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

more Json stuff

aeafa56a7e56024782a8737557455a8fa9565392 authored almost 2 years ago by Samuel Wein <[email protected]>

Merge branch 'fix_sql' of https://github.com/cbielow/OpenMS into fix_sql

8cd67ea58ebc8749f3d3721d3a0f718f7064a74b authored almost 2 years ago by bielow <[email protected]>

export include dir of SQLite to TOPP/UTILS etc

6c7e902998e87f5e6bc1fb1408005acf60a3e9be authored almost 2 years ago by bielow <[email protected]>

cleanup

4e6f490dabee853789ac4b559bc9c0489315d147 authored almost 2 years ago by bielow <[email protected]>

fix compile errors on gcc

ecbaeeb8fa904fa65b04580635cf821677cb27f6 authored almost 2 years ago by bielow <[email protected]>

Merge pull request #6337 from poshul/feature/new_thiols

Feature/new thiols

7cbd92c5fdec750905e24086eceffae69eb45e58 authored almost 2 years ago by Samuel Wein <[email protected]>

split out terminal thiol test

5b5457b6911a44ce738254bc03b6f3f9845ee155 authored almost 2 years ago by Samuel Wein <[email protected]>

Merge branch 'develop' into fix_sql

d38c0df7d3daf063f5696b756c77d900ba39d51a authored almost 2 years ago by Chris Bielow <[email protected]>

minor

0b214ac6ee8f27f20a0c1a626d9e5c63e485c340 authored almost 2 years ago by bielow <[email protected]>

fix: create tmp db, since we need to delete the oms file before creating a db on it (sqlite cannot delete existing files, but will open them instead)

f0f5878940e324a40c58687169aaa0d8e285c596 authored almost 2 years ago by bielow <[email protected]>

fix bug

1c45d9c26ece3415f8f1241db171f482fd0188dc authored almost 2 years ago by bielow <[email protected]>

reverted commenting on getDefaultParameter

9b28110f37cfd1a0394f0a100a52f4fbfd48e7d9 authored almost 2 years ago by Samuel Wein <[email protected]>

fix: reset also after executreStep

c62c560b51a8b9937b4f060a53dd17dc09e19cc1 authored almost 2 years ago by bielow <[email protected]>

bugfix: cannot create index on non-existing table

1ff59b6ee11a26338e95cd3f306b03b526562138 authored almost 2 years ago by bielow <[email protected]>

reset queries after exec, otherwise the next bind() will crash

f661f899cf68acedc5b0bee70cb4e690ae107086 authored almost 2 years ago by bielow <[email protected]>

avoid nested transactions

1750227b4d6d6dbc63d667bf285e3737bf0e6344 authored almost 2 years ago by bielow <[email protected]>

get rid of qt include

36ac99bcdbe0b713f8289c9ed7a0076d6c4b4a5a authored almost 2 years ago by bielow <[email protected]>

remove qcoreapplication

f737368d1b64bcde34b334637ffbda07020bc2cc authored almost 2 years ago by bielow <[email protected]>

convert loading to new interface

ba5e1a4af76132535ae04adda29a21ed59c3ef2c authored almost 2 years ago by bielow <[email protected]>

add reset()

e0d70f10c6252d65f17fe6b3f67d6139e3c0caf6 authored almost 2 years ago by bielow <[email protected]>

spaces fixed

b2e8e456be408053e4c8f6e1a0254dfb1a40e5ba authored almost 2 years ago by rahul799 <[email protected]>

replace tableExists_

eca1517866c391d67e5d63edad799b6b662cf558 authored almost 2 years ago by bielow <[email protected]>

converted OMSFileStore

ab9bbb1075786691a3eb22d1d3257c04aae3cb11 authored almost 2 years ago by bielow <[email protected]>

Merge pull request #6472 from jcharkow/fix/pasefTraMLFlag

[FIX] -pasef flag with TraML file

b46bb751dd865d3d90798f127e0f75ebc9e0416e authored almost 2 years ago by Samuel Wein <[email protected]>

[FIX] -pasef flag with TraML file

Previously bug with -pasef flag using TraML file as ion mobility data
was not able to be accesse...

ec4a7a5164ed6ac8fe4522de7c839a9baafd6e08 authored almost 2 years ago by jcharkow <[email protected]>

fixes

536dabf5f02d8c43a6256d83bc3d83b84c169613 authored almost 2 years ago by rahul799 <[email protected]>

[fix] added tests for thiol-backbones, fixed a-B miscalculation where base n-1 had a thiol backbone

