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

#7098 - [FIX] DatabaseName element in MzIdentMLDOMHandler.cpp

Pull Request - State: closed - Opened by jpfeuffer about 1 year ago - 2 comments

#7095 - [ProteomicsLFQ] Parameterize min. proportion for requant.

Pull Request - State: closed - Opened by jpfeuffer about 1 year ago

#7094 - make UBSan errors to fail tests

Pull Request - State: closed - Opened by timosachsenberg about 1 year ago

#7093 - SageAdapter fixes

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

#7092 - libqt5core is missing from the image

Issue - State: open - Opened by shubham1637 about 1 year ago - 9 comments

#7091 - Bump THIRDPARTY from `402992f` to `a3e6ffb`

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

#7090 - Keep main score in PercolatorAdapter

Pull Request - State: closed - Opened by jpfeuffer about 1 year ago - 7 comments

#7089 - fix ASAN bug in MapAlignmentAlgorithmIdentification.h

Pull Request - State: closed - Opened by timosachsenberg about 1 year ago

#7088 - Expand EICExtractor

Issue - State: closed - Opened by timosachsenberg about 1 year ago - 50 comments
Labels: beginner tasks

#7087 - UBSan fixes

Pull Request - State: closed - Opened by timosachsenberg about 1 year ago

#7086 - Update SemanticValidator.h

Pull Request - State: closed - Opened by timosachsenberg about 1 year ago

#7085 - Fix asan bug in SageAdapter.cpp

Pull Request - State: closed - Opened by timosachsenberg about 1 year ago

#7084 - add mandatory context message to Exception::InvalidSize

Issue - State: open - Opened by cbielow about 1 year ago
Labels: sprint candidate

#7083 - add SpectraMerger tests

Issue - State: open - Opened by cbielow about 1 year ago
Labels: sprint candidate

#7082 - SpectraMerger: fix empty ms-levels which lead to exception

Pull Request - State: closed - Opened by cbielow about 1 year ago

#7081 - Update AddressSanitizer.cmake

Pull Request - State: closed - Opened by timosachsenberg about 1 year ago

#7080 - expose error in ResidueDB code

Pull Request - State: closed - Opened by timosachsenberg about 1 year ago - 1 comment

#7079 - Prot quant comment lines

Pull Request - State: closed - Opened by timosachsenberg about 1 year ago

#7078 - [doc] ProteomicsLFQ.cpp

Pull Request - State: closed - Opened by timosachsenberg about 1 year ago

#7077 - include UndefinedBehaviorSanitizer

Pull Request - State: closed - Opened by timosachsenberg about 1 year ago - 5 comments

#7076 - restore TOPPAS tutorial

Pull Request - State: closed - Opened by cbielow about 1 year ago - 1 comment

#7075 - Bump contrib from `04d64c6` to `69e61f2`

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

#7074 - fix some remaining occurances of util

Pull Request - State: closed - Opened by timosachsenberg about 1 year ago

#7073 - rename some of the old UTIL tests to TOPP tests

Pull Request - State: closed - Opened by timosachsenberg about 1 year ago

#7072 - fix ProteinQuantifier

Pull Request - State: closed - Opened by timosachsenberg about 1 year ago - 3 comments

#7071 - update Deisotoper python documentation and throw exception for unrealistic tolerances

Issue - State: closed - Opened by timosachsenberg about 1 year ago - 1 comment
Labels: sprint candidate

#7070 - fixes bug in string conversion

Pull Request - State: closed - Opened by timosachsenberg about 1 year ago

#7069 - FeatureFinderMetaboIdent seems to add a proton to input molecular formulas

Issue - State: open - Opened by YasinEl about 1 year ago - 5 comments

#7068 - Update Main.doxygen

Pull Request - State: closed - Opened by timosachsenberg about 1 year ago

#7067 - Switch to SPDX license format

Pull Request - State: closed - Opened by cbielow about 1 year ago - 1 comment

#7065 - fix #7051 (repairs #7035)

Pull Request - State: closed - Opened by cbielow about 1 year ago - 1 comment

#7064 - make internal calibration plots more robust

Pull Request - State: closed - Opened by cbielow about 1 year ago - 1 comment

#7063 - [FIX] Sage charge states and spec refs and general spec ref handling

Pull Request - State: closed - Opened by jpfeuffer about 1 year ago

#7062 - Inconsistent behavior in DeistopeAndSingleCharge function

Issue - State: closed - Opened by birdday about 1 year ago - 6 comments
Labels: bug

