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

make mzData more robust against wrong 'length' attributes for binary data

cbielow opened this pull request about 1 year ago

SageAdapter: No accession found

elrubio opened this issue about 1 year ago

Wrong m/z calculation when loading sage/percolator files

elrubio opened this issue about 1 year ago

update changelog helper for 2023

mr-c opened this pull request about 1 year ago

readded HTML tutorial parts

poshul opened this pull request about 1 year ago

Update SIMDe to 2023-10-02 snapshot of 0.7.7

mr-c opened this pull request about 1 year ago

Update CHANGELOG

timosachsenberg opened this pull request about 1 year ago

SAGe updated restricted to null

ypriverol opened this pull request about 1 year ago

[FIX][SageAdapter] Use `restrict: null`

jpfeuffer opened this pull request about 1 year ago

bring back OpenMS dev tutorial

cbielow opened this issue about 1 year ago

add option to extract decoy features in FFID, filter by feature score in ProteomicsLFQ

timosachsenberg opened this pull request about 1 year ago

SageAdapter option to keep json as debug output

timosachsenberg opened this pull request about 1 year ago

Deisotope Fragment Tolerance Exception

matteopilz opened this pull request about 1 year ago

Update SageAdapter.cpp

timosachsenberg opened this pull request about 1 year ago

MzIdentML parser error for DatabaseName/userParam

elrubio opened this issue about 1 year ago

[FIX] DatabaseName element in MzIdentMLDOMHandler.cpp

jpfeuffer opened this pull request about 1 year ago

IDFileConverter: Unexpected internal error (Could not convert string '' to a double value)

elrubio opened this issue about 1 year ago

ProteaseDigestion looses a tryptic peptide contained in a bigger tryptic peptide

Roman-Si opened this issue about 1 year ago

[ProteomicsLFQ] Parameterize min. proportion for requant.

jpfeuffer opened this pull request about 1 year ago

make UBSan errors to fail tests

timosachsenberg opened this pull request about 1 year ago

SageAdapter fixes

timosachsenberg opened this pull request about 1 year ago

libqt5core is missing from the image

shubham1637 opened this issue about 1 year ago

Bump THIRDPARTY from `402992f` to `a3e6ffb`

dependabot[bot] opened this pull request about 1 year ago

Keep main score in PercolatorAdapter

jpfeuffer opened this pull request about 1 year ago

fix ASAN bug in MapAlignmentAlgorithmIdentification.h

timosachsenberg opened this pull request about 1 year ago

Expand EICExtractor

timosachsenberg opened this issue about 1 year ago

UBSan fixes

timosachsenberg opened this pull request about 1 year ago

Update SemanticValidator.h

timosachsenberg opened this pull request about 1 year ago

Fix asan bug in SageAdapter.cpp

timosachsenberg opened this pull request about 1 year ago

add mandatory context message to Exception::InvalidSize

cbielow opened this issue about 1 year ago

add SpectraMerger tests

cbielow opened this issue about 1 year ago

SpectraMerger: fix empty ms-levels which lead to exception

cbielow opened this pull request about 1 year ago

Update AddressSanitizer.cmake

timosachsenberg opened this pull request about 1 year ago

expose error in ResidueDB code

timosachsenberg opened this pull request about 1 year ago

Prot quant comment lines

timosachsenberg opened this pull request about 1 year ago

[doc] ProteomicsLFQ.cpp

timosachsenberg opened this pull request about 1 year ago

include UndefinedBehaviorSanitizer

timosachsenberg opened this pull request about 1 year ago

restore TOPPAS tutorial

cbielow opened this pull request about 1 year ago

Bump contrib from `04d64c6` to `69e61f2`

dependabot[bot] opened this pull request about 1 year ago

fix some remaining occurances of util

timosachsenberg opened this pull request about 1 year ago

rename some of the old UTIL tests to TOPP tests

timosachsenberg opened this pull request about 1 year ago

fix ProteinQuantifier

timosachsenberg opened this pull request about 1 year ago

update Deisotoper python documentation and throw exception for unrealistic tolerances

timosachsenberg opened this issue about 1 year ago

fixes bug in string conversion

timosachsenberg opened this pull request about 1 year ago

FeatureFinderMetaboIdent seems to add a proton to input molecular formulas

YasinEl opened this issue about 1 year ago

Update Main.doxygen

timosachsenberg opened this pull request about 1 year ago

Switch to SPDX license format

cbielow opened this pull request about 1 year ago

Does OpenMS support the deconvolution of sparse labeling C13 or N15 peptide mass spectrum?

