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

Merge pull request #765 from FabianAicheler/feature/DB_removal

[FEATURE] removed database support

cf6a7a9162b3b0e52cc4973ca8030c6717b748ee authored over 10 years ago by Stephan Aiche <[email protected]>
replaced remnant DoubleReal

ba000c9e6529c9176b1fdacf32f8008dcc2262d2 authored over 10 years ago by Chris Bielow <[email protected]>
replaced remnant DoubleReal

e7c7e007157dc1fc2b9148f66eefbc196bbf041b authored over 10 years ago by Chris Bielow <[email protected]>
Merge pull request #776 from hendrikweisser/fix-idpep-mascot

[FIX] fix for IDPosteriorErrorProbability on Mascot search results (#740)

367c203e169666ea37d852d86ddbb3f904394b68 authored over 10 years ago by Stephan Aiche <[email protected]>
Merge branch 'fix-idpep-mascot' of https://github.com/hendrikweisser/OpenMS into FidoAdapter

Need the fix of the "prob_correct" option in IDPosteriorErrorProbability.

7a8f8b78985af766c05d237d830d9e8bc0aa1a1c authored over 10 years ago by Hendrik Weisser <[email protected]>
[FEATURE] Added new TOPP tool FidoAdapter (runs the protein inference engine Fido).

Work in progress.

520def7ee03dd3664d0266512de6fad6e70d691c authored over 10 years ago by Hendrik Weisser <[email protected]>
changes after rebase onto develop

40ceb4be115ec4967bc68be87012479e2a6f0923 authored over 10 years ago by Chris Bielow <[email protected]>
minor optimizations to DTAExtractor

07e5d84e3672726a6adb49853883810539ac1449 authored over 10 years ago by Chris Bielow <[email protected]>
removed sysinfo remnants

d807e3fb3c445643c7c6a89698372e1409f3bfea authored over 10 years ago by Chris Bielow <[email protected]>
removed hopefully all 'RT' and 'MZ' metavalues

Conflicts:
src/openms/source/METADATA/PeptideIdentification.cpp
src/tests/class_tests/openms/s...

e1bb72a0e773ffcabc983d8cc08e55f4590aeb78 authored over 10 years ago by Chris Bielow <[email protected]>
removed hopefully all 'RT' and 'MZ' metavalues

Conflicts:
src/openms/source/METADATA/PeptideIdentification.cpp
src/tests/class_tests/openms/s...

1ed87d64e0f01dd83113a9c5c5fff96159a48894 authored over 10 years ago by Chris Bielow <[email protected]>
Merge pull request #789 from cbielow/winDoc

small fix to Win install doc for VS2013

5c1276c9e5f21dd328a8193dfb3960461866fae3 authored over 10 years ago by Hannes Roest <[email protected]>
added additional safety measure, which we can remove when releasing

Conflicts:
src/openms/source/METADATA/PeptideIdentification.cpp

e6b711dab52117f59ec80cba397490f5c08fd91a authored over 10 years ago by Chris Bielow <[email protected]>
small fix to Win install doc for VS2013

8b454be6b16074a66c36a3e1b474a1bee30b69f2 authored over 10 years ago by Chris Bielow <[email protected]>
minor

3ae27df09751e44f450408fb20a8daec364dc11c authored over 10 years ago by Chris Bielow <[email protected]>
renamed

92a952e93602f3319053ba9a276a228df84fdf97 authored over 10 years ago by Chris Bielow <[email protected]>
minor

c25c4f36f63ba9ed29461e0703988b899e5da010 authored over 10 years ago by Chris Bielow <[email protected]>
[API] simplify API of MSDataCachedConsumer

- it is now longer necessary to know the number of spectra and
chromatograms beforehand

98ea3b36cc2ecdaff5b075aa8eeb78b1cc1a5b31 authored over 10 years ago by Hannes Roest <[email protected]>
[DOC] clearer documentation

b14cef596856b4ec57fb3cb8c626d032d60f89a9 authored over 10 years ago by Hannes Roest <[email protected]>
[FEATURE] change file format of cached files

- write spectra and chromatogram number at the end of the file
- allows to start writing spectra...

c9bf03ae81fdfcbf761132e82c7b8b1afb9c9b80 authored over 10 years ago by Hannes Roest <[email protected]>
added generic R Node to GenericWrapper, along with an exemplary R script and TOPPAS pipeline

4a7be7184643a8df3f5073f4eb22d58bdd216bee authored over 10 years ago by Chris Bielow <[email protected]>
[FEATURE,PARAM,TEST,DOC] Added option to annotate protein hits with target/decoy tags in PeptideIndexer.

