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

add for test

2e334b47d79cc23faccbf0e1185de72a7856da19 authored over 1 year ago by Timo Sachsenberg <[email protected]>
Update cibuild.cmake

da3ac232080c83e58175bdcb9f326364457da9ef authored over 1 year ago by Timo Sachsenberg <[email protected]>
Merge pull request #6612 from OpenMS/feature/QuadtreeFeatureOverlapFilter

* [FEATURE] Add a filter class that can filter FeatureMaps on overlaps

* Replace the FFMID O(...

346646db051985f2af038be241aa51bbfd52b1f8 authored over 1 year ago by Timo Sachsenberg <[email protected]>
Merge branch 'develop' into jpfeuffer-patch-1

85a44567d0d6a169aa92b0799473e20835280361 authored over 1 year ago by Timo Sachsenberg <[email protected]>
Merge pull request #6620 from cbielow/fix_warnings

Fix compile warnings

2dbfcf7b1e0984f1790ea998ed0775face218d66 authored over 1 year ago by Chris Bielow <[email protected]>
fix more warnings for implicitly deleted functions

c5bcf0537b5c3b2dfdff4f448152c5364b12c58f authored over 1 year ago by Chris Bielow <[email protected]>
minor docs

01152836aa164284922cf5e97771915c18cd3eb5 authored over 1 year ago by Chris Bielow <[email protected]>
make dtor virtual

e0436744850f110ed5913bfcaafecb41f9e09cc6 authored over 1 year ago by Chris Bielow <[email protected]>
fix non-virtual desctructor warning

72eae325450a64fe1daa65afd52bd93484561655 authored over 1 year ago by Chris Bielow <[email protected]>
fix binned spectrum test

c3935c4593af8bacf2e38cb4ae66bb6177b22af3 authored over 1 year ago by Chris Bielow <[email protected]>
fix compile error

e6be7f29e3cf16ffa88c2c0b0b305ed8b56336ae authored over 1 year ago by Chris Bielow <[email protected]>
fix thirdparty ref

3ef26da0baa78a85e48614f2dc6decc799358be1 authored over 1 year ago by Samuel Wein <[email protected]>
fixed ambiguity parsing

8c67ad7d4c8ab45561eef2dba95ee0cc756322a9 authored over 1 year ago by Samuel Wein <[email protected]>
[FIX] WinInstaller Default Alluser and no docs

7cd656e65a02c36722685d995548ac98c5168dc4 authored over 1 year ago by Julianus Pfeuffer <[email protected]>
updated JSON parsing

47b46a9b60b6aee6e60fccf701079c2ce75a0341 authored over 1 year ago by Samuel Wein <[email protected]>
[CI] remove Win parallel limit on GH actions (#6623)

After test memory usage was fixed

475270c90926c50a91961ead6aadd22014ebb011 authored over 1 year ago by Julianus Pfeuffer <[email protected]>
fix last test

82d72a75ce32c4f0b4bc242b7292a0c307a8a0e8 authored over 1 year ago by Timo Sachsenberg <[email protected]>
attempt to make sorting stable

271147ae136f55e6bb2f709de12578fd77a6c255 authored over 1 year ago by Timo Sachsenberg <[email protected]>
add another default for the feature comparator

574514a2d76b210f278ddcd65a539887a967f188 authored over 1 year ago by Timo Sachsenberg <[email protected]>
annotate removed by overlap

bbdf2e00e848d0282fa02ad21f4c12ae7fd6f790 authored over 1 year ago by Timo Sachsenberg <[email protected]>
add back information on ambigious ids

4c5e79edd833ffd58cda0f88d199ae325ee75a24 authored over 1 year ago by Timo Sachsenberg <[email protected]>
Merge branch 'develop' into feature/QuadtreeFeatureOverlapFilter

c6f8aefa6aaaf8099e1b9871b670a03561026592 authored over 1 year ago by Timo Sachsenberg <[email protected]>
additional test data to generate overlap cases (#6622)

