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github.com/OpenMS/OpenMS-1

The codebase of the OpenMS project
https://github.com/OpenMS/OpenMS-1

[FIX] Suppress -Wpessimizing-move in tests (#5953)

* fix: suppress pessimizing move warning

* chore: remove debug messages

* chore: add comme...

2d945f995f9c5882cdc5775e90a77947ae7bc286 authored over 2 years ago by Matchy <[email protected]>
attempt to fix linux pyopenms-wheel action (#5958)

9ec498e632a4f9a69f9f8a17a5848ae1c3bcc8b6 authored over 2 years ago by Timo Sachsenberg <[email protected]>
set initial value for np.amax (#5957)

c122c5ead0ee67e100c465e0beba1832f672d06a authored over 2 years ago by axelwalter <[email protected]>
Merge branch 'develop' into feature/TSGDialogTest

781e2e8d79eef89047ba35c946bf19913232409e authored over 2 years ago by Tom Waschischeck <[email protected]>
space in error msg

ca39aa88dfd856932fdaab146ba745bd9d2aff6b authored over 2 years ago by Tom Waschischeck <[email protected]>
use ordered map for pairs mapping

5efa56703b12af13d8a45829ccb8ec6d6a4ed211 authored over 2 years ago by axelwalter <[email protected]>
[DOC] Require and document the actually required min Qt version (#5954)

* [FIX] bump qt min version

fixes #5604

* [DOC] doc min qt version

efb290910348a3b6ce44472d4fbb13919c1d470b authored over 2 years ago by Julianus Pfeuffer <[email protected]>
Feature/isotopes (#5890)

* [FEATURE] allow modification of ElementDB

* [FIX] prevent memory leak

* [PYOPENMS] allow...

a502c6facf4b2a1e4317e8c9023812de88347666 authored over 2 years ago by Hannes Roest <[email protected]>
Merge pull request #5949 from Waschi97/fix/MoveDBSuitTOPPTest

Move most of the TOPP test for DatabaseSuitability to THIRDPARTY

bd91ff64b0a814165263012017d21bb796c77774 authored over 2 years ago by Julianus Pfeuffer <[email protected]>
Merge pull request #5928 from cbielow/fix_logscale

Minor refactor

afb097c7f129ef59ba4fa64112dbf353f52120d7 authored over 2 years ago by Timo Sachsenberg <[email protected]>
Update src/tests/topp/CMakeLists.txt

b71bf8249594817ccbc9eff91438921c13e6d1f9 authored over 2 years ago by Julianus Pfeuffer <[email protected]>
Merge pull request #5952 from OpenMS/mac_ci_fix

add check for empty dylib list

ad7ba40c1e5f3cbe9f55c08a472d288b3cab50ba authored over 2 years ago by Timo Sachsenberg <[email protected]>
Update .github/workflows/openms-ci.yml

Co-authored-by: Julianus Pfeuffer <[email protected]>

9426491d328656c60e2ba1dd5aa87196d6ecc095 authored over 2 years ago by Timo Sachsenberg <[email protected]>
add check for empty dylib list

e36d8fd635428dd37ef10e73a7f43d069e056ba5 authored over 2 years ago by Timo Sachsenberg <[email protected]>
specify stringstream input

e6be94cf6bdf0714e545e36a47b6806fce44a1f5 authored over 2 years ago by axelwalter <[email protected]>
fix GNPSExport_4_out_pairs

377f0258e00bb003b00fb137915524dec0c59e78 authored over 2 years ago by axelwalter <[email protected]>
Merge pull request #5948 from OpenMS/fix/warning_mac

Update DBSuitability.cpp

3635baa96437baf4c94eef3fb9519cd3d4c6418d authored over 2 years ago by Timo Sachsenberg <[email protected]>
add missing include for OPENMS_GUI_DLLAPI

625716a174218baa8613cbfe14c53fdd27bf027d authored over 2 years ago by bielow <[email protected]>
new DBSuit topp test without correction (no Comet dependency)

