Ecosyste.ms: OpenCollective

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

OpenMS

Make mass spectrometry analysis accessible to anyone
Collective - Host: opensource - https://opencollective.com/openms - Website: https://openms.org - Code: https://github.com/openms

more doxygen fixes

github.com/OpenMS/OpenMS - aef65f5e1f8946c17308efa5eeac8e4971687e8e authored 9 months ago by Chris Bielow <[email protected]>
fix undetected writing to bad filestream

add/fix class instantatiations

github.com/OpenMS/OpenMS - f88ca90637140ebcd6452ef46ea0299dfec760dc authored 9 months ago by Chris Bielow <[email protected]>
prepare for markdown support in doxygen (indents are problematic)

github.com/OpenMS/OpenMS - 2da05f50fa77b6da9c3800e4f04b7450c8c2df42 authored 9 months ago by Chris Bielow <[email protected]>
fix more doxygen warnings

github.com/OpenMS/OpenMS - df8f43c6503468a3597ae9a922c96f3fd1783372 authored 9 months ago by Chris Bielow <[email protected]>
remove references to PeakPickerWavelet

github.com/OpenMS/OpenMS - 23789e1403f07b8640cc1cde8936548a55350e5c authored 9 months ago by Chris Bielow <[email protected]>
doygen warning fixes

github.com/OpenMS/OpenMS - 53b9b6b3eee6c21cc7e7042ab673be1f1da27536 authored 9 months ago by Chris Bielow <[email protected]>
better handling of missing DOT (doxygen):

- avoid doxygen warning when its missing

github.com/OpenMS/OpenMS - 676b5a1945567f418207e00cc60fe5488fb99192 authored 9 months ago by Chris Bielow <[email protected]>
updated user FAQ

github.com/OpenMS/OpenMS - 6cef09742d10ab4983ef51b8da738a0afd11b414 authored 9 months ago by Chris Bielow <[email protected]>
more doxygen fixes

github.com/OpenMS/OpenMS - a38d610804407872630cf71308252300f816054c authored 9 months ago by Chris Bielow <[email protected]>
Merge pull request #7209 from enetz/feature/csv_comments

Feature/csv comments

github.com/OpenMS/OpenMS - 60e2905a7571d7b6a479dcd69141dfd2ea220b66 authored 9 months ago by Timo Sachsenberg <[email protected]>
Merge pull request #7286 from OpenMS/license_header

License header

github.com/OpenMS/OpenMS - 0b7828d3dbbfa6a94b98a7de512881afd7af6653 authored 9 months ago by Timo Sachsenberg <[email protected]>
Bump tj-actions/changed-files in /.github/workflows (#7279)

Bumps [tj-actions/changed-files](https://github.com/tj-actions/changed-files) from 34.6.1 to 41....

github.com/OpenMS/OpenMS - cdaeb90068ccfcc6c343edbc5d8fbc0af512a574 authored 9 months ago by dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
wf not needed anymore

github.com/OpenMS/OpenMS - 0205bb6c3cfcb51bc3dc976931eca3dacc7870ed authored 9 months ago by Timo Sachsenberg <[email protected]>
update license header. omit end date

github.com/OpenMS/OpenMS - d5b97af403971ef65913e064a81eda88da7378d7 authored 9 months ago by Timo Sachsenberg <[email protected]>
more doxygen fixes

github.com/OpenMS/OpenMS - 787001e36886176614cc341b08dd42044ca55203 authored 9 months ago by Chris Bielow <[email protected]>
fix undetected writing to bad filestream

add/fix class instantatiations

github.com/OpenMS/OpenMS - 67cb0533e13cd03d4eea1e7133a57987bb7a4589 authored 9 months ago by Chris Bielow <[email protected]>
not derived from DefaultParamHandler... thus no params to document

github.com/OpenMS/OpenMS - 9c92143685ca37627e74955f64adbba0cf2d6346 authored 9 months ago by Chris Bielow <[email protected]>
a lot more doxygen fixes

github.com/OpenMS/OpenMS - 8692173d4863ea18474f46033f409d297b935e05 authored 9 months ago by Chris Bielow <[email protected]>
add missing DefaultParamHandler' derived classes to doc

