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

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

a041d1717f05a6f6de8a40741cae69d8699f3718 authored over 2 years ago by Timo Sachsenberg <[email protected]>

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

4d3863a38f3a520fea49534f666f2a4c91f5ef39 authored over 2 years ago by Timo Sachsenberg <[email protected]>

use std::map interface for accessing elements

e15ce035cbb25f165808e52a6e7927ca9fe60dc8 authored over 2 years ago by Timo Sachsenberg <[email protected]>

use std::map interface for accessing elements

aab5a09a331349e3b68a53343dd8570da4169270 authored over 2 years ago by Timo Sachsenberg <[email protected]>

fix (Enzymes.xml): added synonyms of "no_cut" to "no cleavage" for Comet

b1040d1a6b3b561ab4935f17e64f6efd0f083cd2 authored over 2 years ago by zhuchcn <[email protected]>

more error information in DataValue exception (#5837)

086be4c000c1d5ec75e0d0e246f63d77c156c12b authored over 2 years ago by Timo Sachsenberg <[email protected]>

fix (PeptideIndexing): variable name was spelled wrong

4d4389d9731bed2421adc38d89d6420ac969535b authored over 2 years ago by zhuchcn <[email protected]>

fix (PeptideIndexing): positional parameters missing when calling `search`

98de69ce2ee1cfdfc4fd8dbb6076e01ad765285f authored over 2 years ago by zhuchcn <[email protected]>

fix (PeptideIndexing): 1. allow users to specify nterm clip 2. when enzyme is no cleavage and specificity is full, there must be an exact match

69c2f81b904bda1e2dd38e07ee8b945b4a59bc12 authored over 2 years ago by zhuchcn <[email protected]>

comment out unused parameter

7d917cc9d5a38ccc62f3fc454da09a38e4611f50 authored over 2 years ago by Timo Sachsenberg <[email protected]>

Update SpectrumLookup.cpp

90b222243b97a979a600db7a213ec74bb16beb71 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

[FIX] scan number extraction

94dea2cfff234c6fd515edd39ba4781e8289fc3a authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Merge pull request #5839 from axelwalter/feature/set-thread-num-pyopenms

[Feature] set OpenMP number of threads in pyOpenMS

d3c60f6e1e0fd0d2e42cfa002bdabf8c9d0590c3 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Update src/openms/include/OpenMS/SYSTEM/BuildInfo.h

5355deb005243a6976405b277d1a984a778c9af7 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

fix some compile warnings (#5838)

* fix some compile warnings

* remove from header as well

* Update TOPPViewBase.cpp

cc75c637d81f5cfddfeebe81b6546f01d7fc5676 authored over 2 years ago by Timo Sachsenberg <[email protected]>

Update src/openms/include/OpenMS/SYSTEM/BuildInfo.h

c1b155ffd6484ed9abca88d583a5585bb5226a99 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

add setOpenMPNumThreads to BuildInfo

54d8dee35f9b0b961db9fce5e3348200b4e5613b authored over 2 years ago by axelwalter <[email protected]>

Update CHANGELOG

d203985c7042b885ac1085c30a2d9f36d7609b47 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

forgot to bump version in test

74b2f79cc0eb46c11057f2ba0a473fe2dadbb0f0 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

add extra link to LPwrapper test

3e4d308a92ead740b304abe1c3915962adae59ae authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Version test

e3305910f9f38f2ccc1d8c0bc4678af348c865fd authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Updated changelog

133fe606d3ae82dbfa35f5022832297328fd94e7 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Bump version

84315963eac6bcb0d2e5e780c9d3b48075bb01c0 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

read version from found openms in pyopenms

29b1b6be3deb0b3ff5d998add1f941fb1335f167 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Another missing header

62a0445ca19695323f7d26a245938ed71578e93f authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Major bug in MassTraceDetection.cpp has been fixed. For ms1ft output.

dcc3aa6e5f8b77cd35aa9dbf2275a33df5e1381c authored over 2 years ago by KyowonJeong <[email protected]>

Misspelled

83b9bf5c7ff2ad7bf4a3afcb3152686fc1354a89 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Add missing header to cmake

a77c272121764ef79f45fec76ab626d3df065280 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

add swathmap to swath headers

59877df8ed8ae7eac039cbab05202da3c9288d1b authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Update PULL_REQUEST_TEMPLATE.md (#5824)

716d1deb0c8750039d04b266c4e6b87337c278ce authored over 2 years ago by Chris Bielow <[email protected]>

Adapt test for new implementation of mutual info calculating

c7337905fe34b4369d3293d0abfcf74d6068b5df authored over 2 years ago by khue.nm <[email protected]>