23e499e5fcbe10c513e03fc26b59721b3d06a711 authored over 2 years ago by Tom Waschischeck <[email protected]>
Update DBSuitability.cpp

f9ce1b235f40f8dee79131b38b42349747de17c5 authored over 2 years ago by Timo Sachsenberg <[email protected]>
moved DBSuit topp test to thirdparty tests Comet section

f49189358f491c45a3dcc84dab31b14dba08d508 authored over 2 years ago by Tom Waschischeck <[email protected]>
TSGDialog test files, test added to build system

db5f2430e12f0056849a09d85665f551e70fa073 authored over 2 years ago by Tom Waschischeck <[email protected]>
removed PIMPL ideom to access functions of private member for test

f1fc86d84c3e5d76d6813368f08aebc8816e1767 authored over 2 years ago by Tom Waschischeck <[email protected]>
Merge pull request #5943 from axelwalter/fix/fm-df-pep-values

[FIX] Error in FeatureMap.get_df when PeptideIdentification has no PeptideHits

58f9613e0e03a6e915e5eaab24cc5136a03b20d7 authored over 2 years ago by Timo Sachsenberg <[email protected]>
fix signed/unsigned warning

36772c08753b4e951f2e13330e9de1c2388b9514 authored over 2 years ago by bielow <[email protected]>
Merge branch 'develop' of https://github.com/OpenMS/OpenMS into fix_logscale

9f5ea0a7fcf7e147823d41a3954a13bc9e7d581f authored over 2 years ago by bielow <[email protected]>
include filename and native id

8ee6864e3e7914bed9eb5518e4822c406b555a58 authored over 2 years ago by axelwalter <[email protected]>
fix error when PeptideIdentification has no PeptideHits

d20673b64d5c77c194653ff1bdd9e4896845e1f3 authored over 2 years ago by axelwalter <[email protected]>
fix warning (see #5918)

028f0a5710651b507cf910b8d58d0c77daa534bd authored over 2 years ago by bielow <[email protected]>
minor refactor

b16431cea277da9089906ff88b25c8a730ffbb29 authored over 2 years ago by bielow <[email protected]>
Merge pull request #5840 from OpenMS/jpfeuffer-patch-5

[FIX] scan number extraction

62a701944098259fb7cebd4e6affc6c54f32c361 authored over 2 years ago by Julianus Pfeuffer <[email protected]>
FLASHDeconv 2.0 beta++ version + target_mass option added, thanks to Dave Tabb.

9e83c9e7bef04b7b79ec7e174130ff64341043a1 authored over 2 years ago by kyowonjeong <[email protected]>
annotate ConsensusMap in GNPSExport only

0e66c6f2ed0bd1f3aef149923172f8137fa51806 authored over 2 years ago by axelwalter <[email protected]>
Update SpectrumLookup.cpp

2961f05e13451f63794bd93a37993509b7757a11 authored over 2 years ago by Julianus Pfeuffer <[email protected]>
[FIX] speclookup test for extrScanNr fix

13b7ad866662021b026a74783160fdc143ac605f authored over 2 years ago by Julianus Pfeuffer <[email protected]>
Merge pull request #5912 from bernt-matthias/more-out-prefix

MzMLSplitter and OpenSwathFileSplitter: use output-prefix

889b81e3a431e3223e4571ed5d5e18f718a73244 authored over 2 years ago by Julianus Pfeuffer <[email protected]>
Merge pull request #5923 from Amit0617/develop

[FIX] Warning: unused variables

f60857e912d76053be64b8eee490becca8cf8d57 authored over 2 years ago by Julianus Pfeuffer <[email protected]>
converting group uid to size_t with stoull

19342a1d7c9cfed59db5c70a5c4fc4c2657476ca authored over 2 years ago by axelwalter <[email protected]>
Merge branch 'OpenMS:develop' into develop

