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

minor optimization

242c87d7685808af0f8d71b59eecb3881231818e authored over 1 year ago by Chris Bielow <[email protected]>

fixes #6888

054324c9bafdeaff2b6bf59c0025216beb6e6ea5 authored over 1 year ago by Chris Bielow <[email protected]>

Merge pull request #6876 from SGSSGene/fix/gcc13

Fix gcc13 error and warnings

486453ba208baf28639cc25163ac9c37fb987eb1 authored over 1 year ago by Chris Bielow <[email protected]>

PeakGroup SNR estimation more optimized .

22b228f9c949c44b79f7a23b03f951cc1f41a614 authored over 1 year ago by KyowonJeong <[email protected]>

patch: running clang format on touched files

314ae50c2260cece76456dbec2e4852c0901a909 authored over 1 year ago by Simon Gene Gottlieb <[email protected]>

fix: remove virtual declarations from assignment operators

These virtual doesn't do any thing. The inherited classes have their own
declaration of the assi...

a0d5517d6662520868206dce1802fabfcebaa3a8 authored over 1 year ago by Simon Gene Gottlieb <[email protected]>

fix: adding missing header for gcc13

10b8a8301bb033fa1299eb372f4038a0d962961c authored over 1 year ago by Simon Gene Gottlieb <[email protected]>

patch: remove deprecated std::iterator

59d3f2e341478cafb5db7366a3c9627b7328537a authored over 1 year ago by Simon Gene Gottlieb <[email protected]>

patch: replacing the 'requires' function with 'requirements' since 'requires' is a key word in c++20

ec01689d0645586695f8f2860b2b82165201a413 authored over 1 year ago by Simon Gene Gottlieb <[email protected]>

patch: replace deprecated 'not1' with 'not_fn'

8f909a47222af6ea9623353d2c880da92cf4f82b authored over 1 year ago by Simon Gene Gottlieb <[email protected]>

PeakGroup SNR reimplemented + Julianus comments addressed

babcd11ff0a2dafea4e9378a944c570215bb2d95 authored over 1 year ago by KyowonJeong <[email protected]>

Better logging in RibonucleotideDB.cpp

Added DEBUG level output to show which Custom_RNA_modifications and Modomics files we are using....

4cd8b5bf29b60e41af5ed5d282d48f5a82ab267e authored over 1 year ago by Samuel Wein <[email protected]>

removed white space

d5831b645d2a563a6efbfcbbf8ef952f8fca0ddf authored over 1 year ago by JeeH-K <[email protected]>

DeconvolvedSpectrum_test.cpp test failure fixed

2b827520c15c3dbe5488a13e9b05c02844611230 authored over 1 year ago by KyowonJeong <[email protected]>

Unnecessary harmonic removal removed. Some of magic numbers have removed or/and adjusted.

8f950cbfb01757041c6174267692986b5e014577 authored over 1 year ago by KyowonJeong <[email protected]>

SNR calculation renewed. For signal, first sum intensity then square. For noise, group peaks possibly from the same molecule and sum their intensity before square. Far better to remove harmonic yet to retain signal

4cf6e06bf2ddbbb34c32f5c547f2606cf0324bdf authored over 1 year ago by KyowonJeong <[email protected]>

update FLASHDeconv to the newest version (#6869)

* FLASHDeconv branch is merged (using manual diff). Window test is necessary yet.

* Scan numb...

bc87405780eb75c98a3e1b5de946d374b45598fc authored over 1 year ago by JihyungKim <[email protected]>

Support for consensus maps in .oms (SQLite) files (#6816)

* [FIX] fix handling of IDs (new format) in FeatureMap assignment operator

* [NOP] whitespace...

a497b9971130ec5644d825ad24f89c6f876fec73 authored over 1 year ago by hendrikweisser <[email protected]>

added decoder functionality

14625723d4c31cf884d98689f1597cc8d0a9def9 authored over 1 year ago by Moritz Aubermann <[email protected]>

[FEATURE] Make CMake work with coin from brew. Complete the vcpkg recipe. Fix some warnings.

