Upgrade to numpy 2, github actions and build system

.github/workflows/docs.yml

@@ -0,0 +1,39 @@
+name: Documentation
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+  workflow_dispatch:
+
+jobs:
+  build-docs:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+
+    - name: Set up Python 3.12
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.12"
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -e .[docs]
+
+    - name: Build documentation
+      run: |
+        cd doc
+        make html
+
+    - name: Deploy documentation to GitHub Pages
+      if: github.ref == 'refs/heads/main'
+      uses: peaceiris/actions-gh-pages@v4
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: ./doc/_build/html
+        force_orphan: true

.github/workflows/tests.yml

@@ -0,0 +1,99 @@
+name: Tests
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+  workflow_dispatch:
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: ["3.12", "3.13"]
+        numpy-version: [""]
+        include:
+          # Test Python 3.11 with both numpy 1.x and 2.x
+          - os: ubuntu-latest
+            python-version: "3.11"
+            numpy-version: "<2.0"
+          - os: ubuntu-latest
+            python-version: "3.11"
+            numpy-version: ">=2.0"
+          - os: windows-latest
+            python-version: "3.11"
+            numpy-version: "<2.0"
+          - os: windows-latest
+            python-version: "3.11"
+            numpy-version: ">=2.0"
+          - os: macos-latest
+            python-version: "3.11"
+            numpy-version: "<2.0"
+          - os: macos-latest
+            python-version: "3.11"
+            numpy-version: ">=2.0"
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0  # Fetch full history for setuptools-scm versioning
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Cache pip dependencies
+      uses: actions/cache@v4
+      with:
+        path: ~/.cache/pip
+        key: ${{ runner.os }}-pip-${{ matrix.python-version }}-${{ matrix.numpy-version }}-${{ hashFiles('pyproject.toml') }}
+        restore-keys: |
+          ${{ runner.os }}-pip-${{ matrix.python-version }}-
+          ${{ runner.os }}-pip-
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -e .[tests]
+
+    - name: Install specific numpy version
+      if: matrix.numpy-version != ''
+      run: |
+        pip install "numpy${{ matrix.numpy-version }}"
+
+    - name: Run tests
+      run: |
+        pytest pyexodus/tests
+
+  test-coverage:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+
+    - name: Set up Python 3.12
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.12"
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -e .[tests]
+        pip install pytest-cov
+
+    - name: Run tests with coverage
+      run: |
+        pytest pyexodus/tests --cov=pyexodus --cov-report=xml --cov-report=term-missing
+
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v4
+      with:
+        files: ./coverage.xml
+        fail_ci_if_error: false

.gitignore

@@ -1,4 +1,9 @@
 *.egg-info
 .cache
 pyexodus/RELEASE-VERSION
+pyexodus/_version.py
 doc/_build/
+dist/
+build/
+__pycache__/
+*.pyc

LICENSE.txt

@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright (c) 2016 pyexodus developers
+Copyright (c) 2016-2026 pyexodus developers
 
 Permission is hereby granted, free of charge, to any person obtaining a copy of
 this software and associated documentation files (the "Software"), to deal in

doc/conf.py

@@ -31,11 +31,13 @@
 # ones.
 import pyexodus
 
-import klink
-
-html_theme = "klink"
-html_theme_path = [klink.get_html_theme_path()]
-html_theme_options = {"github": "SalvusHub/pyexodus", "logo": "logo.svg"}
+html_theme = "furo"
+html_theme_options = {
+    "source_repository": "https://github.com/SalvusHub/pyexodus",
+    "source_branch": "main",
+    "source_directory": "doc/",
+}
+html_logo = "_static/logo.svg"
 
 extensions = [
     "sphinx.ext.autodoc",
@@ -62,7 +64,7 @@
 
 # General information about the project.
 project = "pyexodus"
-copyright = "2016, Lion Krischer"
+copyright = "2026 Mondaic Ltd."
 author = "Lion Krischer"
 
 # The version info for the project you're documenting, acts as replacement for
@@ -79,7 +81,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = "en"
 
 # There are two options for replacing |today|: either, you set today to some
 # non-false value, then it is used:
@@ -357,4 +359,4 @@
 
