Ecosyste.ms: OpenCollective

An open API service for software projects hosted on Open Collective.

github.com/OpenMS/OpenMS

The codebase of the OpenMS project
https://github.com/OpenMS/OpenMS

[BUILD] disable python memory leak tests (#4488)

bf584d0410045f44f01e2e3ea76a99bc6a347ea3 authored almost 5 years ago by Hannes Roest <[email protected]>
Merge pull request #4486 from hroest/feature/manylinux2014

Feature/manylinux2014

5e9988c5f4d53145411b2acd700c92e338b8e9b4 authored almost 5 years ago by Hannes Roest <[email protected]>
MS 2 works fine.

ce21c9fe42209aeebe00407f42256826319aea28 authored almost 5 years ago by kyowonjeong <[email protected]>
code restructuring to make arguments independent

4ae239a316bb7335f1dec78bf225f7ac661bdec0 authored almost 5 years ago by M Bernt <[email protected]>
MS 2 works fine.

5603b46c24f4855f0b31dc8c574b442651634f13 authored almost 5 years ago by kyowonjeong <[email protected]>
minor code formatting. converted Range from class to struct. Elements are now parsed using EmpiricalFormula.

7a11bc8a843a5c8fa03f2d84e92859034e4ecf2d authored almost 5 years ago by marcusL <[email protected]>
[FIX] keep TITLE info in nativeID for MGF files

1a6168c5fd77183bec9182d44e9735d4361975a2 authored almost 5 years ago by enetz <[email protected]>
[FIX] Keep MGF title information after loading

4885660a6a837d96ac7bc1a1fc7ce174f8214e1c authored almost 5 years ago by enetz <[email protected]>
fix

12ee26dda7402ed2a6682fc474c8de8564b8dcc8 authored almost 5 years ago by Hannes Roest <[email protected]>
[FIX] should work now for 2.4 release

f0cd6c66fbd2241c99e74c3670a861d3b8fbd6a3 authored almost 5 years ago by Hannes Roest <[email protected]>
[FIX] manylinux2014 dist patch

a7a1ab51ace486e8819233438effc7135285eed4 authored almost 5 years ago by Hannes Roest <[email protected]>
MS 2 works fine.

6aaf0a88849d2ad15b74f409a4f7f18e14bfb700 authored almost 5 years ago by kyowonjeong <[email protected]>
Feature/tsg (#4447)

* [FEATURE] speed up

Substantially speed up "clear" operations for certain workloads then
wh...

dc1f9f2f38a401bcb6f97a6d1e51750880132e02 authored almost 5 years ago by Hannes Roest <[email protected]>
[FIX] MzIdentML peptide evidence start and end range (#4434)

ae25c1f818c87dff2f363f9124a2fa65270a3583 authored almost 5 years ago by Eugen Netz <[email protected]>
Merge branch 'develop' of https://github.com/OpenMS/OpenMS into feature/ffm_improved_isotope_detection

275fe77eace45938bb6a03b940c4a1fd74519e62 authored almost 5 years ago by marcusL <[email protected]>
Update CHANGELOG

Adjusted the format to fit the 2.4 changelog
Added new parameters to OpenPepXLLF that were adde...

8a7c20c689a103f59ab7414902d5baf631cc75e5 authored almost 5 years ago by Eugen Netz <[email protected]>
[PYOPENMS] build for Python 3.8, allow skip check (#4479)

902d437e544b853b55009fe9d65edd4f98dcd471 authored almost 5 years ago by Hannes Roest <[email protected]>
Update FASTAContainer.h

a03d2ea9899b2fccf66a344b427f5ce073b5f042 authored almost 5 years ago by Timo Sachsenberg <[email protected]>
Update CHANGELOG

2fcad6f55973a82d300cb587f00c836fdb8a3869 authored almost 5 years ago by Timo Sachsenberg <[email protected]>
Merge pull request #4476 from bernt-matthias/patch-1

Update AUTHORS

cb1746364fa5d16cecc76a45f7d039b701fa0bbc authored almost 5 years ago by Chris Bielow <[email protected]>
drop gnuplot entirely and just output data

bd8c1d265e5926367fc004042053b808098bc2f5 authored almost 5 years ago by M Bernt <[email protected]>
Update AUTHORS

