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

fix new implementation, which might have reported hits twice (if they contain an AAA).

This was not detected because the outer collection routine used a std::set which removed duplicates.

1b63d1951a3bf6683d15d9a8f3dde25ebcc96e5a authored over 2 years ago by bielow <[email protected]>

fix crash

87d510fa785052dd2e9ab22df1b1ddbf1d5f8458 authored over 2 years ago by bielow <[email protected]>

Update CMakeLists.txt

b91b7f0b1dae1d701cd0aac623ab91be050b32fc authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Update CMakeLists.txt

aa172553578ffa36fe28e4d4e554651a5f19a6de authored over 2 years ago by Julianus Pfeuffer <[email protected]>

[FIX] module dir case

fb555b8f2ebd1020d6133080ee8051162a6935ab authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Merge pull request #5808 from jpfeuffer/fix/pymacdeps

[CMake] Move non-optional simulation models to non-examples share and improve installation granu...

59c65ff4cb9414d35c2291f74b38ea0d8d9c7ba9 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

remove additional target file

f175e3d4a18684f7e2325900ea7de26e13742010 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

some path and export fixes

06d24a43b3b5ad61a2460c3aed8d3b720e298095 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

more cmake install fixes

6c330fb7573b480b28350e2605418faba2e59e86 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Merge branch 'fix/pymacdeps' of https://github.com/jpfeuffer/OpenMS into fix/pymacdeps

788d8d759810d51617d5c4fe7844b1e7013108a1 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Move non-optional simulation models to non-examples share and improve installation granularity

4da5128fd5580e02fe7b7dc32389b3eb53cb8212 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

don't show exception if unknown protein accession encountered (#5807)

9fd86bbc406ee390f3b7cb640f38d63695b33b59 authored over 2 years ago by Timo Sachsenberg <[email protected]>

remove layout from splitter (#5806)

eb81629653754c75284407b6e732545fb591d003 authored over 2 years ago by Timo Sachsenberg <[email protected]>

replace vector of vector with flat vector

b0f3bc647316d8667099f4c496b87a6b7734dd99 authored over 2 years ago by bielow <[email protected]>

Fix/1983 (#5796)

* encode internal comma of stringlists in xml files

* simplify code

* choose different esc...

337fe76788262d76d7feaf997c871d4c2acebc0a authored over 2 years ago by Timo Sachsenberg <[email protected]>

replace map with vector; speedup of 60x for searches with many hits.

9f6f7d29cce2d264d851050b8f66b7e368206209 authored over 2 years ago by bielow <[email protected]>

Merge pull request #5801 from OpenMS/jpfeuffer-patch-5

move WM5 to private libs

c846823cfc54f17f2a9675f102d411d0f38449ba authored over 2 years ago by Julianus Pfeuffer <[email protected]>

move WM5 to private libs

2c33b338c7fca81cdc743f2b47ba17c797013c62 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Merge pull request #5797 from OpenMS/fix/WM5_export

remove WM5 from headers

a5c7ba9a0e4be73f3289b843d8fe388c40af257f authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Merge pull request #5757 from jpfeuffer/fix/pymacdeps

[FEATURE] Complete target-based find modules and CMake-based pyopenms builds

bc7c7fbc13c8068c45c118f1b985ba5ea3f2edb2 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

test with cmath

569cc1512a2f975df4244dea348ea95b8a13f259 authored over 2 years ago by Timo Sachsenberg <[email protected]>

Update LowessSmoothing.cpp

9829cc5fbbccd7f1fab6a98e1bf5917f633308c7 authored over 2 years ago by Timo Sachsenberg <[email protected]>

Apply suggestions from code review

28de690c184fd5814920ccc014f41cbf65234b01 authored over 2 years ago by Timo Sachsenberg <[email protected]>

Var case

1b3ff4e09b3e41368502a168276bfc1ce296ee78 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

remove more seqan

8d34c504303e88347863a70e5cc0bd678c30c7fc authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Update CTestConfig.cmake

47b15df1da79ff86d1f66ccd80d0923493277f48 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Update src/openms/source/MATH/STATISTICS/QuadraticRegression.cpp