 
 # Example configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {"https://docs.python.org/": None}
+intersphinx_mapping = {"python": ("https://docs.python.org/3/", None)}

pyexodus/__init__.py

@@ -2,13 +2,13 @@
 # -*- coding: utf-8 -*-
 """
 :copyright:
-    Lion Krischer (lionkrischer@gmail.com), 2016
+    Lion Krischer (lion.krischer@mondaic.com), 2016-2026
+    Mondaic Ltd. (info@mondaic.com), 2020-2026
 :license:
     MIT License
 """
-from __future__ import absolute_import
+from importlib.metadata import version as _get_version
 
 from .core import exodus  # NOQA
-from .version import get_git_version
 
-__version__ = get_git_version()
+__version__ = _get_version("pyexodus")

pyexodus/compat.py

@@ -2,7 +2,8 @@
 # -*- coding: utf-8 -*-
 """
 :copyright:
-    Lion Krischer (lionkrischer@gmail.com), 2022
+    Lion Krischer (lion.krischer@mondaic.com), 2022-2026
+    Mondaic Ltd. (info@mondaic.com), 2022-2026
 :license:
     MIT License
 """

pyexodus/core.py

@@ -2,7 +2,8 @@
 # -*- coding: utf-8 -*-
 """
 :copyright:
-    Lion Krischer (lionkrischer@gmail.com), 2022
+    Lion Krischer (lion.krischer@mondaic.com), 2022-2026
+    Mondaic Ltd. (info@mondaic.com), 2022-2026
 :license:
     MIT License
 """
@@ -270,7 +271,7 @@ def put_elem_blk_info(
             dtype=np.int32,
             **self._comp_opts
         )
-        self._f.variables[var_name].attrs["elem_type"] = np.string_(elemType)
+        self._f.variables[var_name].attrs["elem_type"] = np.bytes_(elemType)
 
         # Set the status and thus "claim" the element block id.
         self._f.variables["eb_status"][idx - 1] = 1
@@ -934,7 +935,7 @@ def _write_attrs(self, title):
         self._f.attrs["file_size"] = np.array([1], dtype=np.int32)
         self._f.attrs["maximum_name_length"] = np.array([32], dtype=np.int32)
         self._f.attrs["int64_status"] = np.array([0], dtype=np.int32)
-        self._f.attrs["title"] = np.string_(title)
+        self._f.attrs["title"] = np.bytes_(title)
 
     def _create_variables(self):
         # Time steps.
@@ -963,7 +964,7 @@ def _create_variables(self):
             data=[-1] * get_dim_size(self._f, "num_el_blk"),
             **self._comp_opts
         )
-        self._f.variables["eb_prop1"].attrs["name"] = np.string_("ID")
+        self._f.variables["eb_prop1"].attrs["name"] = np.bytes_("ID")
 
         # Coordinate names.
         self._f.create_variable(
@@ -997,7 +998,7 @@ def _create_variables(self):
                 data=[-1] * get_dim_size(self._f, "num_side_sets"),
                 **self._comp_opts
             )
-            self._f.variables["ss_prop1"].attrs["name"] = np.string_("ID")
+            self._f.variables["ss_prop1"].attrs["name"] = np.bytes_("ID")
             self._f.create_variable(
                 "/ss_status",
                 ("num_side_sets",),

pyexodus/tests/__init__.py

@@ -2,7 +2,7 @@
 # -*- coding: utf-8 -*-
 """
 :copyright:
-    Lion Krischer (lionkrischer@gmail.com), 2016
+    Lion Krischer (lion.krischer@mondaic.com), 2016-2026
 :license:
     MIT License
 """

pyexodus/tests/test_reading_exodus.py

@@ -2,7 +2,8 @@
 # -*- coding: utf-8 -*-
 """
 :copyright:
-    Lion Krischer (lionkrischer@gmail.com), 2017
+    Lion Krischer (lion.krischer@mondaic.com), 2017-2026
+    Mondaic Ltd. (info@mondaic.com), 2020-2026
 :license:
     MIT License
 """

pyexodus/tests/test_writing_exodus.py

@@ -2,7 +2,8 @@
 # -*- coding: utf-8 -*-
 """
 :copyright:
-    Lion Krischer (lionkrischer@gmail.com), 2016
+    Lion Krischer (lion.krischer@mondaic.com), 2016-2026
+    Mondaic Ltd. (info@mondaic.com), 2020-2026
 :license:
     MIT License
 """