Merge pull request #31 from GeoStat-Framework/py13_support

Py13 support

Author: MuellerSeb

.github/workflows/main.yml

@@ -19,21 +19,27 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
+        with:
+          fetch-depth: "0"
 
-      - name: Set up Python 3.9
+      - name: Set up Python 3.11
         uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: 3.11
 
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install --editable .[check]
+          pip install -v --editable '.[check]'
 
       - name: black check
         run: |
           python -m black --check --diff --color .
 
+      - name: black preview
+        run: |
+          python -m black --preview --diff --color .
+
       - name: isort check
         run: |
           python -m isort --check --diff --color .
@@ -47,84 +53,126 @@ jobs:
           cython-lint src/pentapy/
 
   build_wheels:
-    name: wheels for ${{ matrix.cfg.os }} / ${{ matrix.cfg.arch }}
-    runs-on: ${{ matrix.cfg.os }}
+    name: wheels for ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        cfg:
-        - { os: ubuntu-latest, arch: x86_64 }
-        - { os: windows-latest, arch: AMD64 }
-        - { os: macos-latest, arch: x86_64 }
-        - { os: macos-latest, arch: arm64 }
-        - { os: macos-latest, arch: universal2 }
+        # macos-13 is an intel runner, macos-latest is apple silicon
+        os: [ubuntu-latest, ubuntu-24.04-arm, windows-latest, macos-13, macos-latest]
 
     steps:
       - uses: actions/checkout@v4
         with:
-          fetch-depth: '0'
+          fetch-depth: "0"
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.17.0
-        env:
-          CIBW_ARCHS: ${{ matrix.cfg.arch }}
+        uses: pypa/cibuildwheel@v2.22.0
         with:
-          output-dir: dist
+          output-dir: dist-wheel-${{ matrix.os }}
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
-          path: ./dist/*.whl
+          name: dist-wheel-${{ matrix.os }}
+          path: ./dist-wheel-${{ matrix.os }}/*.whl
 
   build_sdist:
-    name: sdist on ${{ matrix.os }} with py ${{ matrix.python-version }}
+    name: sdist on ${{ matrix.os }} with py ${{ matrix.ver.py }} numpy${{ matrix.ver.np }}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest]
-        python-version: [3.9]
-
+        os: [ubuntu-latest, windows-latest, macos-13, macos-14]
+        # https://github.com/scipy/oldest-supported-numpy/blob/main/setup.cfg
+        ver:
+          - { py: "3.9", np: "==1.20.0" }
+          - { py: "3.10", np: "==1.21.6" }
+          - { py: "3.11", np: "==1.23.2" }
+          - { py: "3.12", np: "==1.26.2" }
+          - { py: "3.13", np: "==2.1.0" }
+          - { py: "3.13", np: ">=2.1.0" }
+        exclude:
+          - os: macos-14
+            ver: { py: "3.9", np: "==1.20.0" }
+          - os: macos-14
+            ver: { py: "3.10", np: "==1.21.6" }
     steps:
       - uses: actions/checkout@v4
         with:
-          fetch-depth: '0'
+          fetch-depth: "0"
 
-      - name: Set up Python ${{ matrix.python-version }}
+      - name: Set up Python ${{ matrix.ver.py }}
         uses: actions/setup-python@v5
         with:
-          python-version: ${{ matrix.python-version }}
+          python-version: ${{ matrix.ver.py }}
 
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install build coveralls>=3.0.0
-          pip install --editable .[test]
+          pip install build
+
+      - name: Install pentapy
+        run: |
+          pip install -v --editable .[test]
 
       - name: Run tests
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
-          python -m pytest --cov pentapy --cov-report term-missing -v tests/
-          python -m coveralls --service=github
+          pip install "numpy${{ matrix.ver.np }}"
+          python -m pytest -v tests/
 
       - name: Build sdist
         run: |
           # PEP 517 package builder from pypa
-          python -m build --sdist --outdir dist .
+          python -m build --sdist --outdir dist-sdist .
+
+      - uses: actions/upload-artifact@v4
+        if: matrix.os == 'ubuntu-latest' && matrix.ver.py == '3.11'
+        with:
+          name: dist-sdist
+          path: dist-sdist/*.tar.gz
+
+  coverage:
+    name: coverage
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: '0'
 
-      - uses: actions/upload-artifact@v3
-        # if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.9'
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
         with:
-          path: dist/*.tar.gz
+          python-version: 3.11
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install "coveralls>=3.0.0"
+
+      - name: Install pentapy
+        env:
+          PENTAPY_CY_COV: 1
+        run: |
+          pip install -v --editable .[test]
+
+      - name: Run tests
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          pip install "numpy${{ matrix.ver.np }}"
+          python -m pytest --cov pentapy --cov-report term-missing -v tests/
+          python -m coveralls --service=github
 
   upload_to_pypi:
     needs: [build_wheels, build_sdist]
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
         with:
-          name: artifact
+          pattern: dist-*
+          merge-multiple: true
           path: dist
 
