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

#7293 - Bump src/pyOpenMS/pyopenms-docs from `64016e7` to `27dfc2a`

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago - 1 comment
Labels: dependencies, submodules

#7292 - Investigate building snap/flatpak packages for linux

Issue - State: open - Opened by poshul 9 months ago
Labels: BinaryPackages, sprint candidate

#7291 - Fix developer docs and warnings

Pull Request - State: closed - Opened by cbielow 9 months ago - 2 comments

#7290 - Fix Windows installer's extra Dll's from GHA

Issue - State: closed - Opened by cbielow 9 months ago - 14 comments
Labels: blocker

#7289 - Where is MSSimulator?

Issue - State: closed - Opened by Ministreliya131 9 months ago - 2 comments

#7288 - OpenMS File archive not working

Issue - State: closed - Opened by jpfeuffer 9 months ago - 2 comments
Labels: blocker

#7287 - How to write cython code of struct in struct in the type declaration.

Issue - State: closed - Opened by JKVISION1101 9 months ago - 3 comments

#7286 - License header

Pull Request - State: closed - Opened by timosachsenberg 9 months ago - 1 comment

#7284 - Parameter ms1_isotopes ignored

Issue - State: open - Opened by cbielow 9 months ago - 1 comment

#7283 - When making pxd file for wrapping class, question about cimport.

Issue - State: closed - Opened by JKVISION1101 9 months ago - 4 comments

#7282 - Always set working dir in pyopenms tests

Pull Request - State: closed - Opened by jpfeuffer 9 months ago - 2 comments

#7280 - deisotopeAndSingleCharge: Removes Highest Intensity Peaks, bug?

Issue - State: open - Opened by CCranney 9 months ago - 5 comments

#7279 - Bump tj-actions/changed-files from 34.6.1 to 41.0.0 in /.github/workflows

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago
Labels: dependencies, github_actions

#7278 - [ByGitAction] Updated year number in the header of files

Pull Request - State: closed - Opened by github-actions[bot] 9 months ago - 4 comments

#7277 - cmake cleanup

Pull Request - State: closed - Opened by timosachsenberg 9 months ago

#7276 - Is there an elegant way to present the ProteomicsLFQ results?

Issue - State: closed - Opened by liuxiawei 9 months ago - 2 comments

#7275 - fix: remove CWL CI and pregenerated tool description files

Pull Request - State: closed - Opened by SGSSGene 10 months ago - 1 comment

#7274 - Allow different sizes of compressed output in zlib unit tests

Pull Request - State: closed - Opened by timosachsenberg 10 months ago - 1 comment

#7273 - Display proper exit code when external process crashes

Pull Request - State: closed - Opened by cbielow 10 months ago - 2 comments

#7272 - [FEATURE] Concurrent MSGF+ database indexing

Pull Request - State: closed - Opened by cbielow 10 months ago - 5 comments

#7271 - 7 tests fail when using zlib-ng

Issue - State: open - Opened by tuliom 10 months ago - 6 comments

#7270 - Update openms_ci_matrix_full.yml

Pull Request - State: closed - Opened by poshul 10 months ago - 3 comments

#7269 - Bump brew python to 3.12

Pull Request - State: closed - Opened by poshul 10 months ago

#7268 - [NOP] renamed "thirdparty" folder to the more common "extern"

Pull Request - State: closed - Opened by timosachsenberg 10 months ago - 9 comments

#7267 - Bump contrib from `69e61f2` to `5e42765`

Pull Request - State: closed - Opened by dependabot[bot] 10 months ago
Labels: dependencies

#7266 - Delete cmake/Modules/FindHDF5.cmake

Pull Request - State: closed - Opened by timosachsenberg 10 months ago - 1 comment

#7265 - add __repr__

Pull Request - State: closed - Opened by timosachsenberg 10 months ago - 9 comments

#7264 - Bump src/pyOpenMS/pyopenms-docs from `64016e7` to `bb095b8`

Pull Request - State: closed - Opened by dependabot[bot] 10 months ago - 1 comment
Labels: dependencies

