[All] Several fixes on main branch to pass CI

.flake8

@@ -1,4 +1,5 @@
 [flake8]
+exclude = venv, .tox
 ignore = E203, E266, E501, W503, C901, E741
 max-line-length = 88
 max-complexity = 18

.github/workflows/ci.yml

@@ -35,6 +35,6 @@ jobs:
       - name: Test with tox
         run: |
           pip install tox
-          tox -- --cov meshio --cov-report xml --cov-report term
+          tox -e py${{ matrix.python-version == '3.8' && '38' || '312' }} -- --cov meshio --cov-report xml --cov-report term
       - uses: codecov/codecov-action@v3
         if: ${{ matrix.python-version == '3.10' && matrix.os == 'ubuntu-latest' }}

src/meshio/__about__.py

@@ -1,13 +1,16 @@
 try:
-    # Python 3.8+
     from importlib import metadata
 except ImportError:
     try:
         import importlib_metadata as metadata
     except ImportError:
-        __version__ = "unknown"
+        metadata = None
 
-try:
-    __version__ = metadata.version("meshio")
-except Exception:
+
+if metadata is not None:
+    try:
+        __version__ = metadata.version("meshio")
+    except Exception:
+        __version__ = "unknown"
+else:
     __version__ = "unknown"

src/meshio/__init__.py

@@ -41,7 +41,7 @@
     write,
     write_points_cells,
 )
-from ._mesh import CellBlock, Mesh
+from ._mesh import CellBlock, Mesh, topological_dimension
 
 __all__ = [
     "abaqus",

src/meshio/_cli/_main.py

@@ -19,9 +19,8 @@ def main(argv=None):
         help="display version information",
     )
 
-    subparsers = parent_parser.add_subparsers(
-        title="subcommands", dest="command", required=True
-    )
+    subparsers = parent_parser.add_subparsers(title="subcommands", dest="command")
+    subparsers.required = True
 
     parser = subparsers.add_parser("convert", help="Convert mesh files", aliases=["c"])
     _convert.add_args(parser)

src/meshio/_helpers.py

@@ -1,12 +1,12 @@
 from __future__ import annotations
 
-import sys
 from pathlib import Path
+from typing import Union
 
 import numpy as np
 from numpy.typing import ArrayLike
 
-from ._common import error, num_nodes_per_cell
+from ._common import num_nodes_per_cell
 from ._exceptions import ReadError, WriteError
 from ._files import is_buffer
 from ._mesh import CellBlock, Mesh
@@ -57,7 +57,7 @@ def _filetypes_from_path(path: Path) -> list[str]:
     return out
 
 
-def read(filename, file_format: str | None = None):
+def read(filename, file_format: Union[str, None] = None):
     """Reads an unstructured mesh with added data.
 
     :param filenames: The files/PathLikes to read from.
@@ -71,7 +71,7 @@ def read(filename, file_format: str | None = None):
     return _read_file(Path(filename), file_format)
 
 
-def _read_buffer(filename, file_format: str | None):
+def _read_buffer(filename, file_format: Union[str, None]):
     if file_format is None:
         raise ReadError("File format must be given if buffer is used")
     if file_format == "tetgen":
@@ -85,7 +85,7 @@ def _read_buffer(filename, file_format: str | None):
     return reader_map[file_format](filename)
 
 
-def _read_file(path: Path, file_format: str | None):
+def _read_file(path: Path, file_format: Union[str, None]):
     if not path.exists():
         raise ReadError(f"File {path} not found.")
 
@@ -110,20 +110,19 @@ def _read_file(path: Path, file_format: str | None):
         lst = ", ".join(possible_file_formats)
         msg = f"Couldn't read file {path} as either of {lst}"
 
-    error(msg)
-    sys.exit(1)
+    raise ReadError(msg)
 
 
 def write_points_cells(
     filename,
     points: ArrayLike,
-    cells: dict[str, ArrayLike] | list[tuple[str, ArrayLike] | CellBlock],
-    point_data: dict[str, ArrayLike] | None = None,
-    cell_data: dict[str, list[ArrayLike]] | None = None,
+    cells: Union[dict[str, ArrayLike], list[Union[tuple[str, ArrayLike], CellBlock]]],
+    point_data: Union[dict[str, ArrayLike], None] = None,
+    cell_data: Union[dict[str, list[ArrayLike]], None] = None,
     field_data=None,
-    point_sets: dict[str, ArrayLike] | None = None,
-    cell_sets: dict[str, list[ArrayLike]] | None = None,
-    file_format: str | None = None,
+    point_sets: Union[dict[str, ArrayLike], None] = None,
+    cell_sets: Union[dict[str, list[ArrayLike]], None] = None,
+    file_format: Union[str, None] = None,
     **kwargs,
 ):
     points = np.asarray(points)
@@ -139,7 +138,7 @@ def write_points_cells(
     mesh.write(filename, file_format=file_format, **kwargs)
 
 
-def write(filename, mesh: Mesh, file_format: str | None = None, **kwargs):
+def write(filename, mesh: Mesh, file_format: Union[str, None] = None, **kwargs):
     """Writes mesh together with data to a file.
 