108995ec9f72958ffa609e71bfa9753c512ed09a authored over 2 years ago by AMIT KUMAR MISHRA <[email protected]>
[FIX] Warning: unused variables

0aba16a8902bd34a2f9f3d74218dcb3c607add08 authored over 2 years ago by amit0617 <[email protected]>
Merge pull request #5919 from OpenMS/update_pyopenms_wheel_cmake

Update pyopenms-wheels.yml

5655547d8c21ee832401e0cb4468fdec4ab8eb65 authored over 2 years ago by Timo Sachsenberg <[email protected]>
Update pyopenms-wheels.yml

6a4ee8f379bc9d606afe687318c27c6286ca1d1b authored over 2 years ago by Timo Sachsenberg <[email protected]>
Merge pull request #5916 from Amit0617/develop

[FIX] isnan error

d54a36841436c3533da66047065a8bd7a3efc5be authored over 2 years ago by Timo Sachsenberg <[email protected]>
fix error with filtered ConsensusMap

1c0dfcdf226a67e840d90a92a2567d04a6bb4d92 authored over 2 years ago by axelwalter <[email protected]>
Add parentheses

Co-authored-by: Hannes Roest <[email protected]>

4c326565a2672709d5da643b5e0942323a37c7b7 authored over 2 years ago by M Bernt <[email protected]>
Update MQEvidenceExporter.cpp

removed include duplicates

8bd42e7d799e4c1f8c0dfb1d79c60254384a17fd authored over 2 years ago by AMIT KUMAR MISHRA <[email protected]>
fix: 5864, isnan error

9264cfd89cd55dd58898f29b0ea83e1235e43490 authored over 2 years ago by amit0617 <[email protected]>
Merge pull request #5844 from OpenMS/remove_Map

[REFACTOR] replace Map with std::map

3cd3db31efef6241030830388dbceccb3d6ffd4e authored over 2 years ago by Timo Sachsenberg <[email protected]>
update to contrib that removes zlib from boost

5dc6b1d5f15f25a813649443386602766a426d64 authored over 2 years ago by Timo Sachsenberg <[email protected]>
FLASHDeconv 2.0 beta++ version + target_mass option added, thanks to Dave Tabb.

1bf55cd58fd5fc6d07a3cbbfba0a1d6874a84196 authored over 2 years ago by kyowonjeong <[email protected]>
update contrib

5e802dd8220d7d0beec083d2ab0826a11b51a187 authored over 2 years ago by Timo Sachsenberg <[email protected]>
update contrib with zlib patch

35b868af13fe5f8c3ae7e3502526517303cb1457 authored over 2 years ago by Timo Sachsenberg <[email protected]>
clang formatting

0fc35efa85e6e6082e627afa052993f3e500e98c authored over 2 years ago by Matthias Bernt <[email protected]>
use output-prefix for more tools

66dee6ac90396f03760d10f134afe5507567ee0d authored over 2 years ago by Matthias Bernt <[email protected]>
Merge pull request #5466

- merge 'feature/add_elements' into develop

f3910ff6988b4910ced0787a964a8e48ced9262b authored over 2 years ago by Hannes Roest <[email protected]>
[NOP] cleanup of elements

8254a58fd8ada4fae50e643e2ff9583bb62ad0f1 authored over 2 years ago by Hannes Roest <[email protected]>
FLASHDeconv 2.0 beta++ version + target_mass option added, thanks to Dave Tabb.

fc9168a1ea90eb4864358a958b415968d82665b3 authored over 2 years ago by kyowonjeong <[email protected]>
update GNPS tests

3f508b4e7f924bf8b6071745eb3eac097d9d4a8f authored over 2 years ago by axelwalter <[email protected]>
add score for supplementary table

a403c6336c7778595af945c7a0eef713b9bcedd0 authored over 2 years ago by axelwalter <[email protected]>
use static methods for IIMN

