lint fixes

.github/workflows/ci.yml

@@ -13,11 +13,11 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out repo
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
       - name: Run pre-commit
-        uses: pre-commit/action@v2.0.3
+        uses: pre-commit/action@v3.0.0
 
   build:
     needs: [lint]
@@ -27,7 +27,7 @@ jobs:
         os: [ubuntu-latest, windows-latest, macOS-latest]
         python-version: ["3.7", "3.8", "3.9", "3.10"]
     steps:
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Checkout code
@@ -36,5 +36,5 @@ jobs:
         run: |
           pip install tox
           tox -- --cov meshio --cov-report xml --cov-report term
-      - uses: codecov/codecov-action@v1
+      - uses: codecov/codecov-action@v3
         if: ${{ matrix.python-version == '3.10' && matrix.os == 'ubuntu-latest' }}

.pre-commit-config.yaml

@@ -1,16 +1,16 @@
 repos:
   - repo: https://github.com/PyCQA/isort
-    rev: 5.10.1
+    rev: 5.13.2
     hooks:
       - id: isort
 
   - repo: https://github.com/psf/black
-    rev: 22.1.0
+    rev: 24.1.1
     hooks:
       - id: black
         language_version: python3
 
   - repo: https://github.com/PyCQA/flake8
-    rev: 4.0.1
+    rev: 7.0.0
     hooks:
       - id: flake8

justfile

@@ -1,4 +1,4 @@
-version := `python3 -c "from configparser import ConfigParser; p = ConfigParser(); p.read('setup.cfg'); print(p['metadata']['version'])"`
+version := `python -c "import tomllib; print(tomllib.load(open('pyproject.toml', 'rb'))['project']['version'])"`
 
 default:
 	@echo "\"just publish\"?"

src/meshio/abaqus/_abaqus.py

@@ -1,6 +1,7 @@
 """
 I/O for Abaqus inp files.
 """
+
 import pathlib
 from itertools import count
 

src/meshio/ansys/_ansys.py

@@ -3,6 +3,7 @@
 
 <https://romeo.univ-reims.fr/documents/fluent/tgrid/ug/appb.pdf>
 """
+
 import re
 
 import numpy as np

src/meshio/avsucd/_avsucd.py

@@ -2,6 +2,7 @@
 I/O for AVS-UCD format, cf.
 <https://lanl.github.io/LaGriT/pages/docs/read_avs.html>.
 """
+
 import numpy as np
 
 from ..__about__ import __version__ as version

src/meshio/cgns/_cgns.py

@@ -3,6 +3,7 @@
 
 TODO link to specification?
 """
+
 import numpy as np
 
 from .._exceptions import ReadError

src/meshio/dolfin/_dolfin.py

@@ -2,6 +2,7 @@
 I/O for DOLFIN's XML format, cf.
 <https://people.sc.fsu.edu/~jburkardt/data/dolfin_xml/dolfin_xml.html>.
 """
+
 import os
 import pathlib
 import re

src/meshio/exodus/_exodus.py

@@ -5,6 +5,7 @@
 <https://src.fedoraproject.org/repo/pkgs/exodusii/922137.pdf/a45d67f4a1a8762bcf66af2ec6eb35f9/922137.pdf>,
 in particular Appendix A (page 171, Implementation of EXODUS II with netCDF).
 """
+
 import datetime
 import re
 

src/meshio/flac3d/_flac3d.py

@@ -1,6 +1,7 @@
 """
 I/O for FLAC3D format.
 """
+
 from __future__ import annotations
 
 import re
@@ -534,6 +535,7 @@ def _translate_zcells(points, cells):
     normal vectors). Reorder corner points according to sign of scalar triple
     products.
     """
+
     # See <https://stackoverflow.com/a/42386330/353337>
     def slicing_summing(a, b, c):
         c0 = b[:, 1] * c[:, 2] - b[:, 2] * c[:, 1]

src/meshio/gmsh/_gmsh22.py

@@ -2,6 +2,7 @@
 I/O for Gmsh's msh format, cf.
 <http://gmsh.info//doc/texinfo/gmsh.html#File-formats>.
 """
+
 from __future__ import annotations
 
 import numpy as np

src/meshio/gmsh/_gmsh40.py

@@ -2,6 +2,7 @@
 I/O for Gmsh's msh format (version 4.0, as used by Gmsh 4.1.5), cf.
 <http://gmsh.info//doc/texinfo/gmsh.html#MSH-file-format-_0028version-4_0029>.
 """
+
 from __future__ import annotations
 