0b1312c88c84eff367c1946dfa0547206fce3be9 authored over 1 year ago by Timo Sachsenberg <[email protected]>
Merge branch 'OpenMS:develop' into feature/modomicsJSON

d2196ac153a3d0e078841206af023206506d1998 authored over 1 year ago by Samuel Wein <[email protected]>
Merge branch 'develop' into feature/QuadtreeFeatureOverlapFilter

31a8d34b03a95a11e9e7fb5dbc4162090b73f672 authored over 1 year ago by Timo Sachsenberg <[email protected]>
Replace the FFMID O(n*n) overlap check with an efficient, quadtree-based approach (#6619)

* attempt to replace the FFMID overlap check

* produce same result as old method

* update ...

527e9b253672c1a98cc5565f893081d9d01fffc2 authored over 1 year ago by Timo Sachsenberg <[email protected]>
Merge pull request #6607 from matteopilz/develop

Update pyOpenMS plotting

341fc54d1e005cb80ff30ced6287b68332e18e1e authored over 1 year ago by Matteo Pilz <[email protected]>
Merge branch 'develop' into develop

61f8185efbb655554e90237f755d89c9f0a8cdb8 authored over 1 year ago by Matteo Pilz <[email protected]>
start splitting knime package into folder struct with topp,tp,lib

26d0deb65012357bf4484ebab44dd86ea02c3e09 authored over 1 year ago by Julianus Pfeuffer <[email protected]>
remove defaulted move ctor/assignment because they are deleted in the base class for correctness (diamond + double move problem)

e15382feee195b6be5bcb177fafade245c2f11d4 authored over 1 year ago by Chris Bielow <[email protected]>
fix conversion warnings

f79f553d9e52ef66a0acdb38794c76c315b29d9a authored over 1 year ago by Chris Bielow <[email protected]>
fix warning "-Wbitwise-instead-of-logical"

d191a9e5f2d72bd0145be30a190e9e75556ecbf9 authored over 1 year ago by Chris Bielow <[email protected]>
fix conversion warning

c3516abab6ae5e044d7585f9a4e7e11a965c3902 authored over 1 year ago by Chris Bielow <[email protected]>
fix uninitialized warning

7480a381908f1e2e8c96e73c0653af93343d7a58 authored over 1 year ago by Chris Bielow <[email protected]>
fix conversion warning

da6d2f74fe663bd7762db77029b273baf108ebb1 authored over 1 year ago by Chris Bielow <[email protected]>
minor

64c3bf6f19fd3c95b9946c80d6baa92775d7cffc authored over 1 year ago by Chris Bielow <[email protected]>
TOPPView: fixes 3D view zooming (#6616)

* remove useless overrides

* make goto-dialog independent of axis mapping

* simpification
...

5588117a027d0ea563f631332a12a16b0e3370b5 authored over 1 year ago by Chris Bielow <[email protected]>
Apply suggestions from code review

2205ecd5adc57ebef98e36321f914b10c5b2c86f authored over 1 year ago by Chris Bielow <[email protected]>
Merge pull request #6477 from poshul/fix/revertTransformWrapping

reverted commenting on getDefaultParameter

b597256aa8b9be766b09b81a90ff2b5e0c76639e authored over 1 year ago by Samuel Wein <[email protected]>
Merge branch 'develop' into fix/revertTransformWrapping

0ce2597f3fbb81693f3afe7b771d56310a1aa43a authored over 1 year ago by Samuel Wein <[email protected]>
Merge pull request #6618 from cbielow/fix_classtest_RAM

Huge test compilation improvement

9c8fcb880ef8f01716c9947211d023ff1de06932 authored over 1 year ago by Chris Bielow <[email protected]>
move code from macro to function; this saves a LOT of intermediate code when compiling; thus uses way less RAM and compiles much faster.

ef5a5d95211b11fbc70fbe62ec3f1a6ea125f888 authored over 1 year ago by Chris Bielow <[email protected]>
added module docstring

e75d8e1075bc895d875b72efc783cca8f878a997 authored over 1 year ago by matteopilz <[email protected]>
Merge branch 'OpenMS:develop' into develop

3e1dcf73a593e765166214b1ee23a09c4b9a1676 authored over 1 year ago by Matteo Pilz <[email protected]>
[pyOpenMS] simple helper to update scores from a previously exported dataframe (#6613)

* pyopenms update scores from dataframe e.g. for ML

* update tests

* fix tests

* Update...

