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github.com/OpenMS/OpenMS-1

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

Merge pull request #5584 from OpenMS/feat/setModByMass

[Feature] make modifications better for pyopenms

cef7d2efb34c594ffe55a55029b8d3374675b16d authored about 3 years ago by Julianus Pfeuffer <[email protected]>
[FIX] forgot py binding for new methods

8dae186ea52365f855b4e44264ea607d08628847 authored about 3 years ago by jpfeuffer <[email protected]>
ms align parser added

4574cd991a579dad6eaf9303269f0a74082a475b authored about 3 years ago by kyowonjeong <[email protected]>
[FIX] add missing include (#5588)

4983800a82ff90e5033ab8e6ba66fdc1a9297462 authored about 3 years ago by Hannes Roest <[email protected]>
[FEATURE] add all the changes to the AAsequence interface as well

a0b48d5855b69b830d9d46c08b23efef2f8bdb54 authored about 3 years ago by jpfeuffer <[email protected]>
Merge pull request #5586 from OpenMS/jpfeuffer-patch-5

[GH Actions] remove cmake_find_debug

957046f067ab3db7531d868f31c60953f7d49b74 authored about 3 years ago by Julianus Pfeuffer <[email protected]>
[GH Actions] remove cmake_find_debug

1c77c0caf856e5f95a6bb0f663d80ba01c9aa477 authored about 3 years ago by Julianus Pfeuffer <[email protected]>
[action] pyOpenMS wheel patch removed

not needed anymore because of change in __init__.py

34a9624fccda2e94087d4251a8e0b42551e7ccab authored about 3 years ago by Timo Sachsenberg <[email protected]>
make reindexing the default (#5581)

* make reindexing the default

* move reindex functionality to SearchEngineBase

* moved imp...

78da0c9caf3a72069261298efd2d6e57f3b1d475 authored about 3 years ago by Timo Sachsenberg <[email protected]>
amend

041103000d631c1dd3a1e60ffb4069ebdea5d83f authored about 3 years ago by Timo Sachsenberg <[email protected]>
small fix to python wrapping of TransformationModelLinear

56002f9aebc4e5212dfb3924b6027cfc655f2ef5 authored about 3 years ago by Timo Sachsenberg <[email protected]>
[FEATURE] Make Modifications better for pyopenms

bb377fb46b2e0dcaf98e2cfccc376167d535c5d0 authored about 3 years ago by jpfeuffer <[email protected]>
Merge pull request #5583 from OpenMS/jpfeuffer-patch-5

[Pyopenms] Update help in __init__.py

0a9f260b9e096d5f97480a192f5d657eef003424 authored about 3 years ago by Julianus Pfeuffer <[email protected]>
Update help in __init__.py

79b84aeb684c216def299aa00e3cfee7be055d85 authored about 3 years ago by Julianus Pfeuffer <[email protected]>
ms1ft output bug fixed. (scan number report bug)

e169af49dd25ec79902de0a1d0f9209d1e1b73b2 authored about 3 years ago by kyowonjeong <[email protected]>
[Feature] basicproteininference on cxml (#5561)

* Refactor and add first cXML support to Basic Protein inference.

* Smaller fixes

* Add an...

efca0283b43b4fee57429e5bda90a8f393f8bb2c authored about 3 years ago by Julianus Pfeuffer <[email protected]>
[ADD] IDMerger annotate_file_origin default true (#5578)

* [ADD] set true

* [REFACTOR] Flag to StringOption (true,false)

* rm comment

* [FIX] ID...

