Merge pull request #475 from ua-snap/DA_workflow

The branch is named DA_workflow, but the code implements a basic sensitivity analysis.

This branch introduces a new Python module and class (Sensitivity, SensitivityDriver) which help carry out a sensitivity analysis workflow. Additionally there is a Jupyter notebook that demonstrates the usage of the new code.

This also introduces a bunch of changes (additions) to the param_util.py script that improve the Python API.

Dockerfile

@@ -71,6 +71,10 @@ RUN python --version
 RUN pip install -U pip pipenv
 RUN pip install matplotlib numpy pandas bokeh netCDF4 commentjson
 RUN pip install ipython
+RUN pip install jupyter
+RUN pip install lhsmdu
+COPY --chown=develop:develop special_configurations/jupyter_notebook_config.py /home/develop/.jupyter/jupyter_notebook_config.py
+
 #RUN pip install gdal ## Doesn't work...
 #RUN pip install GDAL ## Doesn't work...
 # docker build --target dvmdostem-build --tag dvmdostem-build:0.0.1 .

docker-compose.yml

@@ -27,6 +27,8 @@ services:
     tty: true
     build: .
     image: dvmdostem-run:0.0.1
+    ports:
+      - "8888:8888"
     volumes:
       - sourcecode:/work
       - inputcatalog:/data/input-catalog

docker-install.sh

@@ -0,0 +1,8 @@
+#!/bin/bash 
+# This script will install the docker. 
+# Note: The installation could take a while, please be patient.
+
+docker build --target cpp-dev --tag cpp-dev:0.0.1 .
+docker build --target dvmdostem-build --tag dvmdostem-build:0.0.1 .
+docker build --target dvmdostem-run --tag dvmdostem-run:0.0.1 .
+docker build --tag dvmdostem-mapping-support:0.0.1 -f Dockerfile-mapping-support .

parameters/cmt_calparbgc.txt

@@ -131,9 +131,9 @@
 // soil calibrated parameters
 0.750000     // micbnup: parameter for soil microbial immobilization -8.06e-05of N
 0.091946     // kdcrawc: raw-material (litter) C decompositin rates at reference condition  was 0.068946
-0.0230919    // kdcsoma  was 0.094519
-0.020800     // kdcsompr   was 0.009000 
-0.000005     // kdcsomcr  was 0.000005 
+0.0230919    // kdcsoma:  was 0.094519
+0.020800     // kdcsompr:   was 0.009000 
+0.000005     // kdcsomcr:  was 0.000005 
 //===========================================================
 // CMT06 // Wet Sedge Tundra // Calibrated for Toolik area.
 //Decid      Sedges       Grasses      Forbs        Lichens      Feather      Sphag        PFT7     PFT8      PFT9      // pftnames