Merge pull request nschloe#206 from nschloe/more-test-files

More test files
Gjacquenot · Mar 7, 2018 · 4d69ff6 · 4d69ff6
2 parents b45e06f + d507cc2
commit 4d69ff6
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Showing 28 changed files with 538 additions and 571 deletions.
diff --git a/.pylintrc b/.pylintrc
@@ -1,16 +1,14 @@
 [MESSAGES CONTROL]
 
 disable=
+    duplicate-code,
+    fixme,
     invalid-name,
-    too-many-locals,
+    locally-disabled,
     missing-docstring,
+    no-member,
     too-many-arguments,
+    too-many-branches,
+    too-many-locals,
     too-many-statements,
-    no-member,
-    bad-continuation,
     unused-argument,
-    too-many-branches,
-    duplicate-code,
-    fixme,
-    wildcard-import,
-    locally-disabled
diff --git a/meshio/ansys_io.py b/meshio/ansys_io.py
@@ -81,8 +81,8 @@ def _read_points(f, line, first_point_index_overall, last_point_index):
         # read point data
         total_bytes = dim * bytes_per_item * num_points
         pts = numpy.fromstring(
-                f.read(total_bytes), dtype=dtype
-                ).reshape((num_points, dim))
+            f.read(total_bytes), dtype=dtype
+            ).reshape((num_points, dim))
 
     # make sure that the data set is properly closed
     _skip_close(f, 2)
@@ -104,14 +104,14 @@ def _read_cells(f, line):
     element_type = a[4]
 
     element_type_to_key_num_nodes = {
-            0: ('mixed', None),
-            1: ('triangle', 3),
-            2: ('tetra', 4),
-            3: ('quad', 4),
-            4: ('hexahedron', 8),
-            5: ('pyra', 5),
-            6: ('wedge', 6),
-            }
+        0: ('mixed', None),
+        1: ('triangle', 3),
+        2: ('tetra', 4),
+        3: ('quad', 4),
+        4: ('hexahedron', 8),
+        5: ('pyra', 5),
+        6: ('wedge', 6),
+        }
 
     key, num_nodes_per_cell = \
         element_type_to_key_num_nodes[element_type]
@@ -157,10 +157,10 @@ def _read_cells(f, line):
         total_bytes = \
             bytes_per_item * num_nodes_per_cell * num_cells
         data = numpy.fromstring(
-                f.read(total_bytes),
-                count=(num_nodes_per_cell*num_cells),
-                dtype=dtype
-                ).reshape((num_cells, num_nodes_per_cell))
+            f.read(total_bytes),
+            count=(num_nodes_per_cell*num_cells),
+            dtype=dtype
+            ).reshape((num_cells, num_nodes_per_cell))
 
     # make sure that the data set is properly closed
     _skip_close(f, 2)
@@ -186,11 +186,11 @@ def _read_faces(f, line):
     element_type = a[4]
 
     element_type_to_key_num_nodes = {
-            0: ('mixed', None),
-            2: ('line', 2),
-            3: ('triangle', 3),
-            4: ('quad', 4)
-            }
+        0: ('mixed', None),
+        2: ('line', 2),
+        3: ('triangle', 3),
+        4: ('quad', 4)
+        }
 
     key, num_nodes_per_cell = \
         element_type_to_key_num_nodes[element_type]
@@ -326,10 +326,10 @@ def read(filename):
             elif re.match('(|20|30)10', index):
                 # points
                 pts, first_point_index_overall, last_point_index = \
-                        _read_points(
-                                f, line, first_point_index_overall,
-                                last_point_index
-                                )
+                    _read_points(
+                        f, line, first_point_index_overall,
+                        last_point_index
+                        )
 
                 if pts is not None:
                     points.append(pts)
@@ -384,15 +384,13 @@ def read(filename):
     return points, cells, point_data, cell_data, field_data
 
 
-def write(
-        filename,
-        points,
-        cells,
-        point_data=None,
-        cell_data=None,
-        field_data=None,
-        write_binary=True,
-        ):
+def write(filename,
+          points,
+          cells,
+          point_data=None,
+          cell_data=None,
+          field_data=None,
+          write_binary=True):
     point_data = {} if point_data is None else point_data
     cell_data = {} if cell_data is None else cell_data
     field_data = {} if field_data is None else field_data
@@ -433,13 +431,13 @@ def write(
 
         # Write cells
         meshio_to_ansys_type = {
-                'triangle': 1,
-                'tetra': 2,
-                'quad': 3,
-                'hexahedron': 4,
-                'pyra': 5,
-                'wedge': 6,
-                }
+            'triangle': 1,
+            'tetra': 2,
+            'quad': 3,
+            'hexahedron': 4,
+            'pyra': 5,
+            'wedge': 6,
+            }
         first_index = 0
         binary_dtypes = {
             # numpy.int16 is not allowed

diff --git a/meshio/dolfin_io.py b/meshio/dolfin_io.py
@@ -114,12 +114,7 @@ def read(filename):
     return points, cells, point_data, cell_data, field_data
 
