OpenMS commits | Ecosyste.ms: OpenCollective

[FIX] mzML threading issue (#7011)

* remove dependency on member variable which is being accessed by multiple threads (race conditi...

github.com/OpenMS/OpenMS - 6b0387cd38ee686f4449a0805d3c6dc39d727902 authored about 1 year ago by Chris Bielow <[email protected]>

Merge branch 'Feature/GenericFileLoad' of ssh://github.com/poshul/OpenMS into Feature/GenericFileLoad

github.com/OpenMS/OpenMS - 861b9b68276fc5b2eab1a0716f4367b8e47980b8 authored about 1 year ago by Samuel Wein <[email protected]>

Merge branch 'develop' into Feature/GenericFileLoad

github.com/OpenMS/OpenMS - 04f7978a179f71e6488624197f0be1361dc4e7ff authored about 1 year ago by Samuel Wein <[email protected]>

update topp tests to get rid of remaining .tmp file extensions.

github.com/OpenMS/OpenMS - 9bf752eed95e321148101e25175882f0c6b0cada authored about 1 year ago by Samuel Wein <[email protected]>

Sage MS (#6786)

* reading of version numbers

* scaffold for PercolatorInfile::load

* nop

* minimal pars...

github.com/OpenMS/OpenMS - ef37a651305e95e4ac9b7eedd775e9567e84b5b6 authored about 1 year ago by Timo Sachsenberg <[email protected]>

[fix] update TOPP test file names to use correct extensions

github.com/OpenMS/OpenMS - e68eb34c4961a7af45fdee309db48f3926e6e64e authored about 1 year ago by Samuel Wein <[email protected]>

Merge remote-tracking branch 'upstream/develop' into Feature/GenericFileLoad

github.com/OpenMS/OpenMS - 736d552c67fa357e281974c5067130a159b9bd12 authored about 1 year ago by Samuel Wein <[email protected]>

Update openms-user-tutorial.md (#204)

* Update openms-user-tutorial.md

I have reviewed the tutorial and identified a few minor gram...

github.com/OpenMS/OpenMS-docs - 2c839282d7e8cb79eb3adae9f515fd78d25f0a23 authored about 1 year ago by Ayesha-Feroz <[email protected]>

Merge pull request #6978 from cbielow/base64_simd

[FEATURE] Base64 encoding/decoding using SIMDe

github.com/OpenMS/OpenMS - 69a0ee6e16b93f8af382d11080feb691db7de2b4 authored about 1 year ago by Chris Bielow <[email protected]>

fix bug in Class_test which displays bogus error message even when test passed

github.com/OpenMS/OpenMS - 69a1a31bbbe54cbf0d8f38ea7c2f68537a7d88bd authored about 1 year ago by Chris Bielow <[email protected]>

fix warning

github.com/OpenMS/OpenMS - 8c80dca815714407a40566ca04499336225f99b4 authored about 1 year ago by Chris Bielow <[email protected]>

remove utils. some minor cleanups (#206)

github.com/OpenMS/OpenMS-docs - 2bcda50d8ba98fa3905979095583b25925fcd511 authored about 1 year ago by Timo Sachsenberg <[email protected]>

[discussion] remove utils and model as topp tool with utilities category (#7001)

* move utils to topp tool (adapt category)

* move utils to topp folder and change category

...

github.com/OpenMS/OpenMS - aba1cd5e351913ff16b6cf7bec5383f8f0690f62 authored about 1 year ago by Timo Sachsenberg <[email protected]>

Update openms_clang_format.yml (#7005)

* Update openms_clang_format.yml

github.com/OpenMS/OpenMS - ab14d02ff26879cce9284b0d868e0a03613dda06 authored about 1 year ago by Timo Sachsenberg <[email protected]>

remove tool also from KNIME packaging (#7004)

updates knime_package_support.cmake
apparently had no effect that the tool was missing so this...