70a251ff1f312170b24c4a7f85792441d2402f60 authored almost 2 years ago by Samuel Wein <[email protected]>

implemented suggestions from code review

7038cc3b691166bd8f8534a349d8c35c7d6ee2da authored almost 2 years ago by Samuel Wein <[email protected]>

Merge branch 'develop' into feature/new_thiols

bfcaaec1203a6304ec09bee44206c3cd984310a3 authored almost 2 years ago by Samuel Wein <[email protected]>

DeconvolvedSpectrum.h comments are being addresssed...3 + multi threading for decoy runs + for peak group scoring

5efa3770437a635510c91408435e44a2eaca7561 authored almost 2 years ago by KyowonJeong <[email protected]>

Merge remote-tracking branch 'origin/develop' into feature/FLASHDeconvOnly

16c40f491207fb011c77dc742d873932782aaa6d authored almost 2 years ago by JeeH-K <[email protected]>

DeconvolvedSpectrum.h comments are being addresssed...3 + multi threading for decoy runs.

8b51034a6a4a5d6c129483b269ca081614ccff67 authored almost 2 years ago by KyowonJeong <[email protected]>

DeconvolvedSpectrum.h comments are being addresssed...2

47ebe17d6a4f6959e55f28cde36f0cb1d25b757a authored almost 2 years ago by KyowonJeong <[email protected]>

Merge pull request #6467 from OpenMS/timosachsenberg-patch-1

SpectrumLookup: add regex format to pyOpenMS doc

a10e8ea589c9b25fed2256d78acf4e556a8bc42d authored almost 2 years ago by Timo Sachsenberg <[email protected]>

make sqlite libs static

d6fab5230e417173a1b9b54386a9adfea4f28482 authored almost 2 years ago by bielow <[email protected]>

fix SqliteCPP's CMakeLists export

88ad94b52e1c8fa932b63fb935047d9fc4575903 authored almost 2 years ago by bielow <[email protected]>

use new sqlite lib and forget about qsql and contrib sqlite3

7dd55b35da1d82d550cd5ac2a3317d5b9b61e395 authored almost 2 years ago by bielow <[email protected]>

better docs

34d5f94fc42af1ef402d723b0bac2a08484d772a authored almost 2 years ago by bielow <[email protected]>

added SQLiteCPP thridparty lib

13754db2023cbd44050ef96f7da3b994d0cfbc2f authored almost 2 years ago by bielow <[email protected]>

first parts of json support for RibonucleotideDB. BROKEN

3b2c2c508812228a09a3bad934c1eb63c96567a0 authored almost 2 years ago by Samuel Wein <[email protected]>

Merge pull request #6469 from OpenMS/fix/mztab_file

mztab: fix recently introduced bug

aeb75e44a81b82d96466417e968c48f3d9a87f9c authored almost 2 years ago by Timo Sachsenberg <[email protected]>

update tests

7a1a70c13b013c2b1a500fff496d781d6208fea6 authored almost 2 years ago by Timo Sachsenberg <[email protected]>

fix

c773c2f1b5f1a850c59cb962d815168b4b423f89 authored almost 2 years ago by Timo Sachsenberg <[email protected]>

mztab: fix recently introduced bug

17b74b8ef77d6f87e3104f7cb0ca3f5a79d4bba7 authored almost 2 years ago by Timo Sachsenberg <[email protected]>

Commented 8 lines in main function causing errors

ae51cfac32e3dfd757d826ddcfe2111a6236925e authored almost 2 years ago by AmandaWein <[email protected]>

SpectrumLookup: add regex format to pyOpenMS doc

71b71c4a626446c9454e9c777b45bc70a9f444d5 authored almost 2 years ago by Timo Sachsenberg <[email protected]>

Merge branch 'develop' into feature/new_thiols

a08c9388a392f62712ba4daf9b5002f98bd0aed2 authored almost 2 years ago by Samuel Wein <[email protected]>

DeconvolvedSpectrum.h comments are being addresssed...

