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

inital spellcheck (#5431)

886bf5890c3fb234b405820d74541cb863952caf authored about 3 years ago by Oliver Alka <[email protected]>

Code Arrangement Changes #6 (#5457)

* Code Arrangement Changes #6

* Update IMSAlphabet.cpp

* Update ElementDB.cpp

* Update ...

fe62fff281daa2623977a1f2aafb4444b2c36513 authored about 3 years ago by Aman Kumar <[email protected]>

Merge pull request #5453 from OpenMS/feature/add_D_T

add parsing of D and T in formulas

f53564a01cada2d8591afd831d1f8f1efb56990b authored about 3 years ago by Julianus Pfeuffer <[email protected]>

Merge branch 'develop' into release/2.7.0

c4830f49317f88dbd86dba7769da073f6f2a1229 authored about 3 years ago by Samuel Wein <[email protected]>

Adding Isotope for Zr (#5458)

Co-authored-by: Arraxx <[email protected]>

ef4b42fcce50fefc7cb618e8e4314f26d55761d9 authored about 3 years ago by Aman Kumar <[email protected]>

[FIX] codefactor style

93d6361a33b997eb1861080c293b39045a84e990 authored about 3 years ago by oliveralka <[email protected]>

Merge remote-tracking branch 'upstream/develop' into fix/copyctro_wrapignore

06a0828af36d293f686b41a4d3c7dddb8f8e6bef authored about 3 years ago by oliveralka <[email protected]>

[FIX] copy constructor

77af740ceae135c7d4d01b5f390d4644eb1ee292 authored about 3 years ago by oliveralka <[email protected]>

mod track added, but only for the first mod of each peptide

e19c6c74e45c36a4b8ca211ec176ef881ea000cb authored about 3 years ago by Dhanmoni Nath <[email protected]>

merge remote-tracking branch 'upstream/develop' into develop

f6da2d8a0b145cdfdfd414659f2b6d5b38babc89 authored about 3 years ago by oliveralka <[email protected]>

FLASHDeconv polishing

adf6b74ae939da7704ef43febd83fa1ca4c5abfd authored about 3 years ago by kyowonjeong <[email protected]>

FLASHDeconv polishing

06ef056a6b848378885d68e889b2c96367514570 authored about 3 years ago by kyowonjeong <[email protected]>

[FIX] default (#5454)

904e3715b5fb81f48f4616a8c819ada9d8894e62 authored about 3 years ago by Oliver Alka <[email protected]>

FLASHDeconv polishing

cfaba595ef40f70a1ae8a2902225d2a9fafb6976 authored over 3 years ago by kyowonjeong <[email protected]>

add parsing of D and T in formulas

1da869d65504e34347d4046d7ab02daa6eee67a5 authored over 3 years ago by Timo Sachsenberg <[email protected]>

Add missing elements (#5451)

* Code Arrangement changes #4 (#5438)

Co-authored-by: Arraxx <[email protected]>

...

5af74035975ffb0114b59ecc112fed33a0b9ddd6 authored over 3 years ago by JangJang3 <[email protected]>

Update .gitpod.Dockerfile

a9e07f0a5440aac1ed7fe26cf23f9e5ccd0e9574 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Update .gitpod.yml

23fc940ba1b722ecb6a997f8993d631744f7fce3 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

FLASHDeconv polishing

300a4261d83541708a49f66e786df7b9143deaf4 authored over 3 years ago by kyowonjeong <[email protected]>

Code Arrangement changes #5 (#5449)

* Code Arrangement changes #5

* Update TOFCalibration.cpp

Co-authored-by: Arraxx <kumarama...

66e74389300350dfa21dcafa4b3d055e91424b6e authored over 3 years ago by Aman Kumar <[email protected]>

Merge pull request #5450 from OpenMS/fix/gitpod

[FIX] adapt to new Gitpod version

a03ea57fc084564f2510b6dbd197ef87885926b7 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

build in debug mode so everything is ready to debug

c54a6db4cd1dd48fc206c9f44ec3064b79e1c459 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

[FIX] adapt to new Gitpod version

3ea5a3ebc530edaa9d6584298516b63cee85a979 authored over 3 years ago by jpfeuffer <[email protected]>

Added wrap-doc methods #5 (#5411)

* Added wrap-doc methods

1d5017af63e8f36266497115dbe4145c4f927ee8 authored over 3 years ago by Rahul Agrawal <[email protected]>

Merge remote-tracking branch 'upstream/develop' into fix/copyctro_wrapignore

1cac669d64c280d82676bb59e563661c8675dc32 authored over 3 years ago by oliveralka <[email protected]>

[ADD] missing wrap-ingore to copy ctor

9ada88e5b0ee674d832fb1bd9f9c92a488238506 authored over 3 years ago by oliveralka <[email protected]>

[Add] Additional Python Wrapper (Release 2.7.0) (#5441)

* additional python wrappers

1b7536bb250698f36d5190108bb5626a2af239c9 authored over 3 years ago by Oliver Alka <[email protected]>

[FIX] encoding of 0.0 double values in ini files (#5442)

* Code Arrangement changes #4 (#5438)

Co-authored-by: Arraxx <[email protected]>

...