github.com/OpenMS/OpenMS - da1706b0c13b34a399d4db25d15c3a4d61544cf2 authored 9 months ago by Chris Bielow <[email protected]>
Merge branch 'develop' of https://github.com/OpenMS/OpenMS into fix_devdocs

github.com/OpenMS/OpenMS - 5df2cd5b7e288437a66b2cd3e9fab232353653ba authored 9 months ago by Chris Bielow <[email protected]>
remove references to PeakPickerWavelet

github.com/OpenMS/OpenMS - e47a5687bee79a16a347582f98f6fae0dcbe94c0 authored 9 months ago by Chris Bielow <[email protected]>
doygen warning fixes

github.com/OpenMS/OpenMS - 474e6e1d00637de99b7e0608cf4d7761493287ee authored 9 months ago by Chris Bielow <[email protected]>
better handling of missing DOT (doxygen):

- avoid doxygen warning when its missing

github.com/OpenMS/OpenMS - c4ea88dae399f7764b564b0595d0f17adf6048aa authored 9 months ago by Chris Bielow <[email protected]>
fix more doxygen warnings

github.com/OpenMS/OpenMS - f0b3dc74929dc40c2571e2df83807caf35c88f8b authored 9 months ago by Chris Bielow <[email protected]>
Always set working dir in pyopenms tests (#7282)

fixes #7281

github.com/OpenMS/OpenMS - 3781a02944ec65ec78069cb93698422203dbef04 authored 9 months ago by Julianus Pfeuffer <[email protected]>
a first brush over developer tutorial; readding conding conventions from Wiki

github.com/OpenMS/OpenMS - a1e85394cc3cd1ab735614bb24cab1a5e1f7a770 authored 10 months ago by Chris Bielow <[email protected]>
updated user FAQ

github.com/OpenMS/OpenMS - 67d49b19c24f12c421b9b47816b8c0af9e7b4557 authored 10 months ago by Chris Bielow <[email protected]>
fix doxygen warnings

github.com/OpenMS/OpenMS - 494c92d90135c9ce4d2ee1172ff4f30e5cf5477f authored 10 months ago by Chris Bielow <[email protected]>
prepare for markdown support in doxygen (indents are problematic)

github.com/OpenMS/OpenMS - b8afec980da81c9f6bbdfc66b46ece467b211e18 authored 10 months ago by Chris Bielow <[email protected]>
Merge pull request #18 from OpenMS/dependabot/submodules/umetaflow-gui-8440fc3

Bump umetaflow-gui from `050e0ec` to `8440fc3`

github.com/OpenMS/streamlit-deployment - 4d3e234317ee9c263d268cbdd75ebc0934f666bd authored 10 months ago by axelwalter <[email protected]>
cmake cleanup (#7277)

* cmake cleanup

* Update multithreading.cmake

github.com/OpenMS/OpenMS - c4406b7d8c5b29b89b930723236d14246ca65be5 authored 10 months ago by Timo Sachsenberg <[email protected]>
Bump umetaflow-gui from `050e0ec` to `8440fc3`

Bumps [umetaflow-gui](https://github.com/axelwalter/umetaflow-gui) from `050e0ec` to `8440fc3`.
...

github.com/OpenMS/streamlit-deployment - 87e693a61c21dc55c0d717bcd09a39d5b56dfcbf authored 10 months ago by dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
add __repr__ (#7265)

* add __repr__

* fix __repr__

github.com/OpenMS/OpenMS - 0f13cce7c2fce48722bebb14610ada8c98317ae7 authored 10 months ago by Timo Sachsenberg <[email protected]>
Allow different sizes of compressed output in zlib unit tests (#7274)

* Allow different sizes of compressed output

* Apply suggestions from code review

* Apply ...

github.com/OpenMS/OpenMS - da7603ddb84674c7f1bf143ed1ce91ee40edfc5d authored 10 months ago by Timo Sachsenberg <[email protected]>
Merge pull request #17 from OpenMS/dependabot/submodules/umetaflow-gui-050e0ec