7e94119f598d1477b36452e84557fc790ef422fa authored almost 2 years ago by KyowonJeong <[email protected]>

removed commented codes

32b23392e2c506126e79de31c476f872238bfa59 authored almost 2 years ago by JeeH-K <[email protected]>

Update .gitignore

98adfdaf58ec8adba3612a84fe64707278902ce0 authored almost 2 years ago by Amanda Wein <[email protected]>

Merge branch 'develop' into patch1

c597b160a4a1ba8a95150e1402a22c1cc52307dd authored almost 2 years ago by Amanda Wein <[email protected]>

Add '_' for private function (Chris' comment)

Co-authored-by: Chris Bielow <[email protected]>

f771e194b1b8b62a8148311b5bc6024d7422f29e authored almost 2 years ago by JihyungKim <[email protected]>

Updated DefaultParamHandlerDocumenter.cpp

26901d5632c9f9678cb77b1564138c24048d37bd authored almost 2 years ago by AmandaWein <[email protected]>

Merge pull request #6464 from OpenMS/clang_tidy4

,modernize-use-nullptr,modernize-use-equals-delete,modernize-use-emplace

d61dc569467b26f0a72e0a5b859f2cdfe6d00e48 authored almost 2 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #6461 from OpenMS/jpfeuffer-patch-1

Fix boolean logic

b51cab86f7c1611706cd049c271e536c3958988f authored almost 2 years ago by Julianus Pfeuffer <[email protected]>

Add cmake local files to gitignore

746022d390451d3aeb7c32cd790b862fde2b9c0e authored almost 2 years ago by AmandaWein <[email protected]>

fix

764a9aa91d7fff7a61399877d21136d060de2d8f authored almost 2 years ago by Timo Sachsenberg <[email protected]>

Update TVToolDiscovery.cpp

df3959dbcddc504583af3d9977e0026c5b4147d7 authored almost 2 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #6454 from cbielow/fix_int64_xml

Fix XSD value parsing in XML files

78faa723c217872e37ec7d3f83cf40e7ef9a476a authored almost 2 years ago by Chris Bielow <[email protected]>

Fix boolean logic

9ebaa7fb9fe14f0bfe239ef9b1a367ed4a486ce7 authored almost 2 years ago by Julianus Pfeuffer <[email protected]>

Merge branch 'develop' into feature/FLASHDeconvOnly

ce76fe8e74623336b9fd1c0273de06b44d14c792 authored almost 2 years ago by Samuel Wein <[email protected]>

Merge pull request #6460 from OpenMS/jpfeuffer-patch-1

fix error in mac dependency script when plugin dir is not given

6e4eea277e725e5b8e4a34c9762b2fdd8f4b4890 authored almost 2 years ago by Julianus Pfeuffer <[email protected]>

a change based on Sam's review

4d99dceb2bbc0ed2020b63d66cbc6f530033352b authored almost 2 years ago by JeeH-K <[email protected]>

Merge pull request #4 from poshul/fix/FLASHDeconvOnly

Fix/flash deconv only

411705a9572e33e84a0a52818c254adea8c88842 authored almost 2 years ago by JihyungKim <[email protected]>

Merge branch 'feature/FLASHDeconvOnly' into fix/FLASHDeconvOnly

f4da9ff2691c9c08485194b4f4402a5e13874681 authored almost 2 years ago by JihyungKim <[email protected]>

fix error in mac dependency script when plugin dir is not given

8af41ad0e11f46fdcbf1664238f05837a152979e authored almost 2 years ago by Julianus Pfeuffer <[email protected]>

remove FLASHIda related codes and bug fixing on tests

63a8ad209b9de422955d4c2b38e50fa2094d3e85 authored almost 2 years ago by JeeH-K <[email protected]>

Merge remote-tracking branch 'origin/feature/FLASHDeconv' into feature/FLASHDeconvOnly

b7973192acfc6b801f8310ff700bcdd87ce32171 authored almost 2 years ago by JeeH-K <[email protected]>

Merge branch 'develop' into feature/FLASHDeconvOnly

fcc099dba718458dd35f024cc731fcd9f1b17455 authored almost 2 years ago by JeeH-K <[email protected]>

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

3dc75d53ac8882c2cd8b42a59800ee38483cd73e authored almost 2 years ago by JeeH-K <[email protected]>

Top FD feature file output per ms level recovered. TopPIC needs them all.

