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

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]>

fixes pyopenms visibility and external

b31292c29d91cd8b0912c3ce41602e5bfa8d0277 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

forward declare all svm types (#5762)

* forward declare all svm types

* add missing include

* forward declare svm structs as str...

16a9b45c6405296f598f93d5a433cd49bb576463 authored over 2 years ago by Timo Sachsenberg <[email protected]>

typo fixes (#5763)

* fix typo

* fix #5755

* revert wrong fix

07f980d456ee5fbb70e6afaa41805a0f4428da60 authored over 2 years ago by Chris Bielow <[email protected]>

Fix dir vars

fcac5642588139c55d4b5d2d89452a54638c470e authored over 2 years ago by Julianus Pfeuffer <[email protected]>

fix pyopenms race condition in make. try to fix external test

2e03a2e3785a04386ce981631c67ca1dccc268db authored over 2 years ago by Julianus Pfeuffer <[email protected]>

fix more tests

ffde1c5043da3c71b2d5a4037ada2d05bae9f93b authored over 2 years ago by Julianus Pfeuffer <[email protected]>

fix cmake includes

9050c0ac514c462a7f9e1f5c8497134c3ff1f77d authored over 2 years ago by Julianus Pfeuffer <[email protected]>

I give up. just copy the find module from CMake.

5a02c445b5fec989c3b9039c620ffb82454e3fb6 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Fix tests and potentially HDF5 find

3e3b6466e5f67f339927c208cf4f77ffcb955748 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

upper case boost

5186ec670bc8dbe09dcfb0fe869dfdba2ab41166 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

wrong include from copying

9505bfa40ffd1f1af47fbee663c605657b8d859d authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Readd Xerces find until upstream CMake is merged. Add missing extra links to execs.

a717a0426892f69e3dc8a23e7d16cf404d9f9287 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Update install-linux.doxygen (#5759)

47db3e0ca314219f7693539874c69ca657b32f84 authored over 2 years ago by Timo Sachsenberg <[email protected]>

more fixes

cca3329dcc9b31b719dde59216984c7876a1c882 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

reduce warnings

a5597f19f667e18787a56409949da98cea0a7926 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

more fixes

df88669c5812e57077a1e793872516e82c58b69a authored over 2 years ago by Julianus Pfeuffer <[email protected]>

forgot to remove

8825f6ca413e6d7db7efa893fd24cde3368e86e4 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

forgot to use new var

d2af8b705ad74dd2c612945d9f94c86980133f97 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

more find fixes..

fe60db012457049b461c984ff2e01f90160e6cc7 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Fix superweird FindQt required behaviour. Reduce hdf linking to cpp parts only (also more backwards compat.)

97bc46b3fb3f84e5e07d8acb576a8f686440f559 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Fix PYTHON_EXECUTABLE input

fc685905dc353942bb4d4d530b6fd3c5d39498ee authored over 2 years ago by Julianus Pfeuffer <[email protected]>

forgot to revert path

268a313faab1367bc316524f17ae390894cadaa7 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

fix FindWM5 interface

f3f14e3ee9919bcb318ccd0eb0c0f18821dfa9f7 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Sqlite find override fix?

d56838c4fb98d35b53c636ee02403ea74b2562ed authored over 2 years ago by Julianus Pfeuffer <[email protected]>

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

b45ccf6dcac6dbeb550a8695a804e1ff245cd15d authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Fixes in finding libs

075d0d31478b3aa7f500e80caed43026b05a2d6e authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Merge branch 'develop' into fix/pymacdeps

caff37fa703f0423a26f54b68fa25727e5a4a789 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Also install and use our find modules

a01a7947fa1e8d721c0ff8d3972ccdc985e83c0c authored over 2 years ago by Julianus Pfeuffer <[email protected]>

finished exporting

e71f608b32c3e325b140f1bc88d049c1a3cbc2e3 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

More major refactor for exporting our libraries

0c2d6c8377ee45008dcbee79f3fbf574ab99faa4 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Finished pyopenms build with CMake

eb3e0abe913131adb1c4691b879b9a78db5e7721 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Changes to py CMakelists after cherrypick

2a732bad6d57eaf5f9114114bf70c63e2f74f339 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

merge changes I had on another branch to build pyopenms from cmake

1305a5ee5cf67f1c0689d4a536d0bf1718914022 authored over 2 years ago by Builder <[email protected]>

Major restructure of CMake due to use of imported targets

70c26f3e2324ec92bd4a0cda95fae47c9e046fd8 authored over 2 years ago by Julianus Pfeuffer <[email protected]>

[FEATURE] Add imported targets to all find modules and use CMake's where possible. Also fix fix_dep script

56b6a52bac95d7bb4dec872d08f3bf17a282888c authored over 2 years ago by Julianus Pfeuffer <[email protected]>

Update pyopenms-wheels.yml

7a911a4ca2c3b53a77116eb74ce3f42670d7fd5f authored almost 3 years ago by Julianus Pfeuffer <[email protected]>