OpenMS commits | Ecosyste.ms: OpenCollective

don't run docker containers in github action

github.com/OpenMS/streamlit-template - cd1ad6779ab5d8068f2ab4eade4d38033faab01e authored 12 months ago by axelwalter <[email protected]>

fix typo in docker build action

github.com/OpenMS/streamlit-template - 09b72a46e5f4610bbbd8e069119c5acd5e4d1904 authored 12 months ago by axelwalter <[email protected]>

actions to build docker images for testing

github.com/OpenMS/streamlit-template - f35d93adf34f33142b29e5474f2ee5c83ce63753 authored 12 months ago by axelwalter <[email protected]>

build windows executable only on main branch

github.com/OpenMS/streamlit-template - 83ca30789d7527a0f9408d27c7bd471b6f7248e4 authored 12 months ago by axelwalter <[email protected]>

pylint on PR to main branch

github.com/OpenMS/streamlit-template - 2fc2ad4683196b9ea217cfbdcf93bafb3297bf5c authored 12 months ago by axelwalter <[email protected]>

python version formatting in pylint action

github.com/OpenMS/streamlit-template - 97ad18533f0d4805d19f28855967a1a712894628 authored 12 months ago by axelwalter <[email protected]>

pylint with Python 3.10 only

github.com/OpenMS/streamlit-template - f1d3c57c5a857667935202cc2f2bd6bfb26f7376 authored 12 months ago by axelwalter <[email protected]>

specify dependencies

github.com/OpenMS/streamlit-template - c6e945c1c0eda4a1553f6085fb060d6e7bfaef86 authored 12 months ago by axelwalter <[email protected]>

format code

github.com/OpenMS/streamlit-template - 0e7d599c368866bff9e9aa4c61438d917f605331 authored 12 months ago by axelwalter <[email protected]>

format code

github.com/OpenMS/streamlit-template - 552e01e6a02d4eeb9cf97fe5d0786551ccf288ac authored 12 months ago by axelwalter <[email protected]>

testing wheel search fix

github.com/OpenMS/OpenMS - f8600ec8697ab0aa61fd7d800acaee5b8bc941d4 authored 12 months ago by matteopilz <[email protected]>

Create pylint.yml

github.com/OpenMS/streamlit-template - d3e80c75fa735c73e0b93b29ea71d65e155ac4b6 authored 12 months ago by axelwalter <[email protected]>

Merge remote-tracking branch 'openms/develop' into fix-ubuntu-wheels-test

github.com/OpenMS/OpenMS - c5a33e3cf3782ceea55a2667f927c8b8ca10ae33 authored 12 months ago by matteopilz <[email protected]>

Merge pull request #7154 from SGSSGene/fix/duplicate_option_names

Remove duplicate option names

github.com/OpenMS/OpenMS - fdc30c500ad41dda0468be4c2d347de198dd48ce authored 12 months ago by Samuel Wein <[email protected]>

Merge pull request #7159 from SGSSGene/fix/xvfb_not_starting

fix: xvfb not starting when xvfb is already running

github.com/OpenMS/OpenMS - 84a0b4ac50b005351ca86403477bfabed85bae80 authored 12 months ago by Timo Sachsenberg <[email protected]>

fix test files

github.com/OpenMS/OpenMS - 7fe393b210a810d652b7c8ead61c5fc81a711697 authored 12 months ago by Chris Bielow <[email protected]>

doc: adjusting CHANGELOG

github.com/OpenMS/OpenMS - 8e7b96158ed9d88555429998a76dab31c623ff28 authored 12 months ago by Simon Gene Gottlieb <[email protected]>

fix: rename parameters to avoid duplicates

This fixes duplicates in the applications:
- PeakPickerWavelet `algorithm:optimization` → `algor...

github.com/OpenMS/OpenMS - a128f85e88804c1a3025184c03aa9ed415a2649c authored 12 months ago by Simon Gene Gottlieb <[email protected]>

