Merge pull request #807 from nschloe/remove-cdata-workaround

Remove cdata workaround

Author: nschloe

.flake8

@@ -1,5 +1,5 @@
 [flake8]
-ignore = E203, E266, E501, W503, C901
+ignore = E203, E266, E501, W503, C901, E741
 max-line-length = 88
 max-complexity = 18
 select = B,C,E,F,W,T4,B9

Makefile

@@ -11,7 +11,7 @@ tag:
 	# Always create a github "release" right after tagging so it appears on zenodo
 	curl -H "Authorization: token `cat $(HOME)/.github-access-token`" -d '{"tag_name": "v$(VERSION)"}' https://api.github.com/repos/nschloe/meshio/releases
 
-upload: clean setup.py
+upload: clean
 	# Make sure we're on the master branch
 	@if [ "$(shell git rev-parse --abbrev-ref HEAD)" != "master" ]; then exit 1; fi
 	rm -f dist/*

meshio/_common.py

@@ -157,30 +157,6 @@ def raw_from_cell_data(cell_data):
     return {name: numpy.concatenate(value) for name, value in cell_data.items()}
 
 
-# https://stackoverflow.com/a/30019607/353337
-def CDATA(text=None):
-    element = ET.Element("![CDATA[")
-    element.text = text
-    return element
-
-
-ET._original_serialize_xml = ET._serialize_xml
-
-
-def _serialize_xml(write, elem, qnames, namespaces, short_empty_elements, **kwargs):
-    if elem.tag == "![CDATA[":
-        write("\n<{}{}]]>\n".format(elem.tag, elem.text))
-        if elem.tail:
-            write(ET._escape_cdata(elem.tail))
-    else:
-        return ET._original_serialize_xml(
-            write, elem, qnames, namespaces, short_empty_elements, **kwargs
-        )
-
-
-ET._serialize_xml = ET._serialize["xml"] = _serialize_xml
-
-
 def write_xml(filename, root):
     tree = ET.ElementTree(root)
     tree.write(filename)

meshio/xdmf/main.py

@@ -8,7 +8,7 @@
 
 import numpy
 
-from .._common import CDATA, cell_data_from_raw, raw_from_cell_data, write_xml
+from .._common import cell_data_from_raw, raw_from_cell_data, write_xml
 from .._exceptions import ReadError, WriteError
 from .._helpers import register
 from .._mesh import CellBlock, Mesh
@@ -339,12 +339,12 @@ def __init__(
 
         domain = ET.SubElement(xdmf_file, "Domain")
         grid = ET.SubElement(domain, "Grid", Name="Grid")
-        information = ET.SubElement(
-            grid, "Information", Name="Information", Value=str(len(mesh.field_data))
-        )
+        # information = ET.SubElement(
+        #     grid, "Information", Name="Information", Value=str(len(mesh.field_data))
+        # )
 
         self.points(grid, mesh.points)
-        self.field_data(mesh.field_data, information)
+        # self.field_data(mesh.field_data, information)
         self.cells(mesh.cells, grid)
         self.point_data(mesh.point_data, grid)
         self.cell_data(mesh.cell_data, grid)
@@ -510,13 +510,18 @@ def cell_data(self, cell_data, grid):
             )
             data_item.text = self.numpy_to_xml_string(data)
 
-    def field_data(self, field_data, information):
-        info = ET.Element("main")
-        for name, data in field_data.items():
-            data_item = ET.SubElement(info, "map", key=name, dim=str(data[1]))
-            data_item.text = str(data[0])
-        # information.text = ET.CDATA(ET.tostring(info))
-        information.append(CDATA(ET.tostring(info).decode("utf-8")))
+    # The original idea was to implement field data as XML CDATA. Unfortunately, in
+    # Python's XML, CDATA handled poorly. There are workarounds, e.g.,
+    # <https://stackoverflow.com/a/30019607/353337>, but those mess around with
+    # ET._serialize_xml and lead to bugs elsewhere
+    # <https://github.com/nschloe/meshio/issues/806>.
+    # def field_data(self, field_data, information):
+    #     info = ET.Element("main")
+    #     for name, data in field_data.items():
+    #         data_item = ET.SubElement(info, "map", key=name, dim=str(data[1]))
+    #         data_item.text = str(data[0])
+    #     information.text = ET.CDATA(ET.tostring(info))
+    #     information.append(CDATA(ET.tostring(info).decode("utf-8")))
 
 
 def write(*args, **kwargs):

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = meshio
-version = 4.0.12
+version = 4.0.13
 author = Nico Schlömer et al.
 email = [email protected]
 description = I/O for many mesh formats
@@ -28,9 +28,8 @@ classifiers =
 
 [options]
 packages = find:
-# importlib_metadata can be removed when we support Python 3.8+ only
 install_requires =
-    importlib_metadata
+    importlib_metadata;python_version<"3.8"
     numpy
 python_requires = >=3.5
 setup_requires =

test/test_xdmf.py

@@ -88,33 +88,32 @@ def test_time_series():
                 assert numpy.all(numpy.abs(value - point_data[k][key]) < 1.0e-12)
 
 
-def test_information_xdmf():
-    mesh_out = meshio.Mesh(
-        numpy.array(
-            [[0.0, 0.0, 0.0], [1.0, 0.0, 0.0], [1.0, 1.0, 0.0], [0.0, 1.0, 0.0]]
-        )
-        / 3,
-        [("triangle", numpy.array([[0, 1, 2], [0, 2, 3]]))],
-        field_data={
-            "bottom": numpy.array([1, 1]),
-            "right": numpy.array([2, 1]),
-            "top": numpy.array([3, 1]),
-            "left": numpy.array([4, 1]),
-        },
-    )
-    # write the data
-    points, cells, field_data = mesh_out.points, mesh_out.cells, mesh_out.field_data
-
-    assert cells[0].type == "triangle"
-    meshio.write(
-        "mesh.xdmf",
-        meshio.Mesh(points=points, cells=[cells[0]], field_data=field_data),
-    )
-
-    # read it back in
-    mesh_in = meshio.read("mesh.xdmf")
-
-    assert len(mesh_in.field_data) == len(mesh_out.field_data)
+# def test_information_xdmf():
+#     mesh_out = meshio.Mesh(
+#         numpy.array(
+#             [[0.0, 0.0, 0.0], [1.0, 0.0, 0.0], [1.0, 1.0, 0.0], [0.0, 1.0, 0.0]]
+#         )
+#         / 3,
+#         [("triangle", numpy.array([[0, 1, 2], [0, 2, 3]]))],
+#         field_data={
+#             "bottom": numpy.array([1, 1]),
+#             "right": numpy.array([2, 1]),
+#             "top": numpy.array([3, 1]),
+#             "left": numpy.array([4, 1]),
+#         },
+#     )
+#     # write the data
+#     points, cells, field_data = mesh_out.points, mesh_out.cells, mesh_out.field_data
+#
+#     assert cells[0].type == "triangle"
+#     meshio.write(
+#         "mesh.xdmf",
+#         meshio.Mesh(points=points, cells=[cells[0]], field_data=field_data),
+#     )
+#
+#     # read it back in
+#     mesh_in = meshio.read("mesh.xdmf")
+#     assert len(mesh_in.field_data) == len(mesh_out.field_data)
 
 
 if __name__ == "__main__":