Bump umetaflow-gui from `3eb18e2` to `050e0ec`

github.com/OpenMS/streamlit-deployment - ba56ac574d97fc97bbf8d44a2bff469dd2dea148 authored 10 months ago by axelwalter <[email protected]>
Speedup Ion Mobility OpenSwath Processing (#6479)

* First attempt at modifying DIA scores

Try to forgo filtering by ion mobility by
just compu...

github.com/OpenMS/OpenMS - 79f553adc066425e7bed2c261cdf58cbf46527b2 authored 10 months ago by Joshua Charkow <[email protected]>
Bump umetaflow-gui from `3eb18e2` to `050e0ec`

Bumps [umetaflow-gui](https://github.com/axelwalter/umetaflow-gui) from `3eb18e2` to `050e0ec`.
...

github.com/OpenMS/streamlit-deployment - 079075f2617b1503242cb3d6724acff2e3a0e7f4 authored 10 months ago by dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Update openms_ci_matrix_full.yml

github.com/OpenMS/OpenMS - ec6aa46f858d741f4ff79ff0bc8a5c20796b3684 authored 10 months ago by Samuel Wein <[email protected]>
Update openms_ci_matrix_full.yml

why the heck is it workflow_run when the value is workflow_dispatch?

github.com/OpenMS/OpenMS - 2430fc9fdfc42e539eb11e125346c3104878c5fe authored 10 months ago by Samuel Wein <[email protected]>
Update openms_ci_matrix_full.yml

github.com/OpenMS/OpenMS - b6683178538ccc938908278dcb9b1d96c24b9b83 authored 10 months ago by Samuel Wein <[email protected]>
Update openms_ci_matrix_full.yml

github.com/OpenMS/OpenMS - f416da1ef559555ad615cc8bdd4c5302fce4042a authored 10 months ago by Samuel Wein <[email protected]>
Update openms_ci_matrix_full.yml

refactor where we check inputs to avoid bash issues. Fix assignment instead of equality test in ...

github.com/OpenMS/OpenMS - 39d49fecde40a02fc5e63c11b6ceb9889a905ef6 authored 10 months ago by Samuel Wein <[email protected]>
Update openms_ci_matrix_full.yml

github.com/OpenMS/OpenMS - 997b612ed337c41dca204b35da0dbed32d440824 authored 10 months ago by Samuel Wein <[email protected]>
Update openms_ci_matrix_full.yml

github.com/OpenMS/OpenMS - c55b30bda7999b8587d102a93774d7adf5034a2b authored 10 months ago by Samuel Wein <[email protected]>
Update openms_ci_matrix_full.yml

github.com/OpenMS/OpenMS - 6631511285d428c9673bbc8415e582f3ea23c026 authored 10 months ago by Samuel Wein <[email protected]>
Update openms_ci_matrix_full.yml

github.com/OpenMS/OpenMS - e1a2339c315ff076c2aa10fab18ab132639e95ed authored 10 months ago by Samuel Wein <[email protected]>
Update openms_ci_matrix_full.yml

github.com/OpenMS/OpenMS - 030591fb06ba574b676860dd7431aef2d616f24e authored 10 months ago by Samuel Wein <[email protected]>
Update openms_ci_matrix_full.yml

github.com/OpenMS/OpenMS - 47e53e867917fe9ea3017e29cf004d130909fc89 authored 10 months ago by Samuel Wein <[email protected]>
Update openms_ci_matrix_full.yml

Fix bash issue when running as a push

github.com/OpenMS/OpenMS - 1e8f93e056e8779af2c9877595a6ab88d9f2016b authored 10 months ago by Samuel Wein <[email protected]>
Merge branch 'develop' into release/2.9.1-action

github.com/OpenMS/OpenMS - 42a3788747918b37d6471e55bfd439fc59327bc3 authored 10 months ago by Samuel Wein <[email protected]>
Update openms_ci_matrix_full.yml

Add explicit token

github.com/OpenMS/OpenMS - 1f3302cfc17c31c7ed685670399372d911a336d9 authored 10 months ago by Samuel Wein <[email protected]>
fix: remove CWL CI and pregenerated tool description files (#7275)