1f3aeb409997b009936e75e49683a8e0c5dfb1bc authored over 1 year ago by Timo Sachsenberg <[email protected]>
fixes #6614

23bfae5b70ff389a4281f8132deb1b83de7214d4 authored over 1 year ago by Julianus Pfeuffer <[email protected]>
Merge branch 'develop' into develop

e2000939d6a71c15e66feeb678ceb0cc6ef7e08c authored over 1 year ago by Timo Sachsenberg <[email protected]>
disable some scores not used for MS1 transitions; set max iterations … (#6608)

* disable some scores not used for MS1 transitions; set max iterations for faster EMG fits

* ...

f57a12e1103af6a94b4999e797a5306c1da55940 authored over 1 year ago by Timo Sachsenberg <[email protected]>
[FEATURE] Add a filter class that can filter FeatureMaps on overlaps

ddfdebfeb3feb298f492f294481e0da84166c53d authored over 1 year ago by jpfeuffer <[email protected]>
Merge branch 'develop' into fix/revertTransformWrapping

13d13a5bddb8ed131d43b9c9229b4ae2bab934f1 authored over 1 year ago by Samuel Wein <[email protected]>
disable update check on gh actions

f60393791f05f4e9dc6d8bc1035aa9a7882ff873 authored over 1 year ago by Julianus Pfeuffer <[email protected]>
Update plotting.py

removed leftover #

6793e7f44d9001917585e3ab9c343b221816b1a1 authored almost 2 years ago by Matteo Pilz <[email protected]>
Merge branch 'OpenMS:develop' into develop

65beb0527d18663dacfa944b364ba7c67de644ca authored almost 2 years ago by Matteo Pilz <[email protected]>
alignment parameter - top & bottom spectrum needed to be switched

df419b59823346e739ccf60f1f1a89256fa702fe authored almost 2 years ago by matteopilz <[email protected]>
TOPPView: Remove unsupported flag and fix some warnings (#6597)

* fix redundant inheritance via dominance warnings

* fix uninitialized member warnings

* r...

6a957643f994078472c3f7e54f65163243bd0c4e authored almost 2 years ago by Chris Bielow <[email protected]>
Merge pull request #6599 from bernt-matthias/bump-3rdpty-msgfplus

bump THIRDPARTY

941374b2b019e9e33e1027a482600f38329c21a3 authored almost 2 years ago by Julianus Pfeuffer <[email protected]>
fix test file

fa9eb23a5a6f9b3e1c22a16d9a5d684e25aa2c8a authored almost 2 years ago by Timo Sachsenberg <[email protected]>
bump THIRPARTY

to include latest MSGF+ https://github.com/OpenMS/THIRDPARTY/pull/91

190d34b36b2ed4803b48391c83d3b574989d75f3 authored almost 2 years ago by Matthias Bernt <[email protected]>
remove add_decoys option in MSGF+ (#6557)

* remove add_decoys option in MSGF+

* remove tda parameter

* remove parameter from test fi...

1d46061cfdc2261d7754654043b5955d985bf857 authored almost 2 years ago by Timo Sachsenberg <[email protected]>
simple file downloader (#6564)

* simple file downloader

* fix test filename

* throw exception if file missing

Co-autho...