Also made cosmetic changes in PeptideIndexer documentation/log output and added a test for the p...

cf917ad95c414fd5e93af816a3a69f7b5a5f91a8 authored over 10 years ago by Hendrik Weisser <[email protected]>
doku fixes, remove QtSql from src/openms/cmake_findExternalLibs.cmake .

73b06f6b44266eaabd63387bdf1b83e0493de731 authored over 10 years ago by Fabian Aicheler <[email protected]>
Removed DBConnection, and methods using it, TOPPView buttons, etc

17fc1d5a800380c049cb75a0f6ddfc8d524b990a authored over 10 years ago by Fabian Aicheler <[email protected]>
Removed PersistentObject, and uses etc of it. DBRemoval should be complete

05e93b82cb676b3bdb91a82e177a560ece7f2e44 authored over 10 years ago by Fabian Aicheler <[email protected]>
ripped out DBAdapter (PersistentObject and DBConnection left in until sure that not needed) and removed methods using/building up on DBAdapter, docs, tests, etc

f2ac37c56ebdecca6871c1d5cc21762a7d730f40 authored over 10 years ago by Fabian Aicheler <[email protected]>
DB_TEST FLAG aus doku entfernt, nehme an dass es sich auf die DB Klasse bezieht.

087ff01b7379bc8a697207626b544d67bcb24466 authored over 10 years ago by Fabian Aicheler <[email protected]>
Put VisualStudio error question back into FAQ

cb06428f896523edb450c8738b3e6fea937a3189 authored over 10 years ago by Fabian Aicheler <[email protected]>
removed oxygen entries

451d12021ed3f35a9a53cb619421a60a93aa5a74 authored over 10 years ago by Fabian Aicheler <[email protected]>
Removed db from ToppView Preferences. Removed overlooked DB tests

b57ba46b796069ceb0473e9fcc0cde60b5aaa7a0 authored over 10 years ago by Fabian Aicheler <[email protected]>
[NOP] removed now unused pyopenms.cmake

33064b074fba94ffbc899f7f95d490c30a1bfc52 authored over 10 years ago by Stephan Aiche <[email protected]>
[BUILD,PYOPENMS] moved pyOpenMS to src to allow a proper integration into the build system

0205736a15273e06a1e50009beb2fca988bd1757 authored over 10 years ago by Stephan Aiche <[email protected]>
[FIX] replaced 'DoubleReal' by 'double' in accordance with commit 4d40981a248cf4757f2e68668361f8eb68c40c99

87b6ca839370f049f7fca76351308fb4024a746c authored over 10 years ago by Hendrik Weisser <[email protected]>
Merge branch 'develop' of https://github.com/OpenMS/OpenMS into fix-idpep-mascot

386efe4931c6e49e665e7254ef0cd495456be5c0 authored over 10 years ago by Hendrik Weisser <[email protected]>
[TEST] Speedtest

fix speedcheck

ab3f43c75fa5f2893ffb8c92ef9d1104ef194835 authored over 10 years ago by Hannes Roest <[email protected]>
[TEST] add further tests

d4c22605e74cbf6a2aba5928d2d8944022f513c6 authored over 10 years ago by Hannes Roest <[email protected]>
[TEST] adopt tests to Wm5 splines

b8cb483e490b146076bf4a8b962d3e121d877df5 authored over 10 years ago by Hannes Roest <[email protected]>
[FEATURE] switch to Wm5 splines

9b95c60dda602515a88e8a2727db40a5987834e3 authored over 10 years ago by Hannes Roest <[email protected]>
[FIX] adopt tests for Eigen splines

7340f29a10a8ee4999b1892f543183b08ec0d13f authored over 10 years ago by Hannes Roest <[email protected]>
[TEST] re-add old test files

- add new test files (after change by GSL removal)

f65ea0de1daa1cf832a31cd727d2a899279f6c3b authored over 10 years ago by Hannes Roest <[email protected]>
[FIX] switch to new Eigen spline

- use Eigen splines instead of gsl

0672a478d4ad4c7a25bf2703af452760cece6469 authored over 10 years ago by Hannes Roest <[email protected]>
Merge pull request #785 from timosachsenberg/fix/VS2013CompileFix

[FIX] VS2013 compile fixes

001beee4bac5e4bac5dad2169f78da997370334b authored over 10 years ago by timosachsenberg <[email protected]>
[INTERNAL] move code to cpp file

825f1c7fd63b254e1956e4a508d7b89a85d32c19 authored over 10 years ago by Hannes Roest <[email protected]>
[TEST] remove test to show numerically compatibility

- remove test to show numerically compatibility between the
SignalToNoiseEstimatorMedian and r...