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

# Conflicts:
# src/tests/topp/THIRDPARTY/MSGFPlusAdapter_1_out.idXML

github.com/OpenMS/OpenMS - 105dcfdd03cd0d96965c6aade1a53588e9f8ec31 authored 12 months ago by Chris Bielow <[email protected]>

fix test

github.com/OpenMS/OpenMS - 31e008cbf323e6da8b509fc0822b4299eb5232cd authored 12 months ago by Chris Bielow <[email protected]>

Merge branch 'develop' into fix_mzidentml

github.com/OpenMS/OpenMS - 4a94e96ad7ab8e3d28200731c84e017b0b90f2e7 authored 12 months ago by Chris Bielow <[email protected]>

fix: xvfb not starting when xvfb is already running

github.com/OpenMS/OpenMS - 1fb835649a86a46c35db41871761f5eaaf5569de authored 12 months ago by Simon Gene Gottlieb <[email protected]>

amend changelog for recent PRs

github.com/OpenMS/OpenMS - 65b29a6b967309a42fd1dc01dcb870cb0841b5c8 authored 12 months ago by Chris Bielow <[email protected]>

add conversion of XSD::Boolean to parsing cvParams

github.com/OpenMS/OpenMS - 67dffa01060971b98c000d9b23569129982049b1 authored 12 months ago by Chris Bielow <[email protected]>

use more robust unit conversion in mzIdentML

github.com/OpenMS/OpenMS - c77ca7a88db2a337c6541feea935c26318c19035 authored 12 months ago by Chris Bielow <[email protected]>

move value conversion from mzML to more general XMLHandler for use in other classes

github.com/OpenMS/OpenMS - 81725a57f4f988887b593dc346cf673c2c8ff135 authored 12 months ago by Chris Bielow <[email protected]>

some cleanup

github.com/OpenMS/OpenMS - 81c21d9f36eb1c2bc57ced0e9d70b6e829a5ef52 authored 12 months ago by Chris Bielow <[email protected]>

Merge pull request #7156 from cbielow/info_solver

[INFO] OpenMSInfo: report which ILP lib we use

github.com/OpenMS/OpenMS - bc34c4ae5e8939798c184ecfaf588d767a4dcbe6 authored 12 months ago by Chris Bielow <[email protected]>

Merge pull request #7155 from cbielow/fix_msfragger

[FIX] MSFragger: relative path to database

github.com/OpenMS/OpenMS - c5e870bec5a554d1b652472cf0fc646270019441 authored 12 months ago by Chris Bielow <[email protected]>

Merge pull request #7158 from bernt-matthias/topic/tool-descriptions

improve tool descriptions (slightly)

github.com/OpenMS/OpenMS - 68e0d95863a4c647937211f384ee8c33946242c0 authored 12 months ago by Samuel Wein <[email protected]>

Merge pull request #6780 from poshul/Feature/GenericFileLoad

genericized file loader where possible

github.com/OpenMS/OpenMS - 5c3c0c148e15dc530a0f2a6ac324c0fbcff64270 authored 12 months ago by Samuel Wein <[email protected]>

improve tool descriptions (slightly)

github.com/OpenMS/OpenMS - 985d4f8c1a33d02b1f617541427ca063fcc2cf67 authored 12 months ago by Matthias Bernt <[email protected]>

Merge pull request #8 from axelwalter/main

Update umetaflow submodule

github.com/OpenMS/streamlit-deployment - 12640b9a9f9ddd6cdb73b2211208506b2fb7b3a8 authored 12 months ago by axelwalter <[email protected]>

update umetaflow submodule

github.com/OpenMS/streamlit-deployment - 0229e1a7b857f0ff31fe55821adb0ee87515622a authored 12 months ago by axelwalter <[email protected]>

[INFO] report which ILP lib we use

github.com/OpenMS/OpenMS - 7dabf9decbfb6b9de49932c3f87e8eb38025d2d6 authored 12 months ago by Chris Bielow <[email protected]>