 from functools import partial

src/meshio/gmsh/_gmsh41.py

@@ -2,6 +2,7 @@
 I/O for Gmsh's msh format (version 4.1, as used by Gmsh 4.2.2+), cf.
 <http://gmsh.info/doc/texinfo/gmsh.html#MSH-file-format>.
 """
+
 from functools import partial
 
 import numpy as np
@@ -209,13 +210,15 @@ def _read_elements(
         (num_ele,) = fromfile(f, c_size_t, 1)
         for physical_name, cell_set in cell_sets.items():
             cell_set[k] = np.arange(
-                num_ele
-                if (
-                    physical_tags
-                    and field_data[physical_name][1] == dim
-                    and field_data[physical_name][0] in physical_tags[dim][tag]
-                )
-                else 0,
+                (
+                    num_ele
+                    if (
+                        physical_tags
+                        and field_data[physical_name][1] == dim
+                        and field_data[physical_name][0] in physical_tags[dim][tag]
+                    )
+                    else 0
+                ),
                 dtype=type(num_ele),
             )
         tpe = _gmsh_to_meshio_type[type_ele]

src/meshio/h5m/_h5m.py

@@ -2,6 +2,7 @@
 I/O for h5m, cf.
 <https://www.mcs.anl.gov/~fathom/moab-docs/html/h5mmain.html>.
 """
+
 from datetime import datetime
 
 import numpy as np

src/meshio/mdpa/_mdpa.py

@@ -5,6 +5,7 @@
 The MDPA format is unsuitable for fast consumption, this is why:
 <https://github.com/KratosMultiphysics/Kratos/issues/5365>.
 """
+
 import numpy as np
 
 from .._common import num_nodes_per_cell, raw_from_cell_data, warn

src/meshio/med/_med.py

@@ -2,6 +2,7 @@
 I/O for MED/Salome, cf.
 <https://docs.salome-platform.org/latest/dev/MEDCoupling/developer/med-file.html>.
 """
+
 import numpy as np
 
 from .._common import num_nodes_per_cell

src/meshio/medit/_medit.py

@@ -3,6 +3,7 @@
 Latest official up-to-date documentation and a reference C implementation at
 <https://github.com/LoicMarechal/libMeshb>
 """
+
 import struct
 from ctypes import c_double, c_float
 

src/meshio/nastran/_nastran.py

@@ -1,6 +1,7 @@
 """
 I/O for Nastran bulk data.
 """
+
 from __future__ import annotations
 
 import numpy as np

src/meshio/netgen/_netgen.py

@@ -2,6 +2,7 @@
 I/O for Netgen mesh files
 <https://github.com/NGSolve/netgen/blob/master/libsrc/meshing/meshclass.cpp>.
 """
+
 import numpy as np
 
 from ..__about__ import __version__

src/meshio/neuroglancer/_neuroglancer.py

@@ -3,6 +3,7 @@
 
 Adapted from https://github.com/HumanBrainProject/neuroglancer-scripts/blob/1fcabb613a715ba17c65d52596dec3d687ca3318/src/neuroglancer_scripts/mesh.py (MIT license)
 """
+
 import struct
 
 import numpy as np
@@ -57,7 +58,10 @@ def read_buffer(file):
     if len(buf) != 4 * 3 * num_vertices:
         raise ReadError("The precomputed mesh data is too short")
     flat_vertices = np.frombuffer(buf, "<f")
-    vertices = np.reshape(flat_vertices, (num_vertices, 3),).copy(
+    vertices = np.reshape(
+        flat_vertices,
+        (num_vertices, 3),
+    ).copy(
         order="C"
     )  # TODO remove copy
     # BUG: this could easily exhaust memory if reading a large file that is not

src/meshio/obj/_obj.py

@@ -2,6 +2,7 @@
 I/O for the Wavefront .obj file format, cf.
 <https://en.wikipedia.org/wiki/Wavefront_.obj_file>.
 """
+
 import datetime
 
 import numpy as np

src/meshio/off/_off.py

@@ -3,6 +3,7 @@
 <https://en.wikipedia.org/wiki/OFF_(file_format)>,
 <http://www.geomview.org/docs/html/OFF.html>.
 """
+
 import numpy as np
 