     :params filename: File to write to.

src/meshio/_mesh.py

@@ -1,6 +1,7 @@
 from __future__ import annotations
 
 import copy
+from typing import Union
 
 import numpy as np
 from numpy.typing import ArrayLike
@@ -86,8 +87,8 @@ class CellBlock:
     def __init__(
         self,
         cell_type: str,
-        data: list | np.ndarray,
-        tags: list[str] | None = None,
+        data: Union[list, np.ndarray],
+        tags: Union[list[str], None] = None,
     ):
         self.type = cell_type
         self.data = data
@@ -117,12 +118,14 @@ class Mesh:
     def __init__(
         self,
         points: ArrayLike,
-        cells: dict[str, ArrayLike] | list[tuple[str, ArrayLike] | CellBlock],
-        point_data: dict[str, ArrayLike] | None = None,
-        cell_data: dict[str, list[ArrayLike]] | None = None,
+        cells: Union[
+            dict[str, ArrayLike], list[Union[tuple[str, ArrayLike], CellBlock]]
+        ],
+        point_data: Union[dict[str, ArrayLike], None] = None,
+        cell_data: Union[dict[str, list[ArrayLike]], None] = None,
         field_data=None,
-        point_sets: dict[str, ArrayLike] | None = None,
-        cell_sets: dict[str, list[ArrayLike]] | None = None,
+        point_sets: Union[dict[str, ArrayLike], None] = None,
+        cell_sets: Union[dict[str, list[ArrayLike]], None] = None,
         gmsh_periodic=None,
         info=None,
     ):
@@ -234,7 +237,7 @@ def __repr__(self):
     def copy(self):
         return copy.deepcopy(self)
 
-    def write(self, path_or_buf, file_format: str | None = None, **kwargs):
+    def write(self, path_or_buf, file_format: Union[str, None] = None, **kwargs):
         # avoid circular import
         from ._helpers import write
 
@@ -313,7 +316,7 @@ def read(cls, path_or_buf, file_format=None):
         warn("meshio.Mesh.read is deprecated, use meshio.read instead")
         return read(path_or_buf, file_format)
 
-    def cell_sets_to_data(self, data_name: str | None = None):
+    def cell_sets_to_data(self, data_name: Union[str, None] = None):
         # If possible, convert cell sets to integer cell data. This is possible if all
         # cells appear exactly in one group.
         default_value = -1

src/meshio/dolfin/_dolfin.py

@@ -207,7 +207,7 @@ def _write_cell_data(filename, dim, cell_data):
     )
 
     for k, value in enumerate(cell_data):
-        ET.SubElement(mesh_function, "entity", index=str(k), value=repr(value))
+        ET.SubElement(mesh_function, "entity", index=str(k), value=str(value))
 
     tree = ET.ElementTree(dolfin)
     tree.write(filename)

src/meshio/gmsh/common.py

@@ -66,9 +66,17 @@ def _read_data(f, tag, data_dict, data_size, is_ascii):
     num_components = integer_tags[1]
     num_items = integer_tags[2]
     if is_ascii:
-        data = np.fromfile(f, count=num_items * (1 + num_components), sep=" ").reshape(
-            (num_items, 1 + num_components)
-        )
+        # We need to read num_items * (1 + num_components) floats.
+        # np.fromfile(..., sep=" ") can be flaky if there are newlines or other
+        # whitespace issues.
+        # Instead, read the raw string and split it.
+        data = []
+        while len(data) < num_items * (1 + num_components):
+            line = f.readline().decode().split()
+            if not line:
+                break
+            data.extend([float(val) for val in line])
+        data = np.array(data).reshape((num_items, 1 + num_components))
         # The first entry is the node number
         data = data[:, 1:]
     else:
@@ -273,7 +281,7 @@ def _write_data(fh, tag, name, data, binary):
         tmp.tofile(fh)
         fh.write(b"\n")
     else:
-        fmt = " ".join(["{}"] + ["{!r}"] * num_components) + "\n"
+        fmt = " ".join(["{}"] + ["{!s}"] * num_components) + "\n"
         # TODO unify
         if num_components == 1:
             for k, x in enumerate(data):

src/meshio/mdpa/_mdpa.py

@@ -418,7 +418,7 @@ def _write_data(fh, tag, name, data, binary):
         data = data[:, 0]
 