47ca0202eb7f5e203f0ed2f1bb1823f302253e80 authored about 3 years ago by Oliver Alka <[email protected]>
bug fixed in DeconvolutedSpectrum test + FLASHDeconvWizard icon

commented

fd0e667255bab9527aef5449e3651beba2d3dc27 authored about 3 years ago by KyowonJeong <[email protected]>
Isobaric reporter ion option removed again... MS2 polished

6b65527ee07161b1d3ae7e180086d9f4e94fb18b authored about 3 years ago by kyowonjeong <[email protected]>
Isobaric reporter ion option removed again... MS2 polished

fbb60b3d9d5b08304c3bd66b1dfd5b86f79c9f5e authored about 3 years ago by kyowonjeong <[email protected]>
[Fix] missing cstddef for ptrdiff_t (#5576)

Co-authored-by: Timo Sachsenberg <[email protected]>

16e3051da64f1edec9261b86bbe9ac63d10eb340 authored about 3 years ago by Julianus Pfeuffer <[email protected]>
[Internal] Add ParamCTDFile to write Param to CTD File with only standard dependecies (#5475)

* Add ParamCTDFile class that allows to write Param data to a CTD file with only std dependencie...

f371456f368a6d2df8504752649df4048813266f authored about 3 years ago by Ruben Grünberg <[email protected]>
[FIX] AssayGeneratorMetabo Test (wo SIRIUS) (#5551)

* [FIX] AMG-test

* [ADD] internal sirius_executable check

* [FIX] typo

ddfbb579815265a7273ac99e59605db66555c662 authored about 3 years ago by Oliver Alka <[email protected]>
[refactor] moved percolator in file functionality into library (#5570)

* [refactor] move some Percolator in file functionality to library

* python bindings

* mov...

57e0126ed60b1a77f296e7310d0bd0659db880aa authored about 3 years ago by Timo Sachsenberg <[email protected]>
Merge pull request #5572 from OpenMS/update/sm

update submodule

788310176fcfe3299049c1b246e2cea9797bc2b4 authored about 3 years ago by Julianus Pfeuffer <[email protected]>
update submodule

9fb46c161dc8c157bbb0a1e08a06f2ecc3a559ca authored about 3 years ago by Timo Sachsenberg <[email protected]>
adding-wrap-doc-method-21 (#5545)

* adding-wrap-doc-method-21

* FIX

* Update NLargest.pxd

Co-authored-by: Timo Sachsenber...

7c630702d1cdc744994dcf2621e86408b2b7ae5c authored about 3 years ago by Rahul Agrawal <[email protected]>
Added Unimod Modifications to parameters of MSFraggerAdapter (#5512)

* Added Unimod Modifications to parameters of MSFraggerAdapter

* Update src/utils/MSFraggerAd...

5f9195c967b1d996bab90a824136dc105cde081a authored about 3 years ago by tillenglert <[email protected]>
Merge pull request #5565 from OpenMS/featfix/isoErrPepXML

[FEATURE] Export isotope errors when reading pepXML

ce6c8d6427ca89360523ee97f1110bb80d8b4a89 authored about 3 years ago by Timo Sachsenberg <[email protected]>
[FIX] myrimatch tests

fc303f94e58e148ac3ec96fea58810514930e9b3 authored about 3 years ago by jpfeuffer <[email protected]>
Merge pull request #5559 from OpenMS/feature/enable_LTO

[CMAKE] option to enable LTO

f5626ffbc380c248f0e1f6128ca2018e1c92c920 authored about 3 years ago by Julianus Pfeuffer <[email protected]>
[FIX] PercolatorFeature tests. TODO at MSGF

ea9ea3f9a49d8ba0292ea86c58711d726d25cc10 authored about 3 years ago by jpfeuffer <[email protected]>
remove comment

20bdac1b5480e3b85aa2c228f901be498ef65c9d authored about 3 years ago by jpfeuffer <[email protected]>
add isoerror itself to extracted features for perc for all pepxml SEs

4dc62d1dd085a04a301e4bdba7e25c494a6b2245 authored about 3 years ago by jpfeuffer <[email protected]>
remove unused

22be4896faae72a405c45d766542f1687999d3c9 authored about 3 years ago by jpfeuffer <[email protected]>
Merge branch 'develop' into featfix/isoErrPepXML

7fc55bea58b970576e559c9e6140b52fac06469b authored about 3 years ago by Julianus Pfeuffer <[email protected]>
[FEATURE] Export isotope errors when reading pepXML

42b68b1ff6ec672e81df2633680b63035e86eb8f authored about 3 years ago by jpfeuffer <[email protected]>
Merge pull request #5564 from OpenMS/jpfeuffer-patch-4