13cb7184d4cbd38741d6443ac7fcc1eaf12b54e2 authored over 1 year ago by Julianus Pfeuffer <[email protected]>

[FIX] Param merging with empty subsections (#6873)

* [FIX] Param merging with empty subsections

* add test

* check empty?

74f76cec5178eae044646b10b2a63c2705aa9e7d authored over 1 year ago by Julianus Pfeuffer <[email protected]>

Merge pull request #6872 from OpenMS/dependabot/submodules/src/pyOpenMS/pyopenms-docs-fd4ceca

Bump src/pyOpenMS/pyopenms-docs from `a583c73` to `fd4ceca`

d3de013d4acbf64cf5e7acd4331207df95c4a49a authored over 1 year ago by Julianus Pfeuffer <[email protected]>

Bump src/pyOpenMS/pyopenms-docs from `a583c73` to `fd4ceca`

Bumps [src/pyOpenMS/pyopenms-docs](https://github.com/OpenMS/pyopenms-docs) from `a583c73` to `f...

b56f1250dc6919a9f333aa2cb06c33c9aee267af authored over 1 year ago by dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

reverted changes in test, that was used as workbench

96eac291060a48241233c76adbd93ea1078b43ec authored over 1 year ago by Moritz Aubermann <[email protected]>

coding conventions, comments, last fixes

3b72d702d6b388a73b7175c8cbf1ea8a23e8de67 authored over 1 year ago by Moritz Aubermann <[email protected]>

fixed up compile flags to make simde work

63aa6759a3ca06bbaf910fb39f46f8b22e496915 authored over 1 year ago by Moritz Aubermann <[email protected]>

Merge pull request #6868 from JeeH-K/feature/FLASHDeconvWizard

Adding FLASHDeconvWizard feature

800b1f2b539aad3b068c021c277db48b93dbf304 authored over 1 year ago by Timo Sachsenberg <[email protected]>

Addressing Timo's feedbacks on PR#6868

cf4b634c54a817d97aded5e62a6aafb3cf63a05e authored over 1 year ago by JeeH-K <[email protected]>

remove FLASHDeconvGUILock and use WizardGUILock

ec3276492238de91cb23d0f2874cd82b5a95b870 authored over 1 year ago by JeeH-K <[email protected]>

retrieved FLASHDeconvWizard related files from commit 3d5ebf183c

5a77ea1530101a3cbf4fd342a65965744e28b6a1 authored over 1 year ago by JeeH-K <[email protected]>

fixed encoding

f2d7752e6f374159f74ec95090799416a89f0c8f authored over 1 year ago by Moritz Aubermann <[email protected]>

MetaProSIP: typo (#6862)

26292adaec5da7f398205e977db194ba4f3a9f05 authored over 1 year ago by M Bernt <[email protected]>

[FEATURE] ProtDigest with indices, simpler ModPepGen (#6854)

* [FEATURE] ProtDigest with indices, simpler ModPepGen

* Review comments and fixes

* fix a...

eb7ffacdc9f6f779fe45fd885fc5f6a0243142cc authored over 1 year ago by Julianus Pfeuffer <[email protected]>

code runs now, endianness needs to be fixed

22a194c4240b07b20ee6571b848b54642bc8c73f authored over 1 year ago by Moritz Aubermann <[email protected]>

Merge branch 'develop' of https://github.com/42layerToiltepaper/OpenMS into develop

rumprobieren

0dd830d24a9963856f7cf23eff7ad64773a54dc8 authored over 1 year ago by Moritz Aubermann <[email protected]>

fixes in make file and failed attempt to make our code work

0e93b60b148758abbdbf82307f3641843488b44a authored over 1 year ago by Moritz Aubermann <[email protected]>

repair

9b84bec22b4f72b8ecf2f95eee9627fd50295a56 authored over 1 year ago by Moritz Aubermann <[email protected]>

modify cmake file and note down what needs to be changed partially

6a23386947c33ac790dd61c9d672d5b4091ce03d authored over 1 year ago by Moritz Aubermann <[email protected]>

include thirdparty simde library

2f072dea18c7f0e86d7596a5acc7bdf2210d2673 authored over 1 year ago by Moritz Aubermann <[email protected]>

