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

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]>

do not build automatically on gitpod to be able to debug

871a608831d654223ab12a348515682c77b39031 authored almost 2 years ago by Julianus Pfeuffer <[email protected]>

always use bash

865a9685a5ae8ebf3c3e83cf246fc6c00f5546aa authored almost 2 years ago by Julianus Pfeuffer <[email protected]>

.......

771d7e695e7179d75f51d24239671ce248f29d10 authored almost 2 years ago by Julianus Pfeuffer <[email protected]>

fix dependency excludes

05d6bc83a3967d3c2f42b094eb4bca05fc40d0f8 authored almost 2 years ago by Julianus Pfeuffer <[email protected]>

wrong syntax

54c036cff5c5a74d88b04b579358fb501c94cdef authored almost 2 years ago by Julianus Pfeuffer <[email protected]>

remove useless stuff from sqlitecpp

fec20baec2c71a1ca5bcd763f26b2b0f904aa9f4 authored almost 2 years ago by jpfeuffer <[email protected]>

use downcased repo and remove deprecated set-output

96de91d82d84e783e3b43eaef2d5d0abcc59d6f7 authored almost 2 years ago by Julianus Pfeuffer <[email protected]>

Try using only GH repo as documented

f72a76fac9f03b23aac92c5c87fa68fb21d398f2 authored almost 2 years ago by Julianus Pfeuffer <[email protected]>

exclude sys libs on linux

b41a5ab831e296719c6518289389ab82b9fa955e authored almost 2 years ago by Julianus Pfeuffer <[email protected]>

Merge pull request #6569 from OpenMS/fix/pyomstyping

[FIX] for pyopenms typing

ca28832773a81e37a3b0db2839cd56baf9613d25 authored almost 2 years ago by Julianus Pfeuffer <[email protected]>

wrong name

09b9bb251bc8d9e4e88d6d0e2799d0f6ccf96af1 authored almost 2 years ago by Julianus Pfeuffer <[email protected]>

Update .gitpod.yml

5536c42c4305bd97867cbf3f7d295971a7e1fd47 authored almost 2 years ago by Julianus Pfeuffer <[email protected]>

install pip first

e8408615c71f338ea98a872badaa9c6e587c479c authored almost 2 years ago by Julianus Pfeuffer <[email protected]>

use python -m for pip

59dcc63cbeff651a277209cb4c82b8cbb68fb2a8 authored almost 2 years ago by Julianus Pfeuffer <[email protected]>

install spython?

8d76c38758055a37d21c47218a675abb5bd1a94d authored almost 2 years ago by Julianus Pfeuffer <[email protected]>

fix if case

0451c1182ade06edf52979605bffe4f0b4ba88a0 authored almost 2 years ago by Julianus Pfeuffer <[email protected]>

testing

cea8d2e1ef2b7275c70ea292d874f17a307ecaae authored almost 2 years ago by Julianus Pfeuffer <[email protected]>

[FEATURE] also build singularity images

cf9890c433c0bca670645d03d39858589c309df8 authored almost 2 years ago by Julianus Pfeuffer <[email protected]>

fix setup.py and copying in cmake

039bdc1622fd6557ee1f332387591c44d15113c6 authored almost 2 years ago by Julianus Pfeuffer <[email protected]>

more param doc fixes

f8610cd163b504979c67496597dd76dbbc29e333 authored almost 2 years ago by Chris Bielow <[email protected]>

use the same name as in base class (for doxygen)

b6ace64b44ad7a74486ba861970ba599edc7394f authored almost 2 years ago by Chris Bielow <[email protected]>

do not use circular references to the class itself... doxygen cannot find them...

d531563cc5fce2bf918faac50d334e0a99e6536c authored almost 2 years ago by Chris Bielow <[email protected]>

do not use html tags for anything other than real html tags....

8a30768c5c49c8adc93a8da8ebf2e167c998232c authored almost 2 years ago by Chris Bielow <[email protected]>

more parameters

0bb814a75b94846b9d1f14d729c3c15b856bfa4e authored almost 2 years ago by Chris Bielow <[email protected]>

use pragma once

9fc8e5eca93d37590226e0958e208b873f567b81 authored almost 2 years ago by Chris Bielow <[email protected]>

@hint is not a doxygen command...

e87643791faecd3c8d7e4cf5746728761f23c078 authored almost 2 years ago by Chris Bielow <[email protected]>

fix wrong param doc

a1eb5838deb23d0427017c298752a227f2527929 authored almost 2 years ago by Chris Bielow <[email protected]>

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

6ded55a7c21ea12345e8ddaa7850460ea569f050 authored almost 2 years ago by bielow <[email protected]>

avoid wrong use of @class

1690915396cf9bd0299e1decc1798027d2e08fb1 authored almost 2 years ago by bielow <[email protected]>

Also write an all modules.pyi file for typing.