1af49ae1daba4d3d6214de40d7e577cf0b65c835 authored over 10 years ago by Hannes Roest <[email protected]>
[FEATURE] PeakPickerMaxima

- maxima-searching PeakPicker based on PeakPickerHiRes
- this peak picker uses a cleaner interfa...

7f7d6e716bad0f416ec56b02b27139316b5c4239 authored over 10 years ago by Hannes Roest <[email protected]>
[FIX] performance improvement

- replace std::map with two doubles to keep track of current status of
peak

c130f6b12d2127ce30b98c23aebcd572cb9f7a5e authored over 10 years ago by Hannes Roest <[email protected]>
[FEATURE] SignalToNoiseEstimatorMedianRapid

- A SignalToNoise estimator based on median calculation but
significantly faster than the Sign...

df6e8d5723d16ecd29535a4a4fb7861664a44cd4 authored over 10 years ago by Hannes Roest <[email protected]>
[TEST] add test for SignalToNoiseEstimatorMedianRapid

934dc0e0281f55298994cafc80dede554c3f6016 authored over 10 years ago by Hannes Roest <[email protected]>
[FIX] also add MSNumpress python test to list of tests

- ammend commit 9500476d59d38b5ffe0520d2d7fec8cc52c91d19 (r12099)

a33517ba4167332fff5c3b3e5bfcf7327fe3b757 authored over 10 years ago by Hannes Roest <[email protected]>
[FIX] VS2013 compile fixes

b02a86792e1f876208fdf6f0e8469d8b535b2976 authored over 10 years ago by Timo Sachsenberg <[email protected]>
Merge pull request #749 from hroest/feature/Python3

Feature/python3

1289551cf13e14f4b79d4c3cdb3c0bf05826e216 authored over 10 years ago by Hannes Roest <[email protected]>
[TEST] fix integration and memory tests

60a74feff4548b783805dc13d9eff52ce77ecd55 authored over 10 years ago by Hannes Roest <[email protected]>
[TEST] fix collections and consumer

44f4072e31960ebacbe3b77fd26c56855aa98ef4 authored over 10 years ago by Hannes Roest <[email protected]>
[FEATURE] Python 3 support

- switch to absolute imports
- use print function
- replace cPickle

f6e8c6ceb23bb73ea3f82dadb6ac170f057a232e authored over 10 years ago by Hannes Roest <[email protected]>
[FEATURE] Python 3 support

- switch from str to bytes in addons

354566840ebe418a48528404cd2768ac9057a8d7 authored over 10 years ago by Hannes Roest <[email protected]>
[FEATURE] replace str with bytes in converters

- use now bytes in all custom converter classes

74f0fd767d5ae7cc95304346de2dd240250bff34 authored over 10 years ago by Hannes Roest <[email protected]>
[TEST] switch from str to bytes in tests

14b8022e38405d4b7e6bae41ebb2cc177eb9caf4 authored over 10 years ago by Hannes Roest <[email protected]>
[FIX,BUILD] fix build issue in pyOpenMS

fix Cython code that does not use const in a function which will take
arguments of type "const c...

9d35b73ec389cce943cc163724dde20cd0a26c68 authored over 10 years ago by Hannes Roest <[email protected]>
Merge branch 'develop' of https://github.com/OpenMS/OpenMS into fix-idpep-mascot

33a7a95700421487460a7cb319fcae6df6f91207 authored over 10 years ago by Hendrik Weisser <[email protected]>
[FIX-#782,TEST] Fixed #782 ("IDPosteriorErrorProbability: wrong score annotation if 'prob_correct' is set"), added test case

With "prob_correct", use "Posterior Probability" (without the "Error") as score type and set "is...

