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

Update pyopenms test actions

matteopilz opened this pull request 4 months ago

use contrib from github

timosachsenberg opened this pull request 4 months ago

Fix install numpy <=1.26.4

matteopilz opened this pull request 4 months ago

Numpy install 1.26.4 or earlier

matteopilz opened this pull request 4 months ago

Set pyopenms numpy install<2.0

matteopilz opened this pull request 4 months ago

Revert "Update test_pyopenms.yml"

timosachsenberg opened this pull request 4 months ago

Update test_pyopenms.yml

timosachsenberg opened this pull request 4 months ago

fix etcid encoding with supplemental cv term

timosachsenberg opened this pull request 4 months ago

Support or avoid numpy 2.0 in pyopenms

timosachsenberg opened this issue 4 months ago

update PSI ontology

timosachsenberg opened this pull request 4 months ago

OpenSwathWorkflow command not found in Singularity

HFan11 opened this issue 4 months ago

parse relationship as xref

timosachsenberg opened this pull request 4 months ago

TOPPAS & SageAdapter

TheB1307 opened this issue 4 months ago

update PSI-MS.obo

timosachsenberg opened this pull request 4 months ago

Revert "Update psi-ms.obo"

timosachsenberg opened this pull request 4 months ago

remove deprecated doxygen \includedoc

poshul opened this pull request 4 months ago

Build pyopenmswheels nightly

poshul opened this pull request 4 months ago

always install doxygen

timosachsenberg opened this pull request 4 months ago

Nightly build questions

jpfeuffer opened this issue 4 months ago

Update psi-ms.obo

timosachsenberg opened this pull request 4 months ago

How to select ETCID activation for a TRFP mzML file?

rolivella opened this issue 4 months ago

Update percolator

timosachsenberg opened this issue 5 months ago

Support output directories for TOPP tools and TOPPAS

cbielow opened this pull request 5 months ago

Bump THIRDPARTY from `12eb8d3` to `d6594eb`

dependabot[bot] opened this pull request 5 months ago

Wrong retention time values

luca-annecchino opened this issue 5 months ago

What IDE do you recommend for developing and building openMS(C++) under macOS

suhande opened this issue 5 months ago

Update update_nightly.yml

poshul opened this pull request 5 months ago

make more parameters advanced in MetaProSIP

timosachsenberg opened this pull request 5 months ago

Wrap getvalidstrings

poshul opened this pull request 5 months ago

make IonName(s) consistent. remove old fragmentselectioncode

timosachsenberg opened this pull request 5 months ago

[Feature] Export ion annotations for MSSpectrum DataFrame

axelwalter opened this pull request 5 months ago

Bump src/pyOpenMS/pyopenms-docs from `df06fc8` to `9875a9e`

dependabot[bot] opened this pull request 5 months ago

Comet search engines update.

ypriverol opened this issue 5 months ago

Added support for RNAse4 digestion of RNA. Fixed buggy regex for prot…

poshul opened this pull request 6 months ago

Use macos-13 runner as it's the last x86 mac one

poshul opened this pull request 6 months ago

fix compile warnings

timosachsenberg opened this pull request 6 months ago

update citations

timosachsenberg opened this pull request 6 months ago

Move contrib from abibuilder to GitHub

t0mdavid-m opened this pull request 6 months ago

[Feature] DataFrame export for MSSpectrum and MSChromatogram

axelwalter opened this pull request 6 months ago

Bump THIRDPARTY from `947b56a` to `12eb8d3`

dependabot[bot] opened this pull request 6 months ago

Bump contrib from `f2053b2` to `b786ca3`

dependabot[bot] opened this pull request 6 months ago

Update codium-pr-agent.yml

timosachsenberg opened this pull request 6 months ago

Bump contrib from `5545518` to `f2053b2`

dependabot[bot] opened this pull request 6 months ago

remove some old files, script for unused test files

timosachsenberg opened this pull request 6 months ago

Pyopenms build fails due to recent refactors

jpfeuffer opened this issue 6 months ago

[refactor] merge some ff centroided classes into one file. remove FeatureFinderMRM