3edcb0d5a036436943868a101ae88d3a37b9d714 authored over 3 years ago by Ruben Grünberg <[email protected]>

FLASHDeconv polishing

3caf5927bafa6ea5503bedec19dad0e75aefca6c authored over 3 years ago by kyowonjeong <[email protected]>

FLASHDeconv polishing

05b9b4754a30766ca557356bc43f9b27799becbe authored over 3 years ago by kyowonjeong <[email protected]>

Code Arrangement changes #4 (#5438)

Co-authored-by: Arraxx <[email protected]>

37db195dbf3c66c740b663139f1ecb2d0e195661 authored over 3 years ago by Aman Kumar <[email protected]>

FLASHDeconv polishing

2dd06220b0769bfe99dec5de6c295498212c27f4 authored over 3 years ago by kyowonjeong <[email protected]>

open browser for single accession, show new window that lists all accessions if we have multiple of them; code cleanup

f080bf5111dfba730a82cd951beed1aff9696b52 authored over 3 years ago by Dhanmoni Nath <[email protected]>

protein_to_peptide_id_map created and data is used from this map to send to JS instead of looping through data each time we click on sequence, some debug messages removed

09c4f11ed874a2b118156885a174a390362bb073 authored over 3 years ago by Dhanmoni Nath <[email protected]>

FLASHDeconv polishing

209a40d77744e89216d53e6e05e26f19964a082f authored over 3 years ago by kyowonjeong <[email protected]>

Merge pull request #5437 from OpenMS/jpfeuffer-patch-1

Jpfeuffer patch 1

952ea59d83a46ed7f5bc20d0ae85fe3bb37e2903 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

added TOPP FLASHDeconv tool test

1f1e312a4fd2b475be9ab29e9b3f121263ce5c42 authored over 3 years ago by JeeH-K <[email protected]>

Update knime_package_support.cmake

077bda2e88c01d0d03dac57b992a26d9bd9a09ce authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Try to also copy the OpenMS libs themselves

Somehow CMake just stopped doing it...

4bb967c8f477b5bb2a5dc1e3da633d30efc6050c authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Update PythonExtensionChecker.py (#5433)

* [FIX] test_DIAScoring.py (#5432)

* Update PythonExtensionChecker.py

change what() to get...

84b5bf2d54424be1b81ce28724fcfc6386e94070 authored over 3 years ago by axelwalter <[email protected]>

[FIX] test_DIAScoring.py (#5432)

ab4f3718cae4b24301b3b214e84a98a7e58d532f authored over 3 years ago by Oliver Alka <[email protected]>

[FIX] compiler warnings (#5425)

578ad42ce4b58f84c41d26025a30ddae2cf0b253 authored over 3 years ago by Oliver Alka <[email protected]>

added missing ion names (#5426)

933fdbeba9ec1d5b2e05ef6970202628f0a3620e authored over 3 years ago by Timo Sachsenberg <[email protected]>

added changed params using script on Linux (bash works), added small … (#5427)

* added changed params using script on Linux (bash works), added small workaround for current do...

ee1392beb26e4a81601b289ae314712163afd6ce authored over 3 years ago by Timo Sachsenberg <[email protected]>

Update AUTHORS (#5428)

da6d087f73d232e959290455eb693927c91c88f6 authored over 3 years ago by Timo Sachsenberg <[email protected]>

update rest server helper script to exclude new GUI tools (#5429)

Co-authored-by: timosachsenberg <[email protected]>

e5de580400ebdf238b1241c306f41468b44c4305 authored over 3 years ago by Timo Sachsenberg <[email protected]>

Changelog: main features (#5424)

* main features

* Update CHANGELOG

* Update CH...

e83be6e9a6df6e6ba84fe8546be42d8e93ed33a4 authored over 3 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #5430 from OpenMS/axelwalter-patch-1

Update CMakeLists.txt

d5f27edb1f448cd24a5ab2c69dddbaf572114af8 authored over 3 years ago by axelwalter <[email protected]>

Update CMakeLists.txt

whitelist "version" in mzQC file

c9c3366fe82f3b5947f256e7a61cbabb691170b7 authored over 3 years ago by axelwalter <[email protected]>

Feature/ubuntu warnings (#5422)

* remove PERL_PATH from Doxyfile.in

* remove MSCGEN_PATH from Doxyfile.in

* remove PERL an...

