fix setup.sh script

environment.yml

@@ -1,4 +1,4 @@
-name: epic_env
+name: epic_env2
 channels:
   - conda-forge
   - defaults

geoEpic/dispatcher.py

@@ -4,6 +4,9 @@
 
 # Mapping of modules and functions to their respective relative paths
 script_paths = {
+    "init" : {
+        "init" : "initialize.py"
+    },
     "utility": {
         "crop_csb": "utils/crop_csb.py",
         "gee": "gee/fetch.py"
@@ -38,6 +41,7 @@
     "soil": "usda",
     "sites": "generate",
     "workspace": "run",
+    "init":"init"
 }
 
 class DispatchError(Exception):

geoEpic/initialize.py

@@ -0,0 +1,36 @@
+from geoEpic.io.config_parser import ConfigParser
+import os
+import urllib.request
+
+home_dir = os.path.expanduser("~")
+metadata_dir = os.path.join(home_dir, 'GeoEPIC_metadata')
+root_path = os.path.dirname(__file__)
+
+def setup_metadata():
+    if not os.path.exists(metadata_dir):
+        os.makedirs(metadata_dir)
+        # List of files to download
+        files_to_download = [
+            "https://smarslab-files.s3.amazonaws.com/epic-utils/slope_us.tif",
+            "https://smarslab-files.s3.amazonaws.com/epic-utils/SRTM_1km_US_project.tif",
+            "https://smarslab-files.s3.amazonaws.com/epic-utils/SSURGO.tif"
+        ]
+        # Download the files to the metadata directory
+        for file_url in files_to_download:
+            filename = os.path.join(metadata_dir, os.path.basename(file_url))
+            urllib.request.urlretrieve(file_url, filename)
+    else:
+        print(f"'{metadata_dir}' already exists, skipping file downloads.")
+
+def update_template_config_file():
+
+    config = ConfigParser(os.path.join(f'{root_path}/assets/ws_template/config.yml'))
+
+    config.update({'soil' : {'soil_map': f'{home_dir}/GeoEPIC_metadata/SSURGO.tif',},
+                    'site': {'elevation': f'{home_dir}/GeoEPIC_metadata/SRTM_1km_US_project.tif',
+                            'slope': f'{home_dir}/GeoEPIC_metadata/slope_us.tif',
+        }, })
+
+setup_metadata()
+update_template_config_file()
+

installation_scripts/setup.sh

@@ -1,10 +1,11 @@
 #!/bin/bash
 
 # Environment name
-ENV_NAME="my_project_env"
+ENV_NAME="epic_env2"
 ENV_YML="environment.yml"
 ANACONDA_INSTALLER="Anaconda3-latest-Linux-x86_64.sh"
 ANACONDA_URL="https://repo.anaconda.com/archive/$ANACONDA_INSTALLER"
+GITHUB_PACKAGE_URL="git+https://github.com/smarsGroup/geo-epic.git"
 
 # Function to check if conda is installed
 function check_conda_installed {
@@ -48,13 +49,8 @@ function check_env_exists {
 
 # Function to create the environment from environment.yml
 function create_env {
-    if [[ -f "$ENV_YML" ]]; then
-        echo "Creating Conda environment '$ENV_NAME' from '$ENV_YML'..."
-        conda env create -f "$ENV_YML"
-    else
-        echo "Environment file '$ENV_YML' not found. Please ensure the file exists."
-        exit 1
-    fi
+    echo "Creating Conda environment '$ENV_NAME' ..."
+    conda env create -f https://raw.githubusercontent.com/smarsGroup/geo-epic/master/environment.yml
 }
 
 # Main script
@@ -64,9 +60,17 @@ check_conda_installed
 # 2. Check if the environment exists, if not create it
 if ! check_env_exists; then
     create_env
+else
+    # If environment exists, install the GitHub package via pip
+    echo "Updaing geo_epic package..."
+    conda activate "$ENV_NAME"
+    pip uninstall geo-epic
+    pip install "$GITHUB_PACKAGE_URL"
+    conda deactivate
 fi
 
 # 3. Activate the environment
 echo "Activating environment '$ENV_NAME'..."
 conda activate "$ENV_NAME"
+geo_epic init
 echo "Environment '$ENV_NAME' is activated."