61ae95e15ba1627cf48a792ca74b234ad9af3a67 authored over 2 years ago by axelwalter <[email protected]>
change vertex.uid from String to size_t

b7caf6d89e2b105cdcea00ae028799420abb56f0 authored over 2 years ago by axelwalter <[email protected]>
add IIMN to GNPSExport

e9cdebad3eb3bec5176aabff731b76a03c9f8d89 authored over 2 years ago by axelwalter <[email protected]>
add method to write supplementary pairs table

2694d0d8889e0a8ef82eab01fdb3980f4075fd8a authored over 2 years ago by axelwalter <[email protected]>
add IonIdentityMolecularNetworking::writeFeatureQuantificationTable

d78ecd5565fbb1e684a937ea49ca32a30af6bf4a authored over 2 years ago by axelwalter <[email protected]>
FLASHDeconv 2.0 beta++ version + speed improvement + low charge filtration

c6c23a6adb91c1c0b697dfd74df834adca448604 authored over 2 years ago by kyowonjeong <[email protected]>
add IonIdentitiyMolecularNetworking class with annotateConsensusMap method

48b3a11e7852708bfe4a5e8b41fecd4fd96346a3 authored over 2 years ago by axelwalter <[email protected]>
Apply suggestions from code review

Co-authored-by: Hannes Roest <[email protected]>

a0bc85f001bb9ff073d699d8a6b9917168d39308 authored over 2 years ago by Timo Sachsenberg <[email protected]>
Update src/openms/include/OpenMS/DATASTRUCTURES/sources.cmake

Co-authored-by: Hannes Roest <[email protected]>

9c0dd585078606c20a5a8dc3176f82b8a670c3d6 authored over 2 years ago by Timo Sachsenberg <[email protected]>
Merge pull request #5904 from hroest/feature/fix_monoisotopic

[FIX] test fix after #5891

58eec1738829a7af3a3ec92262bd1508aa5a2b5f authored over 2 years ago by Timo Sachsenberg <[email protected]>
Update AASequence_test.cpp

b5c56edde47b881b45c3b14ddf5d5299bf0332c9 authored over 2 years ago by Timo Sachsenberg <[email protected]>
[FIX] test fix after #5891

- after the change in monoisotopic mass, we have to adjust the test for
monoisotopic mass for se...

0cad5b0ffa21f312517d1f970cd7908f633bce1e authored over 2 years ago by Hannes Roest <[email protected]>
FLASHDeconv 2.0 beta++ version + speed improvement + low charge filtration

4321e5f64cb001b5e0e6376413f66dce46690ced authored over 2 years ago by kyowonjeong <[email protected]>
Revert thirdparty

284b8e477e694b2b916e6d1fbc12b2cc7e9cdc95 authored over 2 years ago by matteopilz <[email protected]>
remove IIMN export in TextExporter

fa2316c49625d878d66e4892e610f1a55a7ca1c4 authored over 2 years ago by axelwalter <[email protected]>
Merge pull request #5898 from hroest/fix/residue

Recalculate average and mono weight in Residue setFormula

ccd08ee5b2c9a53130d5ed46171edf43d707dddc authored over 2 years ago by Timo Sachsenberg <[email protected]>
Merge pull request #5899 from hroest/feature/doc

[DOC] documentation of OpenSwath

d451edd7d8f7a27a59967c525da250694daed85a authored over 2 years ago by Timo Sachsenberg <[email protected]>
Merge pull request #5896 from OpenMS/fix_5894

Fixes 5894

fdd6ec85a191e740abedf8c63263d20770f4b1b1 authored over 2 years ago by Timo Sachsenberg <[email protected]>
[DOC] documentation of OpenSwath

f53e2ce2cf278d34603ee3b4d92d276b8f442739 authored over 2 years ago by Hannes Roest <[email protected]>
[TEST] add test

8e6d3c3a668b74f369fcb069d1e4463f21e57bc2 authored over 2 years ago by Hannes Roest <[email protected]>
fix

