.gitignore

# vim: set foldmethod=marker :
########################################################################
# This file is a compilation of some among the most common ignores
# needed for scientists producing texts in a number of formats (LaTeX,
# Word, Excel, etc.), PDF files, and working with stuff such as Python
# and R. As a bonus, there are some standard ignore patterns for Windows
# and Mac.

# Generated binary files (PDF, Word, etc.) go here {{{1
## Book build output
_book

# For when you want to keep downloaded or received files next to your
# repo without committing them (bc they're usually binaries).
_share
figures
styles

# Jekyll {{{1
_site/
Gemfile.lock
styles
.sass-cache/
.jekyll-cache/
.jekyll-metadata
.vendor/
.bundle/

# eBook build output {{{1
*.epub
*.mobi
*.pdf

# LaTeX {{{ 1
## Core latex/pdflatex auxiliary files: {{{2
*.aux
*.lof
*.log
*.lot
*.fls
*.out
*.toc
*.fmt
*.fot
*.cb
*.cb2
.*.lb

## Intermediate documents: {{{2
*.dvi
*.xdv
*-converted-to.*
# these rules might exclude image files for figures etc.
# *.ps
# *.eps
# *.pdf

## Generated if empty string is given at "Please type another file name for output:"
.pdf

## Bibliography auxiliary files (bibtex/biblatex/biber): {{{2
*.bbl
*.bcf
*.blg
*-blx.aux
*-blx.bib
*.run.xml

## Build tool auxiliary files: {{{2
*.fdb_latexmk
*.synctex
*.synctex(busy)
*.synctex.gz
*.synctex.gz(busy)
*.pdfsync

## Auxiliary and intermediate files from other packages: {{{2
### algorithms
*.alg
*.loa

### achemso
acs-*.bib

### amsthm
*.thm

### beamer
*.nav
*.pre
*.snm
*.vrb

### changes
*.soc

### cprotect
*.cpt

### elsarticle (documentclass of Elsevier journals)
*.spl

### endnotes
*.ent

### fixme
*.lox

### feynmf/feynmp
*.mf
*.mp
*.t[1-9]
*.t[1-9][0-9]
*.tfm

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

### glossaries
*.acn
*.acr
*.glg
*.glo
*.gls
*.glsdefs

### gnuplottex
*-gnuplottex-*

### gregoriotex
*.gaux
*.gtex

### htlatex
*.4ct
*.4tc
*.idv
*.lg
*.trc
*.xref

### hyperref
*.brf

### knitr
*-concordance.tex
# TODO Comment the next line if you want to keep your tikz graphics files
*.tikz
*-tikzDictionary

### listings
*.lol

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

### minitoc
*.maf
*.mlf
*.mlt
*.mtc[0-9]*
*.slf[0-9]*
*.slt[0-9]*
*.stc[0-9]*

### minted
_minted*
*.pyg

### morewrites
*.mw

### nomencl
*.nlg
*.nlo
*.nls

### pax
*.pax

### pdfpcnotes
*.pdfpc

### sagetex
*.sagetex.sage
*.sagetex.py
*.sagetex.scmd

### scrwfile
*.wrt

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

### pdfcomment
*.upa
*.upb

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

### thmtools
*.loe

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

### todonotes
*.tdo

### easy-todo
*.lod

### xmpincl
*.xmpi

### xindy
*.xdy

### xypic precompiled matrices
*.xyc

### endfloat
*.ttt
*.fff

### Latexian
TSWLatexianTemp*

## Editors: {{{2
### WinEdt
*.bak
*.sav

### Texpad
.texpadtmp

### Kile
*.backup

### KBibTeX
*~[0-9]*

## auto folder when using emacs and auctex {{{2
./auto/*
*.el

# expex forward references with \gathertags
*-tags.tex

# standalone packages
*.sta

# generated if using elsarticle.cls
*.spl

# Word processors and other binary cruft {{{1
# LibreOffice locks
.~lock.*#
*.tmp
tmp/

# Word temporary
~$*.doc*

# Word Auto Backup File
Backup of *.doc*

# Excel temporary
~$*.xls*

# Excel Backup File
*.xlk

# PowerPoint temporary
~$*.ppt*

# Node rules: {{{1
## Grunt intermediate storage (http://gruntjs.com/creating-plugins#storing-task-files)
.grunt

## Dependency directory
## Commenting this out is preferred by some people, see
## https://docs.npmjs.com/misc/faq#should-i-check-my-node_modules-folder-into-git
node_modules

# Windows {{{1
# Temporary
.netrwhist
*~
# Auto-generated tag files
tags
# Persistent undo
[._]*.un~
# Windows thumbnail cache files
Thumbs.db
Thumbs.db:encryptable
ehthumbs.db
ehthumbs_vista.db

# Folder config file
[Dd]esktop.ini

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

# Windows shortcuts
*.lnk

# MacOS {{{1
.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

# Python {{{1
# Byte-compiled / optimized / DLL files {{{2
__pycache__/
*.py[cod]
*$py.class

# C extensions {{{2
*.so

# Distribution / packaging {{{2
.Python
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
# lib/
lib64/
parts/
sdist/
var/
wheels/
pip-wheel-metadata/
share/python-wheels/
*.egg-info/
.installed.cfg
*.egg
MANIFEST

# PyInstaller {{{2
#  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 {{{2
htmlcov/
.tox/
.nox/
.coverage
.coverage.*
.cache
nosetests.xml
coverage.xml
*.cover
*.py,cover
.hypothesis/
.pytest_cache/

# Translations {{{2
*.mo
*.pot

# Django stuff: {{{2
*.log
local_settings.py
db.sqlite3
db.sqlite3-journal

# Flask stuff: {{{2
instance/
.webassets-cache

# Scrapy stuff: {{{2
.scrapy

# Sphinx documentation {{{2
docs/_build/

# PyBuilder {{{2
target/

# Jupyter Notebook {{{2
.ipynb_checkpoints

# IPython {{{2
profile_default/
ipython_config.py

# pyenv {{{2
#   For a library or package, you might want to ignore these files since the code is
#   intended to run in multiple environments; otherwise, check them in:
.python-version

# pipenv
#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
#   However, in case of collaboration, if having platform-specific dependencies or dependencies
#   having no cross-platform support, pipenv may install dependencies that don't work, or not
#   install all needed dependencies.
#Pipfile.lock

# PEP 582; used by e.g. github.com/David-OConnor/pyflow {{{2
__pypackages__/

# Celery stuff {{{2
celerybeat-schedule
celerybeat.pid

# SageMath parsed files {{{2
*.sage.py

# Environments {{{2
.env
.venv
env/
venv/
ENV/
env.bak/
venv.bak/

# Spyder project settings {{{2
.spyderproject
.spyproject

# Rope project settings {{{2
.ropeproject

# mkdocs documentation {{{2
/site

# mypy {{{2
.mypy_cache/
.dmypy.json
dmypy.json

# Pyre type checker {{{2
.pyre/

# pytype static type analyzer {{{2
.pytype/

# R {{{1
## 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