86fe5a647b543fb7a8f422f790eea6b51180a44e authored almost 2 years ago by Julianus Pfeuffer <[email protected]>

Create __init__.pyi

25fc852eab71b0c2e46eede24ed2fd5803e55d17 authored almost 2 years ago by Julianus Pfeuffer <[email protected]>

String special case

0a474d641dac67cef970503bb144f5f72f410c81 authored almost 2 years ago by Julianus Pfeuffer <[email protected]>

Merge pull request #6567 from OpenMS/jpfeuffer-patch-4

Fix numpy typing in pyopenms

469b2e06dfa227ce2e7a94cc28b318915602ae01 authored almost 2 years ago by Julianus Pfeuffer <[email protected]>

[FIX] for pyopenms typing

a6163323a28103e74530b29dd81cccc6067e70d8 authored almost 2 years ago by Julianus Pfeuffer <[email protected]>

Update fix_pyi_imports.py

26ee64e020dd0619aa141c26c7c327b912ca51be authored almost 2 years ago by Julianus Pfeuffer <[email protected]>

Update fix_pyi_imports.py

3f79a21fbb05fa718aa68520bc5ed996ba801138 authored almost 2 years ago by Julianus Pfeuffer <[email protected]>

Merge pull request #6561 from OpenMS/poshul-patch-1

Update openms_clang_format.yml

81d4e0a748a7e96e18f2a597e19c772d9952794f authored almost 2 years ago by Timo Sachsenberg <[email protected]>

Fix numpy typing in pyopenms

e47b213bf0ad6419cc3453937ebf69e2c0a86248 authored almost 2 years ago by Julianus Pfeuffer <[email protected]>

Merge pull request #6566 from OpenMS/jpfeuffer-patch-4

Remove `long` type from convProv

a44c392cab913a8f125874a59e3a1d7fcc285bea authored almost 2 years ago by Julianus Pfeuffer <[email protected]>

Remove `long` type from convProv

also removed in py3

49edb10469031bdadc5769f37f1dd506d66cfda4 authored almost 2 years ago by Julianus Pfeuffer <[email protected]>

Merge pull request #6562 from OpenMS/jpfeuffer-patch-4

remove unicode from convProv

7ab7fdeceb91538fbe49cd18c7b312460c0b253f authored almost 2 years ago by Julianus Pfeuffer <[email protected]>

Update special_autowrap_conversionproviders.py

f78eb26faa09d31d99858d19b6f18502c9a1cd8d authored almost 2 years ago by Julianus Pfeuffer <[email protected]>

Merge pull request #6555 from JeeH-K/feature/FLASHDeconv

Updated FLASHDeconv

7d372cd20426cff2c68823e90abc8be6b2f74836 authored almost 2 years ago by Samuel Wein <[email protected]>

Merge pull request #6558 from OpenMS/piwik-script

PIWIK Script added

bf19321e8a302abd16ca0f1227af57f2901e95ff authored almost 2 years ago by Timo Sachsenberg <[email protected]>

Merge branch 'develop' into feature/FLASHDeconv

b0f847bb56e1da77eb59467e075f34b79031f598 authored almost 2 years ago by JihyungKim <[email protected]>

remove unicode from convProv

fixes part of #6559

f5161d5a6846a4cd93838a66b1651f20a9ab365a authored almost 2 years ago by Julianus Pfeuffer <[email protected]>

Update openms_clang_format_add_and_commit.yml

b2b77f4e60dfea6f8e9ebed11abd74df23ff1af0 authored almost 2 years ago by Samuel Wein <[email protected]>

Update openms_clang_format.yml

Bump changed-files version to hopefully fix https://github.com/tj-actions/changed-files/issues/809

aa13ef2ae84ee150760419bbe6d13e0cde8867d8 authored almost 2 years ago by Samuel Wein <[email protected]>

fix permission order

b804acf66fdbb884f704ff8be11d8a009fb0c171 authored almost 2 years ago by Julianus Pfeuffer <[email protected]>

PIWIK Script added

63f0e0e3c7ded52fa5fb5c0559f700e5a6d7c997 authored almost 2 years ago by rahul799 <[email protected]>

Merge pull request #6551 from cbielow/fix_TV

Minor refactor

113d1d73c7447211415f917ea9e37c727f6ca1a8 authored almost 2 years ago by Timo Sachsenberg <[email protected]>

Merge branch 'develop' into patch-1

9dbf0b2aa2f180ab15a879842a02f71f268ff95d authored almost 2 years ago by Aryan Shukla <[email protected]>

Merge branch 'develop' into fix_TV

4e2288471b3ee1e7f1a82fe13fc40cae94754835 authored almost 2 years ago by Timo Sachsenberg <[email protected]>

add write permissions when installing dependency libs

6700c89e4e9492d45a0062ce654fe7946cfe28a2 authored almost 2 years ago by Julianus Pfeuffer <[email protected]>