.gitignore

# Untracked files

# Ignore all the files that match the indicated pattern. Check the
# official documentation for gitignore.
# https://git-scm.com/docs/gitignore

# This gitignore file was created by taken some patterns from
# https://github.com/github/gitignore # which is a collection of
# gitignore files

# ==============================================================
# SciCell++ files
# ==============================================================
src/general/cmake_definitions.h
docs/Makefile

# ==============================================================
# ggtags
# ==============================================================
GPATH
GRTAGS
GSYMS
GTAGS

# ==============================================================
# All files in the build and bin directories
# ==============================================================
bin/
build/
include/
code_report/
test_results/

# ==============================================================
# These include all files on any folder with the bin or build
# name
# ==============================================================
**/build/
**/bin/

# ==============================================================
# Ignore all files in RESLT folders
# ==============================================================
**/RESLT/
**/*RESLT*/

# ==============================================================
# Figures in private folder
# ==============================================================
private/**/*.png

# ==============================================================
# Ignore .dat files
# ==============================================================
**/*.dat

# ==============================================================
# Ignore core files
# ==============================================================
**/core

# ==============================================================
# Some files in the doc directory
# ==============================================================
doc/**/*.html
doc/**/*.htm
doc/*doxy_doc
**/*doxy_doc

# ==============================================================
# Ignore tar files, compressed versions
# ==============================================================
#*.tar.gz

# ==============================================================
# Latex generated files in doc directoy
# ==============================================================
## Core latex/pdflatex auxiliary files:
doc/**/*.aux
doc/**/*.lof
doc/**/*.log
doc/**/*.lot
doc/**/*.fls
doc/**/*.out
doc/**/*.toc
doc/**/*.fmt

private/**/*.aux
private/**/*.lof
private/**/*.log
private/**/*.lot
private/**/*.fls
private/**/*.out
private/**/*.toc
private/**/*.fmt

## Intermediate documents:
doc/**/*.dvi
doc/**/*-converted-to.*
# these rules might exclude image files for figures etc.
# doc/**/*.ps
# doc/**/*.eps
# doc/**/*.pdf

## Bibliography auxiliary files (bibtex/biblatex/biber):
doc/**/*.bbl
doc/**/*.bcf
doc/**/*.blg
doc/**/*-blx.aux
doc/**/*-blx.bib
doc/**/*.brf
doc/**/*.run.xml

private/**/*.bbl
private/**/*.bcf
private/**/*.blg
private/**/*-blx.aux
private/**/*-blx.bib
private/**/*.brf
private/**/*.run.xml

## Build tool auxiliary files:
doc/**/*.fdb_latexmk
doc/**/*.synctex
doc/**/*.synctex.gz
doc/**/*.synctex.gz(busy)
doc/**/*.pdfsync

## Auxiliary and intermediate files from other packages:
# algorithms
doc/**/*.alg
doc/**/*.loa

# achemso
doc/**/acs-*.bib

# amsthm
doc/**/*.thm

# beamer
doc/**/*.nav
doc/**/*.snm
doc/**/*.vrb

# cprotect
doc/**/*.cpt

#(e)ledmac/(e)ledpar
doc/**/*.end
doc/**/*.[1-9]
doc/**/*.[1-9][0-9]
doc/**/*.[1-9][0-9][0-9]
doc/**/*.[1-9]R
doc/**/*.[1-9][0-9]R
doc/**/*.[1-9][0-9][0-9]R
doc/**/*.eledsec[1-9]
doc/**/*.eledsec[1-9]R
doc/**/*.eledsec[1-9][0-9]
doc/**/*.eledsec[1-9][0-9]R
doc/**/*.eledsec[1-9][0-9][0-9]
doc/**/*.eledsec[1-9][0-9][0-9]R