github.com/OpenMS/OpenMS - 5ad0e1ac06bb45b59e237a1d06ff90a5c3767825 authored about 1 year ago by Timo Sachsenberg <[email protected]>

fix test

github.com/OpenMS/OpenMS - 057b92e398e9f4c1ec550d504a65cd3deb2a910a authored about 1 year ago by Chris Bielow <[email protected]>

remove harmful include

github.com/OpenMS/OpenMS - dc27fce6765166c70185327f4849c79e85a8e92c authored about 1 year ago by Chris Bielow <[email protected]>

update simde

github.com/OpenMS/OpenMS - af7a8c7ffa910c3b08c909f200b7b705c8c99714 authored about 1 year ago by Chris Bielow <[email protected]>

comment

github.com/OpenMS/OpenMS - f2c3600ff8561677d3ea42a80e5bebeefd7e28b9 authored about 1 year ago by Julianus Pfeuffer <[email protected]>

allow missing env vars in ci cmake script

github.com/OpenMS/OpenMS - bd43787b7f30b92b96ecafd3977c63d36aa7f75c authored about 1 year ago by Julianus Pfeuffer <[email protected]>

Merge branch 'develop' into base64_simd

github.com/OpenMS/OpenMS - e6f8f14bc8a572df0b3ac0453349c6313ac69047 authored about 1 year ago by Chris Bielow <[email protected]>

move compression code to a better-tested place

github.com/OpenMS/OpenMS - 50859551f000e58a319bd42e867b4bc589057c19 authored about 1 year ago by Chris Bielow <[email protected]>

[DOC] for internals; and saving an include

github.com/OpenMS/OpenMS - f7f30af7ffde2014a899f948baaad7cb28ee7045 authored about 1 year ago by Chris Bielow <[email protected]>

remove useless assign

github.com/OpenMS/OpenMS - 66b33c237713e867b14521a9593ef38585b2e7c0 authored about 1 year ago by Chris Bielow <[email protected]>

fix bug in compression length

github.com/OpenMS/OpenMS - 6d6360f94da48fbdf07b9a75892cd5dff589cf20 authored about 1 year ago by Chris Bielow <[email protected]>

Get rid of dependency on C compilers (#7002)

github.com/OpenMS/OpenMS - 4144268516629de515db4328a141e57459d3ba6f authored about 1 year ago by Julianus Pfeuffer <[email protected]>

fix bug

github.com/OpenMS/OpenMS - 9c6f4259c6fed0f19d7d90c8f1a5c9d0e99bfadb authored about 1 year ago by Chris Bielow <[email protected]>

fix wrong base64 data in test

github.com/OpenMS/OpenMS - b0121bfcaa0b60c493b97b37e662e423f88aeda9 authored about 1 year ago by Chris Bielow <[email protected]>

fix warning

github.com/OpenMS/OpenMS - 39c48fe2f5c20a8f76978a6d5921e0ffe9afb05c authored about 1 year ago by Chris Bielow <[email protected]>

add foldername inference

github.com/OpenMS/OpenMS - a8a8fe98fbb4cfcd155710bf029a09825893f3c5 authored about 1 year ago by Julianus Pfeuffer <[email protected]>

secrets name change

github.com/OpenMS/OpenMS - cf4a9a587b080c2e92f24f74f7ab0296a17c9eb8 authored about 1 year ago by Julianus Pfeuffer <[email protected]>

changes for easier compiler selection

github.com/OpenMS/OpenMS - 1c7935240bb49ccd323432e1172d864ee33022b9 authored about 1 year ago by Julianus Pfeuffer <[email protected]>

finish all steps. just needs testing and potential fixes. minor todos about ssh upload

github.com/OpenMS/OpenMS - 692a346f76b263f6216a7c1857908d76569f661e authored about 1 year ago by Julianus Pfeuffer <[email protected]>

fix compile errors

github.com/OpenMS/OpenMS - 190099063e0c6bace2b68d732a1ca15b5b492cc5 authored about 1 year ago by Chris Bielow <[email protected]>

Merge branch 'develop' into base64_simd

github.com/OpenMS/OpenMS - f6e6301517e21a9d2e3deb0da650f67c5b9700c6 authored about 1 year ago by Chris Bielow <[email protected]>