Update FileHandler_test.cpp

github.com/OpenMS/OpenMS - 2962cc51b4fd4659dc0fb8d5b582f0a05e375ac3 authored 12 months ago by Samuel Wein <[email protected]>

convert relative db names to absolute paths, since msfragger is executed in a new working dir (temp dir)

github.com/OpenMS/OpenMS - b1d1c939127ac33d0123e9fac75d4c78dc4065c3 authored 12 months ago by Chris Bielow <[email protected]>

require MSFragger.jar to exist (or whatever the user specified)

github.com/OpenMS/OpenMS - e91d75a51249d36c1c2489f72746394400268509 authored 12 months ago by Chris Bielow <[email protected]>

improve error message when input files are not found

github.com/OpenMS/OpenMS - 8bfd1d767a7f12da2c0f2a0dad5e3faa25d6372e authored 12 months ago by Chris Bielow <[email protected]>

Remove ref to outdate file_property

github.com/OpenMS/OpenMS - 1821aab90dcf239e98c96aa5a11587a16bb01c38 authored 12 months ago by Samuel Wein <[email protected]>

update Changelog

github.com/OpenMS/OpenMS - b10b578c99e2eec9138e1ad7f4a78a359b80b4fc authored 12 months ago by Chris Bielow <[email protected]>

expose out_type as normal user parameter (do not hide it as advanced)

github.com/OpenMS/OpenMS - 354cf8ead319ba49337ec59850cf9880e25815c0 authored 12 months ago by Chris Bielow <[email protected]>

avoid calling ".toString().toDouble());" on potentially empty DataValue (which would crash)

github.com/OpenMS/OpenMS - af31eba9daf7decdf0ac4e76e1b7719a23ae894f authored 12 months ago by Chris Bielow <[email protected]>

augment #7129 (fixes #7099) since the value was read as "" (which will not count as 'isEmpty()' for a DataValue!

github.com/OpenMS/OpenMS - b730e1028bae1e66cb2f0d6e68be7b0ec3507b05 authored 12 months ago by Chris Bielow <[email protected]>

some internal docs

github.com/OpenMS/OpenMS - ff0c060389ebaab359055038d7173df3d8a339a5 authored 12 months ago by Chris Bielow <[email protected]>

Added new Exception type InvalidFileType

github.com/OpenMS/OpenMS - 7084ddbe475a5cd87af980fb6faa3408e739f02b authored 12 months ago by Samuel Wein <[email protected]>

Update FileTypes.cpp

github.com/OpenMS/OpenMS - e91ef4fe5936488952b649556c0be1960f6127b9 authored 12 months ago by Samuel Wein <[email protected]>

Update FileTypes.h

github.com/OpenMS/OpenMS - 516d111604eecd26ed7484edc160b6cb82013df2 authored 12 months ago by Samuel Wein <[email protected]>

Merge branch 'develop' into Feature/GenericFileLoad

github.com/OpenMS/OpenMS - 6bfff75d4ee4f8e5922f3b564706ed2672cb9e88 authored 12 months ago by Samuel Wein <[email protected]>

Merge pull request #7146 from OpenMS/release/3.1.0

Release/3.1.0

github.com/OpenMS/OpenMS - 443b652db20cf6a61c38b3e3deb4f2154fca3596 authored 12 months ago by Timo Sachsenberg <[email protected]>

Merge pull request #7147 from cbielow/fix_mzquantml

Fix MzQuantMLHandler error when <Modification> element has no "massDelta" attribute)

github.com/OpenMS/OpenMS - f9a11f76cec27f9187c38559c71b26e7e21016dd authored 12 months ago by Chris Bielow <[email protected]>

Merge pull request #7148 from bernt-matthias/rm-compnovo-test-files

remove remnant CompNovo test data

github.com/OpenMS/OpenMS - 7c33681348a14c8434adb0b2563dfdd3d0101c12 authored 12 months ago by Timo Sachsenberg <[email protected]>