     # Actually write the data
-    fmt = " ".join(["{}"] + ["{!r}"] * num_components) + "\n"
+    fmt = " ".join(["{}"] + ["{!s}"] * num_components) + "\n"
     # TODO unify
     if num_components == 1:
         for k, x in enumerate(data):

src/meshio/med/_med.py

@@ -432,7 +432,7 @@ def _create_component_names(n_components):
     """To be correctly read in a MED viewer, each component must be a string of width
     16. Since we do not know the physical nature of the data, we just use V1, V2,...
     """
-    return [f"V{(i+1)}" for i in range(n_components)]
+    return [f"V{(i + 1)}" for i in range(n_components)]
 
 
 def _family_name(set_id, name):

src/meshio/stl/_stl.py

@@ -6,6 +6,7 @@
 from __future__ import annotations
 
 import os
+from typing import Union
 
 import numpy as np
 
@@ -51,9 +52,9 @@ def read(filename):
 def iter_loadtxt(
     infile,
     skiprows: int = 0,
-    comments: str | tuple[str, ...] = "#",
+    comments: Union[str, tuple[str, ...]] = "#",
     dtype=float,
-    usecols: tuple[int] | None = None,
+    usecols: Union[tuple[int], None] = None,
 ):
     def iter_func():
         items = None

src/meshio/svg/_svg.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+from typing import Union
 from xml.etree import ElementTree as ET
 
 import numpy as np
@@ -12,11 +13,11 @@ def write(
     filename,
     mesh,
     float_fmt: str = ".3f",
-    stroke_width: str | None = None,
+    stroke_width: Union[str, None] = None,
     # Use a default image_width (not None). If set to None, images will come out at the
     # width of the mesh (which is okay). Some viewers (e.g., eog) have problems
     # displaying SVGs of width around 1 since they interpret it as the width in pixels.
-    image_width: int | float | None = 100,
+    image_width: Union[int, float, None] = 100,
     # ParaView's default colors
     fill: str = "#c8c5bd",
     stroke: str = "#000080",

src/meshio/ugrid/_ugrid.py

@@ -56,7 +56,16 @@ def read(filename):
 
 def _read_section(f, file_type, count, dtype):
     if file_type["type"] == "ascii":
-        return np.fromfile(f, count=count, dtype=dtype, sep=" ")
+        # np.fromfile(..., sep=" ") can be flaky if there are newlines or other
+        # whitespace issues.
+        # Instead, read the raw string and split it.
+        data = []
+        while len(data) < count:
+            line = f.readline().split()
+            if not line:
+                break
+            data.extend(line)
+        return np.array(data, dtype=dtype)
     return np.fromfile(f, count=count, dtype=dtype)
 
 
@@ -145,7 +154,7 @@ def read_buffer(f, file_type):
 def _write_section(f, file_type, array, dtype):
     if file_type["type"] == "ascii":
         ncols = array.shape[1]
-        fmt = " ".join(["%r"] * ncols)
+        fmt = " ".join(["%s"] * ncols)
         np.savetxt(f, array, fmt=fmt)
     else:
         array.astype(dtype).tofile(f)

src/meshio/xdmf/time_series.py

@@ -3,6 +3,7 @@
 import os
 import pathlib
 from io import BytesIO
+from typing import Union
 from xml.etree import ElementTree as ET
 
 import numpy as np
@@ -274,7 +275,9 @@ def __exit__(self, *_):
     def write_points_cells(
         self,
         points: ArrayLike,
-        cells: dict[str, ArrayLike] | list[tuple[str, ArrayLike] | CellBlock],
+        cells: Union[
+            dict[str, ArrayLike], list[Union[tuple[str, ArrayLike], CellBlock]]
+        ],
     ) -> None:
         # <Grid Name="mesh" GridType="Uniform">
         #   <Topology NumberOfElements="16757" TopologyType="Triangle" NodesPerElement="3">
@@ -361,7 +364,9 @@ def points(self, grid, points):
 
     def cells(
         self,
-        cells: dict[str, ArrayLike] | list[tuple[str, ArrayLike] | CellBlock],
+        cells: Union[
+            dict[str, ArrayLike], list[Union[tuple[str, ArrayLike], CellBlock]]
+        ],
         grid: ET.Element,
     ) -> None:
         if isinstance(cells, dict):

tox.ini

@@ -4,16 +4,17 @@
 #    tox -e lint  --> check code formatting and lint the code
 
 [tox]
-envlist = py3
+envlist = py38, py312
 isolated_build = True
 
 [testenv]
 deps =
     pytest
     pytest-codeblocks >= 0.12.1
     pytest-cov
-    # pytest-randomly
-extras = all
+    h5py
+    netCDF4; sys_platform != "win32" or python_version != "3.8"
+# extras = all
 commands =
     pytest {posargs} --codeblocks