53f42bae6ea8d27c15da5aadd9f9ba0f078091c3 authored almost 5 years ago by M Bernt <[email protected]>
Update CHANGELOG

f85d31dc6d46f15d7448216234c02644a941ee7e authored almost 5 years ago by Timo Sachsenberg <[email protected]>
included new isotope picking method into FeatureFindingMetabo which is based on the set of expected elements in a dataset.

c652d1f1a29ab2dbe2e8b9f1a308a30cf13b1b9b authored almost 5 years ago by marcusL <[email protected]>
[Fix] bug/TODO for reading full TITLE from mgf (#4473)

* Fix bug/TODO for reading full TITLE from mgf

* oops

6074b75d362c4d7534a3e8669708f26c53d798a0 authored almost 5 years ago by jpfeuffer <[email protected]>
Merge pull request #4469 from hroest/feature/perf_fix

ModificationsDB::getInstance performance fix

4333e6d35932e0658b260519cfbcdf6ea641b62f authored almost 5 years ago by jpfeuffer <[email protected]>
masstrace_snr_filtering: is flag (#4455)

according to the discussion in https://github.com/OpenMS/OpenMS/issues/2350
this should be repr...

adbd89d411fb5e2ba411be08860235ef76209114 authored almost 5 years ago by M Bernt <[email protected]>
MetaboliteSpectralMatcher: make database mandatory (#4468)

since the file is not included in the distribution
I guess its better to make the argument mand...

747d1c7df96f42d59333044e2c7ed4e71bce97d6 authored almost 5 years ago by M Bernt <[email protected]>
Feature/py naseq (#4463)

* [PYOPENMS] NASequence / AASequence wrappers

- allow iteration
- allow random access with o...

4eb138dfe2afe123bd35966d1fe4e044979f2e8a authored almost 5 years ago by Hannes Roest <[email protected]>
[FIX] move to cpp file (suggested by @jpfeuffer)

27d8d6624b5d36f7c714e3ae52de481a748e73a7 authored almost 5 years ago by Hannes Roest <[email protected]>
fix outfile variable

5e02e0c4c6680b38b0cecaab0ab40fb702c3f1f8 authored almost 5 years ago by M Bernt <[email protected]>
Merge pull request #4471 from cbielow/doc_writeini

[DOC] update docs for write_ini

73abccd8828b8c30e0beef47376819dcca281087 authored almost 5 years ago by Chris Bielow <[email protected]>
update docs for write_ini (see #4462)

a3573024d6b71f70bcfbd9780a6da422ef5b0db5 authored almost 5 years ago by Chris Bielow <[email protected]>
Merge pull request #4470 from bernt-matthias/topic/test-diff-order

make diff parameter order consistent in tests

940f94480e01e0c2f441abc978a1cdf54d7763ed authored almost 5 years ago by Chris Bielow <[email protected]>
make diff parameter order consistent in tests

d0391cce8e0ada92ec9f022d708c8b7dbd0668fe authored almost 5 years ago by M Bernt <[email protected]>
Forgot s?

51ed3756036b96d500c4a50a4fe154eaf6907548 authored almost 5 years ago by jpfeuffer <[email protected]>
Update ModificationsDB.cpp

34be04b1d8578d6b2fa4f6ff1f42d2b6e7afc7d3 authored almost 5 years ago by Hannes Roest <[email protected]>
[FIX] performance fix for modifications DB

487b6257b737166521a919b379494c5162ef8bc2 authored almost 5 years ago by Hannes Roest <[email protected]>
[FIX,BUILD] re-include Qt SQL package in a build config file (was lost during merge)

e8929bb7a97c676257e5fb0c55d82f608e885415 authored almost 5 years ago by Hendrik Weisser <[email protected]>
Merge branch 'develop' of https://github.com/OpenMS/OpenMS into id-file-format

a384d97c1704a83850c50729d6962413ead3a9d6 authored almost 5 years ago by Hendrik Weisser <[email protected]>
[FEATURE] set SQLite options for efficient writing of .oms files

afc23b0ab0c5a526664229bc9b011d0e549dde66 authored almost 5 years ago by Hendrik Weisser <[email protected]>
[FEATURE] performance optimization: set both 'PRAGMA synchronous = OFF' and 'PRAGMA journal_mode = OFF' when writing .oms files

cfccc8b44afe79b227901c02d9a099a1066cc885 authored almost 5 years ago by Hendrik Weisser <[email protected]>
[INTERNAL] performance testing: set 'PRAGMA journal_mode = MEMORY' when writing .oms files

