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

[FIX] Always add all sourcefiles from mzml (#5819)

* Always add all sourcefiles from mzml

* adds source file (runs)

* preserve sourcefile fro...

f5290386b90dd62881b8b278fb107b31bc824bfb authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Decharger: `-out_fm` not working? Add testfor `-out_fm` and `-outpairs` (#5920)

* Decharder: also test -out_fm and -outpairs

the former seems not to be generated

* rename...

c14c3fdf9a1631d153f38e0d5723d1f6a6001b54 authored over 2 years ago by M Bernt <[email protected]>

Support for overlapping IM and m/z windows (for diaPASEF data) (#5911)

* Add support for PASEF scans

Previously when processing diaPASEF data with overlapping m/z S...

2ea2bde48215362e0450942e47d59ec220f04a3d authored over 2 years ago by Joshua Charkow <[email protected]>

Fix/asan (#5947)

* [FIX] mem-leak

* [FIX] indicate mem-leak

* [FIX] mem-leak

* [FIX]...

2f6c02293ed77bb1da8e102eb8d3dde5967ff823 authored over 2 years ago by Hannes Roest <[email protected]>

export TSGDialog to OpenMS_GUI.lib, additional includes for TSGDialog_test, some GUI testing

ccff141780a2f296aaf05dcd65c9e868de9a25b1 authored over 2 years ago by Tom Waschischeck <[email protected]>

Merge pull request #5983 from OpenMS/jpfeuffer-patch-5

[FIX] No deps pyopenms

7d6c2d79674bcc6fa90a3207487ac2e1803fee80 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

[FIX] screenGeometry is deprecated (#5986)

345edf4dd46f78777529b8780f3254d0f6769758 authored over 2 years ago by AMIT KUMAR MISHRA <[email protected]>

Merge pull request #5884 from axelwalter/feature/annotations-for-IIMN

[Feature] Support for Ion Identity Molecular Networking by GNPS

eb45210f06e3a212a7d81cd58d67d2812b66d191 authored over 2 years ago by axelwalter <[email protected]>

[FIX] suppress buttongroup(int) is deprecated (#5982)

6bc0c8432778c7bfbb8cbf504d61947755be8c2c authored over 2 years ago by AMIT KUMAR MISHRA <[email protected]>

Merge remote-tracking branch 'upstream/develop' into feature/annotations-for-IIMN

2e84a2177e1b8bd7c85e951a12d3d8991ceff4ad authored over 2 years ago by Timo Sachsenberg <[email protected]>

No deps pyopenms

612f0334f3868f2285d90cdeb5a7479cc12b10d3 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

testing gui element construction

cb9d2ed5cb3ba27957ddef61140b6c087a21d1b3 authored over 2 years ago by Tom Waschischeck <[email protected]>

renaming gui elements

4b2a9dc7f2dbc4dc534bfcfe59b8ae8ad92f96f5 authored over 2 years ago by Tom Waschischeck <[email protected]>

[FIX] various Qtime methods deprecated (#5979)

eb3efd772481356c50f1d583154118ae63840872 authored over 2 years ago by AMIT KUMAR MISHRA <[email protected]>

[FIX] suppress similar skipemptyparts (#5980)

719e71ee9b172204a6d5b718dc132f178bf17c60 authored over 2 years ago by AMIT KUMAR MISHRA <[email protected]>

[FIX]suppressing warning toSet() is deprecated (#5977)

5a3c224161c004b4edb99e0bdb5364f892e175f7 authored over 2 years ago by AMIT KUMAR MISHRA <[email protected]>

Pyopenms vis hidden on macos

e75c51ad69e2989096c176fca344d702d10e63ef authored over 2 years ago by Julianus Pfeuffer <[email protected]>

fix: if end

7715a919dcfc2801ef9c6e428aec1989955f06a5 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Suppress -Wunused-variable mac warnings (#5975)

* fix: supress warning for unused variable

* re...