#7061 - CSV File reader does not support comment lines

Issue - State: open - Opened by jpfeuffer about 1 year ago - 11 comments
Labels: major, beginner tasks, sprint candidate

#7060 - Dangling reference to a temporary in OSMFileStore

Issue - State: open - Opened by SGSSGene about 1 year ago - 2 comments

#7059 - MzTab crashes in PLFQ if experimental design is not given

Issue - State: closed - Opened by jonasscheid about 1 year ago - 7 comments

#7058 - Remove BOOST_USE_STATIC

Pull Request - State: closed - Opened by jpfeuffer about 1 year ago - 2 comments

#7057 - Move FDR, IDFilter and IDRipping into ProteomicsLFQ?

Issue - State: open - Opened by jpfeuffer about 1 year ago

#7056 - GHA Upload of docs missing

Issue - State: closed - Opened by jpfeuffer about 1 year ago - 3 comments
Labels: CI, sprint candidate

#7055 - GHA Clang matrix branch is using GCC

Issue - State: open - Opened by jpfeuffer about 1 year ago
Labels: CI, bug

#7054 - GHA and Jenkins overwriting each other

Issue - State: closed - Opened by jpfeuffer about 1 year ago - 3 comments
Labels: critical, CI

#7053 - [FIX] PercolatorInfile reading even more

Pull Request - State: closed - Opened by jpfeuffer about 1 year ago

#7052 - [FIX] CoarseIsotope generation

Pull Request - State: closed - Opened by jpfeuffer about 1 year ago - 1 comment

#7051 - Compilation on g++ < 8 broken due to filesystem header

Issue - State: closed - Opened by jpfeuffer about 1 year ago - 2 comments
Labels: blocker

#7050 - macOS ARM CI for conda

Issue - State: open - Opened by jpfeuffer about 1 year ago - 3 comments
Labels: CI

#7049 - fix ARM64 compile error

Pull Request - State: closed - Opened by cbielow about 1 year ago - 3 comments

#7048 - SIMD nightly build errors on macOS ARM

Issue - State: closed - Opened by jpfeuffer about 1 year ago - 4 comments
Labels: blocker

#7047 - GHA Fix Win Thirdparty

Pull Request - State: closed - Opened by jpfeuffer about 1 year ago
Labels: NoJenkins

#7046 - Update openms_ci_matrix_full.yml

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

#7045 - SageAdapter not tested on Windows

Issue - State: closed - Opened by jpfeuffer about 1 year ago

#7044 - Fix PercolatorInfile loading

Pull Request - State: closed - Opened by jpfeuffer about 1 year ago - 2 comments

#7043 - SageAdapter reading Percolator output error

Issue - State: closed - Opened by jpfeuffer about 1 year ago - 4 comments

#7042 - Update openms_ci_matrix_full.yml

Pull Request - State: closed - Opened by poshul about 1 year ago - 3 comments

#7041 - SageAdapter min and max_peaks settings not passed through

Issue - State: closed - Opened by jpfeuffer about 1 year ago

#7040 - SageAdapter does not find anything on BSA

Issue - State: closed - Opened by jpfeuffer about 1 year ago - 8 comments

#7038 - Bump src/pyOpenMS/pyopenms-docs from `0d5e4f3` to `b44adfe`

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

#7037 - Dockerfile heavily outdated

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

#7036 - [ProteomicsLFQ] allow non-probabilistic scores for basic inference

Pull Request - State: open - Opened by jpfeuffer about 1 year ago - 3 comments

#7035 - [FEATURE] add reporting for read/write speed for mzML

Pull Request - State: closed - Opened by cbielow about 1 year ago - 1 comment

#7034 - [SageAdapter] Pass threads param as (file) batch_size

Pull Request - State: closed - Opened by timosachsenberg about 1 year ago - 6 comments

#7033 - SageAdapter documentation lacking

Issue - State: open - Opened by jpfeuffer about 1 year ago - 5 comments

#7032 - Searchengine parameter names not agreeing

Issue - State: open - Opened by jpfeuffer about 1 year ago - 8 comments

#7031 - SageAdapter does not pass threads

Issue - State: open - Opened by jpfeuffer about 1 year ago - 5 comments

#7030 - Require Qt5.11+?

