Merge branch 'cdo_2.4_miniconda' into 'main'

Cdo 2.4 miniconda

See merge request !1

.gitignore

@@ -4,3 +4,4 @@
 .env
 .venv
 mapfile/*.map
+last_run_timestamp

SEPTREFHUM.py

@@ -180,7 +180,7 @@ subprocess.run(f'cdo -s -aexpr,"WARNING_STATUS = WHS <= 0 ? 0 : -1; WARNING_STAT
 if os.getenv("MASK_FILE") is not None:
     mask_file = os.getenv("MASK_FILE")
     print(f"Applying mask file {mask_file} to result.nc")
-    subprocess.run(f'cdo -maskregion,{mask_file} {tmpfile_path}result_unmasked.nc {tmpfile_path}result.nc', shell=True)
+    subprocess.run(f'cdo -P 6 -maskregion,{mask_file} {tmpfile_path}result_unmasked.nc {tmpfile_path}result.nc', shell=True)
 else:
     os.rename(f"{tmpfile_path}result_unmasked.nc", f"{tmpfile_path}result.nc")
 #"""

conda_environment.yml

+name: SEPTREFHUM
+channels:
+  - conda-forge 
+dependencies:
+  - cdo=2.4.0
+  - Jinja2
+  - netCDF4
+  - pytz
+  - python-dotenv
\ No newline at end of file

run_SEPTREFHUM.sh

@@ -18,42 +18,55 @@
 # Configures environment and logging before running the model
 # @author: Tor-Einar Skog <tor-einar.skog@nibio.no>
 
+# Defines HOME_DIR
+source .env
 
-
-# First: Test that we have CDO and GDAL installed
-if ! command -v cdo &> /dev/null
+# Check for HOME_DIR
+if [ -z "${HOME_DIR}" ]
 then
-    echo "ERROR: CDO could not be found. Exiting."
+    echo "ERROR: \$HOME_DIR is not set. Please declare it in an .env file"
     exit
 fi
 
+# Paths to scripts and requirements
+LOG_FILE=${HOME_DIR}log/SEPTREFHUM.log
+REQUIREMENTS=${HOME_DIR}requirements.txt
+CDO_VERSION=2.4.0
+
+# Test that we have GDAL and Miniconda installed
 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
-
-# Check for HOME_DIR
-if [ -z "${HOME_DIR}" ]
+if ! command -v conda &> /dev/null
 then
-    echo "ERROR: \$HOME_DIR is not set. Please declare it in an .env file"
+    echo "ERROR: Miniconda is not installed. Pleare read: https://code.mpimet.mpg.de/projects/cdo/wiki/Anaconda"
     exit
 fi
 
-# Paths to scripts and requirements
-LOG_FILE=${HOME_DIR}log/SEPTREFHUM.log
-REQUIREMENTS=${HOME_DIR}requirements.txt
-
 cd $HOME_DIR
 
-# Create and activate the virtual environment
-python3 -m venv .venv
-. .venv/bin/activate
-python3 -m pip install -q --upgrade pip
-pip install -q -r $REQUIREMENTS
+# Check if we need to create the virtual environment
+eval "$(conda shell.bash hook)"
+now=$(date +%s)
+if ! conda env list | grep -q "SEPTREFHUM "; then
+    echo "Conda env not found, creating it"
+    conda env create -f conda_environment.yml
+    conda activate SEPTREFHUM
+else
+    # Make sure we catch/update changes in dependencies
+    if [ -e last_run_timestamp ]; then
+        last_run_timestamp=$(<last_run_timestamp)
+        last_modified_env_file=$(stat -c "%Y" conda_environment.yml)
+        if [ $((last_run_timestamp - last_modified_env_file)) -lt 0 ]; then
+            echo "conda_environment.yml file has been updated. Updating the conda env. This may take a while"
+            conda env update --prune -f conda_environment.yml
+        fi
+    fi
+    conda activate SEPTREFHUM
+fi
 
 # Run the model
 echo "==== `date`: Running model" &>> "$LOG_FILE"
@@ -61,4 +74,7 @@ python3 ${HOME_DIR}SEPTREFHUM.py &>> "$LOG_FILE"
 echo "==== `date`: DONE running model" &>> "$LOG_FILE"
 
 # Deactivate the virtual environment
-deactivate
+conda deactivate
+
+# Log this to compare with changes in conda_environment.yml
+echo $now > last_run_timestamp