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

use different plugin install on win

447aaa9d6218a9c66a852aee2454835d4a16241a authored almost 2 years ago by Julianus Pfeuffer <[email protected]>

Add pkg installer and faster, less latexy documentation.

c24a6e28d5e4ae4b4f89ec5788aad6bf5fb7bda4 authored almost 2 years ago by Julianus Pfeuffer <[email protected]>

Only one bundle per RT_DEP possible.

033bd85b219f7cd2dea114e9926afddc02483540 authored almost 2 years ago by Julianus Pfeuffer <[email protected]>

Try collecting GH job status to display overall status

Alternative: Use different workflows.

d2451b3181727381aafb70c0bd199ca60901dc32 authored almost 2 years ago by Julianus Pfeuffer <[email protected]>

Merge pull request #6498 from OpenMS/fix_filesystem

exclude std::filesystem dependent functions

a0e4a0474c709ba845ac4e00d0181f61ce894147 authored almost 2 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #6471 from OpenMS/docstrings-fixed

Docstrings fixed

b10522613611822417a37c94c1e7d9a84878775c authored almost 2 years ago by Julianus Pfeuffer <[email protected]>

exclude std::filesystem dependent functions

8126a7448c58b4cd267c83fc9c4592b4c5031329 authored almost 2 years ago by Timo Sachsenberg <[email protected]>

Update cibuild.cmake

12af1c9242a3473a4590313c8e3d746a3c631617 authored almost 2 years ago by Julianus Pfeuffer <[email protected]>

Merge branch 'develop' into patch2

e401b4bee5ec580443083800034ff40d3b2ed97a authored almost 2 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #6495 from OpenMS/timosachsenberg-patch-1

remove sqlite from linux build instructions

45a1beedec33d99c6562958c3701114978e9818c authored almost 2 years ago by Timo Sachsenberg <[email protected]>

forgot one sqlite occurance in contrib

ed5d002fba43d105844dd9d294f7dbeec656b755 authored almost 2 years ago by Timo Sachsenberg <[email protected]>

remove sqlite from contrib and build instructions

d5a923d824225631aa6abb15835c57447e53e397 authored almost 2 years ago by Timo Sachsenberg <[email protected]>

remove sqlite from linux build instructions

e377ef429ec86c7151870cbde852dada09205a65 authored almost 2 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #6491 from OpenMS/timosachsenberg/update-build-instructions-6490

remove wildmagic from contrib and update build instructions

a4a411c0af2939f48ce467fc2412440d7f7e7623 authored almost 2 years ago by Timo Sachsenberg <[email protected]>

Changed precursorMassCorrector to accept negative charges.

69b32c976127d13266a63aedf0e749f2df0fcf26 authored almost 2 years ago by AmandaWein <[email protected]>

Merge branch 'develop' into timosachsenberg/update-build-instructions-6490

87e9d81af7721ada249657c0f5eeca05bff17ff5 authored almost 2 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #6478 from cbielow/fix_sql

Switch from QtSql to SQLiteCPP

b1c47681cad69b5e023e27e4a45f65cac59f1b2c authored almost 2 years ago by Timo Sachsenberg <[email protected]>

remove wildmagic from contrib

79a27f451be0f6e5bfe97cc7e6c4d5b5bf316f8e authored almost 2 years ago by Timo Sachsenberg <[email protected]>

Merge branch 'develop' into fix_sql

f881e8eebcee1d288644d2e00aceead10e099b30 authored almost 2 years ago by Chris Bielow <[email protected]>

Merge pull request #6486 from axelwalter/feature/sirius-5.6.3-snapshot

[Feature] Update to Sirius 5.6.3 snapshot

cbccabf43fb423a96b556265c2fb7da436e57890 authored almost 2 years ago by Samuel Wein <[email protected]>

remove exposure of private includes

8fafa1e88b2cc57129326e33519c4b5eb189492b authored almost 2 years ago by bielow <[email protected]>

Merge branch 'develop' into fix/pasefCachedFiles

e917908886c079a00f5638c518cf1dd774545bd6 authored almost 2 years ago by Joshua Charkow <[email protected]>

[FIX] cached file loading

OpenSwathWorkflow will not load cached files unless the
-split_file_input flag is specified. Thi...

d7fbf2680e5c0ac494c0560b9e94cbb00180ad44 authored almost 2 years ago by jcharkow <[email protected]>

do not export

dee432d1de9738231ec7df37a0edc1b22716f7eb authored almost 2 years ago by bielow <[email protected]>

remove unneccessary QCoreApp

6cd5dff7c0b83e40cb9d7b0cfd6aa7b63cf60e96 authored almost 2 years ago by bielow <[email protected]>

make SQLiteCPP private (i.e. internal to OpenMS lib)

d834492d4a26368b4676b5b74216c25f82e78d75 authored almost 2 years ago by bielow <[email protected]>

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

# Conflicts:
# doc/doxygen/install/install-linux.doxygen

df5ad1af6ffd04adcb8202829ec6e4e0edae592b authored almost 2 years ago by bielow <[email protected]>

update docs to not require sqlite anymore

3cd9b71b0428124c590f1d98f18e30b8e4226119 authored almost 2 years ago by bielow <[email protected]>

undo qsql plugin requirements

597877e69c47b72100b3f10f24cedc5ab8d07c2b authored almost 2 years ago by bielow <[email protected]>

fix value of empty table cells in JSON (shoudl be "", not "NULL")

fc776adf7078d083c7e03c25c5d0cb453f07aef2 authored almost 2 years ago by bielow <[email protected]>

fix empty statements

402ec8502835f55157f456afe3ce0ff16748481c authored almost 2 years ago by bielow <[email protected]>

fixes some (potential) copies (#6485)

* fixes some (potential) copies

* Update src/openms/source/ANALYSIS/ID/AhoCorasickAmbiguous.c...

4e0d18945199f7f4b7d463dcc547a8260fbccf24 authored almost 2 years ago by Timo Sachsenberg <[email protected]>

update sirius version in files

268b5ed76a4980fcecfc6b5d807d219adb5e0e8a authored almost 2 years ago by axelwalter <[email protected]>

update thirdparty

2b54059abe197e57c3587868b04880bee32e8449 authored almost 2 years ago by axelwalter <[email protected]>

prevent life-time issue by returning by value (#6481)

c5cf570efba89bd39dbed50b9480acba4163aac1 authored almost 2 years ago by Timo Sachsenberg <[email protected]>

Merge branch 'develop' into fix_sql

939100fb9959b49c857576f4d8f6bb69f7a7e214 authored almost 2 years ago by Timo Sachsenberg <[email protected]>

Fix clang ci (#6457)

* fix svm lib related bug

* update build instructions

5ceb2b2eed8fbfbfca7485a6cf80aeadfe2171fe authored almost 2 years ago by Timo Sachsenberg <[email protected]>

meta values of unassigned peptides were not exported properly (#6473)

* meta values of unassigned peptides were not exported properly

* removed debug code

* don...

94b932f6c7f2bf7870005cd90d03da5ec3e0a2fc authored almost 2 years ago by Timo Sachsenberg <[email protected]>

use PIMPL to avoid exposing dependency

8692e03358a46414aa85852624a11b5832effe58 authored almost 2 years ago by bielow <[email protected]>

remove useless includes

11c47f5b65dde008f88b11d068ff69f5a759ce02 authored almost 2 years ago by bielow <[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]>

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]>