[cleanup] remove CompNovo (#6999)

* remove CompNovo

* changelog

* removed additioal files

* Update CHANGELOG

github.com/OpenMS/OpenMS - 846836f804990623049833a0d4346827270c94f7 authored about 1 year ago by Timo Sachsenberg <[email protected]>

Merge branch 'base64_simd' of https://github.com/cbielow/OpenMS into base64_simd

github.com/OpenMS/OpenMS - b97ee07bc8d5ebeca8c86e441a6e1409da217247 authored about 1 year ago by Chris Bielow <[email protected]>

fix compile error

github.com/OpenMS/OpenMS - df9a7898d362526150e33762209a424157b4e153 authored about 1 year ago by Chris Bielow <[email protected]>

Merge branch 'develop' into base64_simd

github.com/OpenMS/OpenMS - 9bd8cc93b68c77bd1c141fddb6df9aa15cdf7867 authored about 1 year ago by Chris Bielow <[email protected]>

[Cleanup] Remove PepNovoAdapter (#6997)

* remove PepNovoAdapter

* clean up non-existing tool entries

* fix test

* Update CHANGELOG

github.com/OpenMS/OpenMS - 179d93c4cd66ffd990fb41664f59e187435aff01 authored about 1 year ago by Timo Sachsenberg <[email protected]>

[Cleanup] Remove some of the eval tools (#6998)

* removed eval tools

* update changelog

* nop

* forgot executable

github.com/OpenMS/OpenMS - cbf37468558842193a53875f20678fabe882c94c authored about 1 year ago by Timo Sachsenberg <[email protected]>

[CI] add initial version of full multijob for GH actions

github.com/OpenMS/OpenMS - d759afdc67780b5a0919adf9d9fc7509a4122d93 authored about 1 year ago by Julianus Pfeuffer <[email protected]>

Bump src/pyOpenMS/pyopenms-docs from `04c8016` to `0d5e4f3`

Bumps [src/pyOpenMS/pyopenms-docs](https://github.com/OpenMS/pyopenms-docs) from `04c8016` to `0...

github.com/OpenMS/OpenMS - 16d5275c032499f6224350b6b337cb8f3da5bbe9 authored about 1 year ago by dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Update docs/source/conf.py

github.com/OpenMS/pyopenms-docs - 0d5e4f3244e70bb41e310090f6a65e9b480ba126 authored about 1 year ago by Julianus Pfeuffer <[email protected]>

automatically add dev tag based on branch (RTD-only)

github.com/OpenMS/pyopenms-docs - 0c624d085763b930333dd9cad93cceabda3daab7 authored about 1 year ago by Julianus Pfeuffer <[email protected]>

add support for endianess when decoding; remove bogus testcase

github.com/OpenMS/OpenMS - b4520d45bb59bcc2537f6431b01d1dcf4a7b781a authored about 1 year ago by Chris Bielow <[email protected]>

NOOP

github.com/OpenMS/OpenMS - 1f716011e271e83938bc32d82ee07c9d15a4a7c9 authored about 1 year ago by Chris Bielow <[email protected]>

Bump THIRDPARTY from `0dda83f` to `402992f` (#6993)

Bumps [THIRDPARTY](https://github.com/OpenMS/THIRDPARTY) from `0dda83f` to `402992f`.
- [Releas...

github.com/OpenMS/OpenMS - 46980c8a5c4f0beb25ff5007ab4d2086174bf990 authored about 1 year ago by dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

update execute flag

github.com/OpenMS/THIRDPARTY - 402992fbb05ac567fb6c5ba4f3dbac679eaf5649 authored about 1 year ago by Timo Sachsenberg <[email protected]>

update sage (#102)

github.com/OpenMS/THIRDPARTY - db56f26ed8593f091e986c8b1c1b6fff49fd8ba2 authored about 1 year ago by Matteo Pilz <[email protected]>

install up to date cmake with mamba (#11)

github.com/OpenMS/streamlit-template - 7866603e0499ffb516547600a6c5a7936d3baf3c authored about 1 year ago by axelwalter <[email protected]>

