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

[FIX] updating to code style, removing built-in inverseMatrix function

f20b4736826f84c8be40fc31ea2c346b2e89afad authored about 4 years ago by Ahmed Khalil <[email protected]>

Remove extra opts

63aa2a3bdb454e973d67889ebbc7026ae94ae033 authored about 4 years ago by jpfeuffer <[email protected]>

Merge pull request #4960 from poshul/ll3_modifications

Ll3 modifications

e83a6198d830636923a4799f8715fe6351c49186 authored about 4 years ago by jpfeuffer <[email protected]>

[fix] removed trailing whitespace

f7956b628c2f88866849c397d32cf9dcc58c1121 authored about 4 years ago by Samuel Wein <[email protected]>

refactor layer annotation; support TOPPView menu entries on/off based on layer type

7af741a971e5645466c43d4d6918e858545b6ff1 authored about 4 years ago by Chris Bielow <[email protected]>

Extension of FlagSet and FileTypes classes

832840ad395b9b0f345edefcd84bf71e8d9af590 authored about 4 years ago by Chris Bielow <[email protected]>

minor cleanup

cff88019798ecaec48f9eee6543d9b30f8e06399 authored about 4 years ago by Chris Bielow <[email protected]>

fix missing newline

7c8bcc906a83392d6665d6307af70f4a7fc1d888 authored about 4 years ago by Samuel Wein <[email protected]>

[fix] reverted to standard 8 module setup

0fb05319fced29ed52bd52e30cef22c33ea7e42a authored about 4 years ago by Samuel Wein <[email protected]>

[fix] reverted ADD_TO_ALL_OTHER back to normal config. Added a handler for the case where NUM_PY_MODULES==1 so that ADD_TO_ALL_OTHER doesn't get erroneously added

8a29e806874e1537cb687d4bbd3f724ba43d2e13 authored about 4 years ago by Samuel Wein <[email protected]>

[fix] fixed python errors so all tests pass under language level 3

4f46877020a296671450d26c1f5234b17ee29e06 authored about 4 years ago by Samuel Wein <[email protected]>

Merge pull request #4955 from jpfeuffer/release/2.6.0

[FIX] Small Epifany fixes

2537a5de76bfd6e6b1e19ee268d217ee08e93c77 authored about 4 years ago by Timo Sachsenberg <[email protected]>

[FIX] removing blank lines to comply with codeFactor

8b08654183ebfb6fb6fd5805a32cb02addc351f0 authored about 4 years ago by Ahmed Khalil <[email protected]>

[FIX] removing blank lines to comply with codeFactor

a59e7a120e61098cce4067cd0ce373aca39e821e authored about 4 years ago by Ahmed Khalil <[email protected]>

Merge pull request #4954 from oliveralka/fix/agm_sirius_index

AGM/SiriusAdapter - FIX (develop branch)

71c4433bc83c807220a44dc0c9e79c7706a0a366 authored about 4 years ago by Timo Sachsenberg <[email protected]>

clean up OSWFile (cleaner interface and more invariants)

ba5763f547f63d851ba1e97f99ca3268cc4d3234 authored about 4 years ago by Chris Bielow <[email protected]>

[FIX] Small Epifany fixes

b18a3715c0cf6e9822a53526996558fa7b0c9f7d authored about 4 years ago by jpfeuffer <[email protected]>

Merge pull request #4952 from oliveralka/fix/agm_sirius_index

AGM/SiriusAdapter: FIX - unidentified masses & scan index not readable

d2a0aec4ff2fbc8d9a30baec8479d4233d881a56 authored about 4 years ago by Timo Sachsenberg <[email protected]>

Update PULL_REQUEST_TEMPLATE.md

38058cb90607e684570e0973ecf3a3ba7d526f0d authored about 4 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #4950 from OpenMS/feature/merge_260

Feature/merge 260

c53be156f0660704a423a52a492c722836511414 authored about 4 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #4953 from poshul/acqFix

[fix] fixed space issue in test_AcquisitionInfo.py and added it to CmakeLists

cf10341c47df2f37ee8e55e33b8fc48631e23013 authored about 4 years ago by Timo Sachsenberg <[email protected]>

[fix] fixed space issue in test_AcquisitionInfo.py and added it to CMakeLists

f783681836957477d01f219d7a255c2348e49e51 authored about 4 years ago by Samuel Wein <[email protected]>

FIX: unidentified masses; index not readable

179fb99080b64ee5b4221aeb834a156fd8166803 authored about 4 years ago by oliveralka <[email protected]>

add test_acquisitionInfo to cmake

f34d3707db12471b75659eb1c004f01cc508a9d0 authored about 4 years ago by Samuel Wein <[email protected]>

Made changes to support compilation of pyOpenMS as a monolithic module

d5884ee9174b756ce75a3ba7fb7f7c047c185f35 authored about 4 years ago by Samuel Wein <[email protected]>

