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

[FEATURE] Concurrent MSGF+ database indexing

cbielow opened this pull request about 1 year ago

7 tests fail when using zlib-ng

tuliom opened this issue about 1 year ago

Update openms_ci_matrix_full.yml

poshul opened this pull request about 1 year ago

Bump brew python to 3.12

poshul opened this pull request about 1 year ago

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

timosachsenberg opened this pull request about 1 year ago

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

dependabot[bot] opened this pull request about 1 year ago

Delete cmake/Modules/FindHDF5.cmake

timosachsenberg opened this pull request about 1 year ago

add __repr__

timosachsenberg opened this pull request about 1 year ago

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

dependabot[bot] opened this pull request about 1 year ago

Aligning Parameters/ New SpectrumGenerator

Trapho opened this pull request about 1 year ago

support tools with multiple headers and cpp files

timosachsenberg opened this pull request about 1 year ago

Move CWL outputs to own build subfolder

jpfeuffer opened this issue about 1 year ago

Error report in XTandemAdapter, IDScoreSwitcher, and ProteomicsLFQ

liuxiawei opened this issue about 1 year ago

Add conversion for MSSpectrum & PeptideHit to spectrum_utils MsmsSpectrum

matteopilz opened this pull request about 1 year ago

Update TOPPAS tutorial

cbielow opened this pull request about 1 year ago

Run example TOPPAS workflows with CI

cbielow opened this issue about 1 year ago

our example mzML files could use an update

cbielow opened this issue about 1 year ago

Running MSGF+ in parallel crashes when input DB is new

cbielow opened this issue about 1 year ago

TOPPView: Running TOPP tools fails

cbielow opened this issue about 1 year ago

fix warning in traml handler

timosachsenberg opened this pull request about 1 year ago

The incomplete documentation makes beginners feel extremely difficult.

liuxiawei opened this issue about 1 year ago

Make ParamIterator a real iterator

timosachsenberg opened this issue about 1 year ago

fix doc

timosachsenberg opened this pull request about 1 year ago

Patch/extend osw output

jcharkow opened this pull request about 1 year ago

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

jpfeuffer opened this issue about 1 year ago

fix wrong OpenMP max_threads in OpenMSInfo TOPP tool

cbielow opened this pull request about 1 year ago

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

Allen188 opened this issue about 1 year ago

Check if this excludes vcpkg from dependabot.yml updates

timosachsenberg opened this pull request about 1 year ago

Bump vcpkg from `64ca152` to `e85cafa`

dependabot[bot] opened this pull request about 1 year ago

Plotting fix - matched peaks highlighting

matteopilz opened this pull request about 1 year ago

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

dependabot[bot] opened this pull request about 1 year ago

Check pyopenms compatibility with Cython < 3.0

jpfeuffer opened this issue about 1 year ago

more robust precursor purity (PR 3 of X)

