.gitignore

## Ignore Visual Studio temporary files, build results, and
## files generated by popular Visual Studio add-ons.

# User-specific files
*.suo
*.user
*.userosscache
*.sln.docstates
.RData
mzkit_old

Rscript/Library/mzkit_app/test/KEGG_maps
Rscript/Library/mzkit_app/assembly

src/mzkit/setup/installer/

# User-specific files (MonoDevelop/Xamarin Studio)
*.userprefs

# Build results
[Dd]ebug/
[Dd]ebugPublic/
[Rr]elease/
[Rr]eleases/
x64/
x86/
bld/
[Bb]in/
[Oo]bj/
[Ll]og/

# Visual Studio 2015 cache/options directory
.vs/
# Uncomment if you have tasks that create the project's static files in wwwroot
#wwwroot/

# MSTest test Results
[Tt]est[Rr]esult*/
[Bb]uild[Ll]og.*

# NUNIT
*.VisualState.xml
TestResult.xml

# Build Results of an ATL Project
[Dd]ebugPS/
[Rr]eleasePS/
dlldata.c

# DNX
project.lock.json
artifacts/

*_i.c
*_p.c
*_i.h
*.ilk
*.meta
*.obj
*.pch
*.pdb
*.pgc
*.pgd
*.rsp
*.sbr
*.tlb
*.tli
*.tlh
*.tmp
*.tmp_proj
*.log
*.vspscc
*.vssscc
.builds
*.pidb
*.svclog
*.scc

# Chutzpah Test files
_Chutzpah*

# Visual C++ cache files
ipch/
*.aps
*.ncb
*.opendb
*.opensdf
*.sdf
*.cachefile
*.VC.db
*.VC.VC.opendb

# Visual Studio profiler
*.psess
*.vsp
*.vspx
*.sap

# TFS 2012 Local Workspace
$tf/

# Guidance Automation Toolkit
*.gpState

# ReSharper is a .NET coding add-in
_ReSharper*/
*.[Rr]e[Ss]harper
*.DotSettings.user

# JustCode is a .NET coding add-in
.JustCode

# TeamCity is a build add-in
_TeamCity*

# DotCover is a Code Coverage Tool
*.dotCover

# NCrunch
_NCrunch_*
.*crunch*.local.xml
nCrunchTemp_*

# MightyMoose
*.mm.*
AutoTest.Net/

# Web workbench (sass)
.sass-cache/

# Installshield output folder
[Ee]xpress/

# DocProject is a documentation generator add-in
DocProject/buildhelp/
DocProject/Help/*.HxT
DocProject/Help/*.HxC
DocProject/Help/*.hhc
DocProject/Help/*.hhk
DocProject/Help/*.hhp
DocProject/Help/Html2
DocProject/Help/html

# Click-Once directory
publish/

# Publish Web Output
*.[Pp]ublish.xml
*.azurePubxml
# TODO: Comment the next line if you want to checkin your web deploy settings
# but database connection strings (with potential passwords) will be unencrypted
*.pubxml
*.publishproj

# Microsoft Azure Web App publish settings. Comment the next line if you want to
# checkin your Azure Web App publish settings, but sensitive information contained
# in these scripts will be unencrypted
PublishScripts/

# NuGet Packages
*.nupkg
# The packages folder can be ignored because of Package Restore
**/packages/*
# except build/, which is used as an MSBuild target.
!**/packages/build/
# Uncomment if necessary however generally it will be regenerated when needed
#!**/packages/repositories.config
# NuGet v3's project.json files produces more ignoreable files
*.nuget.props
*.nuget.targets

# Microsoft Azure Build Output
csx/
*.build.csdef

# Microsoft Azure Emulator
ecf/
rcf/

# Windows Store app package directories and files
AppPackages/
BundleArtifacts/
Package.StoreAssociation.xml
_pkginfo.txt

# Visual Studio cache files
# files ending in .cache can be ignored
*.[Cc]ache
# but keep track of directories ending in .cache
!*.[Cc]ache/

# Others
ClientBin/
~$*
*~
*.dbmdl
*.dbproj.schemaview
*.pfx
*.publishsettings
node_modules/
orleans.codegen.cs

# Since there are multiple workflows, uncomment next line to ignore bower_components
# (https://github.com/github/gitignore/pull/1529#issuecomment-104372622)
#bower_components/

# RIA/Silverlight projects
Generated_Code/

# Backup & report files from converting an old project file
# to a newer Visual Studio version. Backup files are not needed,
# because we have git ;-)
_UpgradeReport_Files/
Backup*/
UpgradeLog*.XML
UpgradeLog*.htm

# SQL Server files
*.mdf
*.ldf

# Business Intelligence projects
*.rdl.data
*.bim.layout
*.bim_*.settings

# Microsoft Fakes
FakesAssemblies/

# GhostDoc plugin setting file
*.GhostDoc.xml

# Node.js Tools for Visual Studio
.ntvs_analysis.dat

# Visual Studio 6 build log
*.plg

# Visual Studio 6 workspace options file
*.opt

# Visual Studio LightSwitch build output
**/*.HTMLClient/GeneratedArtifacts
**/*.DesktopClient/GeneratedArtifacts
**/*.DesktopClient/ModelManifest.xml
**/*.Server/GeneratedArtifacts
**/*.Server/ModelManifest.xml
_Pvt_Extensions

# Paket dependency manager
.paket/paket.exe
paket-files/

# FAKE - F# Make
.fake/

# JetBrains Rider
.idea/
*.sln.iml
/Assembly/ProteoWizard.d/App
.Rproj.user
*.gz
*.zip
/DATA/MetaDNA/MetaDNA/%APPDATA%/Microsoft/Windows/IETldCache
/Assembly/Apps
/App
/Rscript/biodeep/biodeepdb_v3/Rscript/R/Library
/Rscript/R/compound_brites/.R_logs
/src/assembly/Apps
/Rscript/biodeep/biodeepdb_v3/Rscript/R
dist/Rscript/raw/UVtest.cdf
Rscript/R/mzkit/src/mzkit.dll
Rscript/R/mzkit/src/mzPack.o
Rscript/R/mzkit/src/RcppExports.o
dist/Rscript/raw/mzpack_v2/Angiotensin_AllScans.mzPack
DATA/test/aaaaaa.png
DATA/test/aaaaa.png
DATA/test/a.png
/dist/workbench/ms_imaging/HR2MSI mouse urinary bladder S096 - Figure1.ibd
/dist/workbench/ms_imaging/HR2MSI mouse urinary bladder S096 - Figure1.imzML
/dist/workbench/ms_imaging/demo.mzImage
dist/workbench/ms_imaging/HR2MSI_mouse_urinary_bladder-S096.mzImage
Rscript/Library/mzkit_app/test/peakdata.csv
Rscript/Library/mzkit_app/test/cluster_1/cluster.pack
Rscript/Library/mzkit_app/test/cluster_1/spectrum.dat
dist/Rscript/single_cells/brain1.dat
/Rscript/Library/mzkit_app/test/D1.cdf
/Rscript/Library/mzkit_app/test/D1.mzPack
Rscript/Library/mzkit_app/test/decode20231219/demo.dat
Rscript/Library/mzkit_app/test/pubchem/invalid_json.json