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

#7674 - TRFP update test file

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

#7673 - fix TRFP

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

#7672 - Wheels on pr

Pull Request - State: open - Opened by poshul 5 days ago - 9 comments
Labels: Review effort [1-5]: 3

#7671 - Fix RPATH creation in deb package

Pull Request - State: closed - Opened by poshul 6 days ago - 16 comments
Labels: Review effort [1-5]: 2

#7670 - add additional wrapper and fix test

Pull Request - State: closed - Opened by timosachsenberg 6 days ago - 2 comments
Labels: Review effort [1-5]: 3

#7669 - [DOC] Include common CMake flags documentation as doxygen

Pull Request - State: closed - Opened by pjones 8 days ago - 3 comments
Labels: Review effort [1-5]: 1

#7668 - View changes between NuXL branch and develop

Pull Request - State: open - Opened by timosachsenberg 8 days ago

#7667 - Bump src/pyOpenMS/pyopenms-docs from `63fdab2` to `c9b8e09`

Pull Request - State: closed - Opened by dependabot[bot] 11 days ago - 1 comment
Labels: dependencies

#7666 - Pyopenms aaseq

Pull Request - State: open - Opened by jcharkow 11 days ago

#7664 - Pre 3.3 fixes

Pull Request - State: open - Opened by poshul 11 days ago - 3 comments
Labels: Review effort [1-5]: 3

#7663 - enable ms1 code

Pull Request - State: open - Opened by timosachsenberg 11 days ago - 8 comments
Labels: Review effort [1-5]: 2

#7662 - question: role of disabled SWATH code

Issue - State: open - Opened by timosachsenberg 11 days ago

#7661 - Merge to build wheels

Pull Request - State: closed - Opened by poshul 12 days ago

#7660 - add trivial devcontainer config

Pull Request - State: closed - Opened by poshul 12 days ago - 11 comments
Labels: Review effort [1-5]: 1

#7659 - Bump src/pyOpenMS/pyopenms-docs from `63fdab2` to `5c5dfc1`

Pull Request - State: closed - Opened by dependabot[bot] 12 days ago - 2 comments
Labels: dependencies

#7658 - [refactor] removed legacy SWATH chromatogram extraction code

Pull Request - State: closed - Opened by timosachsenberg 12 days ago - 10 comments
Labels: Review effort [1-5]: 3

#7657 - revert small change in MSstatsFile.cpp

Pull Request - State: closed - Opened by timosachsenberg 12 days ago - 4 comments
Labels: Review effort [1-5]: 2

#7656 - Test changes from 3.2

Pull Request - State: closed - Opened by poshul 12 days ago - 2 comments
Labels: Review effort [1-5]: 4

#7655 - Setting up local runners for GHA

Issue - State: open - Opened by poshul 12 days ago - 3 comments

#7654 - fix some warnings

Pull Request - State: closed - Opened by jpfeuffer 13 days ago - 7 comments
Labels: Review effort [1-5]: 2

#7653 - Wheels not getting built with OpenMP

Issue - State: open - Opened by poshul 13 days ago - 2 comments

#7650 - more convenient constructor for AASequence in Python

Pull Request - State: closed - Opened by timosachsenberg 14 days ago - 28 comments
Labels: Review effort [1-5]: 3

#7649 - fix test_equal code (allow comparison of enums)

Pull Request - State: closed - Opened by timosachsenberg 15 days ago - 8 comments
Labels: Review effort [1-5]: 2

#7648 - fix warning in DatabaseFilter.cpp

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

#7647 - Wrap static AASequence::fromString() for easier use in python

Issue - State: closed - Opened by timosachsenberg 15 days ago - 4 comments

#7646 - test: update tests for MRMTransitionGroup

Pull Request - State: closed - Opened by jcharkow 15 days ago

#7645 - improve file list comparison

Pull Request - State: closed - Opened by timosachsenberg 15 days ago - 2 comments
Labels: Review effort [1-5]: 3

#7644 - Non-fatal errors in comet

Issue - State: open - Opened by timosachsenberg 15 days ago - 5 comments

#7643 - added annotate_features param in Deisotoper.cpp

Pull Request - State: closed - Opened by anamaria-uofg 19 days ago - 6 comments
Labels: Review effort [1-5]: 2

#7642 - Enhancements and code simplifications in various files

Pull Request - State: closed - Opened by timosachsenberg 19 days ago - 5 comments
Labels: Review effort [1-5]: 4

