Merge pull request #1241 from nschloe/rich

unify warnings, use rich

.github/workflows/ci.yml

@@ -20,6 +20,7 @@ jobs:
         uses: pre-commit/[email protected]
 
   build:
+    needs: [lint]
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = meshio
-version = 5.1.2
+version = 5.2.0
 author = Nico Schlömer et al.
 author_email = [email protected]
 description = I/O for many mesh formats
@@ -40,6 +40,7 @@ packages = find:
 install_requires =
     importlib_metadata;python_version<"3.8"
     numpy
+    rich
 python_requires = >=3.7
 
 [options.packages.find]

src/meshio/_cli/_ascii.py

@@ -2,6 +2,7 @@
 import pathlib
 
 from .. import ansys, flac3d, gmsh, mdpa, ply, stl, vtk, vtu, xdmf
+from .._common import error
 from .._helpers import _filetype_from_path, read, reader_map
 
 
@@ -49,7 +50,7 @@ def ascii(args):
     elif fmt == "xdmf":
         xdmf.write(args.infile, mesh, data_format="XML")
     else:
-        print(f"Don't know how to convert {args.infile} to ASCII format.")
+        error(f"Don't know how to convert {args.infile} to ASCII format.")
         return 1
 
     size = os.stat(args.infile).st_size

src/meshio/_cli/_compress.py

@@ -2,6 +2,7 @@
 import pathlib
 
 from .. import ansys, cgns, gmsh, h5m, mdpa, ply, stl, vtk, vtu, xdmf
+from .._common import error
 from .._helpers import _filetype_from_path, read, reader_map
 
 
@@ -69,7 +70,7 @@ def compress(args):
             compression_opts=9 if args.max else 4,
         )
     else:
-        print(f"Don't know how to compress {args.infile}.")
+        error(f"Don't know how to compress {args.infile}.")
         exit(1)
 
     size = os.stat(args.infile).st_size

src/meshio/_cli/_decompress.py

@@ -2,6 +2,7 @@
 import pathlib
 
 from .. import cgns, h5m, vtu, xdmf
+from .._common import error
 from .._helpers import _filetype_from_path, read, reader_map
 
 
@@ -38,7 +39,7 @@ def decompress(args):
     elif fmt == "xdmf":
         xdmf.write(args.infile, mesh, data_format="HDF", compression=None)
     else:
-        print(f"Don't know how to decompress {args.infile}.")
+        error(f"Don't know how to decompress {args.infile}.")
         exit(1)
 
     size = os.stat(args.infile).st_size

src/meshio/_cli/_info.py

@@ -1,5 +1,6 @@
 import numpy as np
 
+from .._common import warn
 from .._helpers import read, reader_map
 
 
@@ -24,7 +25,7 @@ def info(args):
     is_consistent = True
     for cells in mesh.cells:
         if np.any(cells.data > mesh.points.shape[0]):
-            print("\nATTENTION: Inconsistent mesh. Cells refer to nonexistent points.")
+            warn("Inconsistent mesh. Cells refer to nonexistent points.")
             is_consistent = False
             break
 
@@ -34,6 +35,6 @@ def info(args):
         for cells in mesh.cells:
             point_is_used[cells.data] = True
         if np.any(~point_is_used):
-            print("ATTENTION: Some points are not part of any cell.")
+            warn("Some points are not part of any cell.")
 
     return 0

src/meshio/_common.py

@@ -1,6 +1,7 @@
 from xml.etree import ElementTree as ET
 
 import numpy as np
+from rich.console import Console
 
 # See <https://github.com/nschloe/meshio/wiki/Node-ordering-in-cells> for the node
 # ordering.
@@ -117,3 +118,13 @@ def _pick_first_int_data(data):
         other = []
 
     return key, other
+
+
+def warn(string, highlight: bool = True) -> None:
+    Console(stderr=True).print(
+        f"[yellow]Warning: {string}[/yellow]", highlight=highlight
+    )
+
+
+def error(string, highlight: bool = True) -> None:
+    Console(stderr=True).print(f"[red]Error: {string}[/red]", highlight=highlight)

src/meshio/_mesh.py

@@ -1,12 +1,11 @@
 from __future__ import annotations
 
 import copy
-import warnings
 
 import numpy as np
 from numpy.typing import ArrayLike
 
-from ._common import num_nodes_per_cell
+from ._common import num_nodes_per_cell, warn
 
 topological_dimension = {
     "line": 1,
@@ -130,8 +129,7 @@ def __init__(
         self.points = np.asarray(points)
         if isinstance(cells, dict):
             # Let's not deprecate this for now.
-            # import warnings
-            # warnings.warn(
+            # warn(
             #     "cell dictionaries are deprecated, use list of tuples, e.g., "
             #     '[("triangle", [[0, 1, 2], ...])]',
             #     DeprecationWarning,
@@ -311,10 +309,7 @@ def read(cls, path_or_buf, file_format=None):
         from ._helpers import read
 
