Merge pull request #725 from nschloe/force-ascii-switch

nschloe · web-flow · commit ef139714df63 · 2020-02-21T14:08:35.000+01:00
force-ascii switch
diff --git a/meshio/__about__.py b/meshio/__about__.py
@@ -1,4 +1,4 @@
-__version__ = "4.0.2"
+__version__ = "4.0.3"
 __original_author__ = "Nico Schlömer"
 __original_author_email__ = "nico.schloemer@gmail.com"
 __copyright__ = "Copyright (c) 2015-2020 meshio developers"
diff --git a/meshio/_cli/_ascii.py b/meshio/_cli/_ascii.py
@@ -59,7 +59,7 @@ def _get_parser():
         "--input-format",
         "-i",
         type=str,
-        choices=list(reader_map.keys()),
+        choices=sorted(list(reader_map.keys())),
         help="input file format",
         default=None,
     )
diff --git a/meshio/_cli/_binary.py b/meshio/_cli/_binary.py
@@ -59,7 +59,7 @@ def _get_parser():
         "--input-format",
         "-i",
         type=str,
-        choices=list(reader_map.keys()),
+        choices=sorted(list(reader_map.keys())),
         help="input file format",
         default=None,
     )
diff --git a/meshio/_cli/_compress.py b/meshio/_cli/_compress.py
@@ -79,7 +79,7 @@ def _get_parser():
         "--input-format",
         "-i",
         type=str,
-        choices=list(reader_map.keys()),
+        choices=sorted(list(reader_map.keys())),
         help="input file format",
         default=None,
     )
diff --git a/meshio/_cli/_convert.py b/meshio/_cli/_convert.py
@@ -37,14 +37,27 @@ def convert(argv=None):
     kwargs = {"file_format": args.output_format}
     if args.float_format is not None:
         kwargs["float_fmt"] = args.float_format
+    if args.ascii:
+        kwargs["binary"] = False
 
     write(args.outfile, mesh, **kwargs)
 
 
 def _get_convert_parser():
+    # Avoid repeating format names
+    # https://stackoverflow.com/a/31124505/353337
+    class CustomHelpFormatter(argparse.HelpFormatter):
+        def _format_action_invocation(self, action):
+            if not action.option_strings or action.nargs == 0:
+                return super()._format_action_invocation(action)
+            default = self._get_default_metavar_for_optional(action)
+            args_string = self._format_args(action, default)
+            return ", ".join(action.option_strings) + " " + args_string
+
     parser = argparse.ArgumentParser(
         description=("Convert between mesh formats."),
-        formatter_class=argparse.RawTextHelpFormatter,
+        # formatter_class=argparse.RawTextHelpFormatter,
+        formatter_class=CustomHelpFormatter,
     )
 
     parser.add_argument("infile", type=str, help="mesh file to be read from")
@@ -53,7 +66,7 @@ def _get_convert_parser():
         "--input-format",
         "-i",
         type=str,
-        choices=list(reader_map.keys()),
+        choices=sorted(list(reader_map.keys())),
         help="input file format",
         default=None,
     )
@@ -62,11 +75,18 @@ def _get_convert_parser():
         "--output-format",
         "-o",
         type=str,
-        choices=list(_writer_map.keys()),
+        choices=sorted(list(_writer_map.keys())),
         help="output file format",
         default=None,
     )
 
+    parser.add_argument(
+        "--ascii",
+        "-a",
+        action="store_true",
+        help="write in ASCII format variant (where applicable, default: binary)",
+    )
+
     parser.add_argument("outfile", type=str, help="mesh file to be written to")
 
     parser.add_argument(
diff --git a/meshio/_cli/_decompress.py b/meshio/_cli/_decompress.py
@@ -53,7 +53,7 @@ def _get_parser():
         "--input-format",
         "-i",
         type=str,
-        choices=list(reader_map.keys()),
+        choices=sorted(list(reader_map.keys())),
         help="input file format",
         default=None,
     )
diff --git a/meshio/_cli/_info.py b/meshio/_cli/_info.py
@@ -43,7 +43,7 @@ def _get_info_parser():
         "--input-format",
         "-i",
         type=str,
-        choices=list(reader_map.keys()),
+        choices=sorted(list(reader_map.keys())),
         help="input file format",
         default=None,
     )
diff --git a/meshio/ansys/_ansys.py b/meshio/ansys/_ansys.py
@@ -461,13 +461,4 @@ def write(filename, mesh, binary=True):
             first_index = last_index + 1
 