7d774719ba0506190fac66e92fd2147542116e56 authored over 3 years ago by axelwalter <[email protected]>

change the year number

0dd6c91506b26ba377ed005b3a876d28a06ffd8f authored over 3 years ago by JeeH-K <[email protected]>

change the version number and added the script for it

5d28a13bac1f4911b4d49012343ff5c0ec442be0 authored over 3 years ago by JeeH-K <[email protected]>

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

7700fd424b0ecd4078d55e4c784e0cdba3f83e87 authored over 3 years ago by oliveralka <[email protected]>

Merge remote-tracking branch 'upstream/develop' into develop

a10ae614bd384150146cee50511a2770a84b7629 authored over 3 years ago by oliveralka <[email protected]>

Code Arrangement changes #3 (#5420)

* Code Arrangement changes #3

* Update PrecursorIonSelectionPreprocessing.cpp

* change in ...

28b1a58ca55a623a72336e374a3e2eeaefe9c893 authored over 3 years ago by Aman Kumar <[email protected]>

Merge remote-tracking branch 'upstream/develop' into develop

bc5664a5f873c98a84b348ad620bae1a898bac10 authored over 3 years ago by oliveralka <[email protected]>

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

ad82037398e2ad7e457a66068dea502a0f245bf0 authored over 3 years ago by oliveralka <[email protected]>

FLASHDeconv bruker testing

05b94c4871715ce61cf09e4d56a6d32bb4f6379e authored over 3 years ago by kyowonjeong <[email protected]>

Style changes (#5415)

83b1f9d3e3949963eaa0d3e01b9a96a504d249fd authored over 3 years ago by Oliver Alka <[email protected]>

[ADD] Docstring example for digestUnmodified (#5418)

* add example digestUnmodified

498b2b8441b20bae5272735fbf5daddd46c81e91 authored over 3 years ago by Oliver Alka <[email protected]>

remove unused parameter (#5417)

050acbf92480b135f93fc889adfddf61420a0e7a authored over 3 years ago by Timo Sachsenberg <[email protected]>

[FIX] Add inheritance to enzyme python wrappers (#5396)

* add inheritance

* fix wrap-doc

* FIX inherited functions

* FIX typo

* Add req chan...

6a0f9a45c4c8a18e070751d21ea5738abb4b0051 authored over 3 years ago by Oliver Alka <[email protected]>

Merge remote-tracking branch 'upstream/develop' into develop

1b570bcec4d5a123f356343a9bc1196ecddef921 authored over 3 years ago by oliveralka <[email protected]>

[Update] SIRIUS to 4.9.0 (#5409)

* Update SIRIUS to 4.9.0

* THIRDPARTY master

* change inline; fix test

a4496d90cf4f1a46218d55994db99e658fd9414d authored over 3 years ago by Oliver Alka <[email protected]>

Added wrap-doc methods #4 (#5407)

* Added wrap-doc methods

5d9d9b88a9d0e06803f404f3b6ea957ab8bbdbda authored over 3 years ago by Rahul Agrawal <[email protected]>

Added subscores for pepXML to idXML conversion// MSFragger Open search features (#5360)

* Added subscores for pepXML to idXML conversion

* MSFragger support in Percolatoradapter &
...

6b9111a7f93d420f8f6b30b6a4106f85896697b0 authored over 3 years ago by tillenglert <[email protected]>

Merge pull request #5414 from OpenMS/feature/mzqc_cv

update CV URL

de98a2732c3ca19f31beef3c9c0854c088009ab6 authored over 3 years ago by axelwalter <[email protected]>

update CV URL

6ef38fe59776d6f83fd319542c54a2553063ae85 authored over 3 years ago by axelwalter <[email protected]>

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

35fac51421847438969a61f648e8e3feed9f53c6 authored over 3 years ago by oliveralka <[email protected]>

FLASHDeconv bruker testing

22d5d0e2b69f19289b54ff1896d0a00ea816e8a2 authored over 3 years ago by kyowonjeong <[email protected]>

FLASHDeconv bruker testing

8c6c2dc0afdc3ce35365b047dc2dfe8505440a8b authored over 3 years ago by kyowonjeong <[email protected]>

Merge pull request #5392 from OpenMS/feature/mzqc_export

Feature/mzqc export

1a93d9cc125d8df3b32b720f5dd7151ee8abf61c authored over 3 years ago by axelwalter <[email protected]>

Update src/openms/include/OpenMS/FORMAT/QcMLFile.h

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

db82a7fe089440acf4cf5d752d9f1392c9263f6b authored over 3 years ago by axelwalter <[email protected]>

Update src/openms/include/OpenMS/FORMAT/QcMLFile.h

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

ee9a815ee7a225e8497d431425af2d42c4f91132 authored over 3 years ago by axelwalter <[email protected]>

add missing include to QcMLFile

acce4ff3c351b1f74cf57c273f16631f3bf907aa authored over 3 years ago by axelwalter <[email protected]>

clean up includes

e33b91bd38785bacb665b538484d7a61f4b24b88 authored over 3 years ago by axelwalter <[email protected]>

qcml export takes in memory data

b082030ae784271f778ad4a7f6b3ba837d637303 authored over 3 years ago by axelwalter <[email protected]>

Added wrap-doc method #3 (#5397)

* added wrap-doc method

* Update src/pyOpenMS/pxds/CVMappings.pxd

Co-authored-by: Oliver A...