#7263 - Aligning Parameters/ New SpectrumGenerator

Pull Request - State: closed - Opened by Trapho 10 months ago

#7262 - support tools with multiple headers and cpp files

Pull Request - State: closed - Opened by timosachsenberg 10 months ago - 3 comments

#7261 - Move CWL outputs to own build subfolder

Issue - State: closed - Opened by jpfeuffer 10 months ago - 9 comments

#7260 - Error report in XTandemAdapter, IDScoreSwitcher, and ProteomicsLFQ

Issue - State: closed - Opened by liuxiawei 10 months ago - 6 comments

#7259 - Add conversion for MSSpectrum & PeptideHit to spectrum_utils MsmsSpectrum

Pull Request - State: open - Opened by matteopilz 10 months ago - 19 comments

#7258 - Update TOPPAS tutorial

Pull Request - State: closed - Opened by cbielow 10 months ago

#7257 - Run example TOPPAS workflows with CI

Issue - State: open - Opened by cbielow 10 months ago

#7256 - our example mzML files could use an update

Issue - State: open - Opened by cbielow 10 months ago

#7255 - Running MSGF+ in parallel crashes when input DB is new

Issue - State: closed - Opened by cbielow 10 months ago - 1 comment

#7254 - TOPPView: Running TOPP tools fails

Issue - State: closed - Opened by cbielow 10 months ago - 3 comments
Labels: blocker

#7253 - fix warning in traml handler

Pull Request - State: closed - Opened by timosachsenberg 10 months ago

#7252 - The incomplete documentation makes beginners feel extremely difficult.

Issue - State: closed - Opened by liuxiawei 10 months ago - 6 comments

#7251 - Make ParamIterator a real iterator

Issue - State: open - Opened by timosachsenberg 10 months ago

#7250 - fix doc

Pull Request - State: closed - Opened by timosachsenberg 10 months ago

#7249 - Patch/extend osw output

Pull Request - State: closed - Opened by jcharkow 10 months ago - 6 comments

#7247 - fix wrong OpenMP max_threads in OpenMSInfo TOPP tool

Pull Request - State: closed - Opened by cbielow 10 months ago

#7246 - How do I perform quantitative analysis on PRM data using OpenMS?

Issue - State: open - Opened by Allen188 10 months ago - 2 comments

#7245 - Check if this excludes vcpkg from dependabot.yml updates

Pull Request - State: closed - Opened by timosachsenberg 10 months ago

#7244 - Bump vcpkg from `64ca152` to `e85cafa`

Pull Request - State: closed - Opened by dependabot[bot] 10 months ago - 1 comment
Labels: dependencies

#7243 - Plotting fix - matched peaks highlighting

Pull Request - State: closed - Opened by matteopilz 10 months ago - 28 comments

#7242 - Bump vcpkg from `64ca152` to `4cac260`

Pull Request - State: closed - Opened by dependabot[bot] 10 months ago - 1 comment
Labels: dependencies

#7241 - Check pyopenms compatibility with Cython < 3.0

Issue - State: open - Opened by jpfeuffer 10 months ago - 1 comment

#7240 - more robust precursor purity (PR 3 of X)

Pull Request - State: closed - Opened by timosachsenberg 10 months ago - 5 comments

#7239 - [cleanup] remove outdated RNPxl tool (PR 2 of X)

Pull Request - State: closed - Opened by timosachsenberg 10 months ago - 2 comments

#7237 - [FEATURE] z* and z' ions for ExD (fixed tests)

Pull Request - State: closed - Opened by timosachsenberg 10 months ago

#7235 - FindCOIN.cmake use imported targets

Pull Request - State: closed - Opened by jpfeuffer 10 months ago - 2 comments

#7234 - SiriusAdapter replaced with SiriusExport and adaptations to AssayGeneratorMetabo