0644c0e5fa72bef1b152f0f1030190c4608e825a authored over 2 years ago by Hannes Roest <[email protected]>
FLASHDeconv 2.0 beta++ version + a bit of speed improve

559469cccdd85f87e48189ecf551c557fa2bb87c authored over 2 years ago by kyowonjeong <[email protected]>
[FIX] update weights after formula changes

95956a1aa8da4b707012c154a0c14de2539abc44 authored over 2 years ago by Hannes Roest <[email protected]>
[DOC] add documentation

ea72a3b0fa63eabb49e2baffd7baff9d1ce7edd1 authored over 2 years ago by Hannes Roest <[email protected]>
FLASHDeconv 2.0 beta++ version + a bit of speed improve

d969bbe5a64de732c793872e56ae20718106eee4 authored over 2 years ago by kyowonjeong <[email protected]>
proper -test mode for FFMetaboID

09265b0094af95b0d92f9086e9b331df8eef1699 authored over 2 years ago by Timo Sachsenberg <[email protected]>
add raw file to FFMetaboID

b662fd70c578ef2702a09da0243b274392602b08 authored over 2 years ago by Timo Sachsenberg <[email protected]>
Update src/pyOpenMS/addons/ADD_TO_ALL.pyx

837003498fb4f0fe278c87815dee0bfcb79199d3 authored over 2 years ago by Hannes Roest <[email protected]>
Corrected spelling error

5ef8488f372b824e69ef286d55b4408c4127a5bb authored over 2 years ago by matteopilz <[email protected]>
Merge remote-tracking branch 'upstream/remove_Map' into remove_Map

2144748db34727eba1fd9542019e023643951db9 authored over 2 years ago by matteopilz <[email protected]>
Simplify double negative std::map find

cf9dbb3695c29c998af5d39cc1b5175b63111486 authored over 2 years ago by matteopilz <[email protected]>
Merge remote-tracking branch 'origin/develop' into remove_Map

8f58d948940676899d96b944ebed8766f8528d0c authored over 2 years ago by Timo Sachsenberg <[email protected]>
FLASHDeconv 2.0 beta++ version.

2723ddb3942fbe753d9b482bd116bd359a4f5d0d authored over 2 years ago by kyowonjeong <[email protected]>
Merge pull request #5891 from hroest/feature/iso_fix

[FEATURE] fix monoisotopic definition

637747ce64bd159309dac7f9f6b3ac728a60dd31 authored over 2 years ago by Timo Sachsenberg <[email protected]>
[FEATURE] fix monoisotopic definition

615bb5734de1d6899820d4e8a4afe2871935f148 authored over 2 years ago by Hannes Roest <[email protected]>
Merge pull request #5892 from oliveralka/fix/SA_Test_10

FIX: SiriusAdapter_test_10

68d3f8056c6ba35747065cbd3505d85d5a04d04e authored over 2 years ago by Timo Sachsenberg <[email protected]>
set "output for per spec" to be printed as default

8b5b32827c2dd51e301754de392d8c1e6cdc1cd6 authored over 2 years ago by JeeH-K <[email protected]>
FIX: SiriusAdapter_test_10

4989be179dd5378b0875b41ceb764ef6a1f10dd3 authored over 2 years ago by oliveralka <[email protected]>
SpectraMerger is now merged into FLASHDeconv tool.

Tested with
- Thermo Std
- Ecoli
- Azo
- Feredrik and Loo MS dataset

15b1335ea4cbbcc1c7c04fab8a4ec513e28b68a5 authored over 2 years ago by kyowonjeong <[email protected]>
[NOP] use same notation

8f5c24371ca8f644f09374192fe3c6cecc6e0314 authored over 2 years ago by Hannes Roest <[email protected]>
[FIX] a few more bugfixes

0cb5badaa8f6af04c0c4c804db4cec728eea2cd9 authored over 2 years ago by Hannes Roest <[email protected]>