#7641 - NASequence.fromString phosphothiolate

Issue - State: closed - Opened by Scott1451 20 days ago - 3 comments

#7640 - Epifany score error

Issue - State: closed - Opened by prvst 21 days ago - 3 comments

#7639 - Correctly do the unit tests in pyopenms-wheels

Pull Request - State: closed - Opened by poshul 21 days ago - 27 comments
Labels: Review effort [1-5]: 2

#7638 - Add check for pandas in cmake

Pull Request - State: closed - Opened by poshul 21 days ago - 3 comments
Labels: Review effort [1-5]: 2

#7637 - INI/CTD files: double NAN's as 'NaN'

Pull Request - State: closed - Opened by cbielow 21 days ago

#7636 - contrib release broken on windows

Issue - State: closed - Opened by timosachsenberg 22 days ago - 4 comments
Labels: blocker

#7636 - contrib release broken on windows

Issue - State: closed - Opened by timosachsenberg 22 days ago - 4 comments
Labels: blocker

#7634 - Upgrade numpy in pyopenms

Issue - State: closed - Opened by uweschmitt 22 days ago - 1 comment

#7633 - Bugs for 3.2.1

Issue - State: open - Opened by poshul 22 days ago - 8 comments

#7632 - Revisit boost serialization bugs

Issue - State: closed - Opened by jpfeuffer 22 days ago

#7631 - Improve flexibility of experimental design matching in PLFQ

Issue - State: open - Opened by jpfeuffer 23 days ago - 5 comments

#7630 - additional convenience functions for MSExperiment

Pull Request - State: closed - Opened by timosachsenberg 25 days ago - 23 comments
Labels: Review effort [1-5]: 4

#7629 - Add support for TMT-32 and 35-plex?

Issue - State: open - Opened by jpfeuffer 25 days ago - 1 comment
Labels: enhancement

#7628 - Fast peak extraction from MSExperiments

Pull Request - State: closed - Opened by timosachsenberg 26 days ago - 1 comment

#7627 - MzTab: preallocate enough memory instead of allocating in the loops

Pull Request - State: closed - Opened by timosachsenberg 27 days ago - 2 comments
Labels: Review effort [1-5]: 2

#7626 - OpenMS does not compile when using GLPK (instead of COINOR)

Pull Request - State: closed - Opened by cbielow 27 days ago - 4 comments
Labels: Review effort [1-5]: 2

#7625 - Cmake fix

Pull Request - State: closed - Opened by cbielow 27 days ago - 5 comments
Labels: Review effort [1-5]: 2

#7624 - add quick check for almost certain out of memory error

Pull Request - State: closed - Opened by timosachsenberg 28 days ago - 2 comments
Labels: Review effort [1-5]: 2

#7623 - KNIME nodes that have NAN for double parameter are broken

Issue - State: closed - Opened by timosachsenberg 28 days ago - 3 comments
Labels: blocker

#7622 - fix KNIME categories

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

#7621 - Categorize branch

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

#7620 - Update containerdeploy.yml to match Release/

Pull Request - State: closed - Opened by poshul about 1 month ago - 4 comments
Labels: enhancement, Review effort [1-5]: 2, configuration changes

#7619 - fix for CI on mac x86

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

#7618 - expose eigen downstream

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

#7617 - make setup.py check for AVX support

Pull Request - State: open - Opened by poshul about 1 month ago - 5 comments
Labels: enhancement, dependencies, Review effort [1-5]: 2

#7616 - Fix remove old pyds

Pull Request - State: closed - Opened by poshul about 1 month ago - 7 comments
Labels: Review effort [1-5]: 1, bug_fix, configuration changes

#7615 - Update pyopenms-wheels.yml

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

#7614 - PyOpenMS 3.2.0 build fails on bioconda due to Eigen3 not found

Issue - State: closed - Opened by jonasscheid about 1 month ago - 16 comments

#7613 - FLASHDeconv msAlign Export

Issue - State: open - Opened by jgpavek about 1 month ago - 1 comment

#7612 - Decoy phosho added to unimod.xml

Pull Request - State: closed - Opened by ypriverol about 1 month ago - 15 comments

#7611 - Release/3.2.0

Pull Request - State: closed - Opened by poshul about 1 month ago

#7610 - Updates unimod and adds back custom mods

Pull Request - State: closed - Opened by timosachsenberg about 1 month ago - 4 comments

#7609 - better variable names

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

#7608 - Wheel action tries to delete wrong libraries

Issue - State: closed - Opened by jpfeuffer about 1 month ago - 2 comments

#7607 - Python wheels still/again packaging dlls for multiple versions

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

#7606 - Update unimod.xml and unimod.obo to "12:08:2024 11:33"

Pull Request - State: closed - Opened by fcyu about 1 month ago - 3 comments
Labels: enhancement

