Merge branch 'master' into develop

Signed-off-by: Johannes Mueller <[email protected]>

Author: johannes-mueller

CHANGELOG.md

@@ -3,6 +3,18 @@
 In this file noteworthy changes of new releases of pyLife are documented since
 2.0.0.
 
+
+## pylife-2.1.3
+
+### Improvements
+
+* Massive performance improvement when reading element connectivity by
+  `odbclient.` Note that also `odbserver` needs to be updated in its
+  environment. (#121)
+
+* Fix some warnings on import
+
+
 ## pylife-2.1.2
 
 ### New features

src/pylife/strength/meanstress.py

@@ -458,6 +458,9 @@ def sum_intervals(iv, ranges, obj):
 
         range_itv_idx, means_itg_idx = resulting_intervals()
 
+        # TODO: remove once we drop python 3.8 support
+        future_stack = {} if pd.__version__ < "2.1" else {'future_stack': True}
+
         if len(self._remaining_names) > 0:
             remaining_idx = self._obj.index.to_frame(index=False).groupby(self._remaining_names).first().index
             result = (
@@ -466,7 +469,9 @@ def sum_intervals(iv, ranges, obj):
             )
             result.index = remaining_idx
             result.columns = pd.MultiIndex.from_arrays([result.columns, means_itg_idx])
-            result = result.stack(['range', 'mean']).reorder_levels(['range', 'mean'] + self._remaining_names)
+            result = result.stack(['range', 'mean'], **future_stack).reorder_levels(
+                ['range', 'mean'] + self._remaining_names
+            )
         else:
             result = range_itv_idx.to_series().apply(lambda iv: sum_intervals(iv, ranges, self._obj))
             result.index = pd.MultiIndex.from_arrays([result.index, means_itg_idx])

tools/odbclient/src/odbclient/odbclient.py

@@ -219,9 +219,19 @@ def element_connectivity(self, instance_name, elset_name=''):
             For every element there is list of node ids that the element is connected to.
 
         """
-        index, connectivity = self._query('get_connectivity', (instance_name, elset_name))
-        return pd.DataFrame({'connectivity': connectivity},
-                            index=pd.Index(index, name='element_id', dtype=np.int64))
+        index, connectivity = self._query(
+            'get_connectivity', (instance_name, elset_name)
+        )
+
+        return pd.DataFrame(
+            {
+                'connectivity': [
+                    conn[conn >= -0].astype(np.int64).tolist() for conn in connectivity
+                ]
+            },
+            index=pd.Index(index, name='element_id', dtype=np.int64),
+        )
+
 
     def nset_names(self, instance_name=''):
         """Query the available node set names.

tools/odbclient/tests/connectivity.csv

@@ -0,0 +1,6 @@
+{
+    "1":{"connectivity":[5,7,3,1,6,8,4,2,24,23,22,21,25,26,27,28,30,29,31,32]},
+    "2":{"connectivity":[9,11,7,5,10,12,8,6,35,34,24,33,36,37,25,38,40,39,29,30]},
+    "3":{"connectivity":[13,15,11,9,14,16,12,10,43,42,35,41,44,45,36,46,48,47,39,40]},
+    "4":{"connectivity":[17,19,15,13,18,20,16,14,51,50,43,49,52,53,44,54,56,55,47,48]}
+}

tools/odbclient/tests/connectivity.json

@@ -106,12 +106,14 @@ def test_odbclient_elset_names_invalid_instance_name(client):
         client.elset_names('nonexistent')
 
 
-@pytest.mark.skip("to be implemented")
 def test_element_connectivity(client):
-    expected = pd.read_csv('tests/connectivity.csv', index_col='element_id')
+    expected = pd.read_json(
+        'tests/connectivity.json', orient="index"
+    )
+    expected.index.names = ["element_id"]
+
     result = client.element_connectivity('PART-1-1')
-    print(result)
-    print(expected)
+
     pd.testing.assert_frame_equal(result, expected)
 
 

tools/odbclient/tests/test_odbclient.py

@@ -22,7 +22,6 @@
 import odbAccess as ODB
 import json
 
-
 class OdbInterface:
 
     def __init__(self, odbfile):
@@ -78,10 +77,11 @@ def connectivity(self, instance_name, element_set_name):
             raise KeyError(element_set_name)
 
         index = np.empty(len(elements), dtype=np.int)
-        connectivity = []
+        connectivity = -np.ones((len(elements), 20))
         for i, el in enumerate(elements):
             index[i] = el.label
-            connectivity.append(list(el.connectivity))
+            conns = list(el.connectivity)
+            connectivity[i, :len(conns)] = conns
 
         return (index, connectivity)