[FIX] Forgot C-term fixed mod lookup in pepXML

90e3bfb4d200a744681a61ce0c9d4bd7f9ab5e8e authored about 3 years ago by Timo Sachsenberg <[email protected]>
Update PepXMLFile.cpp

de8066ff46ec48e3a0258b34419e03593a376123 authored about 3 years ago by Julianus Pfeuffer <[email protected]>
Forgot C-term

2777737cdc009c42a49550bf3b6f280273aac48e authored about 3 years ago by Julianus Pfeuffer <[email protected]>
Merge pull request #5548 from OpenMS/fix/fixedTermModsPepXML

[FIX] Consider fixed mods for terms, reading pepXML

88879fad77cd08d76f354b5d78591752bcd84d45 authored about 3 years ago by Julianus Pfeuffer <[email protected]>
Do not overwrite OPENMS_DATA_PATH in PyOpenMS if it is already set (#5562)

* Do not overwrite OPENMS_DATA_PATH in PyOpenMS if it is already set

Co-authored-by: Timo Sac...

9163f079dd7b5d3022767167c31ba0fc8072e269 authored about 3 years ago by Radu Suciu <[email protected]>
update minimum cmake version

380bfb4c0f6811097530f493f68a4bd2c410f01b authored about 3 years ago by Timo Sachsenberg <[email protected]>
Merge branch 'release/2.7.0' into develop

765d5a5ae6587bc5d7e3b81f7b30e8b7dcaded89 authored about 3 years ago by Timo Sachsenberg <[email protected]>
increase minimum required cmake version

314e2e181cd38850831e351aaeaa3de5d73e7662 authored about 3 years ago by Timo Sachsenberg <[email protected]>
adding-wrap-doc-method-22 (#5560)

5cff225e10bafcb9673635a7eddfd470e5bd8b0b authored about 3 years ago by Rahul Agrawal <[email protected]>
Update CMakeLists.txt

68db1f51f327372799c81f2a14df9da14f9e4ba7 authored about 3 years ago by Timo Sachsenberg <[email protected]>
Merge pull request #5557 from timosachsenberg/feature/pLFQ_overwrite_design_filenames_with_input_filenames

overwrite design file names with input file names (as we know those e…

31fe8b85147fba5a2cd87f9de6fea60246006521 authored about 3 years ago by Julianus Pfeuffer <[email protected]>
fix aaseq python ext. (#5555)

2b91d7cb86dce461a425c1fb29a5260dba513f49 authored about 3 years ago by Julianus Pfeuffer <[email protected]>
Update ProteomicsLFQ.cpp

acf4be80c5d33a84f54bef2e5de9789de97f67d7 authored about 3 years ago by Timo Sachsenberg <[email protected]>
overwrite design file names with input file names (as we know those exist on the filesystem)

d1404ceb729d966978b0ef481d3cef936609f925 authored about 3 years ago by timosachsenberg <[email protected]>
small additions

68eeaf6c6a3b52e6b89fc04fe40c36d8e404a0b3 authored about 3 years ago by jpfeuffer <[email protected]>
Merge pull request #5477 from oliveralka/fix/pyopenms_build_big_sur

[FIX] PyOpenMS macOS 11.5.1 (10.16)

c56977b3745f7a72cc19002a8c1406ea162a8278 authored about 3 years ago by Julianus Pfeuffer <[email protected]>
fix myrimatch tests

3cc603ba3880421be9d5fa9ed68c39cbae9cfffc authored about 3 years ago by jpfeuffer <[email protected]>
Merge pull request #5549 from oliveralka/fix/writeLocationMztabAMS

[FIX] AMS mztab

6af189aa246e85c0a64a6ea2fb867fd505b5c670 authored about 3 years ago by Julianus Pfeuffer <[email protected]>
Try to improve logic for creating spectrum_references

36fae510386e31481db1daedfab7c103e98af6e4 authored about 3 years ago by jpfeuffer <[email protected]>
[cython] link to openmp (#5498)

* [cython] link to openmp

Co-authored-by: oliveralka <[email protected]>
Co-authored-by: ...

