Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / OpenMS/OpenMS issues and pull requests

#7499 - How to select ETCID activation for a TRFP mzML file?

Issue - State: closed - Opened by rolivella 4 months ago - 18 comments

#7498 - Update percolator

Issue - State: open - Opened by timosachsenberg 4 months ago
Labels: critical

#7497 - Support output directories for TOPP tools and TOPPAS

Pull Request - State: open - Opened by cbielow 4 months ago - 14 comments

#7496 - Bump THIRDPARTY from `12eb8d3` to `d6594eb`

Pull Request - State: closed - Opened by dependabot[bot] 4 months ago - 1 comment
Labels: dependencies

#7495 - Wrong retention time values

Issue - State: closed - Opened by luca-annecchino 4 months ago - 1 comment

#7493 - Update update_nightly.yml

Pull Request - State: closed - Opened by poshul 5 months ago - 6 comments
Labels: enhancement, Review effort [1-5]: 2

#7492 - make more parameters advanced in MetaProSIP

Pull Request - State: closed - Opened by timosachsenberg 5 months ago - 11 comments
Labels: enhancement, Review effort [1-5]: 2

#7491 - Wrap getvalidstrings

Pull Request - State: closed - Opened by poshul 5 months ago - 7 comments
Labels: enhancement, Review effort [1-5]: 2

#7490 - make IonName(s) consistent. remove old fragmentselectioncode

Pull Request - State: closed - Opened by timosachsenberg 5 months ago - 9 comments
Labels: enhancement, Review effort [1-5]: 3, bug_fix

#7489 - [Feature] Export ion annotations for MSSpectrum DataFrame

Pull Request - State: closed - Opened by axelwalter 5 months ago - 4 comments
Labels: enhancement, Review effort [1-5]: 3, tests

#7488 - Bump src/pyOpenMS/pyopenms-docs from `df06fc8` to `9875a9e`

Pull Request - State: closed - Opened by dependabot[bot] 5 months ago - 1 comment
Labels: dependencies

#7487 - Comet search engines update.

Issue - State: open - Opened by ypriverol 5 months ago

#7486 - Added support for RNAse4 digestion of RNA. Fixed buggy regex for prot…

Pull Request - State: closed - Opened by poshul 5 months ago - 7 comments
Labels: enhancement, Review effort [1-5]: 3, bug_fix

#7485 - Use macos-13 runner as it's the last x86 mac one

Pull Request - State: closed - Opened by poshul 5 months ago - 15 comments
Labels: enhancement, Review effort [1-5]: 2

#7484 - fix compile warnings

Pull Request - State: closed - Opened by timosachsenberg 5 months ago - 6 comments
Labels: Review effort [1-5]: 2, bug_fix

#7483 - update citations

Pull Request - State: closed - Opened by timosachsenberg 5 months ago - 7 comments
Labels: enhancement, Review effort [1-5]: 2

#7482 - Move contrib from abibuilder to GitHub

Pull Request - State: closed - Opened by t0mdavid-m 5 months ago - 6 comments
Labels: enhancement, Review effort [1-5]: 2

#7481 - [Feature] DataFrame export for MSSpectrum and MSChromatogram

Pull Request - State: closed - Opened by axelwalter 5 months ago - 9 comments
Labels: enhancement, Review effort [1-5]: 4, tests

#7480 - Bump THIRDPARTY from `947b56a` to `12eb8d3`

Pull Request - State: closed - Opened by dependabot[bot] 5 months ago - 1 comment
Labels: dependencies

#7479 - Bump contrib from `f2053b2` to `b786ca3`

Pull Request - State: closed - Opened by dependabot[bot] 5 months ago - 1 comment
Labels: dependencies

#7478 - Update codium-pr-agent.yml

Pull Request - State: closed - Opened by timosachsenberg 5 months ago

#7477 - Bump contrib from `5545518` to `f2053b2`

Pull Request - State: closed - Opened by dependabot[bot] 5 months ago
Labels: dependencies

#7476 - remove some old files, script for unused test files

Pull Request - State: closed - Opened by timosachsenberg 5 months ago

#7475 - Pyopenms build fails due to recent refactors

Issue - State: closed - Opened by jpfeuffer 5 months ago - 2 comments
Labels: blocker