Merge branch 'develop' into Feature/GenericFileLoad

github.com/OpenMS/OpenMS - 9f4b17e84cb7f7f665e466e74afac7d680ffffec authored 12 months ago by Samuel Wein <[email protected]>

remove remnant CompNovo test data

github.com/OpenMS/OpenMS - 35d56bb1af80cd96c5227296e3d95fe1e8776425 authored 12 months ago by Matthias Bernt <[email protected]>

fix #7145 (MzQuantMLHandler error when <Modification> element has no "massDelta" attribute)

github.com/OpenMS/OpenMS - d0643e03fd4017d61bcde0b5b5c4fd8b2b09244d authored 12 months ago by Chris Bielow <[email protected]>

Merge pull request #7 from Arslan-Siraj/main

nuxl-app added

github.com/OpenMS/streamlit-deployment - 69b639794337d39438f5c17635a06cc7db58c18a authored 12 months ago by axelwalter <[email protected]>

nuxl-app added

github.com/OpenMS/streamlit-deployment - 88dca10429246ec458428b70b42935db8969124f authored 12 months ago by Arslan <[email protected]>

Merge pull request #7144 from enetz/fix/asan_errors

Fix a few AddressSanitizer complaints due to uninitialized variables

github.com/OpenMS/OpenMS - 9513f435872e6f02cd5f59cb78ccff30b3f57c73 authored 12 months ago by Timo Sachsenberg <[email protected]>

Update src/openms/include/OpenMS/ANALYSIS/XLMS/OPXLDataStructs.h

github.com/OpenMS/OpenMS - 9bd12ac4ec848cf80716f9fcca0aa5804e72944e authored 12 months ago by Timo Sachsenberg <[email protected]>

[FIX] initialize variable in DeconvolvedSpectrum

github.com/OpenMS/OpenMS - 41231f8bd1753565c9f19c085b5bcaf50475f32c authored 12 months ago by Eugen Netz <[email protected]>

[FIX] initialize variable in PeakGroup

github.com/OpenMS/OpenMS - d6219f8fc170fe86f35bf3db0f5ca2435809ff48 authored 12 months ago by Eugen Netz <[email protected]>

[FIX] initialize variables in OPXLDataStructs

github.com/OpenMS/OpenMS - b55ccb4222e1a23b610c2ac07cfc66bf52bcce43 authored 12 months ago by Eugen Netz <[email protected]>

Merge pull request #7129 from OpenMS/jpfeuffer-patch-5

[mzIdentML] fall back to name element for DatabaseName

github.com/OpenMS/OpenMS - 55094ca9c98949c8d8657d233267a56978f3de8d authored almost 1 year ago by Timo Sachsenberg <[email protected]>

Merge pull request #7142 from cbielow/doc_flash

FlashDeconv: add citation to TOPP tool and more docs

github.com/OpenMS/OpenMS - 0a356e855505b99ddfe37c7688ed6d2e08e33682 authored almost 1 year ago by Timo Sachsenberg <[email protected]>

add citation and more docs

github.com/OpenMS/OpenMS - f64649e618778fb6901a6a29bf98026c44630bd5 authored almost 1 year ago by Chris Bielow <[email protected]>

Merge pull request #7139 from cbielow/fix_TOPPAS_categories

[FEATURE] TOPPAS: search tools by name

github.com/OpenMS/OpenMS - 3d84aa723a87baf383c2cb597e190ddd2a99e409 authored almost 1 year ago by Chris Bielow <[email protected]>

update changelog

github.com/OpenMS/OpenMS - a2881149c21dc33f81831d760cc1d37cf7085b57 authored almost 1 year ago by Chris Bielow <[email protected]>

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

github.com/OpenMS/OpenMS - 28d6dbc32edb13393038073f116d86c7164845d8 authored almost 1 year ago by Chris Bielow <[email protected]>

gcc/clang choke on `inline` in cpp (which VS puts there for some reason when asked to create an implementation)

github.com/OpenMS/OpenMS - 10f545d75fdd7621b932f701a7f58e2fb59329c1 authored almost 1 year ago by Chris Bielow <[email protected]>

