Modernize packaging with pyproject.toml and hatchling (#528)

* Modernize packaging with pyproject.toml and hatchling

- Replace setup.py and MANIFEST.in with comprehensive pyproject.toml using hatchling backend
- Update minimum Python version to 3.10 (drop 3.8, 3.9 support)
- Update GitHub Actions to v4/v5 and use python -m build
- Update tox.ini: remove setup.py from flake8, use black>=22.10.0
- Update Black target version to py310
- Fix .zenodo.json syntax error (missing comma)
- Add CITATION.cff for GitHub citation support
- Update README.rst badges (GitHub Actions, Black, mypy) and installation instructions
- Bump version to 4.1.0

* Fix Christian Bean affiliation to Keele University, fix changelog format

* Apply black formatting for Python 3.10 target

* Pin black==25.1.0 and apply formatting

* Add Python 3.14 testing as main version

* update deploy to py314

Author: jaypantone

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

@@ -9,16 +9,16 @@ jobs:
   build-and-deploy:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
-    - uses: actions/setup-python@v2
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
       with:
-        python-version: "3.13"
+        python-version: "3.14"
     - 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

@@ -9,16 +9,16 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - python: "3.13"
+          - python: "3.14"
             toxenv: flake8
             os: ubuntu-latest
-          - python: "3.13"
+          - python: "3.14"
             toxenv: mypy
             os: ubuntu-latest
-          - python: "3.13"
+          - python: "3.14"
             toxenv: pylint
             os: ubuntu-latest
-          - python: "3.13"
+          - python: "3.14"
             toxenv: black
             os: ubuntu-latest
 
@@ -34,6 +34,9 @@ jobs:
           - python: "3.13"
             toxenv: py313
             os: ubuntu-latest
+          - python: "3.14"
+            toxenv: py314
+            os: ubuntu-latest
 
           - python: "pypy-3.10"
             toxenv: pypy310
@@ -42,17 +45,17 @@ jobs:
             toxenv: pypy311
             os: ubuntu-latest
 
-          - python: "3.13"
-            toxenv: py313
+          - python: "3.14"
+            toxenv: py314
             os: macos-latest
-          - python: "3.13"
-            toxenv: py313
+          - python: "3.14"
+            toxenv: py314
             os: windows-latest
 
     runs-on: ${{ matrix.os }}
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{  matrix.python }}
       - name: Install dependencies from develop branch
@@ -61,22 +64,20 @@ jobs:
           echo "Installing dependencies from develop branches instead of PyPI"
           python -m pip install git+https://github.com/PermutaTriangle/comb_spec_searcher.git@develop
           python -m pip install git+https://github.com/PermutaTriangle/Permuta.git@develop
-          
-          # Optional: Install the project in development mode to work with the new dependencies
+
+          # Install the project in development mode to work with the new dependencies
           python -m pip install -e .
-          
+
           # Verify installed versions
           echo "Checking installed comb_spec_searcher version:"
           python -c "import comb_spec_searcher; print(comb_spec_searcher.__version__)"
           echo "Checking installed permuta version:"
           python -c "import permuta; print(permuta.__version__)"
       - name: install dependencies
-        run: |
-          python -m pip install --upgrade pip tox
-          pip install 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 .

.zenodo.json

@@ -3,7 +3,7 @@
     "title": "tilings",
     "creators": [
         {
-            "affiliation": "Reykjavik University",
+            "affiliation": "Keele University",
             "name": "Christian Bean"
         },
         {
@@ -20,10 +20,10 @@
         {
             "affiliation": "Marquette University",
             "name": "Jay Pantone"
-        }
+        },
         {
             "affiliation": "Reykjavik University",
             "name": "Henning Ulfarsson"
-        },
+        }
     ]
 }