85c2dfd9fc0648e3913a94e1f0b8a923bc39a3b2 authored almost 2 years ago by KyowonJeong <[email protected]>

For FLASHDeconvOnly

37caddd74b1311a8f09da367cb0f7acbc21b4183 authored almost 2 years ago by KyowonJeong <[email protected]>

For FLASHDeconvOnly

8721c8577e0d6bdaa0a6828d26969d26f29e780a authored almost 2 years ago by KyowonJeong <[email protected]>

Merge pull request #6450 from OpenMS/ci_add_clang

Update openms-ci.yml

ee1d1bcd8c1a04639629f02c7d8a2f956c87d0f4 authored almost 2 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #6452 from AmandaWein/AmandaWein-patch-1

Clarified bug/feature reporting in CONTRIBUTING.md

6e9182ac8277f18c44ce12f5b330a23a7204bb45 authored almost 2 years ago by Samuel Wein <[email protected]>

Update openms-ci.yml

fae2ce8ae3a89a4bf563f095f361d085ffbd6e54 authored almost 2 years ago by Timo Sachsenberg <[email protected]>

Update openms-ci.yml

42e2806cb35643a39a8fdbf9b6fee24185d06acd authored almost 2 years ago by Timo Sachsenberg <[email protected]>

Update openms-ci.yml

2c64fb58e45a696e636e509054c1aaf3f657d9f9 authored almost 2 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #6428 from OpenMS/feature/clang_performance

Feature/clang performance

8befb000f9f7f9b380efdb362f880cfcde52e49b authored almost 2 years ago by Timo Sachsenberg <[email protected]>

Update openms-ci.yml

5483c7d326118a3598fcf4dfa5f9e9572126786e authored almost 2 years ago by Timo Sachsenberg <[email protected]>

QScore trainer from decoy

5bbd1ea4f197c584c1b1ac81988228b57e73daaf authored almost 2 years ago by KyowonJeong <[email protected]>

fix

af942e33eaa5a8dfbc49267bcd9268a02fad90b6 authored almost 2 years ago by Timo Sachsenberg <[email protected]>

Update openms-ci.yml

70cb4ec0a83dd998c4252df78ac6dea6245d36cf authored almost 2 years ago by Timo Sachsenberg <[email protected]>

Update openms-ci.yml

390db47816be738994cd3b0124c9141c4f5933a9 authored almost 2 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #6449 from poshul/fix/macCLFIx

Fix/mac clf ix

a058b8a24855bdeacc310567212d5c8327dfa5e4 authored almost 2 years ago by Samuel Wein <[email protected]>

Update openms-ci.yml

1be43e0310b1a8b2e7a27436e831759514109b64 authored almost 2 years ago by Timo Sachsenberg <[email protected]>

Update openms-ci.yml

df9ff2dba5ff4e62b4feb5f55903e792bc04fcf4 authored almost 2 years ago by Timo Sachsenberg <[email protected]>

QScore trainer from decoy

6c50996526f2f65b25b5d5b582c5266422249798 authored almost 2 years ago by KyowonJeong <[email protected]>

Update BayesianProteinInferenceAlgorithm.h

b3c99e12bce5de89f4251f49c3f2c2ded8977945 authored almost 2 years ago by Timo Sachsenberg <[email protected]>

Update openms-ci.yml

1267692345db59296ed51d3422416c2388f80f1d authored almost 2 years ago by Timo Sachsenberg <[email protected]>

QScore trainer from decoy

6d11a8aa458d3187811d8bf7314393549a452311 authored almost 2 years ago by KyowonJeong <[email protected]>

Update BayesianProteinInferenceAlgorithm.h

c562817039c7bf4724c4707eeae1825325a3b4a8 authored almost 2 years ago by Timo Sachsenberg <[email protected]>

Update openms-ci.yml

5c55edb56eb751e4623c8a36e51a97483e60841a authored almost 2 years ago by Timo Sachsenberg <[email protected]>

Merge branch 'develop' into fix_int64_xml

70827b7aabd20c85e06fa4d1b47786107e7b696b authored almost 2 years ago by Chris Bielow <[email protected]>

Merge branch 'develop' into fix/macCLFIx

39eb6c87426cd86a2198fec34c7ab8475c3344a5 authored almost 2 years ago by Samuel Wein <[email protected]>

Update openms-ci.yml

c20ac57c664473c8781895cf1d8f0a9b97817809 authored almost 2 years ago by Timo Sachsenberg <[email protected]>

Update openms-ci.yml

12d91110a6b9665b508c54ea50a9c6007976f006 authored almost 2 years ago by Timo Sachsenberg <[email protected]>

Update openms-ci.yml

8721a70dac5f04cb086c29c92be708aaaab34261 authored almost 2 years ago by Timo Sachsenberg <[email protected]>

refactor code into XMLHandler, where it belongs

39da94135f9284771bc7ece5c329ce1eacc29562 authored almost 2 years ago by bielow <[email protected]>

Update BayesianProteinInferenceAlgorithm.h

5262fa15e0bc68fc0b06f45db1c6c58b1378edb9 authored almost 2 years ago by Timo Sachsenberg <[email protected]>