Update src/openms/source/FORMAT/HANDLERS/MzIdentMLDOMHandler.cpp

github.com/OpenMS/OpenMS - 9a5638236e0c9f89b42ec827e669f07066cac5fd authored almost 1 year ago by Julianus Pfeuffer <[email protected]>

Merge pull request #7140 from OpenMS/disable_failing_sirius

disable failing SIRIUS tests

github.com/OpenMS/OpenMS - 0e12b6ab0c02f46fec7331cd2e87c7d8e9997dc7 authored about 1 year ago by Timo Sachsenberg <[email protected]>

disable_failing_SIRIUS_tests

github.com/OpenMS/OpenMS - 8b7a5afea09d15fdccd2f84a8a5b32b55b403ec1 authored about 1 year ago by Timo Sachsenberg <[email protected]>

Merge branch 'develop' into fix_TOPPAS_categories

github.com/OpenMS/OpenMS - 124f7b3e67e78b652d9b4249c601f0ddf6f7452d authored about 1 year ago by Chris Bielow <[email protected]>

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

github.com/OpenMS/OpenMS - f591e3c0ca50cf9c997c55d0aa8f8aa9e96bb596 authored about 1 year ago by Chris Bielow <[email protected]>

Feature: filter TOPP tools in TOPPAS by name

github.com/OpenMS/OpenMS - 2a9802ad5f1f419bf5b5cd1d280682119a8ad76e authored about 1 year ago by Chris Bielow <[email protected]>

Merge branch 'develop' into jpfeuffer-patch-5

github.com/OpenMS/OpenMS - 777058779f23090ce49352ee20fab15eb053dd74 authored about 1 year ago by Chris Bielow <[email protected]>

Update CHANGELOG

github.com/OpenMS/OpenMS - 17a07f8bdf78e471a26e7869a33004fd046ec510 authored about 1 year ago by Timo Sachsenberg <[email protected]>

Merge pull request #7138 from OpenMS/develop

sync

github.com/OpenMS/OpenMS - 55f52b49f70fa9c049564186d356bdd79965c3da authored about 1 year ago by Timo Sachsenberg <[email protected]>

Merge pull request #7136 from OpenMS/disable_rsync

disable rsync

github.com/OpenMS/OpenMS - cc06e8f422e08fd6c0e39d8060713dad0ece0032 authored about 1 year ago by Timo Sachsenberg <[email protected]>

Merge pull request #7137 from OpenMS/develop

sync with develop

github.com/OpenMS/OpenMS - b9c1ffa944e60280ddc057377e537adea58f4079 authored about 1 year ago by Timo Sachsenberg <[email protected]>

disable rsync

because it led to empty folders in the buildarchive

github.com/OpenMS/OpenMS - 9bdbcd8e64e784fbc2f0272875d3c0e8e090e3de authored about 1 year ago by Timo Sachsenberg <[email protected]>

Merge pull request #7134 from cbielow/fix_TOPPAS_categories

fix FlashDeconv docu (missing parameters)

github.com/OpenMS/OpenMS - a05f1e72e8f9d70e8556a9cc32150f812ba36181 authored about 1 year ago by Chris Bielow <[email protected]>

Merge branch 'develop' into fix_TOPPAS_categories

github.com/OpenMS/OpenMS - 22bfbb9e0ddf3b35054df8db58a746818817879a authored about 1 year ago by Chris Bielow <[email protected]>

fix flash docu (missing parameters)

github.com/OpenMS/OpenMS - bd7ab792d8d8a45fbd63ce9886e469a30fe1fdfb authored about 1 year ago by Chris Bielow <[email protected]>

Merge pull request #7132 from cbielow/fix_TOPPAS_categories

Fix TOPP categories and make OpenMSInfo a TOPP tool

github.com/OpenMS/OpenMS - f7b13a18952a361daae7ba6c0f0a032ea971a36f authored about 1 year ago by Chris Bielow <[email protected]>

Update CHANGELOG

github.com/OpenMS/OpenMS - 8f114b858c369f8637a1f9b0c84b172d4956797e authored about 1 year ago by Timo Sachsenberg <[email protected]>