Merge pull request #5822 from cbielow/tv_refactor

A Painter1D class for Peaks

dc6592789afbfb8d825e573e86456ca91a374c45 authored over 2 years ago by Chris Bielow <[email protected]>

Add SwathMap.h to CMake header list

a5680ef627b9cffeb939aa9344ce52e33a22e7bf authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Merge branch 'develop' into mutualInfoSparse

151c0e1f61569512e1b6c1a6b60b2f82c6012831 authored over 2 years ago by khue.nm <[email protected]>

Merge pull request #5823 from khuenm/mutualInfoTest

[TEST] Mutual info test

292dc0311c0660af1d67341fcc516cd10aadfa95 authored over 2 years ago by Chris Bielow <[email protected]>

Add more tests

8b235fe270053dd23b539f39a97f6e46364adf83 authored over 2 years ago by khue.nm <[email protected]>

Change test equal to real_similar

8091051704a76c808b2032a6a7b52455d2bf3173 authored over 2 years ago by khue.nm <[email protected]>

[FEATURE] add a Painter Class for 1D Canvas (currently for Peak data only; as historically supported)

614ff9d83ecaa3985fd60cfaf3f1aa936d81350a authored over 2 years ago by bielow <[email protected]>

Rename labels

f9ce3bf40b0cd5ef4d693a4aceae58b4b84ca5ff authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Update dockerdeploy.yml

dcb4ca5db658e9ab80fd176aa779d58fad9e513f authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Update dockerdeploy.yml

25ea52f1250f08726d10307e9e11fbf89fe80f87 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

[infrastructure] update to github package repository

2c9adff7758f803f2e03f49eae2dba62ce7a46c8 authored over 2 years ago by Timo Sachsenberg <[email protected]>

Rename tools to executables

ae8b519c5adbe165548da7c6fa1bef8ca4e126ea authored over 2 years ago by Julianus Pfeuffer <[email protected]>

no quotes in docker action

c61419fa734997de55b7a3e93284ae692190645a authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Update dockerdeploy.yml

2d90cf0f05704dd4df9694ccf75c2480fe0c7d67 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Create dockerdeploy.yml

7b57492d04229fa8a0746adc38f5229359a162b1 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

minor spelling

a30d529c0c3dc3845f7e0fb24fb18f6ca4a0e010 authored over 2 years ago by bielow <[email protected]>

clang format mostly

02a70f08d282cbab9ba3236cc43734fd4e88150b authored over 2 years ago by bielow <[email protected]>

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

56bfca1c702ac8d4989ced82dc3f9d59527213e1 authored over 2 years ago by bielow <[email protected]>

include opt

c5d31b42d061894b25649934390307e05a7d6a48 authored over 2 years ago by bielow <[email protected]>

Merge pull request #5809 from cbielow/ac_noSeqan

Optimize PeptideIndexer

932488d3cd7382c5dfe8f2eca71586d76d0d4491 authored over 2 years ago by Chris Bielow <[email protected]>

Apply suggestions from code review

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

d0702cd82bfc951314ccac37ae6d401479cf2347 authored over 2 years ago by Chris Bielow <[email protected]>

Efficiently do "defaultdict" behaviour in Map (#5816)

a035b4f0a290af594b57694a829e2e67a0363759 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Only package found optional qt plugins

004075592322d6a25f8e05443dd2057e63627313 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Merge pull request #5810 from jpfeuffer/fix/cmake

put more cmake find stuff to the beginning

5e27f8f253c60d1dab7e4651e5113ac6520adeff authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Forgot to remove

4e577e20f4c9391fdee0fa55a5038b4dcf9b435d authored over 2 years ago by Julianus Pfeuffer <[email protected]>

put more cmake find stuff to the beginning

73e6b12da2ab73f7d1acf4c332a18194f2f88b1f authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Update cibuild.cmake

c5eb95544693f4cd1f37d950f00fa86cac77cfb2 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

invalidate contrib cache

38d9319c799ee9e4a54a390e0e04041670f5cc68 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

comment out link library hack needed for setup.py (now cmake based)

53e040c5c21b90c23f654958b2430a7bbe41acbb authored over 2 years ago by Julianus Pfeuffer <[email protected]>

fix include path in install tree

c85d53dd64b8a644562e2317d4a57d820600dec3 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Add test to rankedMutualInformation

f92ef702e0673aa1ad5e1bdbe485cda3fb43f8fa authored over 2 years ago by khue.nm <[email protected]>

fix reported peptide count

1f9a477a095dd94579d57e529d3c837cb75bfec9 authored over 2 years ago by bielow <[email protected]>

move wm5 in cmake config to private too

e4ecf85586ba684c4c78e438e00b0b110718e1a2 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

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]>