4382189240845e12b309eacce6c3fb7554b8736c authored about 3 years ago by Julianus Pfeuffer <[email protected]>
[FIX] style

acc78fb830592e96bda56ddd21b753efacd4f444 authored about 3 years ago by oliveralka <[email protected]>
[ADD] MassErrorPPMScore

f5c6b72ea70fc2e9aeeda8e8066d8f08991bf120 authored about 3 years ago by oliveralka <[email protected]>
[FEATURE] Correctly set MSFragger as name.

b373f49ab3a5bb5155df78b38584dc53b47c5355 authored about 3 years ago by jpfeuffer <[email protected]>
[FIX] suggested changes

13296c7d2fddfccc05a9187ac7209635a1fb3d36 authored about 3 years ago by oliveralka <[email protected]>
Merge pull request #5494 from dvdvgt/fix/tests_memory_leaks

[Fix] Remaining memory leaks in tests

0eaa33917ec20fcfc6e29580ea088d600d309844 authored about 3 years ago by Timo Sachsenberg <[email protected]>
[FIX] mztab file

de45e9117a97fa6a4dfcb7e01b8889871aaec0df authored about 3 years ago by oliveralka <[email protected]>
Typo

59fa8b4838ce2edee2959810ca887511898f14df authored about 3 years ago by Julianus Pfeuffer <[email protected]>
Isobaric reporter ion option added

8a45b7b63f87b8c167cd3de32a267a3617179801 authored about 3 years ago by kyowonjeong <[email protected]>
[FIX] Consider fixed mods for terms, reading pepXML

50b6785fb69370873fccca405738f9579a8ad818 authored about 3 years ago by jpfeuffer <[email protected]>
Merge remote-tracking branch 'upstream/develop' into develop

ea989f20d122ba9d0df0231731d814aef65172e2 authored about 3 years ago by oliveralka <[email protected]>
Merge pull request #5544 from OpenMS/jpfeuffer-patch-4

[Feature] Try to add descriptions to Param class repr in pyopenms

d69467f0e22054957aad0425885ee05758ca6104 authored about 3 years ago by Timo Sachsenberg <[email protected]>
Missing parentheses

6fdd421fb6b8d544095cc29d10f51ff1780c4c4a authored about 3 years ago by Julianus Pfeuffer <[email protected]>
Merge pull request #5542 from OpenMS/fix/merge_release270

Merge Release 2.7.0

7a2e4a41d4c9f511306afcb8bb4f1b773ace9b9a authored about 3 years ago by Timo Sachsenberg <[email protected]>
[Feature] Try to add descriptions to Param class repr in pyopenms

7ae3e017194cb9d26a3dee35dc721bdb78df8c88 authored about 3 years ago by Julianus Pfeuffer <[email protected]>
merge release/270

48e09c7806d91eb5fb067c4c1f7f2ff8d96fd592 authored about 3 years ago by Oliver Alka <[email protected]>
Releasing version 2.7.0

da738a3e3ff4ce807f6bf70f5a4f38800a6a3a7d authored about 3 years ago by openms-jenkins-bot <[email protected]>
PLFQ Write chromatograms for debugging (#5536)

* PLFQ Write chromatograms for debugging

* fix var name

81febc20754f87d2ae79ded9c9a8d2967f938a40 authored about 3 years ago by Julianus Pfeuffer <[email protected]>
adding-wrap-doc-method-20 (#5537)

e3b6cfccee047a8394e7cbb2afaa011615a5b8d2 authored about 3 years ago by Rahul Agrawal <[email protected]>
Merge pull request #5533 from poshul/legacy_release

Legacy release

9110e58e6552fd188ddff2335d14cb7790d2a440 authored about 3 years ago by Samuel Wein <[email protected]>
update QCCalculator test for qcML export

c56f5c9d42c374237adbe4550dab58de3ef571c5 authored about 3 years ago by axelwalter <[email protected]>
add legacy cv to QcMLFile, QCExporter and QCImporter

3785dd50ebc65eaea5a8020b456a6684bacd3064 authored about 3 years ago by axelwalter <[email protected]>
[fix] add qc-cv legacy CVs