Issue - State: open - Opened by jpfeuffer about 1 year ago - 1 comment

#7029 - abibuilder8 not working for a long long time

Issue - State: closed - Opened by jpfeuffer about 1 year ago - 5 comments
Labels: critical

#7028 - Building packages with the new Matrix based Github actions CI doesn't work.

Issue - State: closed - Opened by poshul about 1 year ago - 24 comments

#7027 - Poshul test package

Pull Request - State: closed - Opened by poshul about 1 year ago - 4 comments
Labels: NoJenkins, internal

#7026 - nightly OpenMS documentation seems to have issues (not updated?)

Issue - State: closed - Opened by timosachsenberg about 1 year ago - 5 comments
Labels: critical

#7025 - More SIMD/SSE2: removeWhitespace

Pull Request - State: closed - Opened by cbielow about 1 year ago - 1 comment

#7024 - Full multijob matrix gha

Pull Request - State: closed - Opened by poshul about 1 year ago - 3 comments
Labels: NoJenkins

#7023 - Bump contrib from `1240564` to `04d64c6`

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

#7022 - Report active ISA extensions

Pull Request - State: closed - Opened by cbielow about 1 year ago - 3 comments

#7021 - add option to filter spectra by peptide

Pull Request - State: closed - Opened by timosachsenberg about 1 year ago

#7019 - [cleanup] removed EnzymaticDigestionLogModel

Pull Request - State: closed - Opened by timosachsenberg about 1 year ago - 1 comment

#7018 - Fixed broken / deprecated link

Pull Request - State: closed - Opened by matteopilz about 1 year ago

#7017 - fix neon flags (not needed)

Pull Request - State: closed - Opened by cbielow about 1 year ago - 6 comments

#7016 - [cleanup] remove linear mapping PIP

Pull Request - State: closed - Opened by timosachsenberg about 1 year ago - 1 comment

#7015 - [cleanup] remove DocumentIDTagger and IDPool from share

Pull Request - State: closed - Opened by timosachsenberg about 1 year ago - 1 comment

#7014 - remove errorstring from XMLHandler.pxd

Pull Request - State: closed - Opened by timosachsenberg about 1 year ago

#7013 - Fix_sage

Pull Request - State: closed - Opened by timosachsenberg about 1 year ago

#7012 - make idxml user parameter output deterministic

Pull Request - State: closed - Opened by timosachsenberg about 1 year ago - 1 comment

#7011 - [FIX] mzML threading issue

Pull Request - State: closed - Opened by cbielow about 1 year ago - 1 comment

#7010 - MapAlignerPoseClustering can crash with mzML files

Issue - State: open - Opened by axelwalter about 1 year ago - 1 comment

#7009 - [cleanup] remove FIDOAdapter

Pull Request - State: closed - Opened by timosachsenberg about 1 year ago

#7008 - loadExperiment crashes

Issue - State: closed - Opened by uweschmitt about 1 year ago - 17 comments

#7007 - FeatureFinderMultiplex meets bad_alloc problems

Issue - State: open - Opened by liuzy2008 about 1 year ago - 1 comment

#7006 - Fatal Error When Packaging with Pyinstaller

Issue - State: closed - Opened by lingjunli-research about 1 year ago - 11 comments

#7005 - Update openms_clang_format.yml

Pull Request - State: closed - Opened by timosachsenberg about 1 year ago
Labels: NoJenkins

#7004 - remove tool also from KNIME packaging

Pull Request - State: closed - Opened by timosachsenberg about 1 year ago - 1 comment

#7003 - [Feature] IDPEP p-values

Pull Request - State: open - Opened by jpfeuffer about 1 year ago - 1 comment

#7002 - Get rid of dependency on C compilers

Pull Request - State: closed - Opened by jpfeuffer about 1 year ago - 1 comment

#7001 - [discussion] remove utils and model as topp tool with utilities category

Pull Request - State: closed - Opened by timosachsenberg about 1 year ago - 6 comments

#7000 - SiriusAdapter fails in OpenMS 3.0

Issue - State: open - Opened by bernt-matthias about 1 year ago - 11 comments

#6999 - [cleanup] remove CompNovo

Pull Request - State: closed - Opened by timosachsenberg about 1 year ago - 1 comment