 from .._common import warn

src/meshio/permas/_permas.py

@@ -1,6 +1,7 @@
 """
 I/O for PERMAS dat files.
 """
+
 import numpy as np
 
 from ..__about__ import __version__

src/meshio/ply/_ply.py

@@ -3,6 +3,7 @@
 <https://en.wikipedia.org/wiki/PLY_(file_format)>.
 <https://web.archive.org/web/20161221115231/http://www.cs.virginia.edu/~gfx/Courses/2001/Advanced.spring.01/plylib/Ply.txt>.
 """
+
 import collections
 import datetime
 import re
@@ -296,11 +297,13 @@ def _read_binary(
     # Convert strings to proper numpy dtypes
     dts = [
         (
-            endianness + ply_to_numpy_dtype_string[dtype[0]],
-            endianness + ply_to_numpy_dtype_string[dtype[1]],
+            (
+                endianness + ply_to_numpy_dtype_string[dtype[0]],
+                endianness + ply_to_numpy_dtype_string[dtype[1]],
+            )
+            if isinstance(dtype, tuple)
+            else endianness + ply_to_numpy_dtype_string[dtype]
         )
-        if isinstance(dtype, tuple)
-        else endianness + ply_to_numpy_dtype_string[dtype]
         for dtype in cell_data_dtypes
     ]
 
@@ -311,7 +314,7 @@ def _read_binary(
     buffer_position = 0
 
     cell_data = {}
-    for (name, dt) in zip(cell_data_names, dts):
+    for name, dt in zip(cell_data_names, dts):
         if isinstance(dt, tuple):
             buffer_increment, cell_data[name] = _read_binary_list(
                 buffer[buffer_position:], dt[0], dt[1], num_cells, endianness
@@ -370,7 +373,7 @@ def parse_ragged(start, num_cells):
     # `block_dtype` to include the initial counts in each row avoids any
     # wasteful copy operations.
     blocks = []
-    for (start, end) in block_bounds:
+    for start, end in block_bounds:
         if start == end:
             # This should only happen if the element was empty to begin with.
             continue

src/meshio/stl/_stl.py

@@ -2,6 +2,7 @@
 I/O for the STL format, cf.
 <https://en.wikipedia.org/wiki/STL_(file_format)>.
 """
+
 from __future__ import annotations
 
 import os

src/meshio/su2/_su2.py

@@ -2,6 +2,7 @@
 I/O SU2 mesh format
 <https://su2code.github.io/docs_v7/Mesh-File/>
 """
+
 from itertools import chain, islice
 
 import numpy as np

src/meshio/tecplot/_tecplot.py

@@ -3,6 +3,7 @@
 <https://github.com/su2code/SU2/raw/master/externals/tecio/360_data_format_guide.pdf>,
 <http://paulbourke.net/dataformats/tp/>.
 """
+
 import numpy as np
 
 from ..__about__ import __version__ as version

src/meshio/tetgen/_tetgen.py

@@ -2,6 +2,7 @@
 I/O for the TetGen file format, c.f.
 <https://wias-berlin.de/software/tetgen/fformats.node.html>
 """
+
 import pathlib
 
 import numpy as np

src/meshio/ugrid/_ugrid.py

@@ -7,6 +7,7 @@
 Node ordering described in
 [3] <https://www.simcenter.msstate.edu/software/documentation/ug_io/3d_input_output_grids.html>
 """
+
 import numpy as np
 
 from .._common import _pick_first_int_data, warn

src/meshio/vtk/_vtk_42.py

@@ -1,6 +1,7 @@
 """
 I/O for VTK <https://vtk.org/wp-content/uploads/2015/04/file-formats.pdf>.
 """
+
 from functools import reduce
 
 import numpy as np

src/meshio/vtu/_vtu.py

@@ -3,6 +3,7 @@
 <https://vtk.org/Wiki/VTK_XML_Formats>
 <https://vtk.org/wp-content/uploads/2015/04/file-formats.pdf>
 """
+
 import base64
 import re
 import sys

src/meshio/xdmf/__init__.py

@@ -2,6 +2,7 @@
 I/O for XDMF.
 https://xdmf.org/index.php/XDMF_Model_and_Format
 """
+
 from .main import read, write
 from .time_series import TimeSeriesReader, TimeSeriesWriter
 

src/meshio/xdmf/main.py

@@ -2,6 +2,7 @@
 I/O for XDMF.
 https://xdmf.org/index.php/XDMF_Model_and_Format
 """
+
 import os
 import pathlib
 from io import BytesIO