Update style_ini.css

183363254a9b6b4f66dfa2cf0712f6133cd26bfa authored over 1 year ago by Julianus Pfeuffer <[email protected]>

Simply selectversion.js and allow selection on different domains

0c12349221c37a419177f4342c25eda9fcdecb03 authored over 1 year ago by Julianus Pfeuffer <[email protected]>

[DOCS] add version selector

27ae821b1e163f18d44668dedba6b335fc6a47e0 authored over 1 year ago by Julianus Pfeuffer <[email protected]>

improve DecoyDatabase doc (#6844)

* improve DecoyDatabase doc

the tool does not shuffle/reverse the sequence
but only the pept...

e0ac492dc89ae6eecb3c404d1c8e993bc052a8f1 authored over 1 year ago by M Bernt <[email protected]>

Clean up so files after building on manylinux (#6843)

* .so file cleanup

* .so fi...

06dbf1827fa5ca6df79f6f279f716c7d5b29e60a authored over 1 year ago by Matteo Pilz <[email protected]>

Merge pull request #6839 from cbielow/cpp_check

Cpp check fixes

a96aae42d46ecfac09e5cbc41141ae5d412d53cc authored over 1 year ago by Chris Bielow <[email protected]>

fix test

98e2be5d5e930fe917d866ee2252fdfc26a65c23 authored over 1 year ago by Chris Bielow <[email protected]>

fix missing include

569af79e04314df6f9aecd67e5565fbbf2f04df5 authored over 1 year ago by Chris Bielow <[email protected]>

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

6ee7cfe13e196daaf509a501fda1873adf25dade authored over 1 year ago by Chris Bielow <[email protected]>

fix compile error

2831b2b090423b4e1d12c3b1e2426479ca1e5d6d authored over 1 year ago by Chris Bielow <[email protected]>

Bump src/pyOpenMS/pyopenms-docs from `4e49d49` to `a583c73` (#6840)

Bumps [src/pyOpenMS/pyopenms-docs](https://github.com/OpenMS/pyopenms-docs) from `4e49d49` to `a...

bb2d894855aa3e4380d94f7c4c01b853238ee462 authored over 1 year ago by dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

fix cppcheck warnings

2e5a852ea95df71f9f2acb2673f6212498492415 authored over 1 year ago by Chris Bielow <[email protected]>

fix unused init

7632b1db37f1bcdc3c614201f77132accd56010d authored over 1 year ago by Chris Bielow <[email protected]>

fix usused init

2477f084668ba88cf15932997f1341767280f2d9 authored over 1 year ago by Chris Bielow <[email protected]>

fix usused init

088a20ab9695cbcb71531db06673d7e0a1bf3971 authored over 1 year ago by Chris Bielow <[email protected]>

fix unsused assignements

3c529698079f9b9c11bdb5a8d299b33e2abc0e2c authored over 1 year ago by Chris Bielow <[email protected]>

fix usused assignments (cppcheck)

38b49f904e1bbb3549865bd07e31580ba42b2e5d authored over 1 year ago by Chris Bielow <[email protected]>

fix Prefix ++/-- operators should be preferred for non-primitive types.

a7cc3178941635394bf33038441db3bea144956b authored over 1 year ago by Chris Bielow <[email protected]>

fix bug

55e3b266108f8fd743adcaacd988ea8d8b3c55cf authored over 1 year ago by Chris Bielow <[email protected]>

fix cppcheck

dc8cada0a479425e6fc0a78d641d73fb789280e6 authored over 1 year ago by Chris Bielow <[email protected]>

fix ccpcheck (useStl)

b733f02caf323a15d637b1dc6373f86be8041c28 authored over 1 year ago by Chris Bielow <[email protected]>

fix cppcheck

13e1494f31ccd2f0897d699d6cc4720dd4fe5e21 authored over 1 year ago by Chris Bielow <[email protected]>

fix cppcheck

e04eb2ce2e0422c8af45a0cbc519290804f8ea0e authored over 1 year ago by Chris Bielow <[email protected]>

fix multiple cppcheck warnings

b6ccc4d21c6f5c5aa6417a26762bd85696241fea authored over 1 year ago by Chris Bielow <[email protected]>

fix cppcheck

c4b3f88e9e6a58d4436f2a5d63bef94ac53ebf36 authored over 1 year ago by Chris Bielow <[email protected]>

fix cpp check warning

ad2d27e2a6a743bc239eecdcaa45b4864b2c13ab authored over 1 year ago by Chris Bielow <[email protected]>

cpp warning fix

fa4365a2f0117134b5dc42f7f04253a1b123cf7d authored over 1 year ago by Chris Bielow <[email protected]>