#7605 - merge back changes from release branch

Pull Request - State: closed - Opened by timosachsenberg about 1 month ago - 2 comments

#7604 - Retention Time Correction

Issue - State: closed - Opened by LeonSaal about 1 month ago - 6 comments

#7603 - Untargeted Metabolomics for Direct Injection

Issue - State: closed - Opened by felipe-mansoldo about 2 months ago - 5 comments

#7602 - Updated for loop

Pull Request - State: closed - Opened by sa-shaheer-ali about 2 months ago - 4 comments
Labels: enhancement, Review effort [1-5]: 3

#7601 - add isobaric correction defaults for tmt6plex and 11plex

Pull Request - State: closed - Opened by timosachsenberg about 2 months ago - 3 comments
Labels: Review effort [1-5]: 2, bug_fix

#7600 - ImportError with pyOpenMS version 3.2.0 on Windows when PyArrow was imported

Issue - State: open - Opened by RalfG about 2 months ago - 23 comments

#7599 - fix scan number extraction for merged spectra

Pull Request - State: closed - Opened by t0mdavid-m about 2 months ago - 4 comments

#7598 - DONT MERGE Pr 7577

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

#7597 - updating CometAdapter with new parameters

Pull Request - State: open - Opened by MaLLLiYA about 2 months ago - 6 comments
Labels: enhancement, Review effort [1-5]: 3

#7595 - Update FeatureMap.pxd

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

#7594 - FeatureFinderMetabo: param to toggle reporting smoothed intensities

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

#7593 - Bump src/pyOpenMS/pyopenms-docs from `9875a9e` to `63fdab2`

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

#7592 - Update COMET to the latest version

Issue - State: open - Opened by MaLLLiYA 2 months ago - 2 comments

#7591 - OpenMS 3.2 Dockerfiles

Issue - State: closed - Opened by prvst 2 months ago - 10 comments

#7590 - update citation info to OpenMS 3 for GUI apps

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

#7589 - Merge latest release into develop

Pull Request - State: closed - Opened by github-actions[bot] 2 months ago - 1 comment
Labels: feature, automated pr

#7588 - [ByGHAction] Updated OpenMS package version numbers

Pull Request - State: closed - Opened by github-actions[bot] 2 months ago - 3 comments

#7587 - Update/OpenSwathWorkflow IonMobilityScoring Mobilogram Datastructure

Pull Request - State: open - Opened by singjc 2 months ago - 16 comments
Labels: enhancement, Review effort [1-5]: 3

#7586 - Bump THIRDPARTY from `d6594eb` to `6c4aff6`

Pull Request - State: closed - Opened by dependabot[bot] 2 months ago - 6 comments
Labels: dependencies

#7585 - TOPPView: open idXML in same layer as underlying data, if raw mzML is detected …

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

#7584 - Defining more enzymes in OpenMS Comet and SAGE adaptor

Pull Request - State: closed - Opened by MaLLLiYA 2 months ago - 9 comments
Labels: enhancement, Review effort [1-5]: 2

#7583 - FragmentIndex search engine

Pull Request - State: open - Opened by timosachsenberg 2 months ago - 92 comments
Labels: enhancement, Review effort [1-5]: 4, tests

#7582 - FR: report non-smoothed intensities with FFM

Issue - State: closed - Opened by rickhelmus 2 months ago - 2 comments

#7581 - Bottom up fiid [do not merge]

Pull Request - State: closed - Opened by timosachsenberg 2 months ago - 4 comments
Labels: enhancement, Documentation, tests, configuration changes, Review effort [1-5]: 5

#7580 - Update openms_ci_matrix_full.yml

Pull Request - State: closed - Opened by poshul 2 months ago - 8 comments
Labels: enhancement, Review effort [1-5]: 1

#7579 - Parse IM in CometAdapter

Issue - State: open - Opened by jonasscheid 2 months ago - 1 comment

#7578 - Bump src/pyOpenMS/pyopenms-docs from `7628c88` to `63fdab2`

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

#7577 - Updating SageAdapter with new functionality + compatibility with new Sage versions

Pull Request - State: closed - Opened by JohannesvKL 2 months ago - 4 comments
Labels: enhancement, Documentation, Review effort [1-5]: 4

#7576 - fix broken link in pyOpenMS docs

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

#7575 - update Windows release notes

Pull Request - State: closed - Opened by cbielow 3 months ago - 2 comments
Labels: Documentation, Review effort [1-5]: 1

#7574 - libsvm cmake configuration errors on mac

Issue - State: closed - Opened by timosachsenberg 3 months ago - 12 comments
Labels: blocker