Remove_oldsvm (#6990)

* Removed RT and PT predict model

* remove old SVM wrapper code

* update changelog

* re...

github.com/OpenMS/OpenMS - f214cc0887270d8d5fb4d96df49bda032bee3b60 authored about 1 year ago by Timo Sachsenberg <[email protected]>

Merge pull request #6983 from OpenMS/dependabot/submodules/src/pyOpenMS/pyopenms-docs-04c8016

Bump src/pyOpenMS/pyopenms-docs from `577aca4` to `04c8016`

github.com/OpenMS/OpenMS - 1ac310e7fb8654904a9ef40e159e6f6017855a3d authored about 1 year ago by Julianus Pfeuffer <[email protected]>

switch to target_include_directories

github.com/OpenMS/OpenMS - 26742f7ba917a193109c43985d4b8bc7e6c6ed67 authored about 1 year ago by Chris Bielow <[email protected]>

Update docs/source/user_guide/logging.rst

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

github.com/OpenMS/pyopenms-docs - 15accd0523d85992bddae8b6b27c23bc8683b2d2 authored about 1 year ago by Julianus Pfeuffer <[email protected]>

import

github.com/OpenMS/pyopenms-docs - 076fb11a6e89b9b19c227bc7384a54a3048ee8fe authored about 1 year ago by Julianus Pfeuffer <[email protected]>

add page on logging

github.com/OpenMS/pyopenms-docs - 96c765e55d9a600ebfebcd2353026e36fa5f1cd3 authored about 1 year ago by Julianus Pfeuffer <[email protected]>

[CLEANUP] Remove first set of unused tools (#6963)

* remove some files

* remove InclusionExclusionListCreator

* remoe InclusionExclusionListC...

github.com/OpenMS/OpenMS - c7704373f21805c38819c63f1a81cf3a2f0eb318 authored about 1 year ago by Timo Sachsenberg <[email protected]>

Merge pull request #6988 from cbielow/toppas_wording

TOPPAS: better button text to avoid confusion with loading data files

github.com/OpenMS/OpenMS - 6c1f81675e568b3ec803fd26d45db58fd4862538 authored about 1 year ago by Chris Bielow <[email protected]>

better button text to avoid confusion with loading data files

github.com/OpenMS/OpenMS - e99f5fbe649304295feec3add79af2ab3beea201 authored about 1 year ago by Chris Bielow <[email protected]>

make SIMDe includes 'external' i.e. they are not affected by 'C4100: 'i': unreferenced formal parameter'

github.com/OpenMS/OpenMS - 4248a3798c85178f35e548c0bca72aa2da9bf968 authored about 1 year ago by Chris Bielow <[email protected]>

Merge pull request #6955 from OpenMS/dependabot/submodules/THIRDPARTY-0dda83f

Bump THIRDPARTY from `e215209` to `0dda83f`

github.com/OpenMS/OpenMS - 1c64561bc3c9f28a03898c426596d49401a046ee authored about 1 year ago by Samuel Wein <[email protected]>

Update versions on release badges

github.com/OpenMS/OpenMS-website - 0853ade5a49cd1ed7c9dd9083bea955daade0a31 authored about 1 year ago by Radu Suciu <[email protected]>

move SIMDe code to cpp

github.com/OpenMS/OpenMS - a10631a51f64e06290fe0d07bc994a71a298dd7f authored about 1 year ago by Chris Bielow <[email protected]>

update pxds for cython 3 compatibility (#6985)

* update pxds for cython 3 compatibility

* preserve spaces

github.com/OpenMS/OpenMS - b6712b9d5c64ca08430b54f24033635b4f89968d authored about 1 year ago by Timo Sachsenberg <[email protected]>

fix a few compile warnings

github.com/OpenMS/OpenMS - f8b8c0f9c46b6af69fe0c3f6371b7b2a4d0eb280 authored about 1 year ago by Chris Bielow <[email protected]>

add FindModule for SIMDe

github.com/OpenMS/OpenMS - 9106bf17ac40e83884c0477c166c8ab0ea6e9224 authored about 1 year ago by Chris Bielow <[email protected]>