Pull Request - State: closed - Opened by axelwalter 10 months ago - 9 comments

#7232 - Refactoring FragmentIndex

Pull Request - State: closed - Opened by Trapho 10 months ago

#7231 - [SageAdapter] Feature req: Have a load-only functionality

Issue - State: open - Opened by jpfeuffer 10 months ago - 5 comments

#7230 - work around Clang bug

Pull Request - State: closed - Opened by cbielow 10 months ago

#7229 - always print error when MSGF+ fails

Pull Request - State: closed - Opened by jpfeuffer 10 months ago

#7228 - Follow a specification for fragment ion annotations

Issue - State: open - Opened by jpfeuffer 10 months ago - 1 comment

#7227 - move cwl generation into release action

Issue - State: open - Opened by timosachsenberg 10 months ago

#7226 - [FEATURE] z* and z' ions for ExD

Pull Request - State: closed - Opened by jpfeuffer 10 months ago - 18 comments

#7225 - Fix resampler

Pull Request - State: closed - Opened by cbielow 10 months ago

#7224 - vcpkg might have more requirements than our contrib

Issue - State: open - Opened by timosachsenberg 10 months ago - 13 comments
Labels: question

#7223 - Bump src/pyOpenMS/pyopenms-docs from `64016e7` to `5fc3503`

Pull Request - State: closed - Opened by dependabot[bot] 10 months ago - 1 comment
Labels: dependencies

#7222 - OpenSWATH: Differences Between OSW and TSV File Contents

Issue - State: closed - Opened by bruadi 10 months ago - 17 comments

#7221 - [FIX] TOPPView: fix crash when viewing certain Chromatograms

Pull Request - State: closed - Opened by cbielow 11 months ago - 2 comments

#7218 - Handle coinor from brew as well

Pull Request - State: closed - Opened by jpfeuffer 11 months ago - 1 comment

#7217 - how to build pyopenms

Issue - State: closed - Opened by JKVISION1101 11 months ago - 30 comments

#7216 - Fix SpectrumAnnotator small metadata issue

Pull Request - State: closed - Opened by jpfeuffer 11 months ago

#7215 - Fix plotting.py for existing annotations from SpectrumAnnotator

Pull Request - State: closed - Opened by jpfeuffer 11 months ago - 14 comments
Labels: NoJenkins

#7214 - pyopenms 3.1 not available for Silicon macs

Issue - State: open - Opened by jpfeuffer 11 months ago

#7213 - [FIX] TOPPAS: open files in TOPPView

Pull Request - State: closed - Opened by cbielow 11 months ago

#7212 - Update openms_ci_matrix_full.yml

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

#7211 - Resampler uses Da instead of PPM

Issue - State: closed - Opened by cbielow 11 months ago - 1 comment

#7210 - Release action

Pull Request - State: closed - Opened by poshul 11 months ago - 18 comments

#7209 - Feature/csv comments

Pull Request - State: closed - Opened by enetz 11 months ago

#7208 - [NOMERGE] Release3.0.0 winfix

Pull Request - State: closed - Opened by cbielow 11 months ago

#7207 - [fix] add licenses for tool_description_lib

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

#7206 - NOP

Issue - State: closed - Opened by timosachsenberg 11 months ago

#7205 - Bump src/pyOpenMS/pyopenms-docs from `64016e7` to `16607af`

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

#7204 - Install 3.x.0 for single user in windows doesn't create shortcuts

Issue - State: closed - Opened by poshul 11 months ago - 5 comments
Labels: sprint candidate

#7202 - Resolve KNIME THIRDPARTY issues

Issue - State: open - Opened by timosachsenberg 11 months ago - 2 comments

#7201 - Host FLASHViewer

Issue - State: open - Opened by timosachsenberg 11 months ago - 8 comments

#7200 - Review/Work on FragmentIndex PR

Issue - State: open - Opened by timosachsenberg 11 months ago - 1 comment

#7198 - Add mold linker

Pull Request - State: closed - Opened by timosachsenberg 11 months ago - 3 comments
Labels: NoJenkins

#7197 - Remove the rest of ERPairFinder

Pull Request - State: closed - Opened by poshul 11 months ago - 1 comment

#7195 - Bump src/pyOpenMS/pyopenms-docs from `64016e7` to `1d810ae`

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

#7194 - [GHA] Overwrite 1k NSIS without prompt

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