       - name: Publish to Test PyPI
@@ -143,4 +191,4 @@ jobs:
         uses: pypa/gh-action-pypi-publish@release/v1
         with:
           user: __token__
-          password: ${{ secrets.pypi_password }}
+          password: ${{ secrets.pypi_password }}

.gitignore

@@ -119,3 +119,4 @@ src/pentapy/_version.py
 # generated docs
 docs/source/examples/
 docs/source/api/
+docs/source/sg_execution_times.rst

.readthedocs.yml

@@ -8,7 +8,7 @@ build:
 sphinx:
   configuration: docs/source/conf.py
 
-formats: all
+formats: [pdf]
 
 python:
   install:

CHANGELOG.md

@@ -3,6 +3,26 @@
 All notable changes to **pentapy** will be documented in this file.
 
 
+## [1.4.0] - 2025-05
+
+See [#31](https://github.com/GeoStat-Framework/pentapy/pull/31)
+
+### Enhancements
+- added support for python 3.13
+- adding [musllinux](https://musl.libc.org/) wheels
+- adding PyPy wheels (pp39 and pp310)
+  - PyPy needs `setuptools<72.2`: https://github.com/pypa/distutils/issues/283
+- adding 32bit Windows wheels again (still Tier 1 support in Python)
+- adding aarch64 Linux wheels
+
+### Changes
+- dropped python 3.8 support
+
+### Bugfixes
+- use numpy solver for 3x3 matrices
+- set `cdivision=False` in cython solver
+
+
 ## [1.3.0] - 2024-04
 
 See [#21](https://github.com/GeoStat-Framework/pentapy/pull/21)
@@ -100,6 +120,7 @@ This is the first release of pentapy, a python toolbox for solving pentadiagonal
 The solver is implemented in cython, which makes it really fast.
 
 
+[1.4.0]: https://github.com/GeoStat-Framework/pentapy/compare/v1.3.0...v1.4.0
 [1.3.0]: https://github.com/GeoStat-Framework/pentapy/compare/v1.2.0...v1.3.0
 [1.2.0]: https://github.com/GeoStat-Framework/pentapy/compare/v1.1.2...v1.2.0
 [1.1.2]: https://github.com/GeoStat-Framework/pentapy/compare/v1.1.1...v1.1.2

docs/source/changelog.rst

@@ -1 +1,2 @@
-.. mdinclude:: ../../CHANGELOG.md
+.. include:: ../../CHANGELOG.md
+   :parser: myst_parser.docutils_

docs/source/conf.py

@@ -60,7 +60,7 @@ def setup(app):
     "sphinx.ext.napoleon",  # parameters look better than with numpydoc only
     "numpydoc",
     "sphinx_gallery.gen_gallery",
-    "m2r2",
+    "myst_parser",
 ]
 
 # autosummaries from source-files
@@ -89,7 +89,11 @@ def setup(app):
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
-source_suffix = [".rst", ".md"]
+source_suffix = {
+    ".rst": "restructuredtext",
+    ".md": "markdown",
+}
+# source_suffix = [".rst", ".md"]
 # source_suffix = ".rst"
 
 # The master toctree document.
@@ -143,7 +147,7 @@ def setup(app):
     #    'canonical_url': '',
     #    'analytics_id': '',
     "logo_only": False,
-    "display_version": True,
+    "version_selector": True,
     "prev_next_buttons_location": "top",
     #    'style_external_links': False,
     #    'vcs_pageview_mode': '',
@@ -192,11 +196,13 @@ def setup(app):
 # latex_show_urls = 'footnote'
 # http://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-latex-output
 latex_elements = {
-    "preamble": r"""
+    "preamble": (
+        r"""
 \setcounter{secnumdepth}{1}
 \setcounter{tocdepth}{2}
 \pagestyle{fancy}
-""",
+"""
+    ),
     "pointsize": "10pt",
     "papersize": "a4paper",
     "fncychap": "\\usepackage[Glenn]{fncychap}",
@@ -252,9 +258,6 @@ def setup(app):
     "Sphinx": ("http://www.sphinx-doc.org/en/stable/", None),
 }
 
-# -- Sphinx Gallery Options
-from sphinx_gallery.sorting import FileNameSortKey
-
 sphinx_gallery_conf = {
     # only show "print" output as output
     "capture_repr": (),
@@ -267,7 +270,7 @@ def setup(app):
     # Remove the "Download all examples" button from the top level gallery
     "download_all_examples": False,
     # Sort gallery example by file name instead of number of lines (default)
-    "within_subsection_order": FileNameSortKey,
+    "within_subsection_order": "FileNameSortKey",
     # directory where function granular galleries are stored
     "backreferences_dir": None,
     # Modules for which function level galleries are created.  In