79fd6672a212da106e3b31d375400639a072370e authored over 2 years ago by Satvik Singh <[email protected]>

macOS: Try fixing up extracted Qt libs that may contain rpath refs to other Qt libs

3794f56e654799736883cd415e3c58bbd1fc55de authored over 2 years ago by Julianus Pfeuffer <[email protected]>

suppress-unused-function-warnings (#5973)

* suppress-unused-function-warnings

* do-suggested-changes

24480d0c660d6b179ba1704449b181239a443b02 authored over 2 years ago by Pranav Joshi <[email protected]>

[Fix] toList() is deprecated (#5974)

* [Fix] toList() is deprecated

* resolve conflict

* that was supposed to be category_set
...

9c379b9cde95215549935bf9b0ac6554c3e986ff authored over 2 years ago by AMIT KUMAR MISHRA <[email protected]>

metabolic spectrum generation for TOPPView dialog

1ecb790722dad1445af4f50dfc23798f388cdcc6 authored over 2 years ago by Tom Waschischeck <[email protected]>

static fromString() for EmpiricalFormular

ec39d130285d85e486daa2fb53806c14012144fc authored over 2 years ago by Tom Waschischeck <[email protected]>

fixes-array-subscript-for-char-values (#5976)

86e2adaaf45b35007f5058c2e317e2b8848319aa authored over 2 years ago by Pranav Joshi <[email protected]>

Update CMakeLists.txt

211004b9c76eef8fa32e9c585a30571e92a43daf authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Update CMakeLists.txt

be5333fea0cad3359df85aa2ae96886e0156e380 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

add win pyd to manifest for pyopenms?

0ef09011793c0660134ae5474a25777467a9febf authored over 2 years ago by Julianus Pfeuffer <[email protected]>

[Fix] qsort() is deprecated (#5971)

* [Fix] qsort() is deprecated

* Update src/openms_gui/source/VISUAL/APPLICATIONS/TOPPASBase.c...

ee3477f3a7e8cb89a29dc12269a3ef9ef303f8ce authored over 2 years ago by AMIT KUMAR MISHRA <[email protected]>

Remove release/debutg subfolder for pyopenms targets on win

a2e0379e667a761ee7053a826fa77373c5610585 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

wrong dist folder pyopenms action

88ccd1b15965e13b528d3c5667635493093b6565 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Merge pull request #5970 from OpenMS/jpfeuffer-patch-5

Remove deprecated PythonLibs find module usage

ca460562224af9c7dd34010013588ad13f8d1900 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

REmove deprecated PythonLibs find module usage

c742245210e2353366f4dad5b71d0008de8d090e authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Update pyopenms-wheels.yml

a14beacf3e2526c8acd26252fd62b6bb4fe692cb authored over 2 years ago by Julianus Pfeuffer <[email protected]>

[FIX] warning setItemSelected is deprecated (#5969)

d074d98cae0c843f5f40f20d195449cac95ddb16 authored over 2 years ago by AMIT KUMAR MISHRA <[email protected]>

some friend class & include changes to allow PIMPL in TSG

82aa34742941fa41413ed7bb03b66ea421fab93e authored over 2 years ago by Tom Waschischeck <[email protected]>

Try with NO_DEPS instead of deleting all libs

3077346007ae4329d76c007349f2a145af05b6e8 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

[FIX] supress QT::splitbehaviour deprecated warning until 5.14 (#5968)

* [FIX] supress QT::splitbehaviour until 5.14

* [FIX] supress QT::splitbehaviour until 5.14
...

4eece4c0d49f2f5ba248298b0565c23699ae95be authored over 2 years ago by AMIT KUMAR MISHRA <[email protected]>

No-binary option ordering

8220bd4501b666c53687c6ff8e05efe878f93f9e authored over 2 years ago by Julianus Pfeuffer <[email protected]>

attempt to fix unrecognized warnings in visual studio

d8e23c588e9df1cfd7a6e5811c42d933107b8b7b authored over 2 years ago by Timo Sachsenberg <[email protected]>

[FIX] deprecated QTreeWidgetItem::setTextColor (#5967)

c7233288145db34f9beab31a5b951d78b57563be authored over 2 years ago by AMIT KUMAR MISHRA <[email protected]>

add intensity-weighted average peak picker (#5826)

* [NOP] whitespace

* [FEATURE] add ion mobility averaging to PPHiRes

* [TEST] test new IM ...

