Start working on upgrading to Python 3.9

README.md

@@ -1,9 +1,9 @@
 # iSnoda
 iSnobal installation in a local conda environment that allows for editing of:
-* [AWSM](https://github.com/USDA-ARS-NWRC/awsm)
-* [SMRF](https://github.com/USDA-ARS-NWRC/smrf)
+* [AWSM](https://github.com/UofU-Cryosphere/awsm)
+* [SMRF](https://github.com/UofU-Cryosphere/smrf)
 * [PySnobal](https://github.com/USDA-ARS-NWRC/pysnobal)
-* [Weather forecast retrieval](https://github.com/USDA-ARS-NWRC/weather_forecast_retrieval) 
+* [TopoCalc](https://github.com/USDA-ARS-NWRC/topocalc)
 
 ## Conda
 Contains `environment.yml` file and de/activation scripts to setup required
@@ -14,12 +14,6 @@ env variables. Also has an install script to download the above components
 
 Backup of configuration files.
 
-## Docs
-
-Install instructions for:
-* [IPW](https://github.com/USDA-ARS-NWRC/ipw) on Mac OS and Linux environments.  
-* [basin setup](https://github.com/USDA-ARS-NWRC/basin_setup) from source on Linux.
-
 ## Notebooks
 
 Collection of Jupyter notebooks for mostly output analysis.

conda/README.md

@@ -22,7 +22,7 @@ The following steps create a new environment to execute the iSnobal model.
   ./install_isnoda.sh
 ```
 The script takes a user-defined install location as the first argument. The
-default location is: `$HOME/isnoda` if none is provided.
+default location is: `$HOME/iSnobal` if none is provided.
 
 ## Other environments
 ### Basin Setup

conda/basin_setup/basin_setup.yaml

@@ -1,7 +1,6 @@
 name: basin_setup
 channels:
   - conda-forge
-  - defaults
 dependencies:
   - colorama
   - coloredlogs

conda/environment.yml

@@ -1,7 +1,6 @@
 name: isnoda
 channels:
   - conda-forge
-  - defaults
 dependencies:
   - beautifulsoup4
   - cfgrib

conda/environment_p39.yaml

@@ -0,0 +1,25 @@
+name: isnoda
+channels:
+- conda-forge
+dependencies:
+- beautifulsoup4
+- cfgrib
+- cftime=1.5.2
+- coloredlogs
+- cython
+- dateparser=0.7.2
+- make
+- netCDF4
+- numpy<1.23
+- pandas<1.4
+- parallel
+- pip
+- pykrige>1.5
+- python=3.9
+- pytz
+- regex<2021
+- scipy<1.12
+- siphon
+- utm==0.5
+- xarray<2023
+

conda/install_isnoda.sh

@@ -1,15 +1,16 @@
 #!/usr/bin/env bash
 # Script to install all required components from GitHub repositories.
+# Requires to have a fully setup and activated conda environment.
 #
-# These components are installed with the latest from the master branch:
+# The below components are installed with the latest from the master branch:
 #  - AWSM (University of Utah)
 #  - SMRF (University of Utah)
 #  - PySnobal (ARS)
-#  - Weather Forecast Retrieval (University of Utah)
+#  - TopoCalc (ARS)
 #
 # Other packages are installed via the latest available version as pip package.
 # 
-# Install location is given via the first parameter or defaults to $HOME/isnoda
+# Install location is given via the first parameter or defaults to $HOME/iSnobal
 
 set -e
 
@@ -20,14 +21,14 @@ cd $ISNODA_HOME
 
 ######
 # GitHub repositories
-# Will install from source
+# Will install from source and editable
 ######
 
 declare -a repositories=(
   "https://github.com/UofU-Cryosphere/awsm.git"
   "https://github.com/UofU-Cryosphere/smrf.git"
   "https://github.com/USDA-ARS-NWRC/pysnobal.git"
-  "https://github.com/UofU-Cryosphere/weather_forecast_retrieval.git"
+  "https://github.com/USDA-ARS-NWRC/topocalc.git"
 )
 
 for repository in "${repositories[@]}"
@@ -48,16 +49,15 @@ do
 done
 
 #######
-# ISNOBAL components not available via conda package
+# iSnobal components not available via conda package
 #######
 
 declare -a packages=(
   "inicheck"
   "spatialnc"
-  "topocalc"
 )
 
 for package in "${packages[@]}"
 do
-  pip install --no-deps ${package}
+  pip install ${package}
 done