924d180b256805cb42eabcc707951d0236912951 authored almost 2 years ago by Timo Sachsenberg <[email protected]>
IDRipper: prevent unneeded copies (#6594)

* prevent unneeded copies

* update tests

e197db75bd4908fb4697c89a17d2465b90518656 authored almost 2 years ago by Timo Sachsenberg <[email protected]>
fix win actions

6d749f831b03c220c187599a116e43f9db8b78ad authored almost 2 years ago by Julianus Pfeuffer <[email protected]>
[Feature] GH actions ccache (#6112)

* [Feature/CI] try adding ccache to GH actions

* fix ccache actions

* fix ccache install?
...

175dbecba2dbf95fd30a0ad08ad00d5be24ec0bd authored almost 2 years ago by Julianus Pfeuffer <[email protected]>
Update doc/doxygen/parameters/DefaultParamHandlerDocumenter.cpp

6b6e33fdc7de85114c547fcc0c9e5e121a78db26 authored almost 2 years ago by Julianus Pfeuffer <[email protected]>
Merge pull request #6589 from jpfeuffer/fix/nsis

fixes a lot of stuff in NSIS

519c03ff7fb51add183273c8a53c02d00754f247 authored almost 2 years ago by Julianus Pfeuffer <[email protected]>
Merge pull request #6592 from cbielow/fix_logMode

TOPPView: Fix log mode

30cf49b0efb48ed767a4c07a3021466454337b6d authored almost 2 years ago by Chris Bielow <[email protected]>
Merge branch 'develop' into fix_logMode

1e10c1396a187b3045935be606c9803ac8669424 authored almost 2 years ago by Chris Bielow <[email protected]>
fixes #6585

8c7991e338bb0f357543826cd31e7e71ba211b85 authored almost 2 years ago by Chris Bielow <[email protected]>
Feature/id ripper speedup2 (#6590)

* massive speedup

* finished implementation

* also consider file description when mapping
...

001ede33f8b88a045e4c3aba4910d5030d30735f authored almost 2 years ago by Timo Sachsenberg <[email protected]>
Merge branch 'develop' into fix/nsis

767ffcf6d94b24ba857b527d71855332a2839864 authored almost 2 years ago by Julianus Pfeuffer <[email protected]>
More fixes

749da092218c89d3e375e02497871346879a60ea authored almost 2 years ago by jpfeuffer <[email protected]>
update clang format lint action

b159abbb911443530611bb38d0eaa6e5a469098a authored almost 2 years ago by Timo Sachsenberg <[email protected]>
Update NSIS.template.in

8df481c86a0adc19d2740159a23e199b74f85a24 authored almost 2 years ago by Julianus Pfeuffer <[email protected]>
fixes a lot of stuff in NSIS. Todo cleanup and uninstaller not completely working.

205e13865c69d52ef1fbcf95fc1adaa1819531fa authored almost 2 years ago by jpfeuffer <[email protected]>
IDRipper speedup (#6584)

8b18be6a320c192792661cfce4a48fb5b2c4c115 authored almost 2 years ago by Timo Sachsenberg <[email protected]>
Merge pull request #6578 from jcharkow/updateTsvOutput

[FEATURE] add IM output to OpenSwath tsv file

8e61ca3c096ee2517bed5419669efb0e814dfc7e authored almost 2 years ago by Samuel Wein <[email protected]>
Merge pull request #6548 from Telomelonia/patch-1

[DOC] Rename "The OpenMS Proteomics Pipeline" to "The OpenMS PiPeline"

438e21236d8b16d986b4a3f65858180f2fe7fca7 authored almost 2 years ago by Samuel Wein <[email protected]>
Merge pull request #6580 from OpenMS/timosachsenberg/idmapper-much-slower-6072

Timosachsenberg/idmapper-much-slower-6072

5f5521ca427c540416815bce05f1858c0abdb553 authored almost 2 years ago by Julianus Pfeuffer <[email protected]>
Update src/openms/source/ANALYSIS/ID/IDMapper.cpp

70aa120a220c5a5d633866148b1821d33dc1395c authored almost 2 years ago by Julianus Pfeuffer <[email protected]>
use basename for mapping

