3 years ago by jpfeuffer <[email protected]>

Merge pull request #5586 from OpenMS/jpfeuffer-patch-5

[GH Actions] remove cmake_find_debug

957046f067ab3db7531d868f31c60953f7d49b74 authored about 3 years ago by Julianus Pfeuffer <[email protected]>

[GH Actions] remove cmake_find_debug

1c77c0caf856e5f95a6bb0f663d80ba01c9aa477 authored about 3 years ago by Julianus Pfeuffer <[email protected]>

[action] pyOpenMS wheel patch removed

not needed anymore because of change in __init__.py

34a9624fccda2e94087d4251a8e0b42551e7ccab authored about 3 years ago by Timo Sachsenberg <[email protected]>

make reindexing the default (#5581)

* make reindexing the default

* move reindex functionality to SearchEngineBase

* moved imp...

78da0c9caf3a72069261298efd2d6e57f3b1d475 authored about 3 years ago by Timo Sachsenberg <[email protected]>

amend

041103000d631c1dd3a1e60ffb4069ebdea5d83f authored about 3 years ago by Timo Sachsenberg <[email protected]>

small fix to python wrapping of TransformationModelLinear

56002f9aebc4e5212dfb3924b6027cfc655f2ef5 authored about 3 years ago by Timo Sachsenberg <[email protected]>

[FEATURE] Make Modifications better for pyopenms

bb377fb46b2e0dcaf98e2cfccc376167d535c5d0 authored about 3 years ago by jpfeuffer <[email protected]>

Merge pull request #5583 from OpenMS/jpfeuffer-patch-5

[Pyopenms] Update help in __init__.py

0a9f260b9e096d5f97480a192f5d657eef003424 authored about 3 years ago by Julianus Pfeuffer <[email protected]>

Update help in __init__.py

79b84aeb684c216def299aa00e3cfee7be055d85 authored about 3 years ago by Julianus Pfeuffer <[email protected]>

ms1ft output bug fixed. (scan number report bug)

e169af49dd25ec79902de0a1d0f9209d1e1b73b2 authored about 3 years ago by kyowonjeong <[email protected]>

[Feature] basicproteininference on cxml (#5561)

* Refactor and add first cXML support to Basic Protein inference.

* Smaller fixes

* Add an...

efca0283b43b4fee57429e5bda90a8f393f8bb2c authored about 3 years ago by Julianus Pfeuffer <[email protected]>

[ADD] IDMerger annotate_file_origin default true (#5578)

* [ADD] set true

* [REFACTOR] Flag to StringOption (true,false)

* rm comment

* [FIX] ID...

47ca0202eb7f5e203f0ed2f1bb1823f302253e80 authored about 3 years ago by Oliver Alka <[email protected]>

bug fixed in DeconvolutedSpectrum test + FLASHDeconvWizard icon

commented

fd0e667255bab9527aef5449e3651beba2d3dc27 authored about 3 years ago by KyowonJeong <[email protected]>

Isobaric reporter ion option removed again... MS2 polished

6b65527ee07161b1d3ae7e180086d9f4e94fb18b authored about 3 years ago by kyowonjeong <[email protected]>

Isobaric reporter ion option removed again... MS2 polished

fbb60b3d9d5b08304c3bd66b1dfd5b86f79c9f5e authored about 3 years ago by kyowonjeong <[email protected]>

[Fix] missing cstddef for ptrdiff_t (#5576)

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

16e3051da64f1edec9261b86bbe9ac63d10eb340 authored about 3 years ago by Julianus Pfeuffer <[email protected]>

[Internal] Add ParamCTDFile to write Param to CTD File with only standard dependecies (#5475)

* Add ParamCTDFile class that allows to write Param data to a CTD file with only std dependencie...

f371456f368a6d2df8504752649df4048813266f authored about 3 years ago by Ruben Grünberg <[email protected]>

[FIX] AssayGeneratorMetabo Test (wo SIRIUS) (#5551)

* [FIX] AMG-test

* [ADD] internal sirius_executable check

* [FIX] typo

ddfbb579815265a7273ac99e59605db66555c662 authored about 3 years ago by Oliver Alka <[email protected]>

[refactor] moved percolator in file functionality into library (#5570)

* [refactor] move some Percolator in file functionality to library

* python bindings

* mov...

57e0126ed60b1a77f296e7310d0bd0659db880aa authored about 3 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #5572 from OpenMS/update/sm

update submodule

788310176fcfe3299049c1b246e2cea9797bc2b4 authored about 3 years ago by Julianus Pfeuffer <[email protected]>

update submodule

9fb46c161dc8c157bbb0a1e08a06f2ecc3a559ca authored about 3 years ago by Timo Sachsenberg <[email protected]>

adding-wrap-doc-method-21 (#5545)

* adding-wrap-doc-method-21

* FIX

* Update NLargest.pxd

Co-authored-by: Timo Sachsenber...

7c630702d1cdc744994dcf2621e86408b2b7ae5c authored about 3 years ago by Rahul Agrawal <[email protected]>

Added Unimod Modifications to parameters of MSFraggerAdapter (#5512)

* Added Unimod Modifications to parameters of MSFraggerAdapter

* Update src/utils/MSFraggerAd...

5f9195c967b1d996bab90a824136dc105cde081a authored about 3 years ago by tillenglert <[email protected]>

Merge pull request #5565 from OpenMS/featfix/isoErrPepXML

[FEATURE] Export isotope errors when reading pepXML

ce6c8d6427ca89360523ee97f1110bb80d8b4a89 authored about 3 years ago by Timo Sachsenberg <[email protected]>

[FIX] myrimatch tests

fc303f94e58e148ac3ec96fea58810514930e9b3 authored about 3 years ago by jpfeuffer <[email protected]>

Merge pull request #5559 from OpenMS/feature/enable_LTO

[CMAKE] option to enable LTO

f5626ffbc380c248f0e1f6128ca2018e1c92c920 authored about 3 years ago by Julianus Pfeuffer <[email protected]>

[FIX] PercolatorFeature tests. TODO at MSGF

ea9ea3f9a49d8ba0292ea86c58711d726d25cc10 authored about 3 years ago by jpfeuffer <[email protected]>

remove comment

20bdac1b5480e3b85aa2c228f901be498ef65c9d authored about 3 years ago by jpfeuffer <[email protected]>

add isoerror itself to extracted features for perc for all pepxml SEs

4dc62d1dd085a04a301e4bdba7e25c494a6b2245 authored about 3 years ago by jpfeuffer <[email protected]>

remove unused

22be4896faae72a405c45d766542f1687999d3c9 authored about 3 years ago by jpfeuffer <[email protected]>

Merge branch 'develop' into featfix/isoErrPepXML

7fc55bea58b970576e559c9e6140b52fac06469b authored about 3 years ago by Julianus Pfeuffer <[email protected]>