Co-authored-by: Julianus Pfeuffer <[email protected]>

0dc746a7c0a210665fe9cb3d58b57d46e47cf1e0 authored over 2 years ago by Timo Sachsenberg <[email protected]>

use emplace

af9cd04510a37ffe2690e57ce6680ac5beb1b631 authored over 2 years ago by Timo Sachsenberg <[email protected]>

further remove WM5 from headers

42b7a22895be689b7d04272e4ced44cc3bb29b7b authored over 2 years ago by Timo Sachsenberg <[email protected]>

remove occurrence of seqan

3f862ba97a6f26d78d969ed91423a2f431ff3ba3 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Merge branch 'develop' into fix/pymacdeps

636ed5cf11dd5e6823f4685c2a89aafb3204ec36 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

avoid unnecessary copy

0b6a17892618a89deef9c5a975be9f2b715cb8c3 authored over 2 years ago by bielow <[email protected]>

unused variable fix

efc244ee6de61ac92a5fb8d6a26bca7c068831a6 authored over 2 years ago by Timo Sachsenberg <[email protected]>

Remove MIToolbox

f296097cbe7635b76a53068b648c5dcc87444846 authored over 2 years ago by khue.nm <[email protected]>

Merge branch 'develop' into mutualInfoSparse

8d2ef57463e5cb6009b8ad9ea48d276eebef5d93 authored over 2 years ago by khue.nm <[email protected]>

Merge pull request #5792 from cbielow/ac_noSeqan

small cleanup

1a457793ec3c5e010bf9621ab3d31c921f9260d1 authored over 2 years ago by Chris Bielow <[email protected]>

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

# Conflicts:
# src/topp/IDFileConverter.cpp

dc8a058a42bd8f243266ee9d26cd3bdfac150b5f authored over 2 years ago by bielow <[email protected]>

some cleanup

f0c9e86cc58a86f1bbce0bc7bba6bf4d27f707e2 authored over 2 years ago by bielow <[email protected]>

quick fix for wong new line

7bea1126c2d6a92f89894d3999063673edb9edf4 authored over 2 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #5731 from khuenm/swath_merge2

Rewrite MI and XCorr matrices calculation/storing of OpenSwathWorkflow

741914f86d8c565b493739a09bd23317aa262dc8 authored over 2 years ago by Chris Bielow <[email protected]>

TV make sure that accessions are still exported (#5786)

* add mandatory export columns

* fix missing variable

* simplified code

* Update TableV...

dff6b08ca55949a786728108780d0feecfdb2045 authored over 2 years ago by Timo Sachsenberg <[email protected]>

Minor fix

1b2265560866b8ce2314dffafa1f146d021b5052 authored over 2 years ago by khue.nm <[email protected]>

Remove comments

b67b81200fcbfa696b5a3c91cacf48cbb6d58585 authored over 2 years ago by khue.nm <[email protected]>

Move hash function to .hpp

c3e542131410f3fde2ce8e1647d27c7265f67467 authored over 2 years ago by khue.nm <[email protected]>

Rename and document functions in Scoring

68766378b1f6cbe920798e905c25083191600424 authored over 2 years ago by khue.nm <[email protected]>

switch to windows-2022 for now as not all runners seems to be upgraded

91dbdbc62239b28478e8a456ea799271f1b56416 authored over 2 years ago by Timo Sachsenberg <[email protected]>

CometAdapter set No_cut to use @

fd0179385c15a0cf97c4cf221c4027a91318e467 authored over 2 years ago by zhuchcn <[email protected]>

enable setting ezyme to "no cleavage" for XTandemAdapter and CometAdapter

e167bb3c097325911eb9a447197b0fcc1246dbc5 authored over 2 years ago by zhuchcn <[email protected]>

Use simple hash function instead of one from boost

9c16b3aeec6ccfa16ca63da58f4bbc844ee12f00 authored over 2 years ago by khue.nm <[email protected]>

Merge branch 'develop' into swath_merge2

e19c18c0e57e7bb8488999790baf00e1392bf386 authored over 2 years ago by khue.nm <[email protected]>

Fix macros redefinition

4c869bb0c0edc0f6075a105b2fa9d9e51725a186 authored over 2 years ago by khue.nm <[email protected]>

use latest cmake in github action fo rwindows

709a8f4c3c9800c0dfa79dd8d6b1c7b564b017ca authored over 2 years ago by Timo Sachsenberg <[email protected]>

update visual studio version to 17 2022

687501d59715dd7c8239c2477abf2f0c7f8a7af6 authored over 2 years ago by Timo Sachsenberg <[email protected]>

a few fixes (#5782)

* remove superfluous include ?

