github.com/OpenMS/OpenMS-1 commits | Ecosyste.ms: OpenCollective

merging TSGTest to adapt it for metabolic input

7309268e91a897802453e8441b59d3574b829548 authored over 2 years ago by Tom Waschischeck <[email protected]>

Merge pull request #6009 from OpenMS/feature/pyomstyping

[FEATURE] package type stubs with pyopenms

78304b740751603ac5c41b618ec95d0c8e48c51c authored over 2 years ago by Julianus Pfeuffer <[email protected]>

[FEATURE] package type stubs with pyopenms

4b59c3408b935145be7fd238b999f19cc1cfe261 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

[pyopenms] fixes some of the newly introduced bugs (#5997)

* Add support for PASEF scans

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

d39eb52eb4272bcb12190f8496be3cc28d827897 authored over 2 years ago by Timo Sachsenberg <[email protected]>

use contrib_manylinux container from github registry (#6005)

* use contrib_manylinux container from github registry

* also update openms-ci to use new reg...

e0eb614683a4213fa6433344174598c6e1cd8f97 authored over 2 years ago by Timo Sachsenberg <[email protected]>

Update special_autowrap_conversionproviders.py

0c4ce8e9a8bcca1af2662f446df85d7503cf1406 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Add type hints to openms conversion providers

1a8d341cfaaa9803ca51036ae72ab21be29cee98 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

minor comment updates in contrib

1275fe9a1630786e30e0a18c036a9070b87ae73a authored over 2 years ago by Tom Waschischeck <[email protected]>

testing if error message boxes are produced

fb44986de09620f543f61f3be9f326ddab37adf3 authored over 2 years ago by Tom Waschischeck <[email protected]>

[FEATURE] Export annotated spectra from Sirius as mzml

ec7aec3622cfea53a9244f0c63d8538bb9a4d983 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

renamed istope model buttons

75c10eaa66cdb70545b2bb231334bec274669aa5 authored over 2 years ago by Tom Waschischeck <[email protected]>

removed unnecessary vector, some vectors to arrays,'_' for protected members, comments, typos

01fd53b5c67efd7ff0bc40b1e536b7a1da25b811 authored over 2 years ago by Tom Waschischeck <[email protected]>

contrib update, fixed some resulting build errors

af5d263af7be6ed7e4e82afa8c1f9243a664a74e authored over 2 years ago by Tom Waschischeck <[email protected]>

forgot to rename function call

9019815158b40fc18bb96db4358b4b03f0f96271 authored over 2 years ago by Tom Waschischeck <[email protected]>

getParam() -> private getParam_()

699bc34503e4bdcc07209d8f903ae2f1d1bc23f2 authored over 2 years ago by Tom Waschischeck <[email protected]>

some variable renaming and another map to vector

f0afcbd533e67084686d6e53d0734b7db7984d2c authored over 2 years ago by Tom Waschischeck <[email protected]>

map to vector for simplicity

34fde278236b8c9a6ce37f9b206cf17289c4d6ac authored over 2 years ago by Tom Waschischeck <[email protected]>

remove unnecessary link libraries

63a7217d719601e85953ff17f24c8859d3d673db authored over 2 years ago by Tom Waschischeck <[email protected]>

PSMFeatureExtractor add tests (#5087)

* PSMFeatureExtractor differentiate list and single file input

The tool has two input modes s...

ae31f310df4ea7a3e319d97aa063762fc432b0d2 authored over 2 years ago by M Bernt <[email protected]>

contrib update

2008f0a535557126b53dafb2d73021037529a8ff authored over 2 years ago by Tom Waschischeck <[email protected]>

name change of GUI elements

373632d6fc615cd38107a9d8d815b5142ef647f5 authored over 2 years ago by Tom Waschischeck <[email protected]>

comments

9dc965fc150f950cedaceaf76e421314d37f7221 authored over 2 years ago by Tom Waschischeck <[email protected]>

shorter delay for faster test

287ed04ce77c57389646f6f0f99d4aa0c87022c7 authored over 2 years ago by Tom Waschischeck <[email protected]>

testing parameters and spectrum generation, function for GUI testing ions and intensities

a12d824e711d147ae1b1d1aa39d1c5c768d77df7 authored over 2 years ago by Tom Waschischeck <[email protected]>

Revert "[FIX] fix memory leak"

This reverts commit c1ac64b0a5e43cdc30764e965bfdcd9ea7603974.

bc87d11b6e248427ed6706e31b6965e30b1560b0 authored over 2 years ago by Hannes Roest <[email protected]>

run github actions CI for every push/PR (#6000)

b9eca03b649d6abb7b167cac6ca2bee1c7a6de9e authored over 2 years ago by Timo Sachsenberg <[email protected]>

CI warning fixes for pr-5819 (#5999)

* swp warm up: some hopefully easy fixes for continious integration

* Added myself to AUTHORS...

7edc15dde7f48b97665ccc603bd27240edd19e35 authored over 2 years ago by Lenny Kovac <[email protected]>

template function to test spin boxes

83370bf52612729565db9ba35b9fb57c8e383915 authored over 2 years ago by Tom Waschischeck <[email protected]>

testing isotope model, ion type and intensity GUI

0a10de26d14e8541b4e37f269ca651729eb034db authored over 2 years ago by Tom Waschischeck <[email protected]>

new slot clicking on list widget item enables/disables it

9ad4bff1845a88b675caf13f056ad08a16463294 authored over 2 years ago by Tom Waschischeck <[email protected]>

[FIX] few left toSet warnings (#5996)

9e8dbe9c50f1d2ffceb432d55ed0a0c05ddf308a authored over 2 years ago by AMIT KUMAR MISHRA <[email protected]>

[FIX] few more toList() left (#5995)

* [FIX] few more left toList()

a8de8e656e8ce35726816e020949c0ab88204b45 authored over 2 years ago by AMIT KUMAR MISHRA <[email protected]>

[FIX] suppress few left skipemptyparts (#5994)

* [FIX] suppress similar skipemptyparts

* [FIX] some more skipemptyparts

16c2d8048bb625872a007ec33fb491719fa42d6a authored over 2 years ago by AMIT KUMAR MISHRA <[email protected]>

Update sources.cmake

ffae8c67c5b631fcb095acf107466226742b1fc3 authored over 2 years ago by Timo Sachsenberg <[email protected]>

Update MzMLHandler.cpp

edd1bc5377fbaaed58e3b4ddeb89ec973a950625 authored over 2 years ago by Timo Sachsenberg <[email protected]>

fix missing file extension

c91d38cb1a5b9e3743ff2653cdc9bbd0972e11e3 authored over 2 years ago by Timo Sachsenberg <[email protected]>

[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]>