6f254b5d4d2748cabf8dba089b36244a9c3201be authored over 2 years ago by Hannes Roest <[email protected]>

fix some unrestricted boolean parameters (#5965)

fixes https://github.com/OpenMS/OpenMS/issues/5880

cdbedc347f61a6cd7487a204f58fbf837dcc0a6b authored over 2 years ago by M Bernt <[email protected]>

fix for empty py_rpath (#5966)

749d535568877729ce3846e96ab50eee67ae4420 authored over 2 years ago by Timo Sachsenberg <[email protected]>

[FIX] suppress warnings till 5.11 (#5961)

10df3df0e8f3086d95003133c0d12961ee596ff1 authored over 2 years ago by AMIT KUMAR MISHRA <[email protected]>

[FIX] deprecated QDirModel and update with QFileSystemModel (#5962)

d7c750654782ebff7b89891a7c73a7aeb1845990 authored over 2 years ago by AMIT KUMAR MISHRA <[email protected]>

do not build pyopenms again when running pip wheel outside of cmake

a96b0bff6ccf92677951e94a96d95c0eac76db17 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

include to header

4a8e526dd95ef751406a200d268cb28e1be1e30a authored over 2 years ago by Tom Waschischeck <[email protected]>

set input file formats

fa1c67d0f702d6561b4586f174e7d1059ccf43af authored over 2 years ago by axelwalter <[email protected]>

rename parameter

cb9b88da4f5b612a20cac64caf96f2e7c23c4a91 authored over 2 years ago by axelwalter <[email protected]>

sort feature partners

23ef394e68ffabed2068c73def580e753f9db5c4 authored over 2 years ago by axelwalter <[email protected]>

Only require Development.Module for FindPython

manylinux does not include all libs

33311a56b405d2774daa9da99d7ee2912665f539 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

minor

55971b19cff797b739ddc29cd43ee94c9783b3f0 authored over 2 years ago by bielow <[email protected]>

remove useless code

ae5af9351c8f52441b27d81f4ee6a95cd2df8cd8 authored over 2 years ago by bielow <[email protected]>

Update pyopenms-wheels.yml

9be7f8fd1fdffe77ca238708b115b620a2f2bd42 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

minor

45ea2a8d1875ba518723e1742beec3a62b63d53f authored over 2 years ago by bielow <[email protected]>

minor refactor

7d2708252effb3208d00cf8c01c05fee5705adaa authored over 2 years ago by bielow <[email protected]>

FeatureFinderIdentification add test for `-candidates_out` (#5917)

* FeatureFinderIdentification remove unused -candidates_out

* clang linter fixes

* Revert ...

15e5606540e1f238514eb7cc6384465a97e89da2 authored over 2 years ago by M Bernt <[email protected]>

[FIX] suppress [-Wdeprecated-declaration] warnings until Qt5.14 (#5960)

e202e99189e3090fbb1bdfa10fe58eb5432cd9c8 authored over 2 years ago by AMIT KUMAR MISHRA <[email protected]>

Fix/gui (#5955)

* [FIX] bugfix (wrong dtor)

* [FIX] bugfix (use after free)

- fix segfault where layer obj...

c3a4e5677135626ba3c9e141dadfdb3337393eee authored over 2 years ago by Hannes Roest <[email protected]>

Update pyopenms-wheels.yml

793ab65ac51a27444368efd6191e471bc6718e9c authored over 2 years ago by Julianus Pfeuffer <[email protected]>

[FIX] add move constructor and assignment operator (#5825)

09dbdefe10a4dfde8a2654715dba57992b330dfd authored over 2 years ago by Hannes Roest <[email protected]>

Update pyopenms-wheels.yml

705647b45e4a28e2035110e60d49da64d4b82214 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Update pyopenms-wheels.yml

259e7549cd4e3a259842736ad082a3bd8b4a03cc authored over 2 years ago by Julianus Pfeuffer <[email protected]>

[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]>