 
-register(
-    "ansys",
-    [],
-    read,
-    {
-        "ansys": lambda f, m, **kwargs: write(f, m, **kwargs, binary=True),
-        "ansys-ascii": lambda f, m, **kwargs: write(f, m, **kwargs, binary=False),
-        "ansys-binary": lambda f, m, **kwargs: write(f, m, **kwargs, binary=True),
-    },
-)
+register("ansys", [], read, {"ansys": write})
diff --git a/meshio/gmsh/_gmsh22.py b/meshio/gmsh/_gmsh22.py
@@ -378,7 +378,8 @@ def _write_elements(fh, cells, tag_data, binary):
                     form.format(
                         consecutive_index + k + 1,
                         " ".join([str(val) for val in fcd[k]]),
-                        " ".join([str(cc + 1) for cc in c]),
+                        # a bit clumsy for `c+1`, but if c is uint64, c+1 is float64
+                        " ".join([str(cc) for cc in c + numpy.array(1, dtype=c.dtype)]),
                     ).encode("utf-8")
                 )
 
diff --git a/meshio/gmsh/main.py b/meshio/gmsh/main.py
@@ -1,11 +1,11 @@
 import struct
 
-from .._exceptions import ReadError
+from .._exceptions import ReadError, WriteError
 from .._helpers import register
 from . import _gmsh22, _gmsh40, _gmsh41
 
-_readers = {"2": _gmsh22, "2.2": _gmsh22, "4": _gmsh40, "4.0": _gmsh40, "4.1": _gmsh41}
-_writers = {"2": _gmsh22, "2.2": _gmsh22, "4": _gmsh41, "4.0": _gmsh40, "4.1": _gmsh41}
+_readers = {"2.2": _gmsh22, "4.0": _gmsh40, "4.1": _gmsh41}
+_writers = {"2.2": _gmsh22, "4.0": _gmsh40, "4.1": _gmsh41}
 
 
 def read(filename):
@@ -30,6 +30,7 @@ def read_buffer(f):
     if line != "$MeshFormat":
         raise ReadError()
     fmt_version, data_size, is_ascii = _read_header(f)
+    print(fmt_version, data_size, is_ascii)
 
     try:
         reader = _readers[fmt_version]
@@ -90,9 +91,9 @@ def write(filename, mesh, fmt_version="4.1", binary=True):
         writer = _writers[fmt_version]
     except KeyError:
         try:
-            writer = _writers[fmt_version.split(".")[0]]
+            writer = _writers[fmt_version]
         except KeyError:
-            raise ValueError(
+            raise WriteError(
                 "Need mesh format in {} (got {})".format(
                     sorted(_writers.keys()), fmt_version
                 )
@@ -106,10 +107,7 @@ def write(filename, mesh, fmt_version="4.1", binary=True):
     [".msh"],
     read,
     {
-        "gmsh": lambda f, m, **kwargs: write(f, m, "4", **kwargs, binary=True),
-        "gmsh2-ascii": lambda f, m, **kwargs: write(f, m, "2", **kwargs, binary=False),
-        "gmsh2-binary": lambda f, m, **kwargs: write(f, m, "2", **kwargs, binary=True),
-        "gmsh4-ascii": lambda f, m, **kwargs: write(f, m, "4", **kwargs, binary=False),
-        "gmsh4-binary": lambda f, m, **kwargs: write(f, m, "4", **kwargs, binary=True),
+        "gmsh22": lambda f, m, **kwargs: write(f, m, "2.2", **kwargs),
+        "gmsh": lambda f, m, **kwargs: write(f, m, "4.1", **kwargs),
     },
 )
diff --git a/meshio/ply/_ply.py b/meshio/ply/_ply.py
@@ -403,13 +403,4 @@ def write(filename, mesh, binary=True):  # noqa: C901
                 fh.write(out.encode("utf-8"))
 
 
-register(
-    "ply",
-    [".ply"],
-    read,
-    {
-        "ply-ascii": lambda f, m, **kwargs: write(f, m, **kwargs, binary=False),
-        "ply-binary": lambda f, m, **kwargs: write(f, m, **kwargs, binary=True),
-        "ply": lambda f, m, **kwargs: write(f, m, **kwargs, binary=True),
-    },
-)
+register("ply", [".ply"], read, {"ply": write})
diff --git a/meshio/stl/_stl.py b/meshio/stl/_stl.py
@@ -231,13 +231,4 @@ def _binary(filename, points, cells):
                 fh.write(numpy.uint16(0))
 