* fix compiler warnings

* fix failing test due to invalid v...

9a1ff47a0286830e5044e1c5139774f6e180a5a7 authored over 2 years ago by Chris Bielow <[email protected]>

fix compile error for linux

eefc4d4f6d8f10d528607d425a6689ea4e1764ff authored over 2 years ago by bielow <[email protected]>

fix error message for new id data structure tool

"QSqlDatabase: an instance of QCoreApplication is required for loading driver plugins"

0ed7b05324af9783996d88ce2c2ec62daaa50613 authored over 2 years ago by bielow <[email protected]>

Upper_bound incorrect usages have been fixed.

Targeted mode implemented in FLASHIda.cpp and FLASHDeconvAlgorithm.cpp

Many minor bug fix.

49ead71a3454f640a42d936d0ca451c59d8fd592 authored over 2 years ago by KyowonJeong <[email protected]>

fix buggy comparison operator

838ac883b9eeb90b315390a9caabc68fc72ad34f authored over 2 years ago by bielow <[email protected]>

disable 5min test in debug mode

e3e0bab3d14d4bcbcf5379ba826e4d951a96f1c0 authored over 2 years ago by bielow <[email protected]>

fix failing test due to invalid vector access

3ca8fa13c39f8f45c6c2e13c2cac11adeef57bbc authored over 2 years ago by bielow <[email protected]>

fix compiler warnings

ff6412e9af8ab691c43d8ba96dadbdfdf86dee40 authored over 2 years ago by bielow <[email protected]>

Merge pull request #5780 from jpfeuffer/feat/noDepsOptionPyOMS

[FEATURE] add pyopenms option to not bundle dependencies. removes need for patch in conda

9cde7f3de4ae4041635c90761b6aace4ba79e0dc authored over 2 years ago by Julianus Pfeuffer <[email protected]>

remove superfluous include ?

d3fe1d65116ccd8cc928790479c537eecb1bda9f authored over 2 years ago by bielow <[email protected]>

rename vars

a418e4d7694f5e062443402cbb2f00cb762060b0 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

better cython find and to retry CI

7ff834a26c665803c3873c05767a854394589c5c authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Merge pull request #5779 from cbielow/ac_noSeqan

Remove seqan library from OpenMS

c3876fab9a66ee46450481c6d9b09f17dd20f713 authored over 2 years ago by Chris Bielow <[email protected]>

add pyopenms option to not bundle dependencies. removes need for patch in conda

22cbcef742d31cf265384db0c71c943ead746e35 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

removed seqan library from OpenMS

367b768ce1bf211afebeb78b837bcdbfef6079b1 authored over 2 years ago by bielow <[email protected]>

Update GNPSExport.cpp (#5777)

I deleted quite a lot of things to make it simpler for users (also some parts were repeated or l...

e55b2959334f80f812aebc2868fc0b1d08cda176 authored over 2 years ago by Efi Kontou <[email protected]>

Merge pull request #5776 from cbielow/ac_noSeqan

Rewrite of PeptideIndexer; supports AAA's in Peptides;

b14ec03b1b9a886ff664d48f20ec835177f76e53 authored over 2 years ago by Chris Bielow <[email protected]>

add File.h include to avoid compile error

00f9420dc4525410591bf09c7c2780ee664b4bf8 authored over 2 years ago by bielow <[email protected]>

remove template specializations

ebb0d38f673dfda189efa1143bbb0e13c91c4fff authored over 2 years ago by bielow <[email protected]>

[FEATURE] complete rewrite of AhoCorascik algorithm; its about twice as

fast as the previous implementation (which used SeqAn), uses less memory
and supports ambiguous A...

141bbdf3b856db7e0cb6b1012808ebce1bca97bb authored over 2 years ago by bielow <[email protected]>

Merge branch 'develop' into fix/pymacdeps

18b1940cdf5dbf546b2db25fa7d5ac9fca806346 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

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

9275fe4cf1e5436ab61938e894137e4a1486dfa8 authored over 2 years ago by bielow <[email protected]>

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

803c3a6442b4cb81caeebe874e1d343cd5794bc3 authored over 2 years ago by bielow <[email protected]>

more reduction of test output (#5771)

019abf34857bd73b0b3cdb43afc4e7c7aa2126f1 authored over 2 years ago by Timo Sachsenberg <[email protected]>

[Fix] MS3 TMT IdMapping (#5773)

* [FIX] annotate correct precursor charge for MS3 TMT and try scan_id based mapping

* request...

