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

#7529 - Add zip option for packaging

Pull Request - State: open - Opened by t0mdavid-m 4 days ago - 7 comments
Labels: enhancement, Review effort [1-5]: 3

#7527 - KNIME Plugin needs update

Issue - State: open - Opened by cbielow 5 days ago

#7526 - Filtering by Scan Number not working as intended?

Issue - State: open - Opened by pesavent 6 days ago - 4 comments

#7525 - Porting from Qt5 to Qt6

Pull Request - State: open - Opened by cbielow 6 days ago - 8 comments

#7524 - Deprecate XTandemAdapter.cpp

Pull Request - State: closed - Opened by cbielow 8 days ago - 4 comments
Labels: Documentation, Review effort [1-5]: 1

#7523 - Update CHANGELOG

Pull Request - State: closed - Opened by timosachsenberg 8 days ago - 2 comments
Labels: Documentation, Review effort [1-5]: 1

#7522 - Pypifixes

Pull Request - State: closed - Opened by poshul 11 days ago - 3 comments
Labels: enhancement, Bug fix, Review effort [1-5]: 3

#7521 - Correct name of pyopenms-wheels-and-packages

Pull Request - State: closed - Opened by poshul 11 days ago - 2 comments
Labels: Review effort [1-5]: 1, configuration changes

#7520 - Update openms_ci_matrix_full.yml to properly set source archive name

Pull Request - State: closed - Opened by timosachsenberg 13 days ago - 3 comments
Labels: enhancement, Review effort [1-5]: 2, configuration changes

#7519 - Update pyopenms test actions

Pull Request - State: closed - Opened by matteopilz 13 days ago - 2 comments
Labels: enhancement, dependencies, Review effort [1-5]: 2

#7518 - use contrib from github

Pull Request - State: closed - Opened by timosachsenberg 13 days ago - 2 comments
Labels: enhancement, Review effort [1-5]: 2, configuration changes

#7517 - Fix install numpy <=1.26.4

Pull Request - State: closed - Opened by matteopilz 14 days ago - 2 comments
Labels: Bug fix, Review effort [1-5]: 1, configuration changes

#7516 - Numpy install 1.26.4 or earlier

Pull Request - State: closed - Opened by matteopilz 14 days ago - 3 comments
Labels: enhancement, Review effort [1-5]: 2, configuration changes

#7515 - Set pyopenms numpy install<2.0

Pull Request - State: closed - Opened by matteopilz 14 days ago - 3 comments
Labels: enhancement, Review effort [1-5]: 2, configuration changes

#7514 - Revert "Update test_pyopenms.yml"

Pull Request - State: closed - Opened by timosachsenberg 14 days ago - 2 comments
Labels: Review effort [1-5]: 1, configuration changes

#7513 - Update test_pyopenms.yml

Pull Request - State: closed - Opened by timosachsenberg 14 days ago - 2 comments
Labels: Review effort [1-5]: 1, configuration changes

#7512 - fix etcid encoding with supplemental cv term

Pull Request - State: closed - Opened by timosachsenberg 15 days ago - 2 comments
Labels: enhancement, Bug fix, Review effort [1-5]: 2

#7511 - Support or avoid numpy 2.0 in pyopenms

Issue - State: closed - Opened by timosachsenberg 15 days ago - 8 comments

#7510 - update PSI ontology

Pull Request - State: closed - Opened by timosachsenberg 15 days ago - 2 comments
Labels: enhancement, Bug fix, Review effort [1-5]: 4

#7509 - OpenSwathWorkflow command not found in Singularity

Issue - State: closed - Opened by HFan11 18 days ago - 1 comment

#7508 - parse relationship as xref

Pull Request - State: closed - Opened by timosachsenberg 18 days ago - 2 comments
Labels: enhancement, Review effort [1-5]: 3

#7507 - TOPPAS & SageAdapter

Issue - State: closed - Opened by TheB1307 18 days ago - 3 comments

#7506 - update PSI-MS.obo

Pull Request - State: closed - Opened by timosachsenberg 18 days ago - 7 comments
Labels: enhancement, Review effort [1-5]: 2, tests

#7505 - Revert "Update psi-ms.obo"

Pull Request - State: closed - Opened by timosachsenberg 18 days ago - 2 comments
Labels: Bug fix, Review effort [1-5]: 2

#7504 - remove deprecated doxygen thing

Pull Request - State: closed - Opened by poshul 18 days ago

#7503 - Build pyopenmswheels nightly

Pull Request - State: closed - Opened by poshul 18 days ago - 2 comments
Labels: enhancement, Review effort [1-5]: 2, configuration changes

#7502 - always install doxygen

Pull Request - State: closed - Opened by timosachsenberg 18 days ago - 2 comments
Labels: enhancement, Review effort [1-5]: 2, configuration changes

#7501 - Nightly build questions

Issue - State: open - Opened by jpfeuffer 20 days ago - 5 comments

#7500 - Update psi-ms.obo

Pull Request - State: closed - Opened by timosachsenberg 20 days ago - 2 comments
Labels: enhancement, Review effort [1-5]: 2

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

Issue - State: closed - Opened by rolivella 21 days ago - 16 comments

#7498 - Update percolator

Issue - State: open - Opened by timosachsenberg 27 days ago
Labels: critical

#7497 - Support output directories for TOPP tools and TOPPAS

Pull Request - State: open - Opened by cbielow 28 days ago - 12 comments

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

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

#7495 - Wrong retention time values

Issue - State: closed - Opened by luca-annecchino about 1 month ago - 1 comment

#7494 - What IDE do you recommend for developing and building openMS(C++) under macOS

Issue - State: closed - Opened by suhande about 1 month ago - 1 comment

#7493 - Update update_nightly.yml

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

#7491 - Wrap getvalidstrings

Pull Request - State: closed - Opened by poshul about 2 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 about 2 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 about 2 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] about 2 months ago - 1 comment
Labels: dependencies

#7487 - Comet search engines update.