         # 2021-02-21
-        warnings.warn(
-            "meshio.Mesh.read is deprecated, use meshio.read instead",
-            DeprecationWarning,
-        )
+        warn("meshio.Mesh.read is deprecated, use meshio.read instead")
         return read(path_or_buf, file_format)
 
     def sets_to_int_data(self):
@@ -335,7 +330,7 @@ def sets_to_int_data(self):
             for item in intfun:
                 num_default = np.sum(item == default_value)
                 if num_default > 0:
-                    warnings.warn(
+                    warn(
                         f"{num_default} cells are not part of any cell set. "
                         f"Using default value {default_value}."
                     )
@@ -353,7 +348,7 @@ def sets_to_int_data(self):
                 intfun[cc] = i
 
             if np.any(intfun == default_value):
-                warnings.warn(
+                warn(
                     "Not all points are part of a point set. "
                     f"Using default value {default_value}."
                 )

src/meshio/_vtk_common.py

@@ -1,8 +1,6 @@
-import warnings
-
 import numpy as np
 
-from ._common import num_nodes_per_cell
+from ._common import num_nodes_per_cell, warn
 from ._exceptions import ReadError
 from ._mesh import CellBlock
 
@@ -113,7 +111,7 @@ def vtk_cells_from_data(connectivity, offsets, types, cell_data_raw):
         try:
             meshio_type = vtk_to_meshio_type[types[start]]
         except KeyError:
-            warnings.warn(
+            warn(
                 f"File contains cells that meshio cannot handle (type {types[start]})."
             )
             continue

src/meshio/ansys/_ansys.py

@@ -3,12 +3,12 @@
 
 <https://romeo.univ-reims.fr/documents/fluent/tgrid/ug/appb.pdf>
 """
-import logging
 import re
 
 import numpy as np
 
 from ..__about__ import __version__
+from .._common import warn
 from .._exceptions import ReadError, WriteError
 from .._files import open_file
 from .._helpers import register_format
@@ -357,23 +357,23 @@ def read(filename):  # noqa: C901
                     cells.append((key, data[key]))
 
             elif index == "39":
-                logging.warning("Zone specification not supported yet. Skipping.")
+                warn("Zone specification not supported yet. Skipping.")
                 _skip_close(f, line.count("(") - line.count(")"))
 
             elif index == "45":
                 # (45 (2 fluid solid)())
                 obj = re.match("\\(45 \\([0-9]+ ([\\S]+) ([\\S]+)\\)\\(\\)\\)", line)
                 if obj:
-                    logging.warning(
+                    warn(
                         "Zone specification not supported yet (%r, %r). " "Skipping.",
                         obj.group(1),
                         obj.group(2),
                     )
                 else:
-                    logging.warning("Zone specification not supported yet.")
+                    warn("Zone specification not supported yet.")
 
             else:
-                logging.warning("Unknown index %r. Skipping.", index)
+                warn("Unknown index %r. Skipping.", index)
                 # Skipping ahead to the next line with two closing brackets.
                 _skip_close(f, line.count("(") - line.count(")"))
 

src/meshio/avsucd/_avsucd.py

@@ -2,12 +2,10 @@
 I/O for AVS-UCD format, cf.
 <https://lanl.github.io/LaGriT/pages/docs/read_avs.html>.
 """
-import logging
-
 import numpy as np
 
 from ..__about__ import __version__ as version
-from .._common import _pick_first_int_data
+from .._common import _pick_first_int_data, warn
 from .._files import open_file
 from .._helpers import register_format
 from .._mesh import CellBlock, Mesh
@@ -147,7 +145,7 @@ def _read_data(f, num_entities, entity_ids):
 
 def write(filename, mesh):
     if len(mesh.points.shape) > 1 and mesh.points.shape[1] == 2:
-        logging.warning(
+        warn(
             "AVS-UCD requires 3D points, but 2D points given. "
             "Appending 0 third component."
         )
@@ -165,7 +163,7 @@ def write(filename, mesh):
         key, other = _pick_first_int_data(mesh.cell_data)
         if key and other:
             other_string = ", ".join(other)
-            logging.warning(
+            warn(
                 "AVS-UCD can only write one cell data array. "
                 f"Picking {key}, skipping {other_string}."
             )

src/meshio/dolfin/_dolfin.py

@@ -2,14 +2,14 @@
 I/O for DOLFIN's XML format, cf.
 <https://people.sc.fsu.edu/~jburkardt/data/dolfin_xml/dolfin_xml.html>.
 """
-import logging
 import os
 import pathlib
 import re
 from xml.etree import ElementTree as ET
 
 import numpy as np
 
+from .._common import warn
 from .._exceptions import ReadError, WriteError
 from .._helpers import register_format
 from .._mesh import Mesh
@@ -71,7 +71,7 @@ def _read_mesh(filename):
             assert cell_tags is not None
             cells[0][1][k] = [elem.attrib[t] for t in cell_tags]
         else:
-            logging.warning("Unknown entry %s. Ignoring.", elem.tag)
+            warn("Unknown entry %s. Ignoring.", elem.tag)
 
         elem.clear()
 