* fix: remove cwl CI and prebuild workflows

* fix: remove CWL testing

it was comparing aga...

github.com/OpenMS/OpenMS - ea6c611d7e1cc4884209fc47bb93846d381940e4 authored 10 months ago by Simon Gene Gottlieb <[email protected]>
support tools with multiple headers and cpp files (#7262)

* support splitting tools into multiple files

* nop

* Update src/topp/CMakeLists.txt

* ...

github.com/OpenMS/OpenMS - 198a676845fece78b6e5d2babb79120c0bfa6aff authored 10 months ago by Timo Sachsenberg <[email protected]>
fix conversion to number (instead of ASCII code, since `operator<<(QString, char)` seems to be used for `int`, which leads to "(exit code: ÿ)." (#7273)

github.com/OpenMS/OpenMS - c106320a1374bd1de9f2c97bf61c21520b6156cc authored 10 months ago by Chris Bielow <[email protected]>
renamed "thirdparty" folder to the more common "extern" (#7268)

github.com/OpenMS/OpenMS - 3ed1396024f6b039b92ee282a548d4eba67fb40d authored 10 months ago by Timo Sachsenberg <[email protected]>
Update CHANGELOG

github.com/OpenMS/OpenMS - 6625421116cae3770fa70de7aa9fb64f6ee639f4 authored 10 months ago by Chris Bielow <[email protected]>
[FEATURE] Concurrent MSGF+ database indexing (#7272)

* minor update

* add locking to fasta index creation, allowing multiple adapters to run in pa...

github.com/OpenMS/OpenMS - d999ae56eb83278f534121bbc2401315cc518b83 authored 10 months ago by Chris Bielow <[email protected]>
Plotting fix - matched peaks highlighting (#7243)

* Fix plotting.py for existing annotations from SpectrumAnnotator

* remove debug

* added m...

github.com/OpenMS/OpenMS - 117f7a1d814633432583dfce19db5e73240a495b authored 10 months ago by Matteo Pilz <[email protected]>
Merge pull request #14 from OpenMS/dependabot/submodules/umetaflow-gui-3eb18e2

Bump umetaflow-gui from `6cc740f` to `3eb18e2`

github.com/OpenMS/streamlit-deployment - 5aff85a3d0092b50d8c31bc446e762b329e2a6c3 authored 10 months ago by axelwalter <[email protected]>
Bump umetaflow-gui from `6cc740f` to `3eb18e2`

Bumps [umetaflow-gui](https://github.com/axelwalter/umetaflow-gui) from `6cc740f` to `3eb18e2`.
...

github.com/OpenMS/streamlit-deployment - d884c2075b9e6d35df062f3b226ce63bdff3f581 authored 10 months ago by dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Merge branch 'develop' into release/2.9.1-action

github.com/OpenMS/OpenMS - 9d776b1a6c51ac909a57ded337560709b60dc2db authored 10 months ago by Samuel Wein <[email protected]>
Merge pull request #7269 from OpenMS/nightlyfix

Bump brew python to 3.12

github.com/OpenMS/OpenMS - 7bce5149fe0b9472b0bc62597891f004db1b85fe authored 10 months ago by Samuel Wein <[email protected]>
Bump brew python to 3.12

github.com/OpenMS/OpenMS - 2774fcfa2c2cb8418f784b0b5fac0e76fabd57dc authored 10 months ago by Samuel Wein <[email protected]>
Merge branch 'develop' into release/2.9.1-action

github.com/OpenMS/OpenMS - 4dda488158d7319999ec6511fbcd01571e7cd539 authored 10 months ago by Samuel Wein <[email protected]>
Merge pull request #123 from JeeH-K/fq_add_installer_link

Added link to FLASHQuant installer files

github.com/OpenMS/OpenMS-website - a7d764cf98ca49ccb2a6161fd7997da06e5dd305 authored 10 months ago by Jihyung Kim <[email protected]>
Bump contrib from `69e61f2` to `5e42765` (#7267)

Bumps [contrib](https://github.com/OpenMS/contrib) from `69e61f2` to `5e42765`.
- [Commits](htt...

