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

OpenSwath uis score testing

jcharkow opened this issue 8 months ago

[refactor] SpectraFilterScaler and rename Scaler to RankScaler

timosachsenberg opened this pull request 8 months ago

[refactor] remove msquantifications / mzquantml

timosachsenberg opened this pull request 8 months ago

Bump contrib from `8d83037` to `ea62162`

dependabot[bot] opened this pull request 8 months ago

bug fixes...

cbielow opened this pull request 8 months ago

[refactor] remove or hide redundant identification classes

timosachsenberg opened this pull request 8 months ago

Fix bug running TOPP tools in TOPPView.

poshul opened this pull request 8 months ago

[remove] standarddeclarations file

timosachsenberg opened this pull request 8 months ago

Bump contrib from `8d83037` to `00c21bb`

dependabot[bot] opened this pull request 8 months ago

[FEATURE] Binning and reporting of IonMobility

cbielow opened this pull request 8 months ago

[refactor] remove old filter code (de novo low res)

timosachsenberg opened this pull request 8 months ago

Bump contrib from `5545518` to `8d83037`

dependabot[bot] opened this pull request 8 months ago

Python 3.12 related fixes

poshul opened this pull request 8 months ago

Three twelve fixes

poshul opened this pull request 8 months ago

Create AssignSourceGroups.cmake

timosachsenberg opened this pull request 8 months ago

started to work on IM code in FFID

timosachsenberg opened this pull request 8 months ago

[refactor] move statistics and math funcitons into math root

timosachsenberg opened this pull request 8 months ago

[refactor] move interpolation code

timosachsenberg opened this pull request 8 months ago

[refactor] move regression code into ML

timosachsenberg opened this pull request 8 months ago

[refactor] Remove averagepos

timosachsenberg opened this pull request 8 months ago

[refactor] remove transformations folder

timosachsenberg opened this pull request 8 months ago

[refactor] flatten comparison

timosachsenberg opened this pull request 8 months ago

[refactor] move ROCcurve

timosachsenberg opened this pull request 8 months ago

[refactor] mv MSNumpress from math to format

timosachsenberg opened this pull request 8 months ago

[refactor] move gridsearch to ML folder

timosachsenberg opened this pull request 8 months ago

[refactor] move peakpicker

timosachsenberg opened this pull request 8 months ago

[refactor] move binnedspectrum to kernel

timosachsenberg opened this pull request 8 months ago

adding RANSAC to ML folder

timosachsenberg opened this pull request 8 months ago

move svm and clustering to ml folder

timosachsenberg opened this pull request 8 months ago

FileConverter fails for symlinked raw input

bernt-matthias opened this issue 8 months ago

playground: change folder structure

timosachsenberg opened this pull request 8 months ago

[remove] proteinresolver code

timosachsenberg opened this pull request 9 months ago

[remove] PSProteinInference (parsimony-based approach)

timosachsenberg opened this pull request 9 months ago

prune the whole share for pyopenms

poshul opened this pull request 9 months ago

question: feasible to update to newer manylinux?

timosachsenberg opened this issue 9 months ago

[REFACTOR] rename RAW2PEAK to CENTROIDING

timosachsenberg opened this pull request 9 months ago

Use system contrib libs for Mac wheel

poshul opened this pull request 9 months ago

Update python_versions.json

timosachsenberg opened this pull request 9 months ago

Bump version of checkout action

poshul opened this pull request 9 months ago

Add RNAse T1 + Phosphatase as an enzyme choice.

poshul opened this pull request 9 months ago

Debian package download stalling

jpfeuffer opened this issue 9 months ago

[FEATURE/FIX] TOPPView can show MSn ion mobility frames

cbielow opened this pull request 9 months ago

[TOPPView] showing an Ion mobility frame with MS level = 2 fails

cbielow opened this issue 9 months ago

export IM from sage

timosachsenberg opened this pull request 9 months ago

fix windows build error

cbielow opened this pull request 9 months ago

[FEATURE, API] TOPPView: offer Ion mobility view from 2D spectra view

cbielow opened this pull request 9 months ago

Standarizing enzymes for three major search engines COMET MSGF+ and SAGE

ypriverol opened this pull request 9 months ago

[refactor] move SVM from ANALYSIS to MATH folder

timosachsenberg opened this pull request 9 months ago

[quantms,core] add IM support to FeatureFInderIdentification and FeaturteFinderMetaboIdent

timosachsenberg opened this issue 9 months ago

The tests for mono fails in gitpod because mono is not installed

ypriverol opened this issue 9 months ago

pyOpenMS: Log warnings in pure Python code with warnings.warn instead of print

RalfG opened this pull request 9 months ago

pyopenms and nightly update CI broken

jpfeuffer opened this issue 9 months ago

pyopenms build failing in windows. (unresolved external symbol "__declspec(dllimport) public:)

