Add virtualenv, use of .env and logging

.gitignore

 *.nc
 *.tif
 *.tif.aux.xml
+.env
+.venv
 mapfile/SEPTREFHUM.map

log/.gitignore

+*
+*/
+!.gitignore
\ No newline at end of file

requirements.txt

+Jinja2
+netCDF4
+pytz
\ No newline at end of file

run_SEPTREFHUM.sh

+#!/bin/bash
+
+# First: Test that we have CDO and GDAL installed
+if ! command -v cdo &> /dev/null
+then
+    echo "ERROR: CDO could not be found. Exiting."
+    exit
+fi
+
+if ! command -v gdal_merge.py &> /dev/null
+then
+    echo "ERROR: GDAL is either not installed, or not built with Python support. Exiting."
+    exit
+fi
+
+# Defines HOME_DIR
+source .env
+
+# Paths to scripts and requirements
+APP_PATH=$HOME_DIR/SEPTREFHUM
+LOG_FILE=$APP_PATH/log/SEPTREFHUM.log
+REQUIREMENTS=$APP_PATH/requirements.txt
+
+cd $APP_PATH
+
+# Create and activate the virtual environment
+python3 -m venv .venv
+. .venv/bin/activate
+python3 -m pip install --upgrade pip
+pip install -r $REQUIREMENTS
+
+# Run the model
+echo "==== `date`: Running model" &>> "$LOG_FILE"
+python3 $APP_PATH/SEPTREFHUM.py &>> "$LOG_FILE"
+echo "==== `date`: DONE running model" &>> "$LOG_FILE"
+
+# Deactivate the virtual environment
+deactivate