github.com/OpenMS/OpenMS - af95149b2d0b2aa24a37da75ade82d7ae6d07cbc authored 10 months ago by dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
update hdf5 (#135)

Co-authored-by: timosachsenberg <[email protected]>

github.com/OpenMS/contrib - 5e427652cf36043007c7366b5e97b445fe84a7a4 authored 10 months ago by Timo Sachsenberg <[email protected]>
trying to fix the netlify error

github.com/OpenMS/OpenMS-website - cab50bbcd0664a55a10a96b800dc47b93c76b2c3 authored 10 months ago by JeeH-K <[email protected]>
changed the button for download page

github.com/OpenMS/OpenMS-website - 4af6cfb87ded1083ab13152f5e4c68ba29497d60 authored 10 months ago by JeeH-K <[email protected]>
Merge pull request #125 from enetz/fix/useless_footer_mailbox

Removed email signup field in the footer

github.com/OpenMS/OpenMS-website - cfa3fc05f5595e2affa36e0a478b758c20ed3697 authored 10 months ago by Eugen Netz <[email protected]>
Merge pull request #124 from enetz/fix/oms_logo

Replaced outdated OpenMS logo

github.com/OpenMS/OpenMS-website - 37d3a4df5b4504c7631ba2cbf31381a0c6b2270c authored 10 months ago by Eugen Netz <[email protected]>
removed reference to isotopewavelet (#425)

github.com/OpenMS/pyopenms-docs - bb095b81f273c80f035cba9b8ea6e63bbe75a0c2 authored 10 months ago by Timo Sachsenberg <[email protected]>
Merge pull request #121 from matteopilz/main

Fix Quick Facts for Users

github.com/OpenMS/OpenMS-website - 8f040fb524e974de221544addc3c747946131207 authored 10 months ago by Matteo Pilz <[email protected]>
Merge remote-tracking branch 'openms/main' into main

# Conflicts:
# layouts/partials/quick-facts.html

github.com/OpenMS/OpenMS-website - 24d7b208112d9ed42f95c94ac21dfe9f97b2f9e5 authored 10 months ago by matteopilz <[email protected]>
Removed email signup field in the footer

github.com/OpenMS/OpenMS-website - 824b7e23c8685573a94897060c7b3687f63becb1 authored 10 months ago by Eugen Netz <[email protected]>
Replaced outdated OpenMS logo

github.com/OpenMS/OpenMS-website - e5606c7c6611befc81cca421bd59b576693b3956 authored 10 months ago by Eugen Netz <[email protected]>
Reverted change without an effect and cleaned up unused code

github.com/OpenMS/OpenMS - 79c67b88f79883a8891107949d02685b7b2ac980 authored 10 months ago by enetz <[email protected]>
[FEATURE] Optional support for comment lines in TextFile

Moved comment line support from CsvFile to TextFIle as an optional parameter.
CsvFile and Intern...

github.com/OpenMS/OpenMS - 6d3bda4a169961aa0506dac027c1f45a9fad551a authored 10 months ago by enetz <[email protected]>
Added link to FLASHQuant installer files

github.com/OpenMS/OpenMS-website - 2260445c5e0251034a8dcc1e5109dc396f17883b authored 11 months ago by JeeH-K <[email protected]>
Merge branch 'develop' into release/2.9.1-action

github.com/OpenMS/OpenMS - 072a28e0d88e20b78febe22c39e615420997ed7e authored 11 months ago by Samuel Wein <[email protected]>
Merge pull request #7258 from cbielow/doc_toppas

Update TOPPAS tutorial

github.com/OpenMS/OpenMS - 57817d632cf70d45eeb52817c3f6afc2f54921f4 authored 11 months ago by Timo Sachsenberg <[email protected]>
update workflows to latest TOPP version

github.com/OpenMS/OpenMS - 3b3a3a6667d9732efc18d7954367d092eb6c323d authored 11 months ago by Chris Bielow <[email protected]>
remove references to OMSSA, replace by Comet.

