.gitignore

# Created by https://www.toptal.com/developers/gitignore/api/python,dotenv,visualstudiocode,macos,windows,linux,juputernotebooks,r
# Edit at https://www.toptal.com/developers/gitignore?templates=python,dotenv,visualstudiocode,macos,windows,linux,juputernotebooks,r

### dotenv ###
.env

#!! ERROR: juputernotebooks is undefined. Use list command to see defined gitignore types !!#

### 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

### 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/
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
*.py,cover
.hypothesis/
.pytest_cache/
cover/

# Translations
*.mo
*.pot

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

# Flask stuff:
instance/
.webassets-cache

# Scrapy stuff:
.scrapy

# Sphinx documentation
docs/_build/

# PyBuilder
.pybuilder/
target/

# Jupyter Notebook
.ipynb_checkpoints

# IPython
profile_default/
ipython_config.py

# pyenv
#   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

# poetry
#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
#   This is especially recommended for binary packages to ensure reproducibility, and is more
#   commonly ignored for libraries.
#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
#poetry.lock

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

# Celery stuff
celerybeat-schedule
celerybeat.pid

# SageMath parsed files
*.sage.py

# Environments
.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/

# pytype static type analyzer
.pytype/

# Cython debug symbols
cython_debug/

# PyCharm
#  JetBrains specific template is maintainted in a separate JetBrains.gitignore that can
#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
#  and can be added to the global gitignore or merged into this file.  For a more nuclear
#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
#.idea/

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

# Session Data files
.RData
.RDataTmp

# 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/
*.Rproj

# 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/
!cache/html_pages/coverage_images
!cache/html_pages/nt_predictions

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

# R Environment Variables
.Renviron

# pkgdown site
#docs/

# translation temp files
po/*~

# RStudio Connect folder
rsconnect/

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

### VisualStudioCode ###
.vscode/*

# Local History for Visual Studio Code
.history/

# Built Visual Studio Code Extensions
*.vsix

### VisualStudioCode Patch ###
# Ignore all local history of files
.history
.ionide

# Support for Project snippet scope

### 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

# End of https://www.toptal.com/developers/gitignore/api/python,dotenv,visualstudiocode,macos,windows,linux,juputernotebooks,r


### autoenv
.autoenv*

### private files not to share on github
private/

### markdown files inside docs overwrite 
!docs/*md

### result files – removing them one directory at a time
results/cell_gallery
results/completeness
results/movies
results/movie-descriptions
results/html_pages
results/gallery-descriptions
results/cell_gallery
results/fig_summary
results/eyemap
results/gallery
results/cov_compl
results/html_pages

### NeuVid Mesh Cache
neuVidNeuronMeshes/
neuVidRoiMeshes/
neuVidSynapseMeshes/
*-frames/
*-frames*/*png
*-frames*/preview-done
*-frames*/done
*.blend
*.blend1
src/movies/*avi



### Excel temp files
params/\~.*

### snakemake
.snakemake
workflow/.*
logs/*