[INTERNAL] FeatureFinderIdentification: avoid reconversion to old ID formats if input is idXML

92acc129e02c93884e43f1df28b982f2edf2845f authored about 4 years ago by Hendrik Weisser <[email protected]>

Merge remote-tracking branch 'origin/release/2.6.0' into develop

2d84aec148663d1eef0a5d662167e63ca8cfa76d authored about 4 years ago by Timo Sachsenberg <[email protected]>

[TEST] updated .oms test files (IDMerger and MapAlignerIdentification tests)

06cbbe3c44836170bc7a4043af5990a7536b9abf authored about 4 years ago by Hendrik Weisser <[email protected]>

Merge pull request #4949 from cbielow/toppview_refactor

Toppview Chromatogram Speedup

9773440508b8d5ac79414c13251673aa38d40241 authored about 4 years ago by Timo Sachsenberg <[email protected]>

[API] IdentificationData renaming: MoleculeParentMatch to ParentMatch

875200cf5ddf46eadcf8caacc28f1b978569e998 authored about 4 years ago by Hendrik Weisser <[email protected]>

[API] IdentificationData renaming: updated names in comments/doc

1979ece771fe1e356c2f63dc66b426ee81f7a926 authored about 4 years ago by Hendrik Weisser <[email protected]>

[API] IdentificationData renaming: ParentMoleculeGrouping to ParentGroupSet

d35ea8d6cca834b22e0b32327f53fd6521e141e5 authored about 4 years ago by Hendrik Weisser <[email protected]>

[API] IdentificationData renaming: ParentMolecule to ParentSequence, ParentMoleculeGroup to ParentGroup

b6cd9754fbe24f05cb5fce7b97a5dabc8a5c873e authored about 4 years ago by Hendrik Weisser <[email protected]>

[API] IdentificationData renaming: MoleculeQueryMatch to InputMatch

d4f579a1fe38546dd7e055a95c36d2a1eec7f10c authored about 4 years ago by Hendrik Weisser <[email protected]>

[API] IdentificationData renaming: DataProcessingStep to ProcessingStep

b01d5cf83c243770a6fac2b35dfa87fd03f004db authored about 4 years ago by Hendrik Weisser <[email protected]>

[DOC] data flow chart for SwathWizard

556a59427efdb1e3d69404e12a4500ecf9dc93d0 authored about 4 years ago by Chris Bielow <[email protected]>

avoid intermediate painting of chrom (by addLayer without proper chrom-data being set)

900893d4f12c762089880e98b074c2cfed9dae48 authored about 4 years ago by Chris Bielow <[email protected]>

make 2D view of 500k (!) chromatograms smooth!

- from 6 seconds canvas paint time to 2ms
- selecting the currently hovered chromatogram: 2 secon...

88cc95b17c1c38b8eb7bbea215d11933016d48b0 authored about 4 years ago by Chris Bielow <[email protected]>

fix: cache on all chrom data, not just the visible stuff

08afc71f30c3a7554264feb42bf8746b31fcf065 authored about 4 years ago by Chris Bielow <[email protected]>

remove redundant code

a9b32ee90e9b6d96946c9e799ea5bd2025a4438c authored about 4 years ago by Chris Bielow <[email protected]>

[API] IdentificationData renaming: DataProcessingSoftware to ProcessingSoftware

6f2c6a7abaaa6c1efc13c2572823a15aaa9231c6 authored about 4 years ago by Hendrik Weisser <[email protected]>

[API] IdentificationData renaming: DataQuery to InputItem

7d4e7c002c249de6a19ab89cd58e326f211ca3a1 authored about 4 years ago by Hendrik Weisser <[email protected]>

Merge pull request #4943 from cbielow/toppview_refactor

Toppview refactor

7fc14ab58d7b2350f3901627e77b26b315e2ba60 authored about 4 years ago by Timo Sachsenberg <[email protected]>

remove implementation to cpp

103ee701e3fa47e577191380c8880f9dc93439fc authored about 4 years ago by Chris Bielow <[email protected]>

add comment about gfortran on mac for building CoinOR

e1c41387303a797849b0697f427cf866ca9cd458 authored about 4 years ago by jpfeuffer <[email protected]>

[FIX] compiler error abs GCC6

maybe specific combo of stdlib version and c++ std version

edecbfe6601b20f2a262651a64713539f3cfa685 authored about 4 years ago by jpfeuffer <[email protected]>

fix CI

0e76dd8cca8232ddd8d82f658e6270018569cd94 authored about 4 years ago by Chris Bielow <[email protected]>