64c1470848eb1c39345615efe4d74dd8ab28e85f authored over 10 years ago by Hendrik Weisser <[email protected]>
[BUILD] fixed linker error due to variable shadowing

924d70df90db890f723f17459531500248a36168 authored over 10 years ago by Stephan Aiche <[email protected]>
[fix] removed another function from AASequence

2b82528643e38385a8f37863903d60c4ba21e556 authored over 10 years ago by Timo Sachsenberg <[email protected]>
[BUILD,NOP] reduced verbosity of openms_add_library function and added documentation

5e7bc0f18f11878151b82d4eb82d86e84c2b9231 authored over 10 years ago by Stephan Aiche <[email protected]>
[BUILD] implemented installation of config files

* allows to compile easily against OpenMS after installation
* fixed some minor installation i...

3684538912ec0cdc2999a16e8e8bd30726faed6d authored over 10 years ago by Stephan Aiche <[email protected]>
[BUILD] cleanup of export macros

883156b852f66eac75b8edfc36aec99a38ad0ef7 authored over 10 years ago by Stephan Aiche <[email protected]>
[BUILD] redesigned export of targets

Conflicts:
CMakeLists.txt
src/openms/CMakeLists.txt
src/openms_gui/CMakeLists.txt
src/opensw...

169586049ec0bd06ae9697262a0331abcd116c27 authored over 10 years ago by Stephan Aiche <[email protected]>
[BUILD] switched OpenMS to new openms_add_library function

7917e16349aa6cfa43a918abed6784e8daab36f1 authored over 10 years ago by Stephan Aiche <[email protected]>
[BUILD] fixed dependency issue after renaming library collections

* e.g., OPENMS_LIRBRARIES -> OpenMS_LIBRARIES

8399fe253ed6df241fd278d3e9492bc87f6e2396 authored over 10 years ago by Stephan Aiche <[email protected]>
[BUILD] added some verbosity to openms_add_library macro

ffad177312c80c3e6a2bb0c0a191628c9cc19a36 authored over 10 years ago by Stephan Aiche <[email protected]>
[BUILD] removed cuda and tbb support for FFIsotopeWavelet

7a75774ee7f4655d667623061bc1a7e5f5bee7a6 authored over 10 years ago by Stephan Aiche <[email protected]>
[BUILD] switched OpenMS_GUI to new openms_add_library function

d3dd5cef96845b4badd316e27894aa88dffd568f authored over 10 years ago by Stephan Aiche <[email protected]>
[BUILD] switched SuperHirn to new openms_add_library function

54cd4da6c84aca4435cde4865971220e979f6ac4 authored over 10 years ago by Stephan Aiche <[email protected]>
[BUILD] switched OpenSwathAlgo config to auto generated

3e442e8eaf1e353df6803cd44bf71d159801a15a authored over 10 years ago by Stephan Aiche <[email protected]>
[BUILD] created OpenMS specific add library function

* manages headers and system includes
* exports the necessary variables for use by other subpr...

c26388520c295393acf58355ead1438fb007e5f3 authored over 10 years ago by Stephan Aiche <[email protected]>
[BUILD] enabled unity build in openms_add_library function

* moved unity build and copy_dll code to add_library_macros.cmake file

0661ba9ce382eea10c630b72245c15d706e4d4ed authored over 10 years ago by Stephan Aiche <[email protected]>
[FIX] removed redundant methods from AASequence interface

5049d2ce8ef02781850b800f0258feafe5e8288e authored over 10 years ago by Timo Sachsenberg <[email protected]>
[FIX] fix Swath window estimation

- store center of a window in a SwathMap
- allow reading of Swath windows in any random order (m...

86c362e926052fc7a870b55e09c6d9e9ca9b2546 authored over 10 years ago by Hannes Roest <[email protected]>
Merge pull request #781 from hroest/fix/OpenSwathFixes

Fix/open swath fixes

c29f8622b536d2b540b5e3518191ba81c1ca6701 authored over 10 years ago by Hannes Roest <[email protected]>
Merge pull request #779 from timosachsenberg/feature/DoubleRealRemoval

[FIX] replaced DoubleReal and Real by double and float.

