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Pre-requisites for ubuntu install #2

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621b8df
comments on prerequisites for ubuntu install
Oct 8, 2020
7ced6fe
Update of install instruction + new swatplus_wgn.sqlite source
Oct 16, 2020
4259d81
customize install dir in my conda environment
Apr 23, 2021
7b9f905
update import of osgeo modules
Apr 23, 2021
ff903d6
Update install.sh
jphuart Oct 5, 2021
dd2eeb7
change variable name to avoid confusion
Oct 5, 2021
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1 change: 1 addition & 0 deletions .gitignore
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*.pyc
46 changes: 30 additions & 16 deletions install.sh
100644 → 100755
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#!/bin/bash

# To isolate this from other Python projects, create a specific user on your machine
# and install libraries at user level, excepted qgis, python3-pip and mpich packages.
#
# Before launching this script make sure that the following packages have been installed
#
# For Ubuntu 20.04
# sudo apt install qgis python3-pip mpich
# pip3 install --user geopandas peewee cython scipy
#
# set version to download
version="1.0.4"
# set swat home
export SWAT_AW_HOME="~/dev/conda/pesteaux_conda/swat_tools"

rm -r "$HOME/.SWAT/SWATPlus"
rm -r "$HOME/.local/share/swatplus"
rm -r "$SWAT_AW_HOME/.SWAT/SWATPlus"
rm -r "$SWAT_AW_HOME/.local/share/swatplus"

mkdir -p "$HOME/.SWAT/SWATPlus"
mkdir -p "$HOME/.local/share/swatplus"
mkdir -p "$SWAT_AW_HOME/.SWAT/SWATPlus"
mkdir -p "$SWAT_AW_HOME/.local/share/swatplus"

wget -c "https://github.com/celray/swatplus-automatic-workflow/archive/v$version.zip"
wget -c "https://github.com/celray/swatplus-automatic-workflow/releases/download/v$version/TauDEM5Bin_Linux.zip"
wget -c "https://github.com/celray/swatplus-automatic-workflow/raw/master/editor_api/swatplus_wgn.sqlite"
# wget -c "https://github.com/celray/swatplus-automatic-workflow/raw/master/editor_api/swatplus_wgn.sqlite"
wget -c "https://bitbucket.org/swatplus/swatplus.editor/downloads/swatplus_wgn.sqlite"

unzip "./v$version.zip"
unzip "./TauDEM5Bin_Linux.zip"

echo "copying files"
mv "./swatplus-automatic-workflow-$version" "$HOME/.SWAT/SWATPlus/Workflow"
mv "./TauDEM5Bin" "$HOME/.local/share/swatplus/TauDEM5Bin"
mv "./swatplus_wgn.sqlite" "$HOME/.SWAT/SWATPlus/Workflow/editor_api/"
chmod 777 "$HOME/.SWAT/SWATPlus/Workflow/swatplus_aw.sh"
chmod -R 777 "$HOME/.local/share/swatplus/TauDEM5Bin"
mv "./swatplus-automatic-workflow-$version" "$SWAT_AW_HOME/.SWAT/SWATPlus/Workflow"
mv "./TauDEM5Bin" "$SWAT_AW_HOME/.local/share/swatplus/TauDEM5Bin"
mv "./swatplus_wgn.sqlite" "$SWAT_AW_HOME/.SWAT/SWATPlus/Workflow/editor_api/"
chmod 777 "$SWAT_AW_HOME/.SWAT/SWATPlus/Workflow/swatplus_aw.sh"
chmod -R 777 "$SWAT_AW_HOME/.local/share/swatplus/TauDEM5Bin"

# cleanup
echo "cleaning up"
rm "$HOME/.SWAT/SWATPlus/Workflow/.gitattributes"
rm "$HOME/.SWAT/SWATPlus/Workflow/swatplus_aw.bat"
rm "$HOME/.SWAT/SWATPlus/Workflow/code_of_conduct.md"
rm -r "$HOME/.SWAT/SWATPlus/Workflow/.github"
rm "$SWAT_AW_HOME/.SWAT/SWATPlus/Workflow/.gitattributes"
rm "$SWAT_AW_HOME/.SWAT/SWATPlus/Workflow/swatplus_aw.bat"
rm "$SWAT_AW_HOME/.SWAT/SWATPlus/Workflow/code_of_conduct.md"
rm -r "$SWAT_AW_HOME/.SWAT/SWATPlus/Workflow/.github"
rm "./TauDEM5Bin_Linux.zip"
rm "./v$version.zip"

