github.com/OpenMS/OpenMS issues | Ecosyste.ms: OpenCollective

Get toppview tool output extension from out type

poshul opened this pull request 1 day ago

trim .* from file extension in toppview

poshul opened this pull request 4 days ago

TOPPView run tool on visible area

timosachsenberg opened this issue 4 days ago

Question: ARM Linux Support?

thomaspttn opened this issue 5 days ago

feature: add option to ouput only psms that reached some PSM-FDR threshold

timosachsenberg opened this pull request 6 days ago

Try to use system install of qt5 for deb

poshul opened this pull request 6 days ago

Fix cmake choco version

poshul opened this pull request 7 days ago

Fix choco cmake installation

poshul opened this pull request 7 days ago

Update install-linux.doxygen

jcharkow opened this pull request 9 days ago

feature: score switching to general score types - add option to perform protein inference on non-main scores

timosachsenberg opened this pull request 10 days ago

Bump src/pyOpenMS/pyopenms-docs from `16aa3e8` to `57c4d18`

dependabot[bot] opened this pull request 10 days ago

Try to fix mac runner python issue

poshul opened this pull request 11 days ago

Update test000.py

timosachsenberg opened this pull request 11 days ago

Fix pyOpenMS

cbielow opened this pull request 11 days ago

Sage: fix tolerance annotation

timosachsenberg opened this pull request 12 days ago

Dont include qt in deb

poshul opened this pull request 12 days ago

try forcing disabling of library validation

poshul opened this pull request 13 days ago

[refactor] remove getMZ alias from chromatograms

timosachsenberg opened this pull request 13 days ago

Feature/im ipf scoring

singjc opened this pull request 13 days ago

Feature/im peakpicking

singjc opened this pull request 13 days ago

new TOPP failure codes for missing external tools

cbielow opened this pull request 13 days ago

fix: add msfragger enzyme name

timosachsenberg opened this pull request 13 days ago

Update devcontainer.json to use manylinux 2.34

poshul opened this pull request 14 days ago

quickfix of codium-pr-agent.yml

timosachsenberg opened this pull request 14 days ago

Ignore warnings in extern libs

poshul opened this pull request 14 days ago

Feat/cwl produce default values

SGSSGene opened this pull request 14 days ago

Choco's CMake 3.31.2 is bugged. Force use of 3.31.1

poshul opened this pull request 14 days ago

https://bugreports.qt.io/browse/QTBUG-110118 marked as fixed in qt6 r…

poshul opened this pull request 15 days ago

Add cwl package

poshul opened this pull request 16 days ago

Bump src/pyOpenMS/pyopenms-docs from `c9b8e09` to `16aa3e8`

dependabot[bot] opened this pull request 16 days ago

Bump contrib from `b786ca3` to `3cdef5c`

dependabot[bot] opened this pull request 16 days ago

fix pyOpenMS CMakeLists.txt

timosachsenberg opened this pull request 16 days ago

qt6: Update pyopenms-wheels.yml

timosachsenberg opened this pull request 17 days ago

Release/3.3.0

poshul opened this pull request 17 days ago

Update pyopenms-wheels.yml

timosachsenberg opened this pull request 17 days ago

put the cwl files in the right folder and generate them whenever we b…

poshul opened this pull request 17 days ago

Feature/osw auto addup spec

singjc opened this pull request 17 days ago

Bump src/pyOpenMS/pyopenms-docs from `c9b8e09` to `46ff112`

dependabot[bot] opened this pull request 17 days ago

Use adhoc mac signing identity

poshul opened this pull request 17 days ago

fix Dockerfile

timosachsenberg opened this pull request 18 days ago

Bump src/pyOpenMS/pyopenms-docs from `c9b8e09` to `f971933`

dependabot[bot] opened this pull request 18 days ago

docs: update linux contrib requirements for qt-6

jcharkow opened this pull request 18 days ago

SequenceCoverageCalculator: write annotated proteins to idXML

timosachsenberg opened this pull request 18 days ago

improve python developer experience

cbielow opened this pull request 18 days ago

TOPPView crashing on MacOS 14 with code signing issue

RonanDaly opened this issue 19 days ago

Add signing identity to cibuild.cmake

jpfeuffer opened this pull request 19 days ago

Silence warnings from install_name_tool. Fix indentation in add_mac_b…

poshul opened this pull request 20 days ago

Fix mac signing 33

poshul opened this pull request 20 days ago

Revert "add some debug output"