1e1f1e5a75078595b90f61215d35268666f721d2 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

[NOP] better warning message

b0629e408cbb0f5d2d655d93f5721757d7ea1437 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Merge branch 'OpenMS:develop' into develop

35e5b964f97ddf8390610bf1dff4e21793c07dc6 authored over 2 years ago by Chris Bielow <[email protected]>

Set fillIntensity to non-member function

25efe01ecdc64469fb2bf701b5e8a25065b90918 authored over 2 years ago by khue.nm <[email protected]>

Change storing structure of joinStateCounts to unordered_map

5e7a7bc6b945e33caeff6417b1e94e6e67e62ad9 authored over 2 years ago by khue.nm <[email protected]>

Set fillIntensity to non-member function

e233146e26dda5c4840a7f8acfc463fde4a0570e authored over 2 years ago by khue.nm <[email protected]>

replace boost with std variant (#5768)

* replace boost with std variant

* reduce output of MorphologicalFilter_test

* use binary ...

52e6c131b633ff26302d10f6e04f78fb83f58270 authored over 2 years ago by Timo Sachsenberg <[email protected]>

Disable successful test lines by default (#5767)

* disable output via OPENMS_TEST_SUPPRESS_SUCCESS

* inverted logic

* Update MorphologicalF...

08ed8a1c256c8f24a6008b85fb507aef06616f17 authored over 2 years ago by Timo Sachsenberg <[email protected]>

remove pxd for AhoCorasickAmbigous as it pulls in Seqan headers and is disfunctional (#5769)

8ca8b8aa3cc04c14e99587c641d56f1ac38fc972 authored over 2 years ago by Timo Sachsenberg <[email protected]>

Merge branch 'develop' into fix/pymacdeps

534507aff1424a5814d80c33fe24777bde5dd877 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

forgot to adapt includes

4ed75c170edc277ec125946e4a418a9a004e4cae authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Add another module because Cmake is so slow updating theirs.

36d5b287ad5081ecf52c3e9d7fb13d5dd899fb09 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Docs in external test

c1103fe2452d5a4ac2e65fef47c4cc037de887f4 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

remove unneded include

09c00a0b52e529714d04512173b17d010e3101eb authored over 2 years ago by Timo Sachsenberg <[email protected]>

Require OPENMS_TEST_VERBOSE_SUCCESS env variable set if output of successful test executions should be printed (#5765)

* expect OPENMS_TEST_VERBOSE_SUCCESS env variable set if output of successful test executions sh...

ef6c218851f2d0e2bfc89c07a2101ee94e17bd5d authored over 2 years ago by Timo Sachsenberg <[email protected]>

move Wm5 dep to cpp (#5754)

* make seqan private and move Wm5 dep to cpp

* removed uneeded seqanwrapper include

* move...

86b1d86d0b522fb83a42594faf46ecd77f31becc authored over 2 years ago by Timo Sachsenberg <[email protected]>

try some external code fixes

185f64f67b7672e141af54d27ee02e5059f85ae8 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Merge pull request #5766 from OpenMS/revert-5764-fix/compile_warnings

Revert "compile fixes"

c2286d5758553877a8277beb68b09082569b12b3 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Revert "compile fixes (#5764)"

This reverts commit c19574f1d94779d5fce3df82bfcb762cee60559b.

978ccbb87b8f1939db3257a767083b13ce867fb2 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

finish rename and fix tests

06ea0c327c9bad13662ff8688f38f512eaf47d9d authored over 2 years ago by Julianus Pfeuffer <[email protected]>

rename var for consistency

10388890779b7b9be0b3dad5375f41f503bce81e authored over 2 years ago by Julianus Pfeuffer <[email protected]>

compile fixes (#5764)

* compile fixes

* Apply suggestions from code review

Co-authored-by: Julianus Pfeuffer <pf...

c19574f1d94779d5fce3df82bfcb762cee60559b authored over 2 years ago by Timo Sachsenberg <[email protected]>

First working version of separate pyopenms build. Fix pyopenms warnings.

e9099ac842646d205dd2b3b9a114d0e29ad7a698 authored over 2 years ago by Julianus Pfeuffer <[email protected]>