CHANGELOG.md

@@ -5,13 +5,22 @@ 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 
+## [Unreleased]
+
+## [4.1.0] - 2026-01-15
 ### Changed
 - new GriddedPerm.contains_patt function checks positions first, then pattern
   and as a result can lead to huge 2x - 4x speed improvement in specification
   finding
+- Migrated to modern pyproject.toml packaging with hatchling backend
+- Minimum Python version is now 3.10 (dropped 3.8, 3.9 support)
+- Updated GitHub Actions to use latest action versions (checkout@v4, setup-python@v5)
+- Updated Black target version to Python 3.10
+
+### Removed
+- Removed legacy setup.py and MANIFEST.in files
 
-## [4.0.0 - 2025-03-13]
+## [4.0.0] - 2025-03-13
 ### Added
 - python3.9 are deprecated, python3.10 - python3.13 are supported
 - added `TileScopePack.requirement_and_row_and_col_placements`

CITATION.cff

@@ -0,0 +1,32 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+type: software
+title: "tilings: A Python library for gridded permutations and tilings"
+url: "https://github.com/PermutaTriangle/Tilings"
+repository-code: "https://github.com/PermutaTriangle/Tilings"
+license: BSD-3-Clause
+authors:
+  - given-names: "Christian"
+    family-names: "Bean"
+    affiliation: "Keele University"
+  - given-names: "Jon Steinn"
+    family-names: "Eliasson"
+    affiliation: "Reykjavik University"
+  - given-names: "Tomas Ken"
+    family-names: "Magnusson"
+  - given-names: "Émile"
+    family-names: "Nadeau"
+    affiliation: "Reykjavik University"
+  - given-names: "Jay"
+    family-names: "Pantone"
+    affiliation: "Marquette University"
+  - given-names: "Henning"
+    family-names: "Ulfarsson"
+    affiliation: "Reykjavik University"
+identifiers:
+  - type: doi
+    value: "10.5281/zenodo.4948344"
+    description: "DOI for all versions"
+  - type: url
+    value: "https://zenodo.org/badge/latestdoi/121506164"
+    description: "Latest Zenodo DOI"

MANIFEST.in

@@ -1,22 +1,25 @@
 Tilings
 =======
 
-.. image:: https://travis-ci.org/PermutaTriangle/Tilings.svg?branch=master
-    :alt: Travis
-    :target: https://travis-ci.org/PermutaTriangle/Tilings
-.. image:: https://coveralls.io/repos/github/PermutaTriangle/Tilings/badge.svg?branch=master
+.. image:: https://github.com/PermutaTriangle/Tilings/actions/workflows/test.yml/badge.svg
+    :alt: Tests
+    :target: https://github.com/PermutaTriangle/Tilings/actions/workflows/test.yml
+.. image:: https://img.shields.io/badge/code%20style-black-000000.svg
+    :alt: Code style: black
+    :target: https://github.com/psf/black
+.. image:: https://img.shields.io/badge/mypy-checked-blue
+    :alt: mypy: checked
+    :target: https://mypy-lang.org/
+.. image:: https://img.shields.io/coveralls/github/PermutaTriangle/Tilings.svg
     :alt: Coveralls
-    :target: https://coveralls.io/github/PermutaTriangle/Tilings?branch=master
+    :target: https://coveralls.io/github/PermutaTriangle/Tilings
 .. image:: https://img.shields.io/pypi/v/Tilings.svg
     :alt: PyPI
     :target: https://pypi.python.org/pypi/Tilings
 .. image:: https://img.shields.io/pypi/l/Tilings.svg
     :target: https://pypi.python.org/pypi/Tilings
 .. image:: https://img.shields.io/pypi/pyversions/Tilings.svg
     :target: https://pypi.python.org/pypi/Tilings
-.. image:: https://requires.io/github/PermutaTriangle/Tilings/requirements.svg?branch=master
-     :target: https://requires.io/github/PermutaTriangle/Tilings/requirements/?branch=master
-     :alt: Requirements Status
 .. image:: https://zenodo.org/badge/121506164.svg
    :target: https://zenodo.org/badge/