Add a few local variables to template.cupid

These will eventually be populated from an env_?.xml file, but for now starting
a list of variables we want the user to be able to set.

Also added two minor updates:
1. unset PYTHONPATH to ensure we are only using conda-installed python packages
2. The API for the script to generate the ADF config file has been changed - we
now point to the directory containing a CUPiD config file rather than the CUPiD
example

machines/config_workflow.xml

@@ -71,6 +71,7 @@
   <workflow_jobs id="case.cupid" prepend="default">
     <job name="case.cupid">
       <template>template.cupid</template>
+      <hidden>false</hidden>
       <dependency>case.st_archive</dependency>
       <prereq>1</prereq>
       <runtime_parameters MACH="derecho">

machines/template.cupid

@@ -1,12 +1,47 @@
-#!/bin/bash
+#!/bin/bash -e
 
 # Batch system directives
 {{ batchdirectives }}
 
+# Set environment for CESM
 source .env_mach_specific.sh
+
+# Use cupid-infrastructure environment for running these scripts
+# Note: on derecho, the cesmdev module creates a python conflict
+#       by setting $PYTHONPATH; since this is conda-based we
+#       want an empty PYTHONPATH environment variable
+MACH=`./xmlquery --value MACH`
+unset PYTHONPATH
 conda activate cupid-infrastructure
-{{ srcroot }}/tools/CUPiD/helper_scripts/generate_cupid_config_for_cesm_case.py \
-    --cesm-root {{ SRCROOT }}
 
-cupid-timeseries
-cupid-diagnostics
+# Set variables that should eventually come from environment file
+CUPID_EXAMPLE=key_metrics
+RUN_CUPID_ANALYSIS=TRUE
+RUN_CUPID_TIMESERIES=TRUE
+
+if [ "${RUN_CUPID_ANALYSIS}" == "TRUE" ]; then
+  # 1. Generate CUPiD config file
+  {{ srcroot }}/tools/CUPiD/helper_scripts/generate_cupid_config_for_cesm_case.py \
+      --cesm-root {{ SRCROOT }}
+
+  # 2. Generate ADF config file
+  {{ srcroot }}/tools/CUPiD/helper_scripts/generate_adf_config_file.py \
+      --cesm-root {{ SRCROOT }} \
+      --cupid-config-loc ${PWD} \
+      --adf-template {{ SRCROOT }}/tools/CUPiD/externals/ADF/config_amwg_default_plots.yaml \
+      --out-file adf_config.yml
+
+  # 3. Generate timeseries files and run ADF
+  if [ "${RUN_CUPID_TIMESERIES}" == "TRUE" ]; then
+    cupid-timeseries
+  fi
+  conda deactivate
+  conda activate cupid-analysis
+  {{ SRCROOT }}/tools/CUPiD/externals/ADF/run_adf_diag adf_config.yml
+
+  # 4. Run CUPiD and build webpage
+  conda deactivate
+  conda activate cupid-infrastructure
+  cupid-diagnostics
+  cupid-webpage
+fi