timosachsenberg opened this pull request about 1 year ago

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

timosachsenberg opened this pull request about 1 year ago

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

timosachsenberg opened this pull request about 1 year ago

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

timosachsenberg opened this pull request about 1 year ago

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

timosachsenberg opened this pull request about 1 year ago

FindCOIN.cmake use imported targets

jpfeuffer opened this pull request about 1 year ago

SiriusAdapter replaced with SiriusExport and adaptations to AssayGeneratorMetabo

axelwalter opened this pull request about 1 year ago

Refactoring FragmentIndex

Trapho opened this pull request about 1 year ago

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

jpfeuffer opened this issue about 1 year ago

work around Clang bug

cbielow opened this pull request about 1 year ago

always print error when MSGF+ fails

jpfeuffer opened this pull request about 1 year ago

Follow a specification for fragment ion annotations

jpfeuffer opened this issue about 1 year ago

move cwl generation into release action

timosachsenberg opened this issue about 1 year ago

[FEATURE] z* and z' ions for ExD

jpfeuffer opened this pull request about 1 year ago

Fix resampler

cbielow opened this pull request about 1 year ago

vcpkg might have more requirements than our contrib

timosachsenberg opened this issue about 1 year ago

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

dependabot[bot] opened this pull request about 1 year ago

OpenSWATH: Differences Between OSW and TSV File Contents

bruadi opened this issue about 1 year ago

[FIX] TOPPView: fix crash when viewing certain Chromatograms

cbielow opened this pull request about 1 year ago

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

AmmarkoV opened this issue about 1 year ago

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

jpfeuffer opened this issue about 1 year ago

Handle coinor from brew as well

jpfeuffer opened this pull request about 1 year ago

how to build pyopenms

JKVISION1101 opened this issue about 1 year ago

Fix SpectrumAnnotator small metadata issue

jpfeuffer opened this pull request about 1 year ago

Fix plotting.py for existing annotations from SpectrumAnnotator

jpfeuffer opened this pull request about 1 year ago

pyopenms 3.1 not available for Silicon macs

jpfeuffer opened this issue about 1 year ago

[FIX] TOPPAS: open files in TOPPView

cbielow opened this pull request about 1 year ago

Update openms_ci_matrix_full.yml

poshul opened this pull request about 1 year ago

Resampler uses Da instead of PPM

cbielow opened this issue about 1 year ago

Release action

poshul opened this pull request about 1 year ago

Feature/csv comments

enetz opened this pull request about 1 year ago

[NOMERGE] Release3.0.0 winfix

cbielow opened this pull request about 1 year ago

[fix] add licenses for tool_description_lib

poshul opened this pull request about 1 year ago

NOP

timosachsenberg opened this issue about 1 year ago

Bump src/pyOpenMS/pyopenms-docs from `64016e7` to `16607af`

dependabot[bot] opened this pull request about 1 year ago

Install 3.x.0 for single user in windows doesn't create shortcuts

poshul opened this issue about 1 year ago

Improve spectrum visualization and also provide in streamlit template

timosachsenberg opened this issue about 1 year ago

Resolve KNIME THIRDPARTY issues

timosachsenberg opened this issue about 1 year ago

Host FLASHViewer

timosachsenberg opened this issue about 1 year ago

Review/Work on FragmentIndex PR

timosachsenberg opened this issue about 1 year ago

Replace SIRIUSAdapter with SIRIUSExporter, adapt AssayGeneratorMetabo and reimplement DIAMetalyzer workflow with it

timosachsenberg opened this issue about 1 year ago

Add mold linker

timosachsenberg opened this pull request about 1 year ago

Remove the rest of ERPairFinder

poshul opened this pull request about 1 year ago

Loading pepxml files : RuntimeError: the value 'B' was used but is not valid; Modification '': origin must be a letter from A to Y, excluding B and J.

coalooball opened this issue about 1 year ago

Bump src/pyOpenMS/pyopenms-docs from `64016e7` to `1d810ae`

dependabot[bot] opened this pull request about 1 year ago

[GHA] Overwrite 1k NSIS without prompt

poshul opened this pull request about 1 year ago

Update openms_ci_matrix_full.yml

poshul opened this pull request about 1 year ago

Win installer: check for correct NSIS version

cbielow opened this pull request about 1 year ago

Feature/includes

hroest opened this pull request about 1 year ago

[GHA] use custom NSIS for Windows installer

cbielow opened this pull request about 1 year ago

Fix win installer

cbielow opened this pull request about 1 year ago

Expose MetaboliteAdductDecharger functionality in pyOpenMS

timosachsenberg opened this issue about 1 year ago

Ontology based tool annotation

bernt-matthias opened this issue about 1 year ago

[CLEANUP] remove unused and outdated wavelet code

timosachsenberg opened this pull request about 1 year ago

rename peakpickermrm to peakpickerchromatogram

timosachsenberg opened this pull request about 1 year ago

fix some compile warnings and add sage citation

timosachsenberg opened this pull request about 1 year ago

[DOC] Annotate SpectraFilter tools

cbielow opened this pull request about 1 year ago

SageAdapter crashes

cbielow opened this issue about 1 year ago

suggestion: rename PeakPickerMRM to PeakPickerChromatogram

timosachsenberg opened this issue about 1 year ago

ParamEditor: Move getting-tags-part to avoid error from a node (subsection param)

JeeH-K opened this pull request about 1 year ago

Bump src/pyOpenMS/pyopenms-docs from `4bc75aa` to `64016e7`

dependabot[bot] opened this pull request about 1 year ago

IdentificationData bug

cbielow opened this issue about 1 year ago

EICExtractor use trapezoid integration

timosachsenberg opened this pull request about 1 year ago

[FIX] make FileConverter more robust

cbielow opened this pull request about 1 year ago

Fix PyPi Publish Warnings

matteopilz opened this pull request about 1 year ago

Update python_versions.json to rotate with 3.12

jpfeuffer opened this pull request about 1 year ago

Bump src/pyOpenMS/pyopenms-docs from `b44adfe` to `4bc75aa`

dependabot[bot] opened this pull request about 1 year ago

fix compile error in MzQCFile.cpp for clang11(linux)

cbielow opened this pull request about 1 year ago