@@ -138,7 +138,7 @@ def _write_mesh(filename, points, cell_type, cells):
 
     if any(c.type != cell_type for c in cells):
         discarded_cell_types = {c.type for c in cells if c.type != cell_type}
-        logging.warning(
+        warn(
             "DOLFIN XML can only handle one cell type at a time. "
             "Using %s, discarding %s.",
             cell_type,
@@ -215,7 +215,7 @@ def _write_cell_data(filename, dim, cell_data):
 
 
 def write(filename, mesh):
-    logging.warning("DOLFIN XML is a legacy format. Consider using XDMF instead.")
+    warn("DOLFIN XML is a legacy format. Consider using XDMF instead.")
 
     if any("tetra" == c.type for c in mesh.cells):
         cell_type = "tetra"

src/meshio/exodus/_exodus.py

@@ -7,11 +7,11 @@
 """
 import datetime
 import re
-import warnings
 
 import numpy as np
 
 from ..__about__ import __version__
+from .._common import warn
 from .._exceptions import ReadError
 from .._helpers import register_format
 from .._mesh import Mesh
@@ -122,7 +122,7 @@ def read(filename):  # noqa: C901
                 # For now only take the first value
                 pd[idx] = value[0]
                 if len(value) > 1:
-                    warnings.warn("Skipping some time data")
+                    warn("Skipping some time data")
             elif key == "name_elem_var":
                 value.set_auto_mask(False)
                 cell_data_names = [b"".join(c).decode("UTF-8") for c in value[:]]
@@ -139,7 +139,7 @@ def read(filename):  # noqa: C901
                 cd[idx][block] = value[0]
 
                 if len(value) > 1:
-                    warnings.warn("Skipping some time data")
+                    warn("Skipping some time data")
             elif key == "ns_names":
                 value.set_auto_mask(False)
                 ns_names = [b"".join(c).decode("UTF-8") for c in value[:]]

src/meshio/flac3d/_flac3d.py

@@ -1,15 +1,13 @@
 """
 I/O for FLAC3D format.
 """
-import logging
 import struct
 import time
-from warnings import warn
 
 import numpy as np
 
 from ..__about__ import __version__ as version
-from .._common import _pick_first_int_data
+from .._common import _pick_first_int_data, warn
 from .._files import open_file
 from .._helpers import register_format
 from .._mesh import Mesh
@@ -170,10 +168,13 @@ def read_buffer(f, binary):
     ]
 
     if len(cell_sets) > 0:
-        # Can only deal with sequential cell_ids for now. If the order is messed
-        # up, or if some indices are missing, cell_sets will be wrong.
-        if not np.all(np.arange(cell_ids[0], cell_ids[-1] + 1) == cell_ids):
-            warn("FLAC3D cell IDs not sequential. Cell sets probably messed up.")
+        # Can only deal with arange cell_ids for now.
+        if not np.array_equal(np.arange(0, cell_ids[-1] + 1), cell_ids):
+            warn(
+                "FLAC3D cell IDs not arange (0, 1, 2, ..., n). "
+                + "Cell sets probably messed up.",
+                highlight=False,
+            )
 
     # cell_sets contains the indices into the global cell list. Since this is
     # split up into blocks, we need to split the cell_sets, too.
@@ -278,9 +279,7 @@ def write(filename, mesh: Mesh, float_fmt: str = ".16e", binary: bool = False):
     """Write FLAC3D f3grid grid file."""
     skip = [c.type for c in mesh.cells if c.type not in meshio_only["zone"]]
     if skip:
-        logging.warning(
-            f'FLAC3D format only supports 3D cells. Skipping {", ".join(skip)}.'
-        )
+        warn(f'FLAC3D format only supports 3D cells. Skipping {", ".join(skip)}.')
 
     # Pick out material
     material = None
@@ -289,7 +288,7 @@ def write(filename, mesh: Mesh, float_fmt: str = ".16e", binary: bool = False):
         if key:
             material = np.concatenate(mesh.cell_data[key])
             if other:
-                logging.warning(
+                warn(
                     "FLAC3D can only write one cell data array. "
                     f'Picking {key}, skipping {", ".join(other)}.'
                 )