.gitignore

##########################
# Project Input and Output
##########################

# Exclude data folder, since it should all be pulled automatically (unless in the manual folder)
/data/*
!/data/manual/

# Exclude output directory since it's should generated automatically
/output/*

# Exclude PDFs generated from source LaTeX files, which are kept in the reports directory
/reports/*.pdf

# Secrets saved in environment files
.env*

# Other
temp*.csv
*/_build/
*/_notebook_build/
drafts/draft_bp.pdf

##############
#Excluded PDFs
##############
# I've decided to exclude all PDFs unless they're in the literature or papers directory.
# http://stackoverflow.com/questions/1248570/git-ignore-everything-except-subdirectory

# !/related_literature/*
# !/related_literature/
# !/related_literature/*/*
# !/Papers/*
# !/papers/*
# !/literature/*

##############
# LaTex Files
##############
reports/*.aux
reports/*.bbl
reports/*.blg
reports/*.fdb_latexmk
reports/*.fls
reports/*.log
reports/*.out
reports/*.nav
reports/*.pdfsync
reports/*.synctex.gz
reports/*.bak
reports/*.snm
reports/*.toc
reports/*.tdo
reports/*.run.xml
reports/*.loe


##########
# R Files
##########
.Rproj.user
.Rhistory
.RData
.Rapp.history
.Ruserdata
# RStudio files
.Rproj.user/
# produced vignettes
vignettes/*.html
vignettes/*.pdf
# R Environment Variables
.Renviron

# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
.httr-oauth

# knitr and R markdown default cache directories
*_cache/
/cache/

# Temporary files created by R markdown
*.utf8.md
*.knit.md

# Output files from R CMD check
/*.Rcheck/


########
# MISC.
########
# *.zip
# *.tar.gz
\.pytest_cache/

# Pydoit
.doit.*

# Exclude Sublime Text project files
*.sublime*

# Exclude Mac OSX system files
.DS_Store

# IPython/Jupyter Checkpoints
.ipynb_checkpoints
.ipynb_checkpoints/

# Vagrant
.vagrant/


# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]

# Distribution / packaging
.Python
env/
build/
develop-eggs/
dist/
downloads/
eggs/
lib/
lib64/
parts/
sdist/
var/
*.egg-info/
.installed.cfg
*.egg

# PyInstaller
#  Usually these files are written by a python script from a template
#  before PyInstaller builds the exe, so as to inject date/other infos into it.
*.manifest
*.spec

# Installer logs
pip-log.txt
pip-delete-this-directory.txt

# Unit test / coverage reports
htmlcov/
.tox/
.coverage
.cache
nosetests.xml
coverage.xml

# Sphinx documentation
docs/
/docs_src/apidocs


# PyBuilder
target/

# emacs
*~
# C extensions
*.so