Updating jedi log data reader (#182)

## Description
We attempted to produce diagnostics from jedi logs we've generated, and
we found ourselves running into issues with the associated reader. A few
modifications have allowed us to successfully generate jedi log
diagnostics.

List of changes:
- Added `residual_norm` to list of variables to be built
- Added `var_array` resize if `len(var_array) > total_iter`
- Keeping list of variables that are saved in the convergence dataset to
be used in the normalization logic later on
- Added test config and example log to eva's test cases

src/eva/data/jedi_log.py

@@ -237,6 +237,13 @@ def parse_convergence(self):
             var_position.append(1)
             var_dtype.append('float32')
 
+            # Residual norm
+            var_names.append('residual_norm')
+            var_search_criteria.append('Residual norm (')
+            var_split.append('=')
+            var_position.append(1)
+            var_dtype.append('float32')
+
             # Norm reduction
             var_names.append('norm_reduction')
             var_search_criteria.append('Norm reduction (')
@@ -278,6 +285,7 @@ def parse_convergence(self):
         # Concatenate chunks to simplify search algorithm
         min_and_j_chunks = minimizer_chunks + j_chunks
 
+        ds_vars = []
         for var_ind, var in enumerate(var_names):
             var_array = []
             for min_and_j_chunk in min_and_j_chunks:
@@ -291,7 +299,12 @@ def parse_convergence(self):
             if var_array:
                 gn = f'convergence::{var_names[var_ind]}'  # group::variable name
                 convergence_ds[gn] = xr.DataArray(np.zeros(total_iter, dtype=var_dtype[var_ind]))
+
+                # If var is greater than total_iter, clip var array
+                if len(var_array) > total_iter:
+                    var_array = var_array[0:total_iter]
                 convergence_ds[gn].data[:] = var_array
+                ds_vars.append(var)
 
         # Create special case variables
 
@@ -316,10 +329,12 @@ def parse_convergence(self):
 
         # Normalized versions of data
         # ---------------------------
-        normalize_var_names = ['gradient_reduction', 'norm_reduction', 'j', 'jb', 'jojc']
+        normalize_var_names = ['gradient_reduction', 'residual_norm',
+                               'norm_reduction', 'j', 'jb', 'jojc']
 
         for normalize_var_name in normalize_var_names:
-            if normalize_var_name in var_names:
+            if (normalize_var_name in var_names) and (normalize_var_name in ds_vars):
+
                 # Index in lists for the variable being normalized
                 var_ind = var_names.index(normalize_var_name)
 

src/eva/tests/config/testJediLog2.yaml

@@ -0,0 +1,57 @@
+datasets:
+
+- type: JediLog
+  collection_name: jedi_log_test
+  jedi_log_to_parse: ${data_input_path}/jedi_variational_log.txt
+  data_to_parse:
+    convergence: true
+
+graphics:
+
+  plotting_backend: Emcpy
+  figure_list:
+
+  - figure:
+      layout: [3,1]
+      figure size: [12,10]
+      title: 'Residual norm and Norm Reduction Plots'
+      output name: jedi_log/convergence/norm_gradient_reduction.png
+    plots:
+      - add_xlabel: 'Total inner iteration number'
+        add_ylabel: 'Residual norm'
+        layers:
+        - type: LinePlot
+          x:
+            variable: jedi_log_test::convergence::total_iteration
+          y:
+            variable: jedi_log_test::convergence::residual_norm
+          color: 'black'
+
+      - add_xlabel: 'Total inner iteration number'
+        add_ylabel: 'Norm reduction'
+        layers:
+        - type: LinePlot
+          x:
+            variable: jedi_log_test::convergence::total_iteration
+          y:
+            variable: jedi_log_test::convergence::norm_reduction
+          color: 'black'
+
+      - add_xlabel: 'Total inner iteration number'
+        add_ylabel: 'Normalized Value'
+        add_legend:
+        layers:
+        - type: LinePlot
+          x:
+            variable: jedi_log_test::convergence::total_iteration
+          y:
+            variable: jedi_log_test::convergence::residual_norm_normalized
+          color: 'red'
+          label: 'Normalized residual norm'
+        - type: LinePlot
+          x:
+            variable: jedi_log_test::convergence::total_iteration
+          y:
+            variable: jedi_log_test::convergence::norm_reduction_normalized
+          color: 'blue'
+          label: 'Normalized norm reduction'