# glossaries
doc/**/*.acn
doc/**/*.acr
doc/**/*.glg
doc/**/*.glo
doc/**/*.gls

# gnuplottex
doc/**/*-gnuplottex-*

# hyperref
doc/**/*.brf

# knitr
doc/**/*-concordance.tex
doc/**/*.tikz
doc/**/*-tikzDictionary

# listings
doc/**/*.lol

# makeidx
doc/**/*.idx
doc/**/*.ilg
doc/**/*.ind
doc/**/*.ist

# minitoc
doc/**/*.maf
doc/**/*.mtc
doc/**/*.mtc[0-9]
doc/**/*.mtc[1-9][0-9]

# minted
doc/**/_minted*
doc/**/*.pyg

# morewrites
doc/**/*.mw

# mylatexformat
doc/**/*.fmt

# nomencl
doc/**/*.nlo

# sagetex
doc/**/*.sagetex.sage
doc/**/*.sagetex.py
doc/**/*.sagetex.scmd

# sympy
doc/**/*.sout
doc/**/*.sympy
doc/**/sympy-plots-for-*.tex/

# pdfcomment
doc/**/*.upa
doc/**/*.upb

#pythontex
doc/**/*.pytxcode
doc/**/pythontex-files-*/

# Texpad
doc/**/.texpadtmp

# TikZ & PGF
doc/**/*.dpth
doc/**/*.md5
doc/**/*.auxlock

# todonotes
doc/**/*.tdo

# xindy
doc/**/*.xdy

# xypic precompiled matrices
doc/**/*.xyc

# WinEdt
doc/**/*.bak
doc/**/*.sav

# endfloat
doc/**/*.ttt
doc/**/*.fff

# Latexian
doc/**/TSWLatexianTemp*

# Kile
doc/**/*.kilepr

# Doxygen generated files
doc/*doxy_doc

# ==============================================================
# C++
# ==============================================================
# Compiled Object files
*.slo
*.lo
*.o
*.obj

# Precompiled Headers
*.gch
*.pch

# Compiled Dynamic libraries
*.so
*.dylib
*.dll

# Fortran module files
*.mod

# Compiled Static libraries
*.lai
*.la
*.a
*.lib

# Executables
*.exe
*.out
*.app

# ==============================================================
# C
# ==============================================================
# Object files
*.o
*.ko
*.obj
*.elf

# Precompiled Headers
*.gch
*.pch

# Libraries
*.lib
*.a
*.la
*.lo

# Shared objects (inc. Windows DLLs)
*.dll
*.so
*.so.*
*.dylib

# Executables
*.exe
*.out
*.app
*.i*86
*.x86_64
*.hex

# Debug files
*.dSYM/

# ==============================================================
# CMake
# ==============================================================
CMakeCache.txt
CMakeFiles
CMakeScripts
Makefile
cmake_install.cmake
install_manifest.txt

# ==============================================================
# Emacs
# ==============================================================
# Emacs temporary files
*~
# This requires a '\' because the first character is a #
\#*\#
.#*

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

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

# 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

# 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

# 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

# ==============================================================
# Qt related files
# ==============================================================

# Qt-es

/.qmake.cache
/.qmake.stash
*.pro.user
*.pro.user.*
*.qbs.user
*.qbs.user.*
*.moc
moc_*.cpp
moc_*.h
qrc_*.cpp
ui_*.h
Makefile*
*build-*

# QtCreator

*.autosave

# QtCtreator Qml
*.qmlproject.user
*.qmlproject.user.*

# QtCtreator CMake
CMakeLists.txt.user*

# **************************************************************
# **************************************************************
# ==============================================================
# Exceptions
# ==============================================================
# **************************************************************
# **************************************************************
# !bin/clean_distro.py
# !bin/plot_bp_p0.py
# !bin/plot_multiple_break_probability.py
# !bin/plot_one_bp_density_vs_current_and_velocity.py
# !bin/plot_time_space.py
!bin/
bin/*
!bin/*.py
demos/**/bin/
private/**/bin/
private/**/*.dat
private/**/*.vtu

# ==============================================================
# .dat files in demos folder
# ==============================================================
!demos/**/*.dat