228e638b573e0df96fe0ee24b9dbd72f5264dfda authored almost 5 years ago by Hendrik Weisser <[email protected]>
Revert "[INTERNAL] performance testing: use 'execBatch' for writing peak annotations to .oms files"

This reverts commit dc7b7f473f36df34b78a2832281e387e6c76612f.

f05fad706b5a0dfd5ccd2f9996328a3d5b27180a authored almost 5 years ago by Hendrik Weisser <[email protected]>
[INTERNAL] performance testing: set 'PRAGMA synchronous = OFF' when writing .oms files

f4ebbf45e07467e61f87437e85e7c59eb8d00f5c authored almost 5 years ago by Hendrik Weisser <[email protected]>
[INTERNAL] performance testing: use 'execBatch' for writing peak annotations to .oms files

dc7b7f473f36df34b78a2832281e387e6c76612f authored almost 5 years ago by Hendrik Weisser <[email protected]>
IDMAssAccuracy: explicitly specify gnuplot script

therefor combine data and gnuplot script in one file

a89ee09e323ef799172cabe1496cdca4de38d6aa authored almost 5 years ago by M Bernt <[email protected]>
[COMMENT] try disabling constraint checks when writing .oms files (for performance)?

3c747050d876cc92eda2157ddd986bd77cfae547 authored almost 5 years ago by Hendrik Weisser <[email protected]>
Merge pull request #4466 from bernt-matthias/topic/improve-FeatureFinderAlgorithm-warning

[DOC] FFCentroided: a bit clearer warning message

a61e786e1d70fc42156d0d5f669dee6ae729715c authored almost 5 years ago by Chris Bielow <[email protected]>
a bit clearer warning message

follow up to https://github.com/OpenMS/OpenMS/issues/4461

7d134c45b676caf822a1c860edbd14cc66b2c334 authored almost 5 years ago by M Bernt <[email protected]>
[FIX] as suggested by Chris

3078e748bbeafa5a5f805e84f726a5a424e61272 authored almost 5 years ago by Hannes Roest <[email protected]>
[DOC] clearer warning

bb839e49935916e1a074b699abcd5ecb3eeec307 authored almost 5 years ago by Hannes Roest <[email protected]>
[FIX]

d6f3ef4f7f61a8714b94134e62f69edde7969ed4 authored almost 5 years ago by Hannes Roest <[email protected]>
[FEATURE] speed optimization

- instead of reporting all modifications only report the first one (and
store flag if more tha...

9b47282815393978423733e40301ef0773d59871 authored almost 5 years ago by Hannes Roest <[email protected]>
[FEATURE] speedup

0ba5914246784a537b439e10bf00622fe7bea9da authored almost 5 years ago by Hannes Roest <[email protected]>
[FEATURE] speedup

store the ptr to the ModificationsDB once and re-use the ptr

7fb4afa45813f5ac670a7deec9d70f81c977cafa authored almost 5 years ago by Hannes Roest <[email protected]>
[FEATURE] speedup

- use only a single lookup in ResidueDB for the fast code path

70d8fb3a66def1ab82d893592bf8049ff4ce02c9 authored almost 5 years ago by Hannes Roest <[email protected]>
Merge pull request #4451 from bernt-matthias/topic/OpenPep-xml

OpenPepXL, OpenPepXLLF: remove xml from valid extensions

43a2f1cbcb232474476b8fb00eb4b2f20b6db4b7 authored almost 5 years ago by jpfeuffer <[email protected]>
[TEST]

0f546aa9ca099ee06a3d3312eeeac79037ef53bb authored almost 5 years ago by Hannes Roest <[email protected]>
[FIX] commit fix

d2046bc790172e28521195ba205b1f9319fa2327 authored almost 5 years ago by Hannes Roest <[email protected]>
register spec.xml filetype

e8b565774845a27034e1a566dda2e878046a53e4 authored almost 5 years ago by M Bernt <[email protected]>
OpenPepXL: remove xml from valid extensions

since https://github.com/OpenMS/OpenMS/blob/c19b545636e76a5770f095f944e0b196b9b56c82/src/openms/...