Fix some formatting issues.

github.com/OpenMS/OpenMS - 36b955e2d5ee449f2874c1ffe273dcece0a74297 authored 11 months ago by Chris Bielow <[email protected]>
update images to latest TOPPAS version

github.com/OpenMS/OpenMS - ffc38209dc8f56133a681481f527bd979e7dc659 authored 11 months ago by Chris Bielow <[email protected]>
re-index mzML file and avoid CV warning

github.com/OpenMS/OpenMS - ca0704238b02e6a4eafb0a7d585ccb029696de26 authored 11 months ago by Chris Bielow <[email protected]>
fix warning in traml handler (#7253)

github.com/OpenMS/OpenMS - e084a3572e9b2b5f7ba24cce567012929b5cea5f authored 11 months ago by Timo Sachsenberg <[email protected]>
fix doc (#7250)

github.com/OpenMS/OpenMS - 7903e31382d351232916906b4b6f813d5b111552 authored 11 months ago by Timo Sachsenberg <[email protected]>
fix wrong OpenMP max_threads in OpenMSInfo TOPP tool (introduced in #7132) (#7247)

github.com/OpenMS/OpenMS - 77d16b62158d404e46eddc19824685d163f66dfa authored 11 months ago by Chris Bielow <[email protected]>
Update openms_ci_matrix_full.yml

explicitly add write permissions to github.token

github.com/OpenMS/OpenMS - 194a0a07f1ba3eb49e40279ca2b0cd01adef0f16 authored 11 months ago by Samuel Wein <[email protected]>
Check if this excludes vcpkg from dependabot.yml updates (#7245)

github.com/OpenMS/OpenMS - 1ff4cde0264f121202e7c16928d89d4354463f26 authored 11 months ago by Timo Sachsenberg <[email protected]>
Fix syntax for gh

github.com/OpenMS/OpenMS - 5b44fdc308182d355362a3d3184074a8e68dac79 authored 11 months ago by Samuel Wein <[email protected]>
fixed (hopefully) tag syntax

github.com/OpenMS/OpenMS - 5cbb23dbe089983f5abf10436508e8666a9e475d authored 11 months ago by Samuel Wein <[email protected]>
correct how we get the shas

github.com/OpenMS/OpenMS - dc7f1c59a10951a9c79dd536fd346bd55f6ea872 authored 11 months ago by Samuel Wein <[email protected]>
fix ref to removed tool

github.com/OpenMS/OpenMS - 7be700288f3d1d1f47648c1a2c3e63a26717a20b authored 11 months ago by Samuel Wein <[email protected]>
fix spacing

github.com/OpenMS/OpenMS - 7668be62b09555aa8056346dfdb11b5345c875f2 authored 11 months ago by Samuel Wein <[email protected]>
Merge branch 'release/2.9.1-action' of ssh://github.com/OpenMS/OpenMS into release/2.9.1-action

github.com/OpenMS/OpenMS - e5674c0f1a4c4078da26b9e7b1787c4b422f7fc0 authored 11 months ago by Samuel Wein <[email protected]>
move changelog creation up and add checks for nonsensical inputs. Fail if trying to mark_latest on a version that already exists

github.com/OpenMS/OpenMS - 04ce8680bbdbdbe48740509a1fa75f0ba89aa064 authored 11 months ago by Samuel Wein <[email protected]>
Merge branch 'develop' into release/2.9.1-action

github.com/OpenMS/OpenMS - ede64fc12626383ac5f27437a72aafd0d6cecae6 authored 11 months ago by Samuel Wein <[email protected]>
more robust precursor purity (PR 3 of X) (#7240)

* minor refactoring

* removed RNPxl

* make precursor purity calculation more robust

* U...

github.com/OpenMS/OpenMS - 39b23207571ffd9f871d4531b21a6f79412b1c77 authored 11 months ago by Timo Sachsenberg <[email protected]>
[cleanup] remove outdated RNPxl tool (PR 2 of X) (#7239)

* minor refactoring

* removed RNPxl

* fix pxds

* also remove topp test

---------

...

github.com/OpenMS/OpenMS - c3bb6b01a2bc6f3cbf8d4c32293a88e5204f8059 authored 11 months ago by Timo Sachsenberg <[email protected]>