7780b7cb3cd4d252d761641bbb38ca0e33304478 authored almost 2 years ago by Timo Sachsenberg <[email protected]>
use basename for filename mapping

c9bbf3233b98f4274508c877aee8ef6d61f6c0f5 authored almost 2 years ago by Timo Sachsenberg <[email protected]>
only enforce file names for TMT case

666bda7385435ca28a0120849334ff77fac733b5 authored almost 2 years ago by Timo Sachsenberg <[email protected]>
update logic

eafacd8bfad87c088cd48ece6d6f7881cb8ed613 authored almost 2 years ago by Timo Sachsenberg <[email protected]>
use ID_MERGE_INDEX constant

f257ecb092d6b6bbc23b648e2d5b79ab5a09d737 authored almost 2 years ago by Timo Sachsenberg <[email protected]>
faster mapping for TMT data

8dde17b0c7a8ac975425dbd7932456f7f31bdb90 authored almost 2 years ago by Timo Sachsenberg <[email protected]>
small fix to make slow meta value comparisons last

f0fb5fbe45826b22ba85ea21d64076c7cc6619f5 authored almost 2 years ago by Timo Sachsenberg <[email protected]>
[FEATURE] add IM output to OpenSwath tsv file

Recently in https://github.com/OpenMS/OpenMS/pull/6268 added extra
output to OpenSwath .osw file...

9c72e99e33a3f8a212b2a11cd906177b319f85b2 authored almost 2 years ago by jcharkow <[email protected]>
Merge pull request #6575 from OpenMS/feat/singularity

[Feature] direct singularity images on ghcr.io

e1d5db34907273658e9c8c585be3557cebb1ace7 authored almost 2 years ago by Julianus Pfeuffer <[email protected]>
different delimiter

1cf1359593c198159640b2ed625f4e4293b4e031 authored almost 2 years ago by Julianus Pfeuffer <[email protected]>
wrong file

8eb2b58cd6241dd87b8eb34b13245ac5ad4d4fdc authored almost 2 years ago by Julianus Pfeuffer <[email protected]>
use sed to "pass" branch/tag args like in docker

f4938548097b550b30499fa1601cfdca7a95e3ab authored almost 2 years ago by Julianus Pfeuffer <[email protected]>
???? login between pushes

923f00eb4ece205ff0efcb8987f5d9f96641dee0 authored almost 2 years ago by Julianus Pfeuffer <[email protected]>
yet another delimiter..........

59740f795f1a1f93e734bc88cad196907636cb59 authored almost 2 years ago by Julianus Pfeuffer <[email protected]>
Update .gitpod.yml

4053fba52107b514b8327b4023e9f6991037c0c4 authored almost 2 years ago by Julianus Pfeuffer <[email protected]>
use different delimiter

3f34e0b2feba3d3b30bbc756f543ccde40c28610 authored almost 2 years ago by Julianus Pfeuffer <[email protected]>
Merge pull request #6576 from OpenMS/jpfeuffer-patch-4

fix pthreads difference with sqlitecpp

b280f3779978ab60d49d97bf2a46b28dbe0d6047 authored almost 2 years ago by Julianus Pfeuffer <[email protected]>
use localimage

95c1daa77ec9aeb8b5bb6d011604f284101921ba authored almost 2 years ago by Julianus Pfeuffer <[email protected]>
prepare for building tools image

some sed will be necessary to build from local container

5f349b923a1e7e0c5cd2b4c294baea7791104e64 authored almost 2 years ago by Julianus Pfeuffer <[email protected]>
fix pthreads difference with sqlitecpp

4735dd626f0fe12969df0b0e081bc1b082164162 authored almost 2 years ago by Julianus Pfeuffer <[email protected]>
Fix doc warnings (#6573)

* avoid wrong use of @class

* Doxygen's autolink does not use namespaces. Just Class::Functio...

84ae75526d9af20511b04f6f00a51b459e485c95 authored almost 2 years ago by Chris Bielow <[email protected]>