 
-register(
-    "stl",
-    [".stl"],
-    read,
-    {
-        "stl-ascii": lambda f, m, **kwargs: write(f, m, **kwargs, binary=False),
-        "stl-binary": lambda f, m, **kwargs: write(f, m, **kwargs, binary=True),
-        "stl": lambda f, m, **kwargs: write(f, m, **{"binary": True, **kwargs}),
-    },
-)
+register("stl", [".stl"], read, {"stl": write})
diff --git a/meshio/vtk/_vtk.py b/meshio/vtk/_vtk.py
@@ -739,13 +739,4 @@ def _write_field_data(f, data, binary):
         f.write(b"\n")
 
 
-register(
-    "vtk",
-    [".vtk"],
-    read,
-    {
-        "vtk": lambda f, m, **kwargs: write(f, m, **kwargs, binary=True),
-        "vtk-ascii": lambda f, m, **kwargs: write(f, m, **kwargs, binary=False),
-        "vtk-binary": lambda f, m, **kwargs: write(f, m, **kwargs, binary=True),
-    },
-)
+register("vtk", [".vtk"], read, {"vtk": write})
diff --git a/meshio/vtu/_vtu.py b/meshio/vtu/_vtu.py
@@ -561,13 +561,4 @@ def text_writer(f):
     tree.write(filename)
 
 
-register(
-    "vtu",
-    [".vtu"],
-    read,
-    {
-        "vtu": lambda f, m, **kwargs: write(f, m, **kwargs, binary=True),
-        "vtu-ascii": lambda f, m, **kwargs: write(f, m, **kwargs, binary=False),
-        "vtu-binary": lambda f, m, **kwargs: write(f, m, **kwargs, binary=True),
-    },
-)
+register("vtu", [".vtu"], read, {"vtu": write})
diff --git a/meshio/xdmf/main.py b/meshio/xdmf/main.py
@@ -526,17 +526,5 @@ def write(*args, **kwargs):
 else:
     # TODO register all xdmf except hdf outside this try block
     register(
-        "xdmf",
-        [".xdmf", ".xmf"],
-        read,
-        {
-            "xdmf": write,
-            "xdmf-binary": lambda f, m, **kwargs: write(f, m, data_format="Binary"),
-            "xdmf-hdf": lambda f, m, **kwargs: write(f, m, data_format="HDF"),
-            "xdmf-xml": lambda f, m, **kwargs: write(f, m, data_format="XML"),
-            "xdmf3": write,
-            "xdmf3-binary": lambda f, m, **kwargs: write(f, m, data_format="Binary"),
-            "xdmf3-hdf": lambda f, m, **kwargs: write(f, m, data_format="HDF"),
-            "xdmf3-xml": lambda f, m, **kwargs: write(f, m, data_format="XML"),
-        },
+        "xdmf", [".xdmf", ".xmf"], read, {"xdmf": write},
     )
diff --git a/test/helpers.py b/test/helpers.py
@@ -306,6 +306,8 @@ def write_read(writer, reader, input_mesh, atol, extension=".dat"):
     # to make sure we are testing same type of cells we sort the list
     for cells0, cells1 in zip(sorted(input_mesh.cells), sorted(mesh.cells)):
         assert cells0.type == cells1.type
+        print(cells0.data)
+        print(cells1.data)
         assert numpy.array_equal(cells0.data, cells1.data)
 
     for key in input_mesh.point_data.keys():
diff --git a/test/test_cli.py b/test/test_cli.py
@@ -18,19 +18,19 @@ def is_same_mesh(mesh0, mesh1, atol):
 def test_info():
     input_mesh = helpers.tri_mesh
     infile = tempfile.NamedTemporaryFile().name
-    meshio.write(infile, input_mesh, file_format="gmsh4-ascii")
+    meshio.write(infile, input_mesh, file_format="gmsh")
     meshio._cli.info([infile, "--input-format", "gmsh"])
 
 
 def test_convert():
     input_mesh = helpers.tri_mesh
     infile = tempfile.NamedTemporaryFile().name
-    meshio.write(infile, input_mesh, file_format="gmsh4-ascii")
+    meshio.write(infile, input_mesh, file_format="gmsh")
 