Merge pull request #6980 from radusuciu/add_pyopenms_project_urls

Add some project urls to pyopenms package

github.com/OpenMS/OpenMS - 3f8beaec6e88915dca902819ce35f324de697e60 authored about 1 year ago by Julianus Pfeuffer <[email protected]>

Merge branch 'develop' into Feature/GenericFileLoad

github.com/OpenMS/OpenMS - 8035eda12136921fa6c92df5985e50bb5e7f0827 authored about 1 year ago by Samuel Wein <[email protected]>

Merge pull request #6984 from OpenMS/poshul-patch-1

Update CHANGELOG

github.com/OpenMS/OpenMS - a41bf873dc68e964188cd326a566065b31a671ea authored about 1 year ago by Timo Sachsenberg <[email protected]>

Merge branch 'develop' into dependabot/submodules/src/pyOpenMS/pyopenms-docs-04c8016

github.com/OpenMS/OpenMS - 1494526da78c01f75336f5526528a6c3278f4ebc authored about 1 year ago by Samuel Wein <[email protected]>

Update src/pyOpenMS/setup.py

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

github.com/OpenMS/OpenMS - 64817e1cc69fdae5793022785a06ec2d2b7ba685 authored about 1 year ago by Timo Sachsenberg <[email protected]>

Update CHANGELOG

[nop] correct release date for 3.0

github.com/OpenMS/OpenMS - b4c60403d4f9de627650c59f6dc564ac679bab1a authored about 1 year ago by Samuel Wein <[email protected]>

Merge branch 'develop' into dependabot/submodules/THIRDPARTY-0dda83f

github.com/OpenMS/OpenMS - 061bc600e598409bc3ca52faaa9a349a8a38c04c authored about 1 year ago by Samuel Wein <[email protected]>

Merge pull request #6981 from radusuciu/fix_pyopenms_description_link

Fix link in pyopenms package description

github.com/OpenMS/OpenMS - 91a3e1344615a4188fda8ef16118766fd600e9f1 authored about 1 year ago by Timo Sachsenberg <[email protected]>

Bump src/pyOpenMS/pyopenms-docs from `577aca4` to `04c8016`

Bumps [src/pyOpenMS/pyopenms-docs](https://github.com/OpenMS/pyopenms-docs) from `577aca4` to `0...

github.com/OpenMS/OpenMS - 4019222367cf55bb9b2bca1fc7ea1cf9fde30836 authored about 1 year ago by dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Fix link in pyopenms package description

github.com/OpenMS/OpenMS - a8116462b7cd0d4837db73552f31b0ec7bb123f3 authored about 1 year ago by Radu Suciu <[email protected]>

Add some project urls to pyopenms package

github.com/OpenMS/OpenMS - 95a6aace5cc908282b787b00c98062e2afedbed3 authored about 1 year ago by Radu Suciu <[email protected]>

Update supported versions of python

github.com/OpenMS/pyopenms-docs - 04c8016d6dd22cf38b71ce6374b22bf445100f26 authored about 1 year ago by Radu Suciu <[email protected]>

switch to using a library-interface for SIMDe to avoid `...thirdparty\simde\simde\x86\sse.h(3363,39): error C4100: 'i': unreferenced formal parameter ` on MSVC due to external includes since we are using /we4100 and /we4189

github.com/OpenMS/OpenMS - f71a92a3a5262df45d1579142324634bf42fa0be authored about 1 year ago by Chris Bielow <[email protected]>

fix compile errors

github.com/OpenMS/OpenMS - 77aa60326119db96d2ed968d6dbc284a2cb3089e authored about 1 year ago by Chris Bielow <[email protected]>

dumb SSE version of skipping non-whitespaces to make removeWhitespaces faster (this is currently limited to skipping a whitespace-free prefix

