Merge pull request #1454 from nschloe/fix-new-numpy

numpy fix

Author: nschloe

.github/workflows/ci.yml

@@ -13,21 +13,21 @@ 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]
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
         os: [ubuntu-latest, windows-latest, macOS-latest]
-        python-version: ["3.7", "3.8", "3.9", "3.10"]
+        python-version: ["3.8", "3.12"]
     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\"?"

pyproject.toml

@@ -1,33 +1,46 @@
+[build-system]
+requires = ["setuptools>=42", "wheel"]
+build-backend = "setuptools.build_meta"
+
 [project]
 name = "meshio"
-version = "5.0.0"
+version = "5.3.5"
 description = "I/O for many mesh formats"
 readme = "README.md"
-requires-python = ">=3.7"
+requires-python = ">=3.8"
 license = {file = "LICENSE.txt"}
-keywords = ["mesh", "file formats", "scientific", "engineering", "fem", "finite elements"]
+keywords = [
+  "mesh",
+  "file formats",
+  "scientific",
+  "engineering",
+  "fem",
+  "finite elements"
+]
 authors = [
   {email = "[email protected]"},
   {name = "Nico Schlömer"}
 ]
 classifiers = [
-  "Development Status :: 4 - Beta",
-  "Programming Language :: Python",
   "Development Status :: 5 - Production/Stable",
+  "Programming Language :: Python",
   "Intended Audience :: Science/Research",
   "License :: OSI Approved :: MIT License",
   "Operating System :: OS Independent",
   "Programming Language :: Python",
   "Programming Language :: Python :: 3",
-  "Programming Language :: Python :: 3.7",
   "Programming Language :: Python :: 3.8",
   "Programming Language :: Python :: 3.9",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
   "Topic :: Scientific/Engineering",
-  "Topic :: Utilities"
+  "Topic :: Utilities",
 ]
 dependencies = [
   "importlib_metadata; python_version<'3.8'",
-  "numpy>=1.20.0"
+  "numpy>=1.20.0",
+  "rich",
 ]
 
 [project.optional-dependencies]
@@ -40,14 +53,13 @@ all = [
 homepage = "https://github.com/nschloe/meshio"
 code = "https://github.com/nschloe/meshio"
 issues = "https://github.com/nschloe/meshio/issues"
-funding = "https://github.com/sponsors/nschloe"
 
 [project.entry-points.console_scripts]
 meshio = "meshio._cli:main"
 
-[build-system]
-requires = ["setuptools>=42", "wheel"]
-build-backend = "setuptools.build_meta"
-
 [tool.isort]
 profile = "black"
+
+# [options.data_files]
+# share/paraview-5.9/plugins =
+#     tools/paraview-meshio-plugin.py

setup.cfg

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

src/meshio/abaqus/_abaqus.py

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

src/meshio/ansys/_ansys.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/avsucd/_avsucd.py

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

src/meshio/cgns/_cgns.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/dolfin/_dolfin.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/exodus/_exodus.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/flac3d/_flac3d.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/_gmsh22.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/_gmsh40.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/gmsh/_gmsh41.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/h5m/_h5m.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