     outfile = tempfile.NamedTemporaryFile().name
 
     meshio._cli.convert(
-        [infile, outfile, "--input-format", "gmsh", "--output-format", "vtk-binary"]
+        [infile, outfile, "--input-format", "gmsh", "--output-format", "vtk"]
     )
 
     mesh = meshio.read(outfile, file_format="vtk")
diff --git a/test/test_gmsh.py b/test/test_gmsh.py
@@ -47,7 +47,7 @@ def gmsh_periodic():
 )
 @pytest.mark.parametrize("binary", [False, True])
 def test_gmsh22(mesh, binary):
-    writer = partial(meshio.gmsh.write, fmt_version="2", binary=binary)
+    writer = partial(meshio.gmsh.write, fmt_version="2.2", binary=binary)
     helpers.write_read(writer, meshio.gmsh.read, mesh, 1.0e-15)
 
 
@@ -134,7 +134,7 @@ def test_reference_file(filename, ref_sum, ref_num_cells, binary):
     assert list(map(len, mesh.cell_data["gmsh:geometrical"])) == ref_num_cells
     assert list(map(len, mesh.cell_data["gmsh:physical"])) == ref_num_cells
 
-    writer = partial(meshio.gmsh.write, fmt_version="2", binary=binary)
+    writer = partial(meshio.gmsh.write, fmt_version="2.2", binary=binary)
     helpers.write_read(writer, meshio.gmsh.read, mesh, 1.0e-15)
 
 

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-__version__ = "4.0.2"`
	`1`	`+__version__ = "4.0.3"`
`2`	`2`	`__original_author__ = "Nico Schlömer"`
`3`	`3`	`__original_author_email__ = "[email protected]"`
`4`	`4`	`__copyright__ = "Copyright (c) 2015-2020 meshio developers"`
Original file line number	Diff line number	Diff line change
`@@ -59,7 +59,7 @@ def _get_parser():`
`59`	`59`	`"--input-format",`
`60`	`60`	`"-i",`
`61`	`61`	`type=str,`
`62`		`- choices=list(reader_map.keys()),`
	`62`	`+ choices=sorted(list(reader_map.keys())),`
`63`	`63`	`help="input file format",`
`64`	`64`	`default=None,`
`65`	`65`	`)`
Original file line number	Diff line number	Diff line change
`@@ -79,7 +79,7 @@ def _get_parser():`
`79`	`79`	`"--input-format",`
`80`	`80`	`"-i",`
`81`	`81`	`type=str,`
`82`		`- choices=list(reader_map.keys()),`
	`82`	`+ choices=sorted(list(reader_map.keys())),`
`83`	`83`	`help="input file format",`
`84`	`84`	`default=None,`
`85`	`85`	`)`
Original file line number	Diff line number	Diff line change
`@@ -53,7 +53,7 @@ def _get_parser():`
`53`	`53`	`"--input-format",`
`54`	`54`	`"-i",`
`55`	`55`	`type=str,`
`56`		`- choices=list(reader_map.keys()),`
	`56`	`+ choices=sorted(list(reader_map.keys())),`
`57`	`57`	`help="input file format",`
`58`	`58`	`default=None,`
`59`	`59`	`)`
Original file line number	Diff line number	Diff line change
`@@ -43,7 +43,7 @@ def _get_info_parser():`
`43`	`43`	`"--input-format",`
`44`	`44`	`"-i",`
`45`	`45`	`type=str,`
`46`		`- choices=list(reader_map.keys()),`
	`46`	`+ choices=sorted(list(reader_map.keys())),`
`47`	`47`	`help="input file format",`
`48`	`48`	`default=None,`
`49`	`49`	`)`
Original file line number	Diff line number	Diff line change
`@@ -378,7 +378,8 @@ def _write_elements(fh, cells, tag_data, binary):`
`378`	`378`	`form.format(`
`379`	`379`	`consecutive_index + k + 1,`
`380`	`380`	`" ".join([str(val) for val in fcd[k]]),`
`381`		`- " ".join([str(cc + 1) for cc in c]),`
	`381`	+ # a bit clumsy for `c+1`, but if c is uint64, c+1 is float64
	`382`	`+ " ".join([str(cc) for cc in c + numpy.array(1, dtype=c.dtype)]),`
`382`	`383`	`).encode("utf-8")`
`383`	`384`	`)`
`384`	`385`