58073e076b28528a26474bd2097abe34ae035736 authored almost 5 years ago by M Bernt <[email protected]>
recognize .spec.xml

5c61107507a74225106284a8036a5edb3d487f0c authored almost 5 years ago by M Bernt <[email protected]>
OpenPepXLLF: also remove xml from valid extensions

9851d0ee007f884fd26b35fbdf663fb26bcfd4ca authored almost 5 years ago by M Bernt <[email protected]>
Feature/matrix py (#4457)

* [PYOPENMS] fast access to Matrix

* [PYOPENMS] fast access to Matrix

* [TEST] add test an...

735441decb37d3d4501b682e45ac83d767b803f4 authored almost 5 years ago by Hannes Roest <[email protected]>
[FIX] db fix

b4b4da41e388ff054bae78a2e35efdd53d4b8139 authored almost 5 years ago by Hannes Roest <[email protected]>
[PYOPENMS] NASequence / AASequence wrappers

- allow iteration
- allow random access with operator []
- fix RibonucleotideDB

247c3d415511ed3935b5a1a767dab10fe7d1bad8 authored almost 5 years ago by Hannes Roest <[email protected]>
Fixing a bug at sorting peakgroup

7903ff3aeb81aa36362c51e874c34821eb7659e8 authored almost 5 years ago by JeeK <[email protected]>
FIX: filename and sample name mismatch in AbsoluteQuantitationStandards (#4416)

* merge: merged upstream develop

* fix: removed .vs

* fix: small bug identified in accessi...

23906894a689fb82db5f682481021c663d841078 authored almost 5 years ago by Douglas McCloskey <[email protected]>
Update Windows installation instructions for VS2019 (#4454)

* Warn about VS2015 and VS2017 due to OpenMP bug
* Some small fixes

3eaea8a5258e967028ca778b968a3fadaa276540 authored almost 5 years ago by Chris Bielow <[email protected]>
Feature/matrix py (#4453)

* [PYOPENMS] fast access to Matrix

* [PYOPENMS] fast access to Matrix

e392c5c2ed6a0bc280bc527882d41ceb64534e98 authored almost 5 years ago by Hannes Roest <[email protected]>
MS 2 parameters tuned...

ff37d63d44abd1c3f05c6a1807ffbe4b58f8782c authored almost 5 years ago by kyowonjeong <[email protected]>
Merge remote-tracking branch 'origin/feature/FLASHDeconv' into feature/FLASHDeconv

0551ece61b9dae719bbe1bb5e12b7af0a53fb698 authored almost 5 years ago by kyowonjeong <[email protected]>
MS 2 parameters tuned...

de4e80c2c1e7694a0e83cdeaf668ae4e8163f590 authored almost 5 years ago by kyowonjeong <[email protected]>
[FIX] use faster implementation of residuesMatch_

[FIX] use faster implementation of residuesMatch_

c1981c3a14ed0c296b638fcf61378a96a000fceb authored almost 5 years ago by Hannes Roest <[email protected]>
[FIX] faster implementation of residuesMatch_

[FIX] bugfix

0353cb58b2f93428ba897a28a127778d5e7c1ec5 authored almost 5 years ago by Hannes Roest <[email protected]>
[FIX] speedup

5c0fe1aa4b12164e25bd03f5c2d1faf091a8d8ca authored almost 5 years ago by Hannes Roest <[email protected]>
[FIX] speedup

efffc40fe158b9a982e00a66e8203f105bf36959 authored almost 5 years ago by Hannes Roest <[email protected]>
[FIX] speedup

230001b7bd6b0b4c4186c9d722b1f71a445ba22c authored almost 5 years ago by Hannes Roest <[email protected]>
[FIX] speedup