Local variable 'sum' shadows outer function [shadowFunction]

5796f852e09af27e741543282876aab378cd63af authored over 1 year ago by Chris Bielow <[email protected]>

Local variable 'sum' shadows outer function [shadowFunction]

2938a8d2610192984dedaff02226746c37152c27 authored over 1 year ago by Chris Bielow <[email protected]>

Local variable 'sum' shadows outer function [shadowFunction]

4257006ced498c59f2d2eec893a7c34d70cc93f5 authored over 1 year ago by Chris Bielow <[email protected]>

avoid 'style: Local variable 'mean' shadows outer function [shadowFunction]'

9ef5dc06dfea5ba6d72dfcb841214b53166c43fd authored over 1 year ago by Chris Bielow <[email protected]>

Merge pull request #6837 from cbielow/fix_dragExternal

TOPPView: Fix drag external

f94017e5fbd2d102ab96230229b77cdee30922f6 authored over 1 year ago by Chris Bielow <[email protected]>

use a QTimer to finish the dragEvent and avoid blocking the external source (e.g. Explorer) when loading the file in TOPPView

cefdb89dbf4e6657cc0c342e9d010ddd3be5719b authored over 1 year ago by Chris Bielow <[email protected]>

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

d5d49df7ee6363526b8aefbd82700f484c0c539e authored over 1 year ago by Chris Bielow <[email protected]>

Revert "use QueuedConnection (i.e. no direct invocation of loading files before finishing the dropEvent) for drag'n'drop from external sources"

This reverts commit 9e0c3550635420bfd610d8173a9c600fed05527b.

fabf2beba7d8a1699f4a8f91b4b03b8c156eba52 authored over 1 year ago by Chris Bielow <[email protected]>

use QueuedConnection (i.e. no direct invocation of loading files before finishing the dropEvent) for drag'n'drop from external sources

9e0c3550635420bfd610d8173a9c600fed05527b authored over 1 year ago by Chris Bielow <[email protected]>

pin file reader (#6824)

* wip

* more entries

* nop

* Update PercolatorInfile.cpp

* add modification parsing ...

52809bd12e8e2a8db41f81ca1dfb20362bfff1ae authored over 1 year ago by Timo Sachsenberg <[email protected]>

Bump src/pyOpenMS/pyopenms-docs from `19d3537` to `4e49d49` (#6836)

Bumps [src/pyOpenMS/pyopenms-docs](https://github.com/OpenMS/pyopenms-docs) from `19d3537` to `4...

79977f78afcfd483e4afafe503467ce487028f04 authored over 1 year ago by dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

fix gaussFilter's wrong ppm width (#6830)

* fix wrong PPM computation (used 10e-6 which is 10^-5 !!!!)

* modernize tests a bit

* upd...

1e08e9f53a1f720afac3df9f54de74381c8e430e authored over 1 year ago by Chris Bielow <[email protected]>

Fix spec decoder memory leak (#6831)

* another go at fixing mem leak in ElementDB

* remove memory leak in case of exception

---...

7a428a34b566da847b53101fec5ca4d247472c75 authored over 1 year ago by Timo Sachsenberg <[email protected]>

another go at fixing mem leak in ElementDB (#6829)

* another go at fixing mem leak in ElementDB

* Update ElementDB.h

---------

Co-authored...

efc10dca0f06805e490e33f249cc98a271eb5477 authored over 1 year ago by Chris Bielow <[email protected]>

Update ClassTest.h (#6828)

Print name of unexpected std::exceptions

b25e2e9a25640bbc43ddcc71ec83c56943a77b0d authored over 1 year ago by Timo Sachsenberg <[email protected]>

make FFID and map alignment more robust to missing IDs (#6825)

* quick fix attempt

* add test to reproduce issue

* don't fail if not enough RT informatio...