 
-def _write_mesh(
-        filename,
-        points,
-        cell_type,
-        cells
-        ):
+def _write_mesh(filename, points, cell_type, cells):
     stripped_cells = {cell_type: cells[cell_type]}
 
     dolfin = ET.Element(
@@ -136,19 +131,19 @@ def _write_mesh(
         discarded_cells = list(cells.keys())
         discarded_cells.remove(cell_type)
         logging.warning(
-          'DOLFIN XML can only handle one cell type at a time. '
-          'Using %s, discarding %s.',
-          cell_type, ', '.join(discarded_cells)
-          )
+            'DOLFIN XML can only handle one cell type at a time. '
+            'Using %s, discarding %s.',
+            cell_type, ', '.join(discarded_cells)
+            )
 
     dim = 2 if all(points[:, 2] == 0) else 3
 
     mesh = ET.SubElement(
-            dolfin,
-            'mesh',
-            celltype=meshio_to_dolfin_type[cell_type],
-            dim=str(dim)
-            )
+        dolfin,
+        'mesh',
+        celltype=meshio_to_dolfin_type[cell_type],
+        dim=str(dim)
+        )
     vertices = ET.SubElement(mesh, 'vertices', size=str(len(points)))
 
     for k, point in enumerate(points):
@@ -192,23 +187,19 @@ def _numpy_type_to_dolfin_type(dtype):
     return None
 
 
-def _write_cell_data(
-        filename,
-        dim,
-        cell_data
-        ):
+def _write_cell_data(filename, dim, cell_data):
     dolfin = ET.Element(
         'dolfin',
         nsmap={'dolfin': 'https://fenicsproject.org/'}
         )
 
     mesh_function = ET.SubElement(
-            dolfin,
-            'mesh_function',
-            type=_numpy_type_to_dolfin_type(cell_data.dtype),
-            dim=str(dim),
-            size=str(len(cell_data))
-            )
+        dolfin,
+        'mesh_function',
+        type=_numpy_type_to_dolfin_type(cell_data.dtype),
+        dim=str(dim),
+        size=str(len(cell_data))
+        )
 
     for k, value in enumerate(cell_data):
         ET.SubElement(
@@ -223,14 +214,12 @@ def _write_cell_data(
     return
 
 
-def write(
-        filename,
-        points,
-        cells,
-        point_data=None,
-        cell_data=None,
-        field_data=None
-        ):
+def write(filename,
+          points,
+          cells,
+          point_data=None,
+          cell_data=None,
+          field_data=None):
     logging.warning(
         'Dolfin\'s XML is a legacy format. Consider using XDMF instead.'
         )

diff --git a/meshio/exodus_io.py b/meshio/exodus_io.py
@@ -126,8 +126,7 @@ def write(filename,
           cells,
           point_data=None,
           cell_data=None,
-          field_data=None
-          ):
+          field_data=None):
     import netCDF4
 
     point_data = {} if point_data is None else point_data
@@ -163,17 +162,17 @@ def write(filename,
 
     # points
     coor_names = rootgrp.createVariable(
-            'coor_names', 'S1', ('num_dim', 'len_string'),
-            )
+        'coor_names', 'S1', ('num_dim', 'len_string'),
+        )
     coor_names.set_auto_mask(False)
     coor_names[0, 0] = 'X'
     coor_names[1, 0] = 'Y'
     coor_names[2, 0] = 'Z'
     data = rootgrp.createVariable(
-            'coord',
-            numpy_to_exodus_dtype[points.dtype],
-            ('num_dim', 'num_nodes')
-            )
+        'coord',
+        numpy_to_exodus_dtype[points.dtype],
+        ('num_dim', 'num_nodes')
+        )
     data[:] = points.T
 
     # cells
@@ -189,8 +188,8 @@ def write(filename,
         rootgrp.createDimension(dim2, values.shape[1])
         dtype = numpy_to_exodus_dtype[values.dtype]
         data = rootgrp.createVariable(
-                'connect{}'.format(k+1), dtype, (dim1, dim2)
-                )
+            'connect{}'.format(k+1), dtype, (dim1, dim2)
+            )
         data.elem_type = meshio_to_exodus_type[key]
         # Exodus is 1-based
         data[:] = values + 1
@@ -203,8 +202,8 @@ def write(filename,
         rootgrp.createDimension('num_nod_var', num_nod_var)
         # set names
         point_data_names = rootgrp.createVariable(
-                'name_nod_var', 'S1', ('num_nod_var', 'len_string')
-                )
+            'name_nod_var', 'S1', ('num_nod_var', 'len_string')
+            )
         point_data_names.set_auto_mask(False)
         for k, name in enumerate(point_data.keys()):
             for i, letter in enumerate(name):
@@ -215,9 +214,9 @@ def write(filename,
         first_key = list(point_data.keys())[0]
         dtype = numpy_to_exodus_dtype[point_data[first_key].dtype]
         node_data = rootgrp.createVariable(
-                'vals_nod_var', dtype,
-                ('time_step', 'num_nod_var', 'num_nodes')
-                )
+            'vals_nod_var', dtype,
+            ('time_step', 'num_nod_var', 'num_nodes')
+            )
         for k, (name, data) in enumerate(point_data.items()):
             node_data[0, k] = data