Modernize packaging and PyPI release workflow

.github/workflows/build.yml

@@ -15,9 +15,9 @@ jobs:
         os: [ubuntu-latest, windows-latest, macos-latest]
         python-version: ['3.12', '3.13', '3.14']
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
       - name: Display versions
@@ -31,3 +31,49 @@ jobs:
       - name: Run tests with coverage
         if: ${{ matrix.os == 'ubuntu-latest' && matrix.python-version == '3.14' }}
         run: pytest --cov=morphops --cov-report=term-missing --pyargs morphops
+
+  minimum-dependencies:
+    name: ubuntu-latest/py3.12/minimum-dependencies
+    runs-on: ubuntu-latest
+    timeout-minutes: 15
+    steps:
+      - uses: actions/checkout@v6
+      - uses: actions/setup-python@v6
+        with:
+          python-version: '3.12'
+      - name: Install minimum dependencies and package
+        run: |
+          pip install numpy==1.26.4 scipy==1.12.0 pytest
+          pip install --no-deps -e .
+          pip check
+      - name: Run tests
+        run: pytest --pyargs morphops
+
+  package:
+    name: Build and validate package
+    runs-on: ubuntu-latest
+    timeout-minutes: 15
+    steps:
+      - uses: actions/checkout@v6
+      - uses: actions/setup-python@v6
+        with:
+          python-version: '3.14'
+      - name: Build and validate distributions
+        run: |
+          pip install build twine
+          python -m build
+          twine check dist/*
+
+  docs:
+    name: Build documentation
+    runs-on: ubuntu-latest
+    timeout-minutes: 15
+    steps:
+      - uses: actions/checkout@v6
+      - uses: actions/setup-python@v6
+        with:
+          python-version: '3.14'
+      - name: Install package and documentation dependencies
+        run: pip install -e .'[docs]'
+      - name: Build documentation
+        run: sphinx-build -W --keep-going -b html docs/source docs/build/html

.github/workflows/publish.yml

@@ -1,30 +1,40 @@
-# This workflow will upload a Python Package using Twine when a release is created
-# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
-
-name: Upload package to PyPI
+name: Publish package to PyPI
 
 on:
   release:
     types:
       - published
 
 jobs:
-  publish-to-pip:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          persist-credentials: false
+      - uses: actions/setup-python@v6
+        with:
+          python-version: '3.x'
+      - name: Install build tools
+        run: python -m pip install build
+      - name: Build distributions
+        run: python -m build
+      - uses: actions/upload-artifact@v5
+        with:
+          name: python-package-distributions
+          path: dist/
+
+  publish-to-pypi:
+    needs: build
     runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/morphops
+    permissions:
+      id-token: write
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python ${{ runner.python-version }}
-      uses: actions/setup-python@v2
-      with:
-        python-version: '3.x'
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install setuptools wheel twine
-    - name: Build and publish to PyPI
-      env:
-        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
-        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
-      run: |
-        python setup.py sdist bdist_wheel
-        twine upload dist/*
+      - uses: actions/download-artifact@v6
+        with:
+          name: python-package-distributions
+          path: dist/
+      - uses: pypa/gh-action-pypi-publish@release/v1

CHANGELOG.rst

@@ -18,6 +18,9 @@ Changed
 -------
 - Dropped support for Python versions older than 3.12 and updated CI to test
   Python 3.12 through 3.14.
+- Modernized package builds and PyPI publishing, including Trusted Publishing
+  and CI validation for distributions and documentation.
+- Updated the minimum supported dependencies to NumPy 1.26 and SciPy 1.12.
 
 Fixed
 -----

README.rst

@@ -118,8 +118,8 @@ they can now be submitted to various commonly used statistical procedures like
 Principal Components Analysis and various kinds of regression for further
 analysis.
 
-Contributors ✨
-===============
+Contributors
+============
 
 See the project's `contributor acknowledgements <https://github.com/vaipatel/morphops/blob/master/CONTRIBUTORS.md>`_.
 The list is maintained with the `All Contributors bot <https://allcontributors.org/en/bot/overview/>`_.

README_for_docs.rst

@@ -126,8 +126,8 @@ they can now be submitted to various commonly used statistical procedures like
 Principal Components Analysis and various kinds of regression for further
 analysis.
 
-Contributors ✨
-===============
+Contributors
+============
 
 See the project's `contributor acknowledgements <https://github.com/vaipatel/morphops/blob/master/CONTRIBUTORS.md>`_.
 The list is maintained with the `All Contributors bot <https://allcontributors.org/en/bot/overview/>`_.

docs/source/conf.py

@@ -30,7 +30,7 @@
 author = 'Vaibhav Patel'
 
 # The short X.Y version
-version = '0.1'
+version = '.'.join(full_version.split('.')[:2])
 # The full version, including alpha/beta/rc tags
 release = full_version
 
@@ -72,7 +72,7 @@
 #
 # 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'
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -210,5 +210,5 @@
 # Example configuration for intersphinx: refer to the Python standard library.
 intersphinx_mapping = {
     'python': ('https://docs.python.org/3', None),
-    'numpy': ('https://docs.scipy.org/doc/numpy/', None)
+    'numpy': ('https://numpy.org/doc/stable/', None)
 }

pyproject.toml

@@ -0,0 +1,3 @@
+[build-system]
+requires = ["setuptools >= 77.0.3"]
+build-backend = "setuptools.build_meta"

setup.py

@@ -2,16 +2,16 @@
 from setuptools import setup, find_packages
 
 
-with open('README.rst') as readme_file:
+with open('README.rst', encoding='utf-8') as readme_file:
     readme = readme_file.read()
 
 version = {}
-with open("morphops/_version.py") as version_file:
+with open("morphops/_version.py", encoding='utf-8') as version_file:
     exec(version_file.read(), version)
 
 extra_feature_requirements = {
-    "tests": ["coverage >= 5.0", "pytest >= 5.4", "pytest-cov >= 2.8.1", "tox"],
-    "docs": ["sphinx < 2", "sphinx-rtd-theme"],
+    "tests": ["pytest >= 8", "pytest-cov >= 5", "tox >= 4"],
+    "docs": ["sphinx >= 8", "sphinx-rtd-theme >= 3"],
 }
 extra_feature_requirements["dev"] = list(
     chain(*list(extra_feature_requirements.values()))
@@ -33,11 +33,10 @@
         'Programming Language :: Python :: 3.12',
         'Programming Language :: Python :: 3.13',
         'Programming Language :: Python :: 3.14',
-        'License :: OSI Approved :: MIT License',
         'Topic :: Scientific/Engineering'
     ],
     python_requires='>=3.12',
     extras_require=extra_feature_requirements,
-    install_requires=['numpy >= 1.13.3', 'scipy >= 1.3.3'],
+    install_requires=['numpy >= 1.26', 'scipy >= 1.12'],
     include_package_data=True
 )

tox.ini

@@ -1,12 +1,21 @@
 [tox]
-envlist = py312,py313,py314-coverage
+envlist = py312-min,py312,py313,py314-coverage
 
 [testenv]
 deps = 
   pytest
 commands = 
   pytest -q -s --pyargs morphops
 
+[testenv:py312-min]
+basepython = python3.12
+deps =
+  numpy == 1.26.4
+  scipy == 1.12.0
+  pytest
+commands =
+  pytest -q -s --pyargs morphops
+
 [testenv:py314-coverage]
 basepython = python3.14
 deps =