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

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

# 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*
# Allow example environment file
!.env.example*

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

# venv virtual environment folder
/venv/*
/.venv/*
/.venv/*

# Sphinx build files
_docs/


##############
#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/*

#########################
# Exclude Compiled Files
#########################
bin/
*.pyc
*.exe
SourceCode/build/
bin/
a.out

# 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

# Translations
*.mo
*.pot

# Django stuff:
*.log

# Sphinx documentation
docs/
/docs_src/apidocs


# PyBuilder
target/

# emacs
*~
# C extensions
*.so

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


##########
# R Files
##########
.Rproj.user
.Rhistory
.RData
.Rapp.history

################
# Database Files
################
*.hdf5
*.npz

###################################
# Exclude Output From Scripted Jobs
###################################
*.o*

####################################
# Exclude Sublime Text project files
####################################
*.sublime*

####################################
# Exclude Mac OSX system files
####################################
.DS_Store

####################################
# IPython/Jupyter Checkpoints
####################################
.ipynb_checkpoints
.ipynb_checkpoints/

####################################
# Vagrant
####################################
.vagrant/

######################################
## R files ##
######################################
# History files
.Rhistory
.Rapp.history

# Session Data files
.RData

# User-specific files
.Ruserdata

# Example code in package build process
*-Ex.R

# Output files from R CMD build
/*.tar.gz

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

# RStudio files
.Rproj.user/

# produced vignettes
vignettes/*.html
vignettes/*.pdf

# 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

# R Environment Variables
.Renviron

########
# MISC.
########
# *.zip
# *.tar.gz
*.aux
*.bbl
*.bcf
*.blg
*.dat
*.dir
*.fdb_latexmk
*.fls
*.graphml
*.gz
*.ini
*.log
*.out
*.vrb
*.xdv
*.xdv
\.pytest_cache/
~$*

.doit.db.db
.doit-db.sqlite

src/z_scratch_project_template.ipynb

*Thumbs.db

src/z_scratch_pipeline_template.ipynb

# Notebooks that run_notebooks makes from src/*.py and deletes again
src/*_ipynb.ipynb

# The Markdown chartbook docs generate writes before Sphinx runs; a build makes and removes it
_docs_src/