github.com/OpenMS/OpenMS - 785e8aa8704d614ac5e0b0f96acd38fca62759a9 authored about 1 year ago by Chris Bielow <[email protected]>

update PR number

github.com/OpenMS/OpenMS - 2056a0f9ac16ab8d4fd1ce540cfe005711d22b58 authored about 1 year ago by Chris Bielow <[email protected]>

extend test

github.com/OpenMS/OpenMS - 51e66b26a2856e28cd5b6ab8667460e23c979bb4 authored about 1 year ago by Chris Bielow <[email protected]>

document AVX requirement

github.com/OpenMS/OpenMS - cec8aa422aeb5cf576ecbfcf73b75d78b36dfb97 authored about 1 year ago by Chris Bielow <[email protected]>

noop

github.com/OpenMS/OpenMS - 66c98581a5cfcdd15b9ad23037f7c339b4451907 authored about 1 year ago by Chris Bielow <[email protected]>

cleaning up a bit

github.com/OpenMS/OpenMS - 0830d7953ad5700942a32fdf66c22bc08b4fffe5 authored about 1 year ago by Chris Bielow <[email protected]>

Merge branch 'develop' of https://github.com/OpenMS/OpenMS into base64_simd

github.com/OpenMS/OpenMS - 09b846c3eb078637348932503584a3a31fe346c7 authored about 1 year ago by Chris Bielow <[email protected]>

Revert "reverse logic of #6877, to allow pre-configured OpenMS source builds to run without weird error messages"

This reverts commit 30e5def115eea2f71b5703db7596c61a2a6ffb3f.

github.com/OpenMS/OpenMS - b7a8ded865db0933d5425018441e6af585eca14e authored about 1 year ago by Chris Bielow <[email protected]>

Merge pull request #6975 from OpenMS/changeCoinFind

[CMAKE] detect coin-or in different places

github.com/OpenMS/OpenMS - 3965aec2291c113c468c51dfeed75848f89c68ef authored about 1 year ago by Chris Bielow <[email protected]>

Replace #6974

github.com/OpenMS/OpenMS - c55da3e728afe593e12acd7ff355b38920680c34 authored about 1 year ago by Julianus Pfeuffer <[email protected]>

Replace #6974

github.com/OpenMS/OpenMS - 167988b3acecc84ddd6cacdaf11bebb72fede63d authored about 1 year ago by Julianus Pfeuffer <[email protected]>

clean up SIMD compile flags

github.com/OpenMS/OpenMS - 45a2d93a9dffc23f8291fca2b24745d24bf8a70a authored about 1 year ago by Chris Bielow <[email protected]>

useAVX2 on MSVC by default

github.com/OpenMS/OpenMS - 5b75496215d1f3e8c18532f127a6a1148a0842da authored about 1 year ago by Chris Bielow <[email protected]>

fix for clang/gcc

github.com/OpenMS/OpenMS - ebac5ca334350107d003c6288cf44a685b13dbce authored about 1 year ago by Chris Bielow <[email protected]>

fix some compile errors for Win and minor optimizations

github.com/OpenMS/OpenMS - e166dac57e76890546fc88127d64f7f6021163e4 authored about 1 year ago by Chris Bielow <[email protected]>

reverse logic of #6877, to allow pre-configured OpenMS source builds to run without weird error messages

github.com/OpenMS/OpenMS - 30e5def115eea2f71b5703db7596c61a2a6ffb3f authored about 1 year ago by Chris Bielow <[email protected]>

exe support

github.com/OpenMS/streamlit-template - 27ff531cda5471dd6b6cab24b859129566c55a58 authored about 1 year ago by Arslan <[email protected]>

streamlit_exe.md added

github.com/OpenMS/streamlit-template - ff6d0936c3ce29e95c6ce69f9ce1a0f85f7c2a57 authored about 1 year ago by Arslan <[email protected]>

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

github.com/OpenMS/OpenMS - 876c38b8f2dc23d25f88ecbcf07aa56d8bc9601d authored about 1 year ago by Chris Bielow <[email protected]>