#7473 - [refactor] Move deisotoping

Pull Request - State: closed - Opened by timosachsenberg 5 months ago

#7472 - [refactor] rename FILTERING to PROCESSING

Pull Request - State: closed - Opened by timosachsenberg 5 months ago

#7471 - [refactor] Move spectramerging

Pull Request - State: closed - Opened by timosachsenberg 5 months ago

#7470 - [refactor] Move scaling

Pull Request - State: closed - Opened by timosachsenberg 5 months ago

#7469 - [refactor] move resampling code to separate folder

Pull Request - State: closed - Opened by timosachsenberg 5 months ago

#7468 - OpenSwath uis score testing

Issue - State: open - Opened by jcharkow 6 months ago - 16 comments
Labels: OpenSWATH

#7466 - [refactor] remove msquantifications / mzquantml

Pull Request - State: closed - Opened by timosachsenberg 6 months ago

#7465 - Bump contrib from `8d83037` to `ea62162`

Pull Request - State: closed - Opened by dependabot[bot] 6 months ago - 1 comment
Labels: dependencies

#7464 - bug fixes...

Pull Request - State: closed - Opened by cbielow 6 months ago

#7462 - Fix bug running TOPP tools in TOPPView.

Pull Request - State: closed - Opened by poshul 6 months ago - 1 comment

#7461 - [remove] standarddeclarations file

Pull Request - State: closed - Opened by timosachsenberg 6 months ago

#7460 - Bump contrib from `8d83037` to `00c21bb`

Pull Request - State: closed - Opened by dependabot[bot] 6 months ago - 1 comment
Labels: dependencies

#7459 - [FEATURE] Binning and reporting of IonMobility

Pull Request - State: closed - Opened by cbielow 6 months ago - 1 comment

#7458 - [refactor] remove old filter code (de novo low res)

Pull Request - State: closed - Opened by timosachsenberg 6 months ago

#7457 - Bump contrib from `5545518` to `8d83037`

Pull Request - State: closed - Opened by dependabot[bot] 6 months ago
Labels: dependencies

#7456 - Python 3.12 related fixes

Pull Request - State: closed - Opened by poshul 6 months ago - 11 comments

#7455 - Three twelve fixes

Pull Request - State: closed - Opened by poshul 6 months ago

#7454 - Create AssignSourceGroups.cmake

Pull Request - State: closed - Opened by timosachsenberg 6 months ago - 5 comments

#7453 - started to work on IM code in FFID

Pull Request - State: open - Opened by timosachsenberg 6 months ago - 5 comments
Labels: enhancement, Review effort [1-5]: 3

#7451 - [refactor] move interpolation code

Pull Request - State: closed - Opened by timosachsenberg 6 months ago

#7450 - [refactor] move regression code into ML

Pull Request - State: closed - Opened by timosachsenberg 6 months ago

#7449 - [refactor] Remove averagepos

Pull Request - State: closed - Opened by timosachsenberg 6 months ago

#7448 - [refactor] remove transformations folder

Pull Request - State: closed - Opened by timosachsenberg 6 months ago

#7447 - [refactor] flatten comparison

Pull Request - State: closed - Opened by timosachsenberg 6 months ago

#7446 - [refactor] move ROCcurve

Pull Request - State: closed - Opened by timosachsenberg 6 months ago - 1 comment

#7445 - [refactor] mv MSNumpress from math to format

Pull Request - State: closed - Opened by timosachsenberg 6 months ago - 1 comment

#7444 - [refactor] move gridsearch to ML folder

Pull Request - State: closed - Opened by timosachsenberg 6 months ago - 1 comment

#7443 - [refactor] move peakpicker

Pull Request - State: closed - Opened by timosachsenberg 6 months ago - 1 comment

#7442 - [refactor] move binnedspectrum to kernel

Pull Request - State: closed - Opened by timosachsenberg 6 months ago - 1 comment

#7441 - adding RANSAC to ML folder

Pull Request - State: closed - Opened by timosachsenberg 6 months ago - 1 comment

#7440 - move svm and clustering to ml folder

Pull Request - State: closed - Opened by timosachsenberg 6 months ago - 2 comments

#7439 - FileConverter fails for symlinked raw input

Issue - State: open - Opened by bernt-matthias 6 months ago - 7 comments

#7438 - playground: change folder structure

Pull Request - State: closed - Opened by timosachsenberg 6 months ago
Labels: NoJenkins

#7437 - [remove] proteinresolver code

Pull Request - State: closed - Opened by timosachsenberg 6 months ago - 1 comment

#7436 - [remove] PSProteinInference (parsimony-based approach)

Pull Request - State: closed - Opened by timosachsenberg 6 months ago - 1 comment

#7435 - prune the whole share for pyopenms

Pull Request - State: closed - Opened by poshul 6 months ago - 5 comments

#7434 - question: feasible to update to newer manylinux?