Issue - State: open - Opened by ypriverol about 2 months ago

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

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

#7484 - fix compile warnings

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

#7483 - update citations

Pull Request - State: closed - Opened by timosachsenberg about 2 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 2 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 2 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] 2 months ago - 1 comment
Labels: dependencies

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

Pull Request - State: closed - Opened by dependabot[bot] 2 months ago - 1 comment
Labels: dependencies

#7478 - Update codium-pr-agent.yml

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

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

Pull Request - State: closed - Opened by dependabot[bot] 2 months ago
Labels: dependencies

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

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

#7475 - Pyopenms build fails due to recent refactors

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

#7473 - [refactor] Move deisotoping

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

#7472 - [refactor] rename FILTERING to PROCESSING

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

#7471 - [refactor] Move spectramerging

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

#7470 - [refactor] Move scaling

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

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

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

#7468 - OpenSwath uis score testing

Issue - State: open - Opened by jcharkow 2 months ago
Labels: OpenSWATH

#7466 - [refactor] remove msquantifications / mzquantml

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

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

Pull Request - State: closed - Opened by dependabot[bot] 2 months ago - 1 comment
Labels: dependencies

#7464 - bug fixes...

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

#7462 - Fix bug running TOPP tools in TOPPView.

Pull Request - State: closed - Opened by poshul 3 months ago - 1 comment

#7461 - [remove] standarddeclarations file

Pull Request - State: closed - Opened by timosachsenberg 3 months ago

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

Pull Request - State: closed - Opened by dependabot[bot] 3 months ago - 1 comment
Labels: dependencies

#7459 - [FEATURE] Binning and reporting of IonMobility

Pull Request - State: closed - Opened by cbielow 3 months ago - 1 comment

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

Pull Request - State: closed - Opened by timosachsenberg 3 months ago

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

Pull Request - State: closed - Opened by dependabot[bot] 3 months ago
Labels: dependencies

#7456 - Python 3.12 related fixes

Pull Request - State: closed - Opened by poshul 3 months ago - 11 comments

#7455 - Three twelve fixes

Pull Request - State: closed - Opened by poshul 3 months ago

#7454 - Create AssignSourceGroups.cmake

Pull Request - State: closed - Opened by timosachsenberg 3 months ago - 5 comments

#7453 - started to work on IM code in FFID

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

#7451 - [refactor] move interpolation code

Pull Request - State: closed - Opened by timosachsenberg 3 months ago

#7450 - [refactor] move regression code into ML

Pull Request - State: closed - Opened by timosachsenberg 3 months ago

#7449 - [refactor] Remove averagepos

Pull Request - State: closed - Opened by timosachsenberg 3 months ago

#7448 - [refactor] remove transformations folder

Pull Request - State: closed - Opened by timosachsenberg 3 months ago

#7447 - [refactor] flatten comparison

Pull Request - State: closed - Opened by timosachsenberg 3 months ago

#7446 - [refactor] move ROCcurve

Pull Request - State: closed - Opened by timosachsenberg 3 months ago - 1 comment

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

Pull Request - State: closed - Opened by timosachsenberg 3 months ago - 1 comment

#7444 - [refactor] move gridsearch to ML folder

Pull Request - State: closed - Opened by timosachsenberg 3 months ago - 1 comment

#7443 - [refactor] move peakpicker

Pull Request - State: closed - Opened by timosachsenberg 3 months ago - 1 comment

#7442 - [refactor] move binnedspectrum to kernel

Pull Request - State: closed - Opened by timosachsenberg 3 months ago - 1 comment

#7441 - adding RANSAC to ML folder

Pull Request - State: closed - Opened by timosachsenberg 3 months ago - 1 comment

#7440 - move svm and clustering to ml folder

Pull Request - State: closed - Opened by timosachsenberg 3 months ago - 2 comments

#7439 - FileConverter fails for symlinked raw input

Issue - State: open - Opened by bernt-matthias 3 months ago - 5 comments

#7438 - playground: change folder structure

Pull Request - State: closed - Opened by timosachsenberg 3 months ago
Labels: NoJenkins

#7437 - [remove] proteinresolver code

Pull Request - State: closed - Opened by timosachsenberg 3 months ago - 1 comment

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

Pull Request - State: closed - Opened by timosachsenberg 3 months ago - 1 comment

#7435 - prune the whole share for pyopenms

Pull Request - State: closed - Opened by poshul 3 months ago - 5 comments

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

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

#7433 - [REFACTOR] rename RAW2PEAK to CENTROIDING

Pull Request - State: closed - Opened by timosachsenberg 3 months ago

#7432 - Use system contrib libs for Mac wheel

Pull Request - State: closed - Opened by poshul 3 months ago - 2 comments

#7431 - Update python_versions.json

Pull Request - State: closed - Opened by timosachsenberg 3 months ago - 1 comment

#7430 - Bump version of checkout action

Pull Request - State: closed - Opened by poshul 3 months ago - 1 comment