Fix handling of xtime variable in mpas_to_xdmf

conda_package/mpas_tools/viz/mpas_to_xdmf/io.py

@@ -71,6 +71,8 @@ def _load_dataset(mesh_filename, time_series_filenames, variables, xtime_var):
                 data_vars='minimal',
                 coords='minimal',
                 compat='override',
+                decode_times=False,
+                decode_timedelta=False,
             )
 
     ds_mesh = _get_ds_mesh(ds_mesh)
@@ -91,6 +93,8 @@ def _load_dataset(mesh_filename, time_series_filenames, variables, xtime_var):
                 )
             else:
                 selected_vars.add(var)
+        if xtime_var is not None:
+            selected_vars.add(xtime_var)
         ds = ds[list(selected_vars)]
 
     _set_time(ds=ds, xtime_var=xtime_var)

conda_package/mpas_tools/viz/mpas_to_xdmf/templates/xdmf_template.xml

@@ -3,9 +3,9 @@
   <Domain>
     <Grid Name="TimeSeries" GridType="Collection" CollectionType="Temporal">
       {% if times|length > 0 %}
-      {% set t_index = 0 %}
-      {% for t_val in times %}
-      <Grid Name="Step{{ t_index }}" GridType="Uniform">
+    {% for t_val in times %}
+    {% set t_index = loop.index0 %}
+    <Grid Name="Step{{ t_index }}" GridType="Uniform">
         <Time Value="{{ t_val }}"/>
         <Topology TopologyType="Polygon" NumberOfElements="{{ num_elements }}" NodesPerElement="{{ num_verts }}">
           <DataItem Format="HDF" Dimensions="{{ num_elements }} {{ num_verts }}">{{ h5_basename }}:/Cells</DataItem>
@@ -16,7 +16,7 @@
         {% for var in variables %}
         {% if var.has_time %}
         <Attribute Name="{{ var.name }}" AttributeType="Scalar" Center="Cell">
-          <DataItem Format="HDF" Dimensions="{{ num_elements }}">{{ h5_basename }}:/{{ var.name }}_t{{ t_index }}</DataItem>
+      <DataItem Format="HDF" Dimensions="{{ num_elements }}">{{ h5_basename }}:/{{ var.name }}_t{{ t_index }}</DataItem>
         </Attribute>
         {% else %}
         <Attribute Name="{{ var.name }}" AttributeType="Scalar" Center="Cell">
@@ -25,7 +25,6 @@
         {% endif %}
         {% endfor %}
       </Grid>
-      {% set t_index = t_index + 1 %}
       {% endfor %}
       {% else %}
       <Grid Name="Static" GridType="Uniform">

conda_package/mpas_tools/viz/mpas_to_xdmf/time.py

@@ -37,18 +37,21 @@ def _xtime_to_seconds(xtime: xr.DataArray) -> xr.DataArray:
     ----------
     xtime : xr.DataArray
         An array of strings representing time in the format
-        'YYYY-MM-DD_HH:MM:SS.sss'.
+        'YYYY-MM-DD_HH:MM:SS' or 'YYYY-MM-DD_HH:MM:SS.sss'.
 
     Returns
     -------
     xr.DataArray
         An array of seconds since the first entry in `xtime`.
     """
     # Convert xtime strings to datetime objects using datetime.strptime
-    timestamps = [
-        datetime.strptime(time_str, '%Y-%m-%d_%H:%M:%S.%f')
-        for time_str in xtime.values.astype(str)
-    ]
+    timestamps = []
+    for time_str in xtime.values.astype(str):
+        try:
+            timestamp = datetime.strptime(time_str, '%Y-%m-%d_%H:%M:%S.%f')
+        except ValueError:
+            timestamp = datetime.strptime(time_str, '%Y-%m-%d_%H:%M:%S')
+        timestamps.append(timestamp)
     # Calculate seconds since the first timestamp
     seconds_since_start = [
         (ts - timestamps[0]).total_seconds() for ts in timestamps