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setup_recolour_system_conda_python_notebook.sh
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#!/bin/bash -e
#-----------------------------------------------------------------------------------------
# Script information
script_name='RECOLOUR ENVIRONMENT - PYTHON3 LIBRARIES FOR PACKAGE - NOTEBOOK TYPE - CONDA'
script_version="1.6.4"
script_date='2023/05/22'
# Define file reference path according with https link(s) --> https://repo.anaconda.com/miniconda/
fp_env_file_miniconda='https://repo.continuum.io/miniconda/Miniconda3-py37_4.8.2-Linux-x86_64.sh'
#fp_env_file_miniconda='https://repo.continuum.io/miniconda/Miniconda3-py39_23.1.0-1-Linux-x86_64.sh'
# Argument(s) default definition(s)
fp_env_tag_default='recolour_notebook'
fp_env_folder_root_default='./conda/'
fp_env_file_reference_default='%ENV_TAG_settings'
fp_env_folder_libraries_default='%ENV_TAG_libraries'
fp_env_file_requirements_default='requirements_%ENV_TAG.yaml'
# Examples of generic command-line:
# conda create --yes --name $fp_env_folder_libraries numpy scipy pip python=3
# conda create --yes --nama $fp_env_folder_libraries -c conda-forge pyresample pygeobase
# conda install --yes -c conda-forge nbconvert
# conda env export | grep -v "^prefix: " > requirements_fp_env_python.yaml
# conda env create --file $fp_env_file_requirements # create virtual env using yaml file
# conda create -y --name $fp_env_folder_libraries --file $fp_env_file_requirements # create virtual env using ascii file
#-----------------------------------------------------------------------------------------
# ----------------------------------------------------------------------------------------
# Info script start
echo " ==================================================================================="
echo " ==> "$script_name" (Version: "$script_version" Release_Date: "$script_date")"
echo " ==> START ..."
# Get arguments number and values
script_args_n=$#
script_args_values=$@
echo ""
echo " ==> Script arguments number: $script_args_n"
echo " ==> Script arguments values: $script_args_values"
echo ""
echo " ==> ARGS DEFINED:"
echo ""
echo " ==> Script arguments 1 - Tag of virtual environmenf [string: path]-> $1"
echo " ==> Script arguments 2 - Directory of libraries [string: path]-> $2"
echo " ==> Script arguments 3 - Filename of system environment [string: filename] -> $3"
echo " ==> Script arguments 4 - Name of virtual environment [string: name] -> $4"
echo " ==> Script arguments 5 - Filename of system requirements in yaml format [string: name] -> $5"
echo ""
# Get folder root path
if [ $# -eq 0 ]; then
fp_env_tag=$fp_env_tag_default
fp_env_folder_root=$fp_env_folder_root_default
fp_env_file_reference=$fp_env_file_reference_default
fp_env_folder_libraries=$fp_env_folder_libraries_default
fp_env_file_requirements=$fp_env_file_requirements_default
elif [ $# -eq 1 ]; then
fp_env_tag=$1
fp_env_folder_root=$fp_env_folder_root_default
fp_env_file_reference=$fp_env_file_reference_default
fp_env_folder_libraries=$fp_env_folder_libraries_default
fp_env_file_requirements=$fp_env_file_requirements_default
elif [ $# -eq 2 ]; then
fp_env_tag=$1
fp_env_folder_root=$2
fp_env_file_reference=$fp_env_file_reference_default
fp_env_folder_libraries=$fp_env_folder_libraries_default
fp_env_file_requirements=$fp_env_file_requirements_default
elif [ $# -eq 3 ]; then
fp_env_tag=$1
fp_env_folder_root=$2
fp_env_file_reference=$3
fp_env_folder_libraries=$fp_env_folder_libraries_default
fp_env_file_requirements=$fp_env_file_requirements_default
elif [ $# -eq 4 ]; then
fp_env_tag=$1
fp_env_folder_root=$2
fp_env_file_reference=$3
fp_env_folder_libraries=$4
fp_env_file_requirements=$fp_env_file_requirements_default
elif [ $# -eq 5 ]; then
fp_env_tag=$1
fp_env_folder_root=$2
fp_env_file_reference=$3
fp_env_folder_libraries=$4
fp_env_file_requirements=$5
fi
# Set the
fp_env_folder_root=${fp_env_folder_root/'%ENV_TAG'/$fp_env_tag}
fp_env_file_reference=${fp_env_file_reference/'%ENV_TAG'/$fp_env_tag}
fp_env_folder_libraries=${fp_env_folder_libraries/'%ENV_TAG'/$fp_env_tag}
fp_env_file_requirements=${fp_env_file_requirements/'%ENV_TAG'/$fp_env_tag}
echo ""
echo " ==> ARGS SELECTED:"
echo ""
echo " ==> Script arguments 1 - Tag of virtual environmenf [string: path]-> ${fp_env_tag}"
echo " ==> Script arguments 2 - Directory of libraries [string: path]-> ${fp_env_folder_root}"
echo " ==> Script arguments 3 - Filename of system environment [string: filename] -> ${fp_env_file_reference}"
echo " ==> Script arguments 4 - Name of virtual environment [string: name] -> ${fp_env_folder_libraries}"
echo " ==> Script arguments 5 - Filename of system requirements in yaml format [string: name] -> ${fp_env_file_requirements}"
echo ""
# Create root folder
if [ ! -d "$fp_env_folder_root" ]; then
mkdir -p $fp_env_folder_root
fi
# Define folder path(s)
fp_env_folder_root=$fp_env_folder_root
# Define environment filename
fp_env_path_reference=$fp_env_folder_root/$fp_env_file_reference
# multilines comment: if [ 1 -eq 0 ]; then ... fi
#-----------------------------------------------------------------------------------------
# ----------------------------------------------------------------------------------------
# Install python environmente using miniconda
echo " ====> CHECK PYTHON ENVIRONMENT ... "
if [ -d "$fp_env_folder_root/bin/" ] > /dev/null 2>&1 ; then
export PATH="$fp_env_folder_root/bin:$PATH"
if source activate $fp_env_folder_root > /dev/null 2>&1 ; then
echo " ====> CHECK PYTHON ENVIRONMENT ... FOUND."