89e429d289cce4c4dde15ca8384a2d3107e1131d authored almost 5 years ago by Hannes Roest <[email protected]>
Update contrib for use with -A CMake flag for Win VS target arch

2e3f0113f8b8a07af224c110af435b6f4c1510ca authored almost 5 years ago by Julianus Pfeuffer <[email protected]>
Merge branch 'develop' into feature/FLASHDeconv

1e873f06affede372263da8564ddd81992a93883 authored almost 5 years ago by JeeK <[email protected]>
Remove redundant outputs

c4c1c993c0dd5ad7e2b6e69563622610b965a17d authored almost 5 years ago by JeeK <[email protected]>
[FIX] small fix in SQL query (writing .oms files)

c434e978f86d1b3d5f397937f2e3ccfb8b34b53e authored almost 5 years ago by Hendrik Weisser <[email protected]>
[FIX] small fix in SQL query (writing .oms files)

665ca9616ce6ca1059e39fb92980058b23d9479f authored almost 5 years ago by Hendrik Weisser <[email protected]>
[FEATURE] enable SQLite foreign key support when writing .oms files

9efb8745397d03b33b3cd08284974008c42cbb4c authored almost 5 years ago by Hendrik Weisser <[email protected]>
[LOG] support for progress logging when reading/writing .oms files

5bdac4422ee09fa2e31e100887af5e2cf6f0c530 authored almost 5 years ago by Hendrik Weisser <[email protected]>
Merge commit 'e31ccc5fe2' into feature/FLASHDeconv

2a654658f91500d21a92d14c2720b344842b8540 authored almost 5 years ago by JeeK <[email protected]>
Merge with Kyowon's modified FLASHDeconv (MS2 parameters added)

e31ccc5fe282e5d21f8c200f84715bb8f7b97087 authored almost 5 years ago by JeeK <[email protected]>
Update package_nsis.cmake

de5a443f9d43c3e1d80c853febfa67b5936d99e6 authored almost 5 years ago by jpfeuffer <[email protected]>
[IO] added support for .oms output to NucleicAcidSearchEngine (parameter 'db_out')

315cdcec4e623a50b27e0f1d1233a9a17486d393 authored almost 5 years ago by Hendrik Weisser <[email protected]>
Merge pull request #4429 from bernt-matthias/topic/RTEvaluation-missing-option

RTEvaluation add missing argument

c19b545636e76a5770f095f944e0b196b9b56c82 authored almost 5 years ago by Hannes Roest <[email protected]>
Update OpenSwathDIAPreScoring.cpp

1386e6fad450daea981f9a22ae55664b4a23bb8c authored almost 5 years ago by Hannes Roest <[email protected]>
Adapt platform determination during packaging on Win for VS2019

8cc81674f88aefbbc45274a77d1389b551076f34 authored almost 5 years ago by jpfeuffer <[email protected]>
Merge branch 'id-file-format' into mapalignerident-idfile

652b3adf3fb41d5be82def32e3a5caa85f18c1bf authored almost 5 years ago by Hendrik Weisser <[email protected]>
Update refman_overwrite.tex.in

4ce809c5be3852358876b159523321b33d48d741 authored almost 5 years ago by jpfeuffer <[email protected]>
Update refman_overwrite.tex.in

64c28581dc480eb88947a89ad15a0e1ce3fb32a0 authored almost 5 years ago by jpfeuffer <[email protected]>
Merge pull request #4440 from jpfeuffer/fix/evalOrderDecharger

[FIX] make decharger safe for eval order of string manip. stmts

f34dd371f49e93a1183fbb98764380545cd814f8 authored almost 5 years ago by jpfeuffer <[email protected]>
OpenSwathDIAPreScoring: fix outputs

- the `-out` argument was unused
- output is only generated if swath files are given
- make it...

f91a9af7d30b6ead74a6bd0629f3ae4b5f8d752c authored almost 5 years ago by M Bernt <[email protected]>
FileMerger: allow fasta output (#4441)

* FileMerger: allow fasta output

* Update FileMerger.cpp

* Update FileMerger.cpp

Co-aut...

2220b925b7f04d4b49f35f09bfe31aa499e97529 authored almost 5 years ago by M Bernt <[email protected]>