.gitignore

# Created by https://www.gitignore.io/api/r,java,julia,linux,macos,python,windows,pycharm,jupyternotebooks,gradle
# Edit at https://www.gitignore.io/?templates=r,java,julia,linux,macos,python,windows,pycharm,jupyternotebooks,gradle

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

# Log file
*.log

# BlueJ files
*.ctxt

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


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

### Julia ###
# Files generated by invoking Julia with --code-coverage
*.jl.cov
*.jl.*.cov

# Files generated by invoking Julia with --track-allocation
*.jl.mem

# System-specific files and directories generated by the BinaryProvider and BinDeps packages
# They contain absolute paths specific to the host computer, and so should not be committed
deps/deps.jl
deps/build.log
deps/downloads/
deps/usr/
deps/src/

# Build artifacts for creating documentation generated by the Documenter package
docs/build/
docs/site/

# File generated by Pkg, the package manager, based on a corresponding Project.toml
# It records a fixed state of all packages used by the project. As such, it should not be
# committed for packages, but should be committed for applications that require a static
# environment.
Manifest.toml

### JupyterNotebooks ###
# gitignore template for Jupyter Notebooks
# website: http://jupyter.org/

.ipynb_checkpoints
*/.ipynb_checkpoints/*


# Remove previous ipynb_checkpoints
#   git rm -r .ipynb_checkpoints/
#

### Linux ###
*~

# temporary files which can be created if a process still has a handle open of a deleted file
.fuse_hidden*

# KDE directory preferences
.directory

# Linux trash folder which might appear on any partition or disk
.Trash-*

# .nfs files are created when an open file is removed but is still being accessed
.nfs*

### 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

### PyCharm ###
# Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm, CLion, Android Studio and WebStorm
# Reference: https://intellij-support.jetbrains.com/hc/en-us/articles/206544839

# User-specific stuff
../.idea/
.idea/**/workspace.xml
.idea/**/tasks.xml
.idea/**/usage.statistics.xml
.idea/**/dictionaries
.idea/**/shelf

# Generated files
.idea/**/contentModel.xml

# Sensitive or high-churn files
.idea/**/dataSources/
.idea/**/dataSources.ids
.idea/**/dataSources.local.xml
.idea/**/sqlDataSources.xml
.idea/**/dynamic.xml
.idea/**/uiDesigner.xml
.idea/**/dbnavigator.xml

# Gradle
.idea/**/gradle.xml
.idea/**/libraries

# Gradle and Maven with auto-import
# When using Gradle or Maven with auto-import, you should exclude module files,
# since they will be recreated, and may cause churn.  Uncomment if using
# auto-import.
# .idea/modules.xml
# .idea/*.iml
# .idea/modules
# *.iml
# *.ipr

# CMake
cmake-build-*/

# Mongo Explorer plugin
.idea/**/mongoSettings.xml

# File-based project format
*.iws

# IntelliJ
out/

# mpeltonen/sbt-idea plugin
.idea_modules/

# JIRA plugin
atlassian-ide-plugin.xml

# Cursive Clojure plugin
.idea/replstate.xml

# Crashlytics plugin (for Android Studio and IntelliJ)
com_crashlytics_export_strings.xml
crashlytics.properties
crashlytics-build.properties
fabric.properties

# Editor-based Rest Client
.idea/httpRequests

# Android studio 3.1+ serialized cache file
.idea/caches/build_file_checksums.ser

### PyCharm Patch ###
# Comment Reason: https://github.com/joeblau/gitignore.io/issues/186#issuecomment-215987721

# *.iml
# modules.xml
# .idea/misc.xml
# *.ipr

# Sonarlint plugin
.idea/sonarlint

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

# C extensions
*.so

# Distribution / packaging
.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
#  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/
.nox/
.coverage
.coverage.*
.cache
nosetests.xml
coverage.xml
*.cover
.hypothesis/
.pytest_cache/

# Translations
*.mo
*.pot

# Django stuff:
local_settings.py
db.sqlite3
db.sqlite3-journal

# Flask stuff:
instance/
.webassets-cache

# Scrapy stuff:
.scrapy

# Sphinx documentation
docs/_build/

# PyBuilder
target/

# Jupyter Notebook

# IPython
profile_default/
ipython_config.py

# pyenv
.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

# celery beat schedule file
celerybeat-schedule

# SageMath parsed files
*.sage.py

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

# Spyder project settings
.spyderproject
.spyproject

# Rope project settings
.ropeproject

# mkdocs documentation
/site

# mypy
.mypy_cache/
.dmypy.json
dmypy.json

# Pyre type checker
.pyre/

### R ###
# 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.Bookdown Stack ###
# R package: bookdown caching files
/*_files/

### 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

### Gradle ###
.gradle

# Ignore Gradle GUI config
gradle-app.setting

# Avoid ignoring Gradle wrapper jar file (.jar files are usually ignored)
!gradle-wrapper.jar

# Cache of project
.gradletasknamecache

# # Work around https://youtrack.jetbrains.com/issue/IDEA-116898
# gradle/wrapper/gradle-wrapper.properties

### Gradle Patch ###
**/build/

# End of https://www.gitignore.io/api/r,java,julia,linux,macos,python,windows,pycharm,jupyternotebooks,gradle


# Created by https://www.gitignore.io/api/maven
# Edit at https://www.gitignore.io/?templates=maven

### Maven ###
target/
pom.xml.tag
pom.xml.releaseBackup
pom.xml.versionsBackup
pom.xml.next
release.properties
dependency-reduced-pom.xml
buildNumber.properties
.mvn/timing.properties
.mvn/wrapper/maven-wrapper.jar

# End of https://www.gitignore.io/api/maven


# added by hans for general purposes
/data/
/scratch/
/scratch
.snakemake/


# added by Anna for general purposes :)

.config/
.local/
code/notebooks/
!/data/part3/