fp_env_install=false
else
echo " ====> CHECK PYTHON ENVIRONMENT ... FOUND ENVIRONMENT BUT LIBRARIES ARE NOT FOUND."
fp_env_install=false
fi
else
echo " ====> CHECK PYTHON ENVIRONMENT ... NOT FOUND."
fp_env_install=true
fi
echo " ====> INSTALL PYTHON ENVIRONMENT ... "
if $fp_env_install; then
# Download library source codes
echo " =====> GET LIBRARY FILES ... "
wget $fp_env_file_miniconda -O miniconda.sh
echo " =====> GET LIBRARY FILES ... DONE!"
if [ -d "$fp_env_folder_root" ]; then
rm -Rf $fp_env_folder_root;
fi
bash miniconda.sh -b -p $fp_env_folder_root
echo " ====> INSTALL PYTHON ENVIRONMENT ... DONE!"
else
echo " ====> INSTALL PYTHON ENVIRONMENT ... DONE. PREVIOSLY INSTALLED"
fi
# ----------------------------------------------------------------------------------------
# ----------------------------------------------------------------------------------------
# Install python libraries
echo " ====> INSTALL PYTHON LIBRARIES ... "
export PATH="$fp_env_folder_root/bin:$PATH"
if [ -f $fp_env_file_requirements ] ; then
echo " =====> USE OF CONDA REQUIREMENTS FILE YAML: $fp_env_file_requirements"
# source activate $fp_env_folder_libraries
# conda create -y --name $fp_env_folder_libraries --file $fp_env_file_requirements
conda env create --file $fp_env_file_requirements
else
echo " =====> USE OF CONDA GENERIC COMMAND-LINE"
echo " =====> CONDA INSTALLATION ... "
echo " ======> [1/3] CONDA-DEFAULT CHANNEL INSTALLATION ... "
conda create --yes --name $fp_env_folder_libraries numpy scipy pandas seaborn matplotlib=3.1.3 rasterio geopandas cartopy=0.17 netCDF4 pip jupyterlab ipywidgets ipympl nodejs=12 python=3.7
echo " ======> [1/3] CONDA-DEFAULT CHANNEL INSTALLATION ... DONE"
echo " ======> [2/3] PYTHON-PIP INSTALLATION ... "
source activate $fp_env_folder_libraries
pip install cmcrameri
pip install pygeogrids
pip install pytesmo==0.13.4
echo " ======> [2/3] PYTHON-PIP INSTALLATION ... DONE"
echo " ======> [3/3] JUPYTER-NOTEBOOK INSTALLATION ... "
jupyter labextension install @jupyter-widgets/jupyterlab-manager
jupyter lab build
echo " ======> [3/3] JUPYTER-NOTEBOOK INSTALLATION ... DONE"
echo " =====> CONDA INSTALLATION ... DONE"
fi
echo " ====> INSTALL PYTHON LIBRARIES ... DONE!"
# ----------------------------------------------------------------------------------------
# ----------------------------------------------------------------------------------------
# Create environmental file
echo " ====> CREATE ENVIRONMENTAL FILE ... "
# Delete old version of environmental file
cd $fp_env_folder_root
if [ -f $fp_env_file_reference ] ; then
rm $fp_env_file_reference
fi
# Export BINARY PATH(S)
echo "PATH=$fp_env_folder_root/bin:"'$PATH'"" >> $fp_env_file_reference
echo "export PATH" >> $fp_env_file_reference
# Export VENV ACTIVATION
echo "source activate $fp_env_folder_libraries" >> $fp_env_file_reference
echo " ====> CREATE ENVIRONMENTAL FILE ... DONE!"
# ----------------------------------------------------------------------------------------
# ----------------------------------------------------------------------------------------
# Info script end
echo " ==> "$script_name" (Version: "$script_version" Release_Date: "$script_date")"
echo " ==> ... END"
echo " ==> Bye, Bye"
echo " ==================================================================================="
# ----------------------------------------------------------------------------------------