930b5b881bdf531ab0cb295c9fecd1b7eefe5423 authored over 3 years ago by Rahul Agrawal <[email protected]>

mzqc export takes in memory data

401f729d25e5db4ef343bfc33fc8942ea5cfcd92 authored over 3 years ago by axelwalter <[email protected]>

Code Arrangement changes #2 (#5406)

Co-authored-by: Arraxx <[email protected]>

a146aed325d6afb64e6d622d39bcf6c4cefe6b8b authored over 3 years ago by Aman Kumar <[email protected]>

update test mzqc export

e8dce9b30f68743eccb834e4a8cab8b55ff5c4fe authored over 3 years ago by axelwalter <[email protected]>

fix small cp bug

caa4fae964f11ce766bf0e0549714f396ac1a364 authored over 3 years ago by Timo Sachsenberg <[email protected]>

rename getTIC to calculateTIC

65e6d104777ee48a082f15ee2db9e38b97cf5eca authored over 3 years ago by Timo Sachsenberg <[email protected]>

[REFACTOR] move FeatureFinderMetaboIdent code from tool to library (#5230)

* moved ffmetaboid to library

* fix typo

* Update FeatureFinderAlgorithmMetaboIdent.h

*...

60f38cdeeff20fb85259272399bf448b5d4a8af1 authored over 3 years ago by Timo Sachsenberg <[email protected]>

The initial Data visualization is complete using nightingale library

1e5aa74f75794de6ada7ae097153f29a1929b7df authored over 3 years ago by Dhanmoni Nath <[email protected]>

remove now unnecessary code to extract basename (#5393)

* remove now unnecessary code to extract basename

* replaced another occurance

355cc84f918e7f63cc9cd83569dfd51a18aea7ba authored over 3 years ago by Timo Sachsenberg <[email protected]>

Small Code Arrangement changes (#5405)

Co-authored-by: Arraxx <[email protected]>

32991d2d3c150f60ee837bee7f77ea8009681d32 authored over 3 years ago by Aman Kumar <[email protected]>

improvements in IdentificationSummary

48ecba06c39b091cbc2e03713150992b11378daf authored over 3 years ago by axelwalter <[email protected]>

simplify mean rt deviation calculation

28cd323bcc4d8eccfa977e1b257855d4b562e9c2 authored over 3 years ago by axelwalter <[email protected]>

MissedCleavages refactoring

38eb6672584d0927b81258edf7c2792cff805d15 authored over 3 years ago by axelwalter <[email protected]>

[FIX] Class tests memory leaks (#5390)

* [fix] Fix various memory leaks in tests

* Fix numerous memory leaks in tests

* [fix] Fix...

eff53eb5c73fb5971c190ab25bd36c2a3e673e01 authored over 3 years ago by David Voigt <[email protected]>

Correctly setup c17 for pyopenms (#5401)

5548dcf1262ce00aef64b62d574b190e8e7b2bf3 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Update PULL_REQUEST_TEMPLATE.md

1b8c8a059b9f275a88eced93a6068a51f226a8cf authored over 3 years ago by Timo Sachsenberg <[email protected]>

rt mean calculation

7cfddb994016f08e936a8b80784a6ea980d52446 authored over 3 years ago by axelwalter <[email protected]>

annotate members

d6ef15e8b552c55b5af34ba32061790fa220b72f authored over 3 years ago by axelwalter <[email protected]>

compute functions don't read from file

c87e8d796deff8d38309a25dc48cd6f1ed99f390 authored over 3 years ago by axelwalter <[email protected]>

QWidget::grab() (#5394)

e1252f2fa6b24bd3843859914be7e132f9db79d6 authored over 3 years ago by Oliver Alka <[email protected]>

rename qc classes

1183ae4bc1c89ecf7516b1c3b5c39b0c26e986b1 authored over 3 years ago by axelwalter <[email protected]>

Improved docs in pxd's (#5382)

* annotations added

* files added

* files-added

* first-letter-capitalized

* Update ...

aedce62b780ff8089f413ee29e9f78d11b076144 authored over 3 years ago by Rahul Agrawal <[email protected]>

delete Elements.xml

94c9370cafa86578c8f249f45cb7afdd35d7d034 authored over 3 years ago by Timo Sachsenberg <[email protected]>