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

Bump src/pyOpenMS/pyopenms-docs from `229a171` to `6a0aab2`

dependabot[bot] opened this pull request 9 months ago

MSstatsConverter does not allow subset of experimental design in input cXML

jpfeuffer opened this issue 9 months ago

Enhancements in Documentation and Code Readability

cbielow opened this pull request 9 months ago

folders in build archive no accessible

saassli21 opened this issue 9 months ago

Bump src/pyOpenMS/pyopenms-docs from `64016e7` to `229a171`

dependabot[bot] opened this pull request 9 months ago

Comet scores duplicated

jpfeuffer opened this issue 9 months ago

nightly merge action fails

timosachsenberg opened this issue 9 months ago

Enhancements and code simplifications in various files

jpfeuffer opened this pull request 9 months ago

Update update_nightly.yml

poshul opened this pull request 9 months ago

Add action to replace Jenkins at updating the nightly branch every night

poshul opened this pull request 9 months ago

fix compiler issue

poshul opened this pull request 9 months ago

Create codium-pr-agent

timosachsenberg opened this pull request 9 months ago

Migrate Dockerfiles from external repository

radusuciu opened this pull request 9 months ago

Update README

poshul opened this pull request 9 months ago

mgf file from single mzML files

YasinEl opened this issue 9 months ago

OpenSwathWorkflow - swath_windows_file type not restricted!

bruadi opened this issue 9 months ago

[FEATURE] Simple, targeted, fast IsobaricWorkflow

jpfeuffer opened this pull request 9 months ago

[Feature] Loading XML from remote locations

jpfeuffer opened this pull request 9 months ago

Enhancements in MSExperiment and MSSpectrum classes

jpfeuffer opened this pull request 9 months ago

Enhancements in Documentation and Code Readability

cbielow opened this pull request 9 months ago

Linux build instructions could be simplified.

timosachsenberg opened this issue 9 months ago

Bump src/pyOpenMS/pyopenms-docs from `64016e7` to `27dfc2a`

dependabot[bot] opened this pull request 9 months ago

Investigate building snap/flatpak packages for linux

poshul opened this issue 9 months ago

Fix developer docs and warnings

cbielow opened this pull request 9 months ago

Fix Windows installer's extra Dll's from GHA

cbielow opened this issue 9 months ago

Where is MSSimulator?

Ministreliya131 opened this issue 9 months ago

OpenMS File archive not working

jpfeuffer opened this issue 9 months ago

How to write cython code of struct in struct in the type declaration.

JKVISION1101 opened this issue 9 months ago

License header

timosachsenberg opened this pull request 9 months ago

when cythonize, No such file or directory error (wrapping class for pyopenms)

JKVISION1101 opened this issue 9 months ago

Parameter ms1_isotopes ignored

cbielow opened this issue 9 months ago

When making pxd file for wrapping class, question about cimport.

JKVISION1101 opened this issue 9 months ago

Always set working dir in pyopenms tests

jpfeuffer opened this pull request 10 months ago

After building pyopenms, ctest failed, although importing pyopenms worked well,

JKVISION1101 opened this issue 10 months ago

deisotopeAndSingleCharge: Removes Highest Intensity Peaks, bug?

CCranney opened this issue 10 months ago

Bump tj-actions/changed-files from 34.6.1 to 41.0.0 in /.github/workflows

dependabot[bot] opened this pull request 10 months ago

[ByGitAction] Updated year number in the header of files

github-actions[bot] opened this pull request 10 months ago

cmake cleanup

timosachsenberg opened this pull request 10 months ago

Is there an elegant way to present the ProteomicsLFQ results?

liuxiawei opened this issue 10 months ago

fix: remove CWL CI and pregenerated tool description files

SGSSGene opened this pull request 10 months ago

Allow different sizes of compressed output in zlib unit tests

timosachsenberg opened this pull request 10 months ago

Display proper exit code when external process crashes

cbielow opened this pull request 10 months ago

[FEATURE] Concurrent MSGF+ database indexing

cbielow opened this pull request 10 months ago

7 tests fail when using zlib-ng

tuliom opened this issue 10 months ago

Update openms_ci_matrix_full.yml

poshul opened this pull request 10 months ago

Bump brew python to 3.12

poshul opened this pull request 10 months ago

[NOP] renamed "thirdparty" folder to the more common "extern"