JKVISION1101 opened this issue 9 months ago

MSGF+ min_peaks option added

ypriverol opened this pull request 9 months ago

experimental design file

josephineabighanem opened this issue 9 months ago

remove weightwrapper

timosachsenberg opened this pull request 9 months ago

remove simple pair finder

timosachsenberg opened this pull request 9 months ago

remove unneeded includes

timosachsenberg opened this pull request 9 months ago

removed some of the left overs

timosachsenberg opened this pull request 9 months ago

remove TypeAsString

timosachsenberg opened this pull request 9 months ago

windows builds failing. contrib not found (probably IT again)

timosachsenberg opened this issue 9 months ago

remove old denovo marker code

timosachsenberg opened this pull request 9 months ago

remove PeakPickerMaxima

timosachsenberg opened this pull request 9 months ago

[Fix] Remove unused pxd file

axelwalter opened this pull request 9 months ago

fix python types

cbielow opened this pull request 9 months ago

remove proton distribution model

timosachsenberg opened this pull request 9 months ago

Remove old hidden markov model code

timosachsenberg opened this pull request 9 months ago

[FIX] Warn use of bitwise '&' with boolean operands

jpfeuffer opened this pull request 9 months ago

[Fix] GHA MacOS python brew problem

jpfeuffer opened this pull request 9 months ago

MacOS CI failing due to brew+GHA python conflict

jpfeuffer opened this issue 9 months ago

[INTERNAL] Simplify how custom OpenMS types are defined

cbielow opened this pull request 9 months ago

Update existing C++ tutorials

cbielow opened this pull request 9 months ago

[DOC] Ion mobility converter: clarification of input-output data

cbielow opened this pull request 10 months ago

make pyopenms compile again

timosachsenberg opened this pull request 10 months ago

Bump src/pyOpenMS/pyopenms-docs from `e75ffd0` to `df06fc8`

dependabot[bot] opened this pull request 10 months ago

question: how to adapt MatrixDouble.pyx

timosachsenberg opened this issue 10 months ago

Nightly installers aren't getting linked to their respective 'latest'

poshul opened this issue 10 months ago

Remove unnecessary redeclaration of KNIME version

poshul opened this pull request 10 months ago

Revert to targeting KNIME 5.1

poshul opened this pull request 10 months ago

Only try to download the changelog if do_release

poshul opened this pull request 10 months ago

Trigger openms-ci-full after merging from develop

poshul opened this pull request 10 months ago

Update pyopenms-wheels.yml with latest *-artifacts action version

poshul opened this pull request 10 months ago

Bump github-actions-cpu-cores version

poshul opened this pull request 10 months ago

Is it possible to run MSFraggerAdapter as a "Quick scan" workflow?

rolivella opened this issue 10 months ago

[DOC] update citation from OpenMS 2 --> 3

cbielow opened this pull request 10 months ago

Bump src/pyOpenMS/pyopenms-docs from `6a0aab2` to `e75ffd0`

dependabot[bot] opened this pull request 10 months ago

TargetedFileConverter issue

Droslj opened this issue 10 months ago

mzML writer: check that output file is a proper file

sneumann opened this issue 10 months ago

Update openms_ci_matrix_full.yml

timosachsenberg opened this pull request 10 months ago

Update openms_ci_matrix_full.yml

timosachsenberg opened this pull request 10 months ago

attempt to install eigen from chocolatey

timosachsenberg opened this pull request 10 months ago

Update MatrixUtils.h with correct(?) eigen include path

timosachsenberg opened this pull request 10 months ago

mzML writer: no valid checksum

sneumann opened this issue 10 months ago

Think about building develop from time to time for ccache

jpfeuffer opened this issue 10 months ago

Use v4 artifacts in GHA

jpfeuffer opened this issue 10 months ago

SIRIUS output reader fails (SiriusMzTabWriter.read, CsiFingerIdMzTabWriter.read)

NilouJ opened this issue 10 months ago

Bump contrib from `04d64c6` to `5545518`

dependabot[bot] opened this pull request 10 months ago

Update openms_ci_matrix_full.yml

poshul opened this pull request 10 months ago

Merge latest release into develop

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

Merge latest release into develop

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