timosachsenberg opened this pull request 20 days ago

Fix residue heisenbug

cbielow opened this pull request 20 days ago

add some debug output

timosachsenberg opened this pull request 20 days ago

OpenMS nightly documentation out of sync

timosachsenberg opened this issue 20 days ago

Question: role of ITransition.h

timosachsenberg opened this issue 20 days ago

Question: role of MSSpectrum in MRMTransitionGroup

timosachsenberg opened this issue 20 days ago

add final to iterators and remove unneeded virtual

timosachsenberg opened this pull request 21 days ago

TheoreticalSpectrumGenerator and AASequence test fails on Windows

timosachsenberg opened this issue 21 days ago

Remove SONAR Functionality from OpenSWATH

jcharkow opened this pull request 23 days ago

`-write_cwl` does not print out default values

t0mdavid-m opened this issue 23 days ago

update: comet

MaLLLiYA opened this pull request 24 days ago

fix Toppas pipelines and add tests

cbielow opened this pull request 25 days ago

TOPPAS to CWL Converter

mr-c opened this issue 25 days ago

Ecoli_Identification.toppas is not under test (and has an error)

mr-c opened this issue 25 days ago

incomplete error message about JSON input error

mr-c opened this issue 26 days ago

release source tarball is surprisingly large, contains many duplicate files

mr-c opened this issue 26 days ago

Generate and publish the CWL tool descriptors for all OpenMS tools

mr-c opened this issue 26 days ago

[ByGHAction] Updated OpenMS package version numbers

github-actions[bot] opened this pull request 26 days ago

Update version to 3.4.0 develop

poshul opened this pull request 26 days ago

Proof/json reader works with all unittests

poshul opened this pull request 26 days ago

add release 3.2 changes to develop

timosachsenberg opened this pull request 26 days ago

Add addMissingIMToPeptideIDs function to SpectrumMetaDataLookup

jonasscheid opened this pull request 27 days ago

Apply fix for msvc issue

poshul opened this pull request 27 days ago

Update pyopenms-wheels.yml

poshul opened this pull request 27 days ago

Residue names, attempt 2

cbielow opened this pull request 27 days ago

add missing ion names to Residue.cpp

timosachsenberg opened this pull request 28 days ago

MassCalculator error

bernt-matthias opened this issue 29 days ago

Docker containers broken

jpfeuffer opened this issue 29 days ago

OpenMS KNIME package, RawFileReader fails to find binary

poshul opened this issue about 1 month ago

Revert "conda: try to add windows builds"

timosachsenberg opened this pull request about 1 month ago

conda: try to add windows builds

timosachsenberg opened this pull request about 1 month ago

Current pyOpenMS errors

timosachsenberg opened this issue about 1 month ago

Mac OS not supported?

btemoshir opened this issue about 1 month ago

openMS install from *.dmg fails with codesigning error or process kill on M1 mac

tentrillion opened this issue about 1 month ago

add Poisson probability scoring to NASE

poshul opened this pull request about 1 month ago

add source path from pepxml

timosachsenberg opened this pull request about 1 month ago

Update CMakeLists.txt

poshul opened this pull request about 1 month ago

Now that we aren't passing the package type during the build just set…

poshul opened this pull request about 1 month ago

Release/3.3.0

poshul opened this pull request about 1 month ago

Throw warning if package is defined with enable_x_testing

poshul opened this pull request about 1 month ago

Unit and TOPP tests are only being run on Ubuntu-22.04-Clang not any of the other matrix entries for CI

poshul opened this issue about 1 month ago

PepXML from MSFragger IDFileConverted to idXML doesn't preserve spectrum filename

timosachsenberg opened this issue about 1 month ago

try to work around gha protection

timosachsenberg opened this pull request about 1 month ago

Update update_version_numbers.yml

poshul opened this pull request about 1 month ago

deployment: create bioconda deploy action

timosachsenberg opened this pull request about 1 month ago

Update update_ini_files_OpenMS_version.sh

poshul opened this pull request about 1 month ago

Release checklist for 3.3.0

poshul opened this issue about 1 month ago

Move pyopenMS building to pyproject.toml

poshul opened this issue about 1 month ago

TRFP update test file

timosachsenberg opened this pull request about 1 month ago

fix TRFP

timosachsenberg opened this pull request about 1 month ago

Wheels on pr

poshul opened this pull request about 1 month ago

Fix RPATH creation in deb package

poshul opened this pull request about 1 month ago