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

# Conflicts:
# src/openms_gui/source/VISUAL/SpectraViewWidget.cpp
# src/openms_gui/source/VISUAL...

345459f93225201cc8eed2b94d4eb937754fb8d5 authored about 4 years ago by Chris Bielow <[email protected]>

add a 'LayerStack' class which encapsulates addition and removal of layers, making it impossible to have an invalid `current_layer_` (as happens many times before)

48346b2683ba4820b4f30dd335f50dbfd721f37d authored about 4 years ago by Chris Bielow <[email protected]>

cache tree widget for Chromatogram data. rebuilding could be very expensive

67a4e725902eb8b5eff63fe961b9943c0c4e2250 authored about 4 years ago by Chris Bielow <[email protected]>

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

7ca2231cd2b565304d50d33654bec6da251e8f9e authored about 4 years ago by Hendrik Weisser <[email protected]>

Merge pull request #4940 from OpenMS/doc/ED

Update documenation for ExperimentalDesign

1c404ecf0d24c1b5fcd0b11c1322e0de6cc787d7 authored about 4 years ago by jpfeuffer <[email protected]>

Update ExperimentalDesign.h

e0be5fcc9295046885875250e4e93d3d31ea8911 authored about 4 years ago by Timo Sachsenberg <[email protected]>

Update ExperimentalDesignFile.h

8f1a1304efd9bd76cdb89320d59833ef2904b018 authored about 4 years ago by Timo Sachsenberg <[email protected]>

Update documenation for ExperimentalDesign

fb322995818e3e0e77cd607547f1d25914e4d5b2 authored about 4 years ago by Timo Sachsenberg <[email protected]>

cache tree widget for Chromatogram data. rebuilding could be very expensive

e7c1d1eeec9934ff2bec0bfab11d64ebdd04d60d authored about 4 years ago by Chris Bielow <[email protected]>

Merge pull request #4937 from jpfeuffer/feature/extraInfo

Extend OpenMSInfo (include build type, openmp info and missing infos on linux and macos)

92546ba1f7625c9e44fbb7f78ea1c0b51fa22b82 authored about 4 years ago by jpfeuffer <[email protected]>

remove win-specifics

340a47dd6a12c9034196d0785bd4b045cd729e1b authored about 4 years ago by Julianus Pfeuffer <[email protected]>

PR comments and more py fixes

5ac6a22936ca322824e592d4d10fe7c6e1f0a800 authored about 4 years ago by Julianus Pfeuffer <[email protected]>

fix more pybindings

702bf8403bd7ba0d10aedd2eafba765a92a0e784 authored about 4 years ago by Julianus Pfeuffer <[email protected]>

make default ctor public for pyopenms

93c1e9fdaa62ffbb87d95a5ce914454b846cff19 authored about 4 years ago by Julianus Pfeuffer <[email protected]>

add python bindings

bff3e58c3be5f75f4aef51244c0fd105ff6fdc93 authored about 4 years ago by Julianus Pfeuffer <[email protected]>

Refactor into class for usage in pyopenms

8b7aa61c4c449712067c000d56207e20a51a9057 authored about 4 years ago by Julianus Pfeuffer <[email protected]>

newline

091c43192ddd4eb27a459c4f8dbeefdd21c99641 authored about 4 years ago by Julianus Pfeuffer <[email protected]>

cleanup

7938983e4ddf31aca653fa188b95924580eed348 authored about 4 years ago by Julianus Pfeuffer <[email protected]>

Extend OpenMSInfo (include build type, openmp info and missing infos on linux and macos)

9ffdddb569a5d726bdf466156ba183d19d8c5e03 authored about 4 years ago by Julianus Pfeuffer <[email protected]>

[FIX] add SwathWizard to StartMenu (#4936)

a9551ba48b7b332f85648f97b2f128201c3eeb7f authored about 4 years ago by Chris Bielow <[email protected]>

fix

3e516069aad5d38e9e2ed18e9bb804a0eef7b38a authored about 4 years ago by Chris Bielow <[email protected]>

[FIX] auto-scale column width in SpectraView

0ca5dd68466b9d3b65954a3aa4e642e3d7ad468e authored about 4 years ago by Chris Bielow <[email protected]>

linear instead of quadratic precursor<> mapping

038380ec861cc3be4022bdde3eceaf54173abad7 authored about 4 years ago by Chris Bielow <[email protected]>

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

# Conflicts:
# src/openms/include/OpenMS/FORMAT/FileTypes.h

6d5998bca7610be584deadf3187aa1237eb22513 authored about 4 years ago by Chris Bielow <[email protected]>

support loading SqMass files in TOPPView

a27cbd17c175071f0a95587546daf1f3578c90f0 authored about 4 years ago by Chris Bielow <[email protected]>

[DOC] updating IsotopeLabelingMDVs class documentation

8d108aa62fa8b4e439252353fd7432f2abf2205d authored about 4 years ago by Ahmed Khalil <[email protected]>

[FIX] CMake warning about sqlite package name (#4933)