4c74c21f9e158921e82eb6e9b95acecc50b95a4c authored over 10 years ago by Hannes Roest <[email protected]>
Merge pull request #784 from aiche/feature/fix-macosx-pyopenms-errors

[FEATURE] fix macosx pyopenms errors

07f4e62b5fd6f480bf09d0f0d0a20a5d7d191264 authored over 10 years ago by Hannes Roest <[email protected]>
[BUILD,PYOPENMS] fixed some more pyopenms compile issues on mac osx

122275f6eb2b2c02e454e0e88de25e9044242678 authored over 10 years ago by Stephan Aiche <[email protected]>
[BUILD,PYOPENMS] made pyopenms.cmake a bit more cmake like

8dd550475e7636e1f3a8dc300c8c75f3679ea1e6 authored over 10 years ago by Stephan Aiche <[email protected]>
[BUILD,PYOPENMS] removed offending link args

6d9dcf2609968d5bb9c2e2399dd07af371f7c2e3 authored over 10 years ago by Stephan Aiche <[email protected]>
[BUILD] fixed macosx extra libs (reduced to subset, CoreServices, CoreFoundation, OpenGL)

dca20c9a2abebdd99b2a6a7303f6442c883ec12c authored over 10 years ago by Stephan Aiche <[email protected]>
[INTERNAL] use 'boost::math::isnan' for NaN test (self-comparison may be optimized out with 'fast-math' compiler flag)

daa19b8c53d25e7953b0cd666af9df610f6d96d9 authored over 10 years ago by Hendrik Weisser <[email protected]>
[fix] replaced DoubleReal and Real in pxd files

ad4f46bc60d3266c09053de5079040471323a311 authored over 10 years ago by Timo Sachsenberg <[email protected]>
[FIX] pyOpenMS changes

960e5983319a821d3d36b43db3b2232d4c52ccb5 authored over 10 years ago by Timo Sachsenberg <[email protected]>
[FIX] allow empty RT input

- OpenSwathWorkflow allows to not specify an iRT input file (it will
simply assume that no iRT...

002d8078ff1d18fa4bd2b15ab1637c704a9889f3 authored over 10 years ago by Hannes Roest <[email protected]>
[FIX] move computation of overlapping features

- perform computation of overlapping features _after_ the boundaries are
re-computed

773c5f2d427251850ddfc11cff9c60b8a9006d56 authored over 10 years ago by Hannes Roest <[email protected]>
[DEBUG] add option to get irt chromatograms for debugging

2f5f47207166192edd2fd457e08ae991bef74db0 authored over 10 years ago by Hannes Roest <[email protected]>
[FIX] replaced DoubleReal and Real by double and float

4d40981a248cf4757f2e68668361f8eb68c40c99 authored over 10 years ago by Timo Sachsenberg <[email protected]>
amend

7b3b99b95c138cc954eeb63c6472e14dab190123 authored over 10 years ago by Timo Sachsenberg <[email protected]>
[FIX] factoring out AASequence parse function

5c0ab7e40dba39bd5178d7ee5d9d871bb427cb9f authored over 10 years ago by Timo Sachsenberg <[email protected]>
Merge pull request #754 from uweschmitt/feature/pyopenms_float64_for_peaks

[PYOPENMS] changed extra methods on MSSpectrum

dfa1d5af5ba59d6b52a15fdd6966483b0f61f90c authored over 10 years ago by Hannes Roest <[email protected]>
Merge branch 'develop' of https://github.com/OpenMS/OpenMS into fix-idpep-mascot

Conflicts:
src/topp/IDPosteriorErrorProbability.cpp

750132b613a9c5957e137412e76f9ef443d1fd49 authored over 10 years ago by Hendrik Weisser <[email protected]>
[FIX] removed redundant functions from AASequence interface

e04c4ff7fc0a301005d88075d16f1af546521c31 authored over 10 years ago by Timo Sachsenberg <[email protected]>
Merge pull request #775 from hroest/fix/typos

[FIX] typos in the CMake file

d99263d948fefd794b12569f47a7025ca9337357 authored over 10 years ago by Stephan Aiche <[email protected]>
[FIX] typos in the CMake file

d6afeeffcea2af98dcac25fbd9995ecf79e4a8e9 authored over 10 years ago by Hannes Roest <[email protected]>
Merge pull request #750 from uweschmitt/fix/pyopenms_streampos_conversion

[PYOPENMS,FIX] fixed streampos->long conversion

9bff51909e9a9547963ee2570919980b85a76df7 authored over 10 years ago by Hannes Roest <[email protected]>
Merge pull request #764 from aiche/feature/libsuperhirn

[FEATURE] lib superhirn

79bb8e8029cd7481d1b3ab610b29849a098de571 authored over 10 years ago by Hannes Roest <[email protected]>