timosachsenberg opened this pull request 10 months ago

Bump contrib from `69e61f2` to `5e42765`

dependabot[bot] opened this pull request 10 months ago

Delete cmake/Modules/FindHDF5.cmake

timosachsenberg opened this pull request 10 months ago

add __repr__

timosachsenberg opened this pull request 10 months ago

Bump src/pyOpenMS/pyopenms-docs from `64016e7` to `bb095b8`

dependabot[bot] opened this pull request 10 months ago

Aligning Parameters/ New SpectrumGenerator

Trapho opened this pull request 10 months ago

support tools with multiple headers and cpp files

timosachsenberg opened this pull request 10 months ago

Move CWL outputs to own build subfolder

jpfeuffer opened this issue 10 months ago

Error report in XTandemAdapter, IDScoreSwitcher, and ProteomicsLFQ

liuxiawei opened this issue 10 months ago

Add conversion for MSSpectrum & PeptideHit to spectrum_utils MsmsSpectrum

matteopilz opened this pull request 11 months ago

Update TOPPAS tutorial

cbielow opened this pull request 11 months ago

Run example TOPPAS workflows with CI

cbielow opened this issue 11 months ago

our example mzML files could use an update

cbielow opened this issue 11 months ago

Running MSGF+ in parallel crashes when input DB is new

cbielow opened this issue 11 months ago

TOPPView: Running TOPP tools fails

cbielow opened this issue 11 months ago

fix warning in traml handler

timosachsenberg opened this pull request 11 months ago

The incomplete documentation makes beginners feel extremely difficult.

liuxiawei opened this issue 11 months ago

Make ParamIterator a real iterator

timosachsenberg opened this issue 11 months ago

fix doc

timosachsenberg opened this pull request 11 months ago

Patch/extend osw output

jcharkow opened this pull request 11 months ago

[Feature request] Add more low-level MSExperiment multidimensional access functions

jpfeuffer opened this issue 11 months ago

fix wrong OpenMP max_threads in OpenMSInfo TOPP tool

cbielow opened this pull request 11 months ago

How do I perform quantitative analysis on PRM data using OpenMS?

Allen188 opened this issue 11 months ago

Check if this excludes vcpkg from dependabot.yml updates

timosachsenberg opened this pull request 11 months ago

Bump vcpkg from `64ca152` to `e85cafa`

dependabot[bot] opened this pull request 11 months ago

Plotting fix - matched peaks highlighting

matteopilz opened this pull request 11 months ago

Bump vcpkg from `64ca152` to `4cac260`

dependabot[bot] opened this pull request 11 months ago

Check pyopenms compatibility with Cython < 3.0

jpfeuffer opened this issue 11 months ago

more robust precursor purity (PR 3 of X)

timosachsenberg opened this pull request 11 months ago

[cleanup] remove outdated RNPxl tool (PR 2 of X)

timosachsenberg opened this pull request 11 months ago

[refactoring] moving files into more appropriate folders (PR 1 of X)

timosachsenberg opened this pull request 11 months ago

[FEATURE] z* and z' ions for ExD (fixed tests)

timosachsenberg opened this pull request 11 months ago

Added port file to use qt from system libraries, fixed bug in LPWrapper cmake files (thanks Julianus)

timosachsenberg opened this pull request 11 months ago

FindCOIN.cmake use imported targets

jpfeuffer opened this pull request 11 months ago

SiriusAdapter replaced with SiriusExport and adaptations to AssayGeneratorMetabo

axelwalter opened this pull request 11 months ago

Refactoring FragmentIndex

Trapho opened this pull request 11 months ago

[SageAdapter] Feature req: Have a load-only functionality

jpfeuffer opened this issue 11 months ago

work around Clang bug

cbielow opened this pull request 11 months ago

always print error when MSGF+ fails

jpfeuffer opened this pull request 11 months ago

Follow a specification for fragment ion annotations

jpfeuffer opened this issue 11 months ago

move cwl generation into release action

timosachsenberg opened this issue 11 months ago

[FEATURE] z* and z' ions for ExD

jpfeuffer opened this pull request 11 months ago

Fix resampler

cbielow opened this pull request 11 months ago

vcpkg might have more requirements than our contrib

timosachsenberg opened this issue 11 months ago

Bump src/pyOpenMS/pyopenms-docs from `64016e7` to `5fc3503`

dependabot[bot] opened this pull request 11 months ago

OpenSWATH: Differences Between OSW and TSV File Contents

bruadi opened this issue 11 months ago

[FIX] TOPPView: fix crash when viewing certain Chromatograms

cbielow opened this pull request 11 months ago

terminate called after throwing an instance of 'std::length_error' what(): vector::_M_range_insert

AmmarkoV opened this issue 11 months ago

Support different proton abstracted, radicalized, ... c/z ions for ECD

jpfeuffer opened this issue 11 months ago

Handle coinor from brew as well

jpfeuffer opened this pull request 11 months ago

how to build pyopenms

JKVISION1101 opened this issue 11 months ago

Fix SpectrumAnnotator small metadata issue

jpfeuffer opened this pull request 11 months ago

Fix plotting.py for existing annotations from SpectrumAnnotator

jpfeuffer opened this pull request 11 months ago

pyopenms 3.1 not available for Silicon macs

jpfeuffer opened this issue 11 months ago