* [FIX] CMake warning about sqlite package name

* Rename FindSQLITE.cmake to FindSQLite.cmake

73e0caa8700734273cef7674e606464a2b734af2 authored about 4 years ago by jpfeuffer <[email protected]>

* some convenience functions for FileTypes

* avoid std::map include

090f8b158993851103857a62d2a069083b579af9 authored about 4 years ago by Chris Bielow <[email protected]>

Copy some fixes from #4922

#4922

c64b9e4de98a136c7b3f73a66823d97011d264aa authored about 4 years ago by jpfeuffer <[email protected]>

some convenience functions for FileTypes

5adc6eeaa2a16dd177181da93c009000882ac64a authored about 4 years ago by Chris Bielow <[email protected]>

Ensamble spectrum processing added

1fa0821e8d7acefbb04dd224cfccf6928c4b67f2 authored about 4 years ago by kyowonjeong <[email protected]>

Merge remote-tracking branch 'origin/feature/FLASHDeconv' into feature/FLASHDeconv

0c7488f20118678901e0031f76661a7155ad1c5e authored about 4 years ago by kyowonjeong <[email protected]>

Ensamble spectrum processing added

63304d2e0b3ba924e9c6397924f7066618e175a2 authored about 4 years ago by kyowonjeong <[email protected]>

function rename

0d20b7460de479b32b9edc56d006ea9682299306 authored about 4 years ago by Chris Bielow <[email protected]>

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

6e04c7511df333edaa0210e6813e842dc84fbdb4 authored about 4 years ago by Chris Bielow <[email protected]>

Merge branch 'feature/FLASHDeconv' of https://github.com/JeeH-K/OpenMS into feature/FLASHDeconv

343717b8b4e1c6f435061c1937ed9b898f2e4a0c authored about 4 years ago by KyowonJeong <[email protected]>

.

901eaabcf7424f11f34b5163e9681ad8e74e328b authored about 4 years ago by KyowonJeong <[email protected]>

.

951e3371b8340a0e779ab1d041734b066c7f1f19 authored about 4 years ago by kyowonjeong <[email protected]>

.

b41de7619c973cea0542fdd39d35370b3e444f7d authored about 4 years ago by kyowonjeong <[email protected]>

filling of viewWidget with less code

b5d84843b73ff58a164f2f836beeeff5acc6b60f authored about 4 years ago by Chris Bielow <[email protected]>

Merge pull request #4885 from cbielow/toppview_refactor

[FIX] Toppview refactoring with bugfixes

903ae0b348a2298d4266aef7c8360dae35efc695 authored about 4 years ago by Chris Bielow <[email protected]>

.

0e53f0ddf70ce339bac13563a502938c65196b6a authored about 4 years ago by kyowonjeong <[email protected]>

Actually test the import. Patch linux for auditwheel

9a3da3bb65e21fe56ae98391a68228756a1ec95f authored about 4 years ago by jpfeuffer <[email protected]>

Merge pull request #4924 from oliveralka/fix/SwathWizardICNSmacos

SwathWizard icns

b326de239c98348158856edd67e94c69cb88dac3 authored about 4 years ago by jpfeuffer <[email protected]>

Merge pull request #4932 from OpenMS/fix/NSIS_doc

update path to documentation

f4002623f44efc7f927dfcb677078e74881456ac authored about 4 years ago by jpfeuffer <[email protected]>

update path to documentation

4e7313f2741c346ee227f74bbf03ac21e2fe7b46 authored about 4 years ago by Timo Sachsenberg <[email protected]>

[API, TEST, DOC] adding encapsulating member functions to IsotopeLabelingMDVs class

20446c34408b6952efb9372599191e711410f42c authored about 4 years ago by Ahmed Khalil <[email protected]>

remove absolute_import from init.py

55849cd2071b760debca9f17c9a4e8064cedc16b authored about 4 years ago by jpfeuffer <[email protected]>

revert pyopenms package prefix

57308563a6f1f52c93bdad7f93fa6f5a23f110e0 authored about 4 years ago by jpfeuffer <[email protected]>

fix CI

952a8544ead95a2f18a6ef981377d149310b00ac authored about 4 years ago by Chris Bielow <[email protected]>

peakpicking removed in FLASHDeconv.cpp. Instead, aggresive overlapping peak groups in PeakGroupScoring.cpp (isotopologues removed)

b4f82b9ac981ca8c19d5cb98fedf2eee1be3dbb6 authored about 4 years ago by kyowonjeong <[email protected]>

actually use the ms_level

40105e3247e8936ae22ffeb17d274768b0c77924 authored about 4 years ago by Chris Bielow <[email protected]>

fix bug

378d1d795cd668c1b584a6fb246daa1d3f773522 authored about 4 years ago by Chris Bielow <[email protected]>