update build systems

.github/workflows/build-and-deploy.yml

@@ -16,9 +16,9 @@ jobs:
     - name: install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install setuptools wheel twine
+        pip install build twine
     - name: build
-      run: python setup.py sdist
+      run: python -m build
     - name: deploy
       env:
         TWINE_USERNAME: __token__

.github/workflows/test.yml

@@ -45,7 +45,7 @@ jobs:
           - python: "3.13"
             toxenv: py313
             os: macos-latest
-          - python: "3.11"
+          - python: "3.13"
             toxenv: py313
             os: windows-latest
 
@@ -56,10 +56,10 @@ jobs:
         with:
           python-version: ${{  matrix.python }}
       - name: install dependencies
-        run: python -m pip install --upgrade pip tox setuptools wheel twine
+        run: python -m pip install --upgrade pip tox
       - name: run
         env:
           TOXENV: ${{ matrix.toxenv }}
         run: tox
       - name: setup
-        run: python setup.py install
+        run: pip install -e .

.gitignore

@@ -104,4 +104,8 @@ ENV/
 .pytest_cache/
 
 # vscode settings
-.vscode/
+.vscode/
+
+# Local Claude instructions
+CLAUDE.local.md
+.claude/

CHANGELOG.md

@@ -5,6 +5,11 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
 ## Unreleased 
+### Changed
+ - Migrated from setup.py to modern pyproject.toml packaging with hatchling backend
+ - Updated minimum Python requirement to 3.10+ (removed support for 3.7-3.9)
+ - Updated GitHub Actions workflows to use modern build tools
+ - Removed legacy packaging files (setup.py, MANIFEST.in)
 
 ## 2.3.0 - 2024-04-03
 ### Changed

CITATION.cff

@@ -0,0 +1,21 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+title: "Permuta: A Python Library for Permutations and Patterns"
+type: software
+authors:
+  - name: "Ragnar Pall Ardal"
+  - name: "Arnar Bjarni Arnarson"
+  - name: "Christian Bean"
+    affiliation: "Keele University"
+  - name: "Alfur Birkir Bjarnason"
+  - name: "Jon Steinn Eliasson"
+  - name: "Bjarki Agust Gudmundsson"
+  - name: "Sigurjón Ingi Jónsson"
+  - name: "Bjarni Jens Kristinsson"
+  - name: "Tomas Ken Magnusson"
+  - name: "Émile Nadeau"
+  - name: "Jay Pantone"
+    affiliation: "Marquette University"
+  - name: "Murray Tannock"
+  - name: "Henning Ulfarsson"
+    affiliation: "Reykjavik University"

README.rst

@@ -2,32 +2,34 @@
 permuta
 #######
 
-.. image:: https://travis-ci.org/PermutaTriangle/Permuta.svg?branch=master
-    :alt: Travis
-    :target: https://travis-ci.org/PermutaTriangle/Permuta
+.. image:: https://github.com/PermutaTriangle/Permuta/workflows/tests/badge.svg
+    :alt: Tests
+    :target: https://github.com/PermutaTriangle/Permuta/actions
 .. image:: https://img.shields.io/pypi/v/Permuta.svg
     :alt: PyPI
     :target: https://pypi.python.org/pypi/Permuta
 .. image:: https://img.shields.io/pypi/l/Permuta.svg
     :target: https://pypi.python.org/pypi/Permuta
 .. image:: https://img.shields.io/pypi/pyversions/Permuta.svg
     :target: https://pypi.python.org/pypi/Permuta
-.. image:: http://img.shields.io/badge/readme-tested-brightgreen.svg
-    :alt: Travis
-    :target: https://travis-ci.org/PermutaTriangle/Permuta
-.. image:: https://requires.io/github/PermutaTriangle/Permuta/requirements.svg?branch=master
-    :target: https://requires.io/github/PermutaTriangle/Permuta/requirements/?branch=master
-    :alt: Requirements Status
+.. image:: https://img.shields.io/badge/code%20style-black-000000.svg
+    :alt: Code style: black
+    :target: https://github.com/psf/black
+.. image:: http://www.mypy-lang.org/static/mypy_badge.svg
+    :alt: Checked with mypy
+    :target: http://mypy-lang.org/
 .. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.4725758.svg
    :target: https://doi.org/10.5281/zenodo.4725758
 
 Permuta is a Python library for working with perms (short for permutations),
 patterns, and mesh patterns.
 
 If this code is useful to you in your work, please consider citing it. To generate a
-BibTeX entry (or another format), click the "DOI" badge above and locate the "Cite As"
+BibTeX entry (or another format), click the "DOI" badge above to go to `Zenodo`_ and locate the "Export"
 section.
 
+.. _Zenodo: https://doi.org/10.5281/zenodo.4725758
+
 If you need support, you can join us in our `Discord support server`_.
 
 .. _Discord support server: https://discord.gg/ngPZVT5
@@ -46,14 +48,13 @@ source code, in which case you run the following after cloning the repository:
 
 .. code-block:: bash
 
-    ./setup.py develop
+    pip install -e .
 
 To run the unit tests:
 
 .. code-block:: bash
 
-    pip install -r test_requirements.txt
-    ./setup.py test
+    tox
 
 Using Permuta
 #############
@@ -522,12 +523,3 @@ License
 
 BSD-3: see the `LICENSE <https://github.com/PermutaTriangle/Permuta/blob/master/LICENSE>`_ file.
 
-Citing
-######
-
-If you found this library helpful with your research and would like to cite us,
-you can use the following `BibTeX`_ or go to `Zenodo`_ for alternative formats.
-
-.. _BibTex: https://zenodo.org/record/4945792/export/hx#.YImTibX7SUk
-
-.. _Zenodo: https://doi.org/10.5281/zenodo.4725758

pyproject.toml

@@ -1,3 +1,57 @@
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "permuta"
+dynamic = ["version"]
+authors = [
+    {name = "Permuta Triangle", email = "[email protected]"},
+]
+description = "A comprehensive high performance permutation library."
+readme = "README.rst"
+license = {text = "BSD-3-Clause"}
+keywords = ["permutation", "perm", "mesh", "pattern", "patt", "avoid", "contain", "occurrence", "statistic"]
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Intended Audience :: Education",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: BSD License",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: Implementation :: CPython",
+    "Programming Language :: Python :: Implementation :: PyPy",
+    "Topic :: Education",
+    "Topic :: Scientific/Engineering :: Mathematics",
+]
+requires-python = ">=3.10"
+dependencies = [
+    "automata-lib==9.0.0",
+]
+
+[project.urls]
+Source = "https://github.com/PermutaTriangle/Permuta"
+Tracker = "https://github.com/PermutaTriangle/Permuta/issues"
+
+[project.scripts]
+permtools = "permuta.cli:main"
+
+[tool.hatch.version]
+path = "permuta/__init__.py"
+
+[tool.hatchling.build.targets.wheel]
+packages = ["permuta"]
+
+[tool.hatchling.build.targets.sdist]
+include = [
+    "/permuta",
+    "/tests",
+    "/README.rst",
+    "/LICENSE",
+]
+
 [tool.black]
 target-version = ['py310']
 include = '\.pyi?$'

tox.ini

@@ -39,7 +39,7 @@ deps =
     flake8
     flake8-isort
 commands =
-    flake8 --isort-show-traceback permuta tests setup.py
+    flake8 --isort-show-traceback permuta tests
 
 [testenv:pylint]
 description = run pylint (static code analysis)