.gitignore

.classpath
.project
.factorypath
.settings/
/.pydevproject
/listserv/
/log4j.properties
/vcell_debug_server.properties
/vcell_localClient.properties
/vfrapPaper/
jsbml.log
target/
node_modules/
.angular
*.pyc
*.so
*.so.*
*.dll
*.dylib
*.exe
*_x64
testzip
ziptool
.idea
.vagrant
/update/
/.checksums
vcell-client/UserDocumentation/originalXML/helpSearchConfig.txt
*.iml
.metadata/

### Eclipse ###
.metadata
bin/
tmp/
*.tmp
*.bak
*.swp
*~.nib
local.properties
.settings/
.loadpath
.recommenders
stdOut.txt
# External tool builders
.externalToolBuilders/

# Locally stored "Eclipse launch configurations"
*.launch

# PyDev specific (Python IDE for Eclipse)
*.pydevproject

# CDT-specific (C/C++ Development Tooling)
.cproject

# CDT- autotools
.autotools

# Java annotation processor (APT)
.factorypath

# PDT-specific (PHP Development Tools)
.buildpath

# sbteclipse plugin
.target

# Tern plugin
.tern-project

# TeXlipse plugin
.texlipse

# STS (Spring Tool Suite)
.springBeans

# Code Recommenders
.recommenders/

# Annotation Processing
.apt_generated/

# Scala IDE specific (Scala & Java development for Eclipse)
.cache-main
.scala_dependencies
.worksheet

### Eclipse Patch ###
# Eclipse Core
.project

# JDT-specific (Eclipse Java Development Tools)
.classpath

# Annotation Processing
.apt_generated

.sts4-cache/

### Java ###
# Compiled class file
*.class

# Log file
*.log

# BlueJ files
*.ctxt

# Mobile Tools for Java (J2ME)
.mtj.tmp/

# Package Files #
*.jar
*.war
*.nar
*.ear
*.zip
*.tar.gz
*.rar

# need this file for testing
!python-utils/tests/fixtures/modeldb-206365-outputs.zip

# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
hs_err_pid*

### macOS ###
# General
.DS_Store
.AppleDouble
.LSOverride

# Icon must end with two \r
Icon

# Thumbnails
._*

# Files that might appear in the root of a volume
.DocumentRevisions-V100
.fseventsd
.Spotlight-V100
.TemporaryItems
.Trashes
.VolumeIcon.icns
.com.apple.timemachine.donotpresent

# Directories potentially created on remote AFP share
.AppleDB
.AppleDesktop
Network Trash Folder
Temporary Items
.apdisk

# JetBrains Tools
.idea*
.run*

### VisualStudioCode ###
.vscode/*
!.vscode/settings.json
!.vscode/tasks.json
!.vscode/launch.json
!.vscode/extensions.json

### VisualStudioCode Patch ###
# Ignore all local history of files
.history

### envFile and Output file ###
# Ignore all local .env and generated output file
.env

### Windows ###
# Windows thumbnail cache files
Thumbs.db
Thumbs.db:encryptable
ehthumbs.db
ehthumbs_vista.db

# Dump file
*.stackdump

# Folder config file
[Dd]esktop.ini

# Recycle Bin used on file shares
$RECYCLE.BIN/

# Windows Installer files
*.cab
*.msi
*.msix
*.msm
*.msp

# Windows shortcuts
*.lnk
!results/.gitkeep
results/*

/status.yml
.java-version
.python-version

Makefile


run_sim.sh

remove_temp.sh

vcell-client/UserDocumentation/originalXML/helpSearchConfig.txt
.vscode/launch.json
.vscode/settings.json

pythonCopasiOpt/vcell-opt/dist/

vcell-core/src/test/resources/org/vcell/sbml/local

# Files generated during execution
temp*.out
temp*.err


vcell-core/src/test/resources/simdata/n5/N5ExportData/
!vcell-core/src/test/resources/simdata/n5/ezequiel23/SimID_1136922340_0_.log
!vcell-core/src/test/resources/simdata/n5/ezequiel23/SimID_1136922340_0_00.zip

docker/swarm/zeke_env.txt

webapp-ng/.nx/

localsolvers/mac64/GNUSparseFile.0/

webapp-ng/.nvmrc

pythonData/test_data/SimID_946368938_0__0.simtask.xml
pythonData/test_data/SimID_946368938_0_.functions
pythonData/test_data/SimID_946368938_0_.fvinput
pythonData/test_data/SimID_946368938_0_.hdf5
pythonData/test_data/SimID_946368938_0_.mesh
pythonData/test_data/SimID_946368938_0_.meshmetrics
pythonData/test_data/SimID_946368938_0_.subdomains
pythonData/test_data/SimID_946368938_0_.vcg
pythonData/test_data/SimID_946368938_mathmodel.vcml

pythonData/test_data/zarr/