# set environmental variables
echo "setting up environmental variables"
echo 'export PATH=$PATH:$HOME/.SWAT/SWATPlus/Workflow' >>~/.bashrc
echo 'export swatplus_wf_dir=$HOME/.SWAT/SWATPlus/Workflow' >>~/.bashrc
echo 'export PATH=$PATH:$SWAT_AW_HOME/.SWAT/SWATPlus/Workflow' >>~/.bashrc
echo 'export swatplus_wf_dir=$SWAT_AW_HOME/.SWAT/SWATPlus/Workflow' >>~/.bashrc
4 changes: 2 additions & 2 deletions main_stages/prepare_project.py
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from glob import glob
from shutil import copyfile, rmtree

import gdal
import osr
from osgeo import gdal
from osgeo import osr

sys.path.insert(0, os.path.join(os.environ["swatplus_wf_dir"], "packages"))
sys.path.append(os.path.join(os.environ["swatplus_wf_dir"]))
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2 changes: 1 addition & 1 deletion packages/helper_functions.py
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import shutil
from glob import glob
from shutil import copyfile, copytree
import gdal
# import gdal
import pickle
import xml.etree.ElementTree as ET
from osgeo import gdal
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61 changes: 47 additions & 14 deletions swatplus_aw.sh
100644 → 100755
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# set the directory of QGIS
# export QGIS_Dir=C:\Program Files\QGIS 3.10
# set ERRORLEVEL=0
# set swat home
export SWAT_AW_HOME="~/dev/conda/pesteaux_conda/swat_tools"

# set variables for project initialisation
export python_script_prepare_qswat=$HOME/.SWAT/SWATPlus/Workflow/main_stages/prepare_project.py
export python_script_make_namelist=$HOME/.SWAT/SWATPlus/Workflow/main_stages/generate_namelist.py
export python_script_run_qswat=$HOME/.SWAT/SWATPlus/Workflow/main_stages/run_qswat.py
export python_script_run_editor=$HOME/.SWAT/SWATPlus/Workflow/main_stages/run_editor.py
export python_script_run_calibration=$HOME/.SWAT/SWATPlus/Workflow/main_stages/run_calibration.py
export python_script_make_figures=$HOME/.SWAT/SWATPlus/Workflow/main_stages/run_make_figures.py
export python_script_clean_up=$HOME/.SWAT/SWATPlus/Workflow/main_stages/run_clean_up.py
export python_script_prepare_qswat=$SWAT_AW_HOME/.SWAT/SWATPlus/Workflow/main_stages/prepare_project.py
export python_script_make_config=$SWAT_AW_HOME/.SWAT/SWATPlus/Workflow/main_stages/generate_config.py
export python_script_run_qswat=$SWAT_AW_HOME/.SWAT/SWATPlus/Workflow/main_stages/run_qswat.py
export python_script_run_editor=$SWAT_AW_HOME/.SWAT/SWATPlus/Workflow/main_stages/run_editor.py
export python_script_run_calibration=$SWAT_AW_HOME/.SWAT/SWATPlus/Workflow/main_stages/run_calibration.py
export python_script_make_figures=$SWAT_AW_HOME/.SWAT/SWATPlus/Workflow/main_stages/run_make_figures.py
export python_script_clean_up=$SWAT_AW_HOME/.SWAT/SWATPlus/Workflow/main_stages/run_clean_up.py

export BASE_DIR=$PWD
export swatplus_wf_dir=$HOME/.SWAT/SWATPlus/Workflow/
export swatplus_wf_dir=$SWAT_AW_HOME/.SWAT/SWATPlus/Workflow/
# add qgis plugins folder to pythonpath
export WF_QGIS=/usr/share/qgis/python/plugins

# # add default plugins and model directory to python path
export PYTHONPATH=$BASE_DIR:$PYTHONPATH
export PYTHONPATH=$BASE_DIR:$WF_QGIS:$PYTHONPATH
# export PATH=%PATH%

# start runing the workflow using PyQGIS

python3 $python_script_prepare_qswat $BASE_DIR
if [ "$?" -ne "0" ];
then
echo "prepare_qswat failed"
exit 1
else
echo 'prepare_qswat done'
python3 $python_script_make_config $BASE_DIR
if [ "$?" -ne "0" ];
then
echo "make_config failed"
exit 1
else
echo 'make_config done'
python3 $python_script_run_qswat $BASE_DIR
if [ "$?" -ne "0" ];
then
echo "run_qswat failed"
exit 1
else
echo 'run_qswat done'
python3 $python_script_run_editor $BASE_DIR
echo 'run_editor done'

python3 $python_script_make_namelist $BASE_DIR
python3 $python_script_run_calibration $BASE_DIR
echo 'un_calibration done'

python3 $python_script_run_qswat $BASE_DIR
python3 $python_script_run_editor $BASE_DIR
python3 $python_script_run_calibration $BASE_DIR
python3 $python_script_make_figures $BASE_DIR
python3 $python_script_make_figures $BASE_DIR
echo 'make_figures done'
fi

fi
fi

python3 $python_script_clean_up $BASE_DIR
echo 'clean_up done'

echo 'This is the end.'