setup_all.sh

#!/usr/bin/env bash

## This script creates Python virtualenv and installs libraries for analysis.
## No deep learning framework will be installed.
##
## The first argument is recognised as the name of virtualenv.

WITH_GIT="yes"
WITH_DVC="yes"

if [[ -z "$1" ]]; then
  VENV="venv"
else
  VENV=$1
fi

echo "-- Create a Python environment"
python -m venv $VENV

echo "-- Activate the Python environment: $VENV"
source $VENV/bin/activate

echo "-- Upgrade pip"
pip install --upgrade pip

echo "-- Install adhoc and required libraries"
pip install https://github.com/stdiff/adhoc/archive/v0.4.zip

echo "-- Install jupyter lab and jupytext"
pip install jupyter==1.0.0
pip install jupyterlab==2.1.4
pip install jupytext==1.5.0

echo "-- Install jupyterlab_spellchecker"
jupyter labextension install @ijmbarr/jupyterlab_spellchecker

echo "-- Install jupyterlab_templates"
pip install jupyterlab_templates==0.2.4
jupyter labextension install jupyterlab_templates@0.2.4
jupyter serverextension enable --py jupyterlab_templates

#echo "-- Install jupyterlab-emacskeys"
#jupyter labextension install jupyterlab-emacskeys

echo "-- Install further libraries"
pip install watermark==2.0.2
pip install click==7.1.2
##pip install scikit-image==0.16.2 pillow==6.2.2

echo "-- create requirements.txt"
pip freeze > requirements.txt

if [ "$WITH_GIT" == "yes" ]; then 
echo "-- initialize git"
git init
cat << EOF > .gitignore
## virtualenv
venv/

## PyCharm
.idea

## Jupyter Notebook Checkpoints
notebooks/.ipynb_checkpoints/

## temporary workspace
tmp/
EOF
echo "Do not forget to add a remote: git remote add origin URL"
git add .gitignore
git add requirements.txt
git commit -m "init"

    if [ "$WITH_DVC" == "yes" ]; then 
    echo "-- install DVC as a Python library"
    pip install dvc[s3]

    echo "-- initialize DVC"
    dvc init --quiet
    dvc install 

    git add .dvc/config
    git commit -m "DVC prepared"
    echo "Do not forget to add a remote: dvc remote add -d default URL"
    fi
fi

echo "-- Deactivate the Python environment"
deactivate

echo "-- Create some directories"
mkdir data
mkdir lib
mkdir notebook
mkdir test
mkdir tmp