Issue - State: closed - Opened by timosachsenberg 6 months ago - 3 comments

#7433 - [REFACTOR] rename RAW2PEAK to CENTROIDING

Pull Request - State: closed - Opened by timosachsenberg 6 months ago

#7432 - Use system contrib libs for Mac wheel

Pull Request - State: closed - Opened by poshul 6 months ago - 2 comments

#7431 - Update python_versions.json

Pull Request - State: closed - Opened by timosachsenberg 6 months ago - 1 comment

#7430 - Bump version of checkout action

Pull Request - State: closed - Opened by poshul 6 months ago - 1 comment

#7429 - Add RNAse T1 + Phosphatase as an enzyme choice.

Pull Request - State: closed - Opened by poshul 6 months ago - 1 comment

#7428 - Debian package download stalling

Issue - State: closed - Opened by jpfeuffer 6 months ago - 3 comments
Labels: BinaryPackages, blocker

#7427 - [FEATURE/FIX] TOPPView can show MSn ion mobility frames

Pull Request - State: closed - Opened by cbielow 6 months ago - 3 comments

#7426 - [TOPPView] showing an Ion mobility frame with MS level = 2 fails

Issue - State: closed - Opened by cbielow 6 months ago - 1 comment

#7425 - export IM from sage

Pull Request - State: closed - Opened by timosachsenberg 6 months ago - 2 comments

#7424 - fix windows build error

Pull Request - State: closed - Opened by cbielow 6 months ago - 4 comments

#7422 - Standarizing enzymes for three major search engines COMET MSGF+ and SAGE

Pull Request - State: closed - Opened by ypriverol 6 months ago - 1 comment

#7421 - [refactor] move SVM from ANALYSIS to MATH folder

Pull Request - State: closed - Opened by timosachsenberg 6 months ago - 1 comment

#7419 - The tests for mono fails in gitpod because mono is not installed

Issue - State: closed - Opened by ypriverol 6 months ago - 2 comments

#7418 - pyOpenMS: Log warnings in pure Python code with warnings.warn instead of print

Pull Request - State: closed - Opened by RalfG 6 months ago - 3 comments

#7417 - pyopenms and nightly update CI broken

Issue - State: closed - Opened by jpfeuffer 6 months ago - 4 comments
Labels: major

#7414 - MSGF+ min_peaks option added

Pull Request - State: closed - Opened by ypriverol 6 months ago - 3 comments

#7413 - experimental design file

Issue - State: open - Opened by josephineabighanem 6 months ago

#7412 - remove weightwrapper

Pull Request - State: closed - Opened by timosachsenberg 6 months ago

#7411 - remove simple pair finder

Pull Request - State: closed - Opened by timosachsenberg 6 months ago

#7410 - remove unneeded includes

Pull Request - State: closed - Opened by timosachsenberg 6 months ago

#7409 - removed some of the left overs

Pull Request - State: closed - Opened by timosachsenberg 6 months ago

#7408 - remove TypeAsString

Pull Request - State: closed - Opened by timosachsenberg 6 months ago

#7406 - remove old denovo marker code

Pull Request - State: closed - Opened by timosachsenberg 7 months ago

#7405 - remove PeakPickerMaxima

Pull Request - State: closed - Opened by timosachsenberg 7 months ago

#7404 - [Fix] Remove unused pxd file

Pull Request - State: closed - Opened by axelwalter 7 months ago

#7403 - fix python types

Pull Request - State: closed - Opened by cbielow 7 months ago - 2 comments

#7402 - remove proton distribution model

Pull Request - State: closed - Opened by timosachsenberg 7 months ago

#7401 - Remove old hidden markov model code

Pull Request - State: closed - Opened by timosachsenberg 7 months ago

#7400 - [FIX] Warn use of bitwise '&' with boolean operands

Pull Request - State: closed - Opened by jpfeuffer 7 months ago

#7399 - [Fix] GHA MacOS python brew problem

Pull Request - State: closed - Opened by jpfeuffer 7 months ago