timosachsenberg opened this pull request 6 months ago

[refactor] Move deisotoping

timosachsenberg opened this pull request 6 months ago

[refactor] rename FILTERING to PROCESSING

timosachsenberg opened this pull request 6 months ago

[refactor] Move spectramerging

timosachsenberg opened this pull request 6 months ago

[refactor] Move scaling

timosachsenberg opened this pull request 6 months ago

[refactor] move resampling code to separate folder

timosachsenberg opened this pull request 6 months ago

OpenSwath uis score testing

jcharkow opened this issue 6 months ago

[refactor] SpectraFilterScaler and rename Scaler to RankScaler

timosachsenberg opened this pull request 6 months ago

[refactor] remove msquantifications / mzquantml

timosachsenberg opened this pull request 6 months ago

Bump contrib from `8d83037` to `ea62162`

dependabot[bot] opened this pull request 6 months ago

bug fixes...

cbielow opened this pull request 6 months ago

[refactor] remove or hide redundant identification classes

timosachsenberg opened this pull request 6 months ago

Fix bug running TOPP tools in TOPPView.

poshul opened this pull request 6 months ago

[remove] standarddeclarations file

timosachsenberg opened this pull request 6 months ago

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

dependabot[bot] opened this pull request 6 months ago

[FEATURE] Binning and reporting of IonMobility

cbielow opened this pull request 6 months ago

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

timosachsenberg opened this pull request 6 months ago

Bump contrib from `5545518` to `8d83037`

dependabot[bot] opened this pull request 6 months ago

Python 3.12 related fixes

poshul opened this pull request 6 months ago

Three twelve fixes

poshul opened this pull request 6 months ago

Create AssignSourceGroups.cmake

timosachsenberg opened this pull request 6 months ago

started to work on IM code in FFID

timosachsenberg opened this pull request 6 months ago

[refactor] move statistics and math funcitons into math root

timosachsenberg opened this pull request 6 months ago

[refactor] move interpolation code

timosachsenberg opened this pull request 6 months ago

[refactor] move regression code into ML

timosachsenberg opened this pull request 6 months ago

[refactor] Remove averagepos

timosachsenberg opened this pull request 6 months ago

[refactor] remove transformations folder

timosachsenberg opened this pull request 6 months ago

[refactor] flatten comparison

timosachsenberg opened this pull request 6 months ago

[refactor] move ROCcurve

timosachsenberg opened this pull request 6 months ago

[refactor] mv MSNumpress from math to format

timosachsenberg opened this pull request 6 months ago

[refactor] move gridsearch to ML folder

timosachsenberg opened this pull request 6 months ago

[refactor] move peakpicker

timosachsenberg opened this pull request 6 months ago

[refactor] move binnedspectrum to kernel

timosachsenberg opened this pull request 6 months ago

adding RANSAC to ML folder

timosachsenberg opened this pull request 6 months ago

move svm and clustering to ml folder

timosachsenberg opened this pull request 6 months ago

FileConverter fails for symlinked raw input

bernt-matthias opened this issue 6 months ago

playground: change folder structure

timosachsenberg opened this pull request 6 months ago

[remove] proteinresolver code

timosachsenberg opened this pull request 6 months ago

[remove] PSProteinInference (parsimony-based approach)

timosachsenberg opened this pull request 6 months ago

prune the whole share for pyopenms

poshul opened this pull request 6 months ago

question: feasible to update to newer manylinux?

timosachsenberg opened this issue 6 months ago

[REFACTOR] rename RAW2PEAK to CENTROIDING

timosachsenberg opened this pull request 6 months ago

Use system contrib libs for Mac wheel

poshul opened this pull request 6 months ago

Update python_versions.json

timosachsenberg opened this pull request 6 months ago

Bump version of checkout action

poshul opened this pull request 6 months ago

Add RNAse T1 + Phosphatase as an enzyme choice.

poshul opened this pull request 6 months ago

Debian package download stalling

jpfeuffer opened this issue 6 months ago

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

cbielow opened this pull request 7 months ago

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

cbielow opened this issue 7 months ago

export IM from sage

timosachsenberg opened this pull request 7 months ago

fix windows build error

cbielow opened this pull request 7 months ago

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

cbielow opened this pull request 7 months ago

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

ypriverol opened this pull request 7 months ago

[refactor] move SVM from ANALYSIS to MATH folder

timosachsenberg opened this pull request 7 months ago

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

timosachsenberg opened this issue 7 months ago