YiqingElroy opened this issue about 1 year ago

fix #7051 (repairs #7035)

cbielow opened this pull request about 1 year ago

make internal calibration plots more robust

cbielow opened this pull request about 1 year ago

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

jpfeuffer opened this pull request about 1 year ago

Inconsistent behavior in DeistopeAndSingleCharge function

birdday opened this issue about 1 year ago

CSV File reader does not support comment lines

jpfeuffer opened this issue about 1 year ago

Dangling reference to a temporary in OSMFileStore

SGSSGene opened this issue about 1 year ago

MzTab crashes in PLFQ if experimental design is not given

jonasscheid opened this issue about 1 year ago

Remove BOOST_USE_STATIC

jpfeuffer opened this pull request about 1 year ago

Move FDR, IDFilter and IDRipping into ProteomicsLFQ?

jpfeuffer opened this issue about 1 year ago

GHA Upload of docs missing

jpfeuffer opened this issue about 1 year ago

GHA Clang matrix branch is using GCC

jpfeuffer opened this issue about 1 year ago

GHA and Jenkins overwriting each other

jpfeuffer opened this issue about 1 year ago

[FIX] PercolatorInfile reading even more

jpfeuffer opened this pull request about 1 year ago

[FIX] CoarseIsotope generation

jpfeuffer opened this pull request about 1 year ago

Compilation on g++ < 8 broken due to filesystem header

jpfeuffer opened this issue about 1 year ago

macOS ARM CI for conda

jpfeuffer opened this issue about 1 year ago

fix ARM64 compile error

cbielow opened this pull request about 1 year ago

SIMD nightly build errors on macOS ARM

jpfeuffer opened this issue about 1 year ago

GHA Fix Win Thirdparty

jpfeuffer opened this pull request about 1 year ago

Update openms_ci_matrix_full.yml

poshul opened this pull request about 1 year ago

SageAdapter not tested on Windows

jpfeuffer opened this issue about 1 year ago

Fix PercolatorInfile loading

jpfeuffer opened this pull request about 1 year ago

SageAdapter reading Percolator output error

jpfeuffer opened this issue about 1 year ago

Update openms_ci_matrix_full.yml

poshul opened this pull request about 1 year ago

SageAdapter min and max_peaks settings not passed through

jpfeuffer opened this issue about 1 year ago

SageAdapter does not find anything on BSA

jpfeuffer opened this issue about 1 year ago

Test and add documentation for new pkg installer on macOS

jpfeuffer opened this issue about 1 year ago

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

dependabot[bot] opened this pull request about 1 year ago

Dockerfile heavily outdated

jpfeuffer opened this issue about 1 year ago

[ProteomicsLFQ] allow non-probabilistic scores for basic inference

jpfeuffer opened this pull request about 1 year ago

[FEATURE] add reporting for read/write speed for mzML

cbielow opened this pull request about 1 year ago

[SageAdapter] Pass threads param as (file) batch_size

timosachsenberg opened this pull request about 1 year ago

SageAdapter documentation lacking

jpfeuffer opened this issue about 1 year ago

Searchengine parameter names not agreeing

jpfeuffer opened this issue about 1 year ago

SageAdapter does not pass threads

jpfeuffer opened this issue about 1 year ago

Require Qt5.11+?

jpfeuffer opened this issue about 1 year ago

abibuilder8 not working for a long long time

jpfeuffer opened this issue about 1 year ago

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

poshul opened this issue about 1 year ago

Poshul test package

poshul opened this pull request about 1 year ago

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

timosachsenberg opened this issue about 1 year ago

More SIMD/SSE2: removeWhitespace

cbielow opened this pull request about 1 year ago

Full multijob matrix gha

poshul opened this pull request about 1 year ago

Bump contrib from `1240564` to `04d64c6`

dependabot[bot] opened this pull request about 1 year ago

Report active ISA extensions

cbielow opened this pull request about 1 year ago

add option to filter spectra by peptide

timosachsenberg opened this pull request about 1 year ago

IDFilter: KeepBestPerPeptide available via pyopenms but not as CLI flag in IDFilter

jonasscheid opened this issue about 1 year ago

[cleanup] removed EnzymaticDigestionLogModel

timosachsenberg opened this pull request about 1 year ago

Fixed broken / deprecated link

matteopilz opened this pull request about 1 year ago

fix neon flags (not needed)

cbielow opened this pull request about 1 year ago

[cleanup] remove linear mapping PIP

timosachsenberg opened this pull request about 1 year ago

[cleanup] remove DocumentIDTagger and IDPool from share

timosachsenberg opened this pull request about 1 year ago

remove errorstring from XMLHandler.pxd

timosachsenberg opened this pull request about 1 year ago