095960fa44c7337db26b830d408ceeebb1355e95 authored about 3 years ago by Samuel Wein <[email protected]>
Merge pull request #5529 from poshul/feature_add_legacy_qcms

[fix] add qc-cv legacy CVs

04733cf52ca54f467156590ae52300d38bc3b856 authored about 3 years ago by Samuel Wein <[email protected]>
adding-wrap-doc-method-19 (#5532)

* adding-wrap-doc-method-19

1bbf4e85496f9dee8e224c853b908a0b9320e518 authored about 3 years ago by Rahul Agrawal <[email protected]>
Use RAIICleanup instead of shared_ptr

26f34febd545535c93280574a1cccca67b124d8a authored about 3 years ago by dvdvgt <[email protected]>
Merge branch 'develop' into feature/FLASHDeconv

8e530784fd972e29f32c69a85fb5e8fb270a7556 authored about 3 years ago by JeeH-K <[email protected]>
update QCCalculator test for qcML export

fef38a0c19580c3a7597b227aa80f7879d926e94 authored about 3 years ago by axelwalter <[email protected]>
Added_wrap-doc _methods_6 (#5439)

* Added wrap-doc methods 6

cd622219b71f6ad12153abfe16298256edc42227 authored about 3 years ago by Rahul Agrawal <[email protected]>
add legacy cv to QcMLFile, QCExporter and QCImporter

4af4d05933d3b0184b657865dc43fd9c678262ca authored about 3 years ago by axelwalter <[email protected]>
Merge branch 'develop' of https://github.com/oliveralka/OpenMS into develop

98397938c653142b426762ab6fa4206ecd861811 authored about 3 years ago by oliveralka <[email protected]>
Merge remote-tracking branch 'upstream/develop' into develop

3f6801cad4d64b61c7688925b16327ec61faa5ff authored about 3 years ago by oliveralka <[email protected]>
[fix] add qc-cv legacy CVs

745631f97a83bcf32bce344058ed907340fb0058 authored about 3 years ago by Samuel Wein <[email protected]>
Removal

56d254843b5b095430e98ae17644b873d15a3652 authored about 3 years ago by Arraxx <[email protected]>
Po,Ra,Fr

dc800a0fbffad9be636b6615d00089e97dea7f42 authored about 3 years ago by Arraxx <[email protected]>
Adding more Elements

32e046f80daadbb05927f1f882f721cf71ce8686 authored about 3 years ago by Arraxx <[email protected]>
Merge remote-tracking branch 'upstream/develop' into develop

e67a6f038900cf4ecbe827474ccb48ffe6b03a0b authored about 3 years ago by oliveralka <[email protected]>
Merge pull request #5527 from OpenMS/fix/epifany_error_dbg_lvl

fix bug in Epifany introduced by new ParamValue class

f5a7a3018e0d14a40edb5dc1fa3a0175aca24f82 authored about 3 years ago by Julianus Pfeuffer <[email protected]>
fix bug in Epifany introduced by new ParamValue class

409b4f63224dbc656e5e89ae2c0ff61456288794 authored about 3 years ago by Timo Sachsenberg <[email protected]>
adding-wrap-doc-method-18 (#5524)

* adding-wrap-doc-method-18

bc60b556c8cba4d2578b291c497042beaa0827fe authored about 3 years ago by Rahul Agrawal <[email protected]>
fix bug if experimental design is given (#5522)

now treated as unfractionated

0593c32d7cc324f98482012812cf8920cf833c7e authored about 3 years ago by Timo Sachsenberg <[email protected]>
adding-wrap-doc-method-17 (#5520)

* adding-wrap-doc-method-17

8bddddd26166fff24fb289a6de44dc25617984ad authored about 3 years ago by Rahul Agrawal <[email protected]>
Code Arrangement changes-15 (#5519)

* Code Arrangement changes-15

* Update src/topp/OpenSwathChromatogramExtractor.cpp

Co-auth...

2d6c4351e18f0355f04fe50f71e3c7d804d20a9f authored about 3 years ago by Aman Kumar <[email protected]>
Feature tracing ppm error

2f58ac1934bb6932bd67e2ceac0fa87956506cea authored about 3 years ago by kyowonjeong <[email protected]>