7e6662f5b1c92418bb902689d3bf6f8ec7ceeaf2 authored over 1 year ago by Timo Sachsenberg <[email protected]>

Merge branch 'develop' into Feature/GenericFileLoad

993455f1400b33d58f8a5aa206cfbe5a9673dd52 authored over 1 year ago by Samuel Wein <[email protected]>

Update LogConfigHandler.pxd docs

0e107d006c5e8e7fc82bf35856de2aa3f2200083 authored over 1 year ago by Julianus Pfeuffer <[email protected]>

add to CHANGELOG

d77d32c84f1907c39bc4a2a0d4aa644dd94ec244 authored over 1 year ago by Samuel Wein <[email protected]>

Merge branch 'Feature/GenericFileLoad' of ssh://github.com/poshul/OpenMS into Feature/GenericFileLoad

3b1de9eca69139e65877b80e2134bd47fb9d782f authored over 1 year ago by Samuel Wein <[email protected]>

Merge branch 'develop' into Feature/GenericFileLoad

e30ead2e5532fcd9d712a3989347b07e75a4fc5b authored over 1 year ago by Samuel Wein <[email protected]>

remove decoy_prefix for proper decoy annotation of comet pin file (#6823)

a80f857975ba2b4e35c4fc05c5f99bda58efe167 authored over 1 year ago by Jonas Scheid <[email protected]>

Merge branch 'develop' into Feature/GenericFileLoad

6eb12e39aa45f0709f3985c9723082db59c77f03 authored over 1 year ago by Samuel Wein <[email protected]>

[fix] fixed memory leaks in RibonucleotideDB class (#6821)

8f57309eed12ce66f27ad2be7094de576894b743 authored over 1 year ago by Samuel Wein <[email protected]>

fix ASAN in ElementsDB (#6820)

* fix ASAN

* Update src/openms/source/CHEMISTRY/ElementDB.cpp

---------

Co-authored-by:...

3f8d264db7758d5d7e27074d9c553d6e2adab37b authored over 1 year ago by Timo Sachsenberg <[email protected]>

Check for IM when -pasef flag set (#6735)

* Check for IM when -pasef flag set

Errors are not properly caught when dealing with PASEF fi...

9d17f4bceac8fc497f24ed6a716a150013dca070 authored over 1 year ago by Joshua Charkow <[email protected]>

remove useless critical section (since protection is incomplete and very hard to achieve anyways). (#6818)

This fixes the ElementDB test which throws an exception inside the former `omp critical section`...

70b7b8f0022619f027aad94342d9d1c07f9a0fac authored over 1 year ago by Chris Bielow <[email protected]>

fix comet tests (#6817)

* fix comet tests

* update IDFileConverter test

* update featuresethelper test

--------...

a223ae55ce0f5ba44fb094d931f86b4a5f573dba authored over 1 year ago by Timo Sachsenberg <[email protected]>

only calculate features if not already annotated by comet (#6814)

e55818d6fbebcd23cad1e92bada66974c6832250 authored over 1 year ago by Timo Sachsenberg <[email protected]>

Add comet tests with new pepxml output (#6815)

e338fec3447ab4fda42a47c99b8e5591b619b6f0 authored over 1 year ago by Jonas Scheid <[email protected]>

parse new comet entries (#6813)

935ee660c4b03548bd89c2526c02a19f7f92277e authored over 1 year ago by Timo Sachsenberg <[email protected]>

[DOC] improved Linux build docs (fixes #6789) (#6812)

* [DOC] improved Linux build docs (fixes #6789)

d3d34b4f631bb24e8df156fef523e23d81ae225d authored over 1 year ago by hendrikweisser <[email protected]>

Adjust cometadapter tests (#6811)

* Adjust cometadapter tests

* Add export_additional_pepxml_scores param for additional search...

26d3411b05b6b91bfee3616b5ae4b4997c0f20cf authored over 1 year ago by Jonas Scheid <[email protected]>

enable mass trace quantification median with smoothing (#6803)

67c1c68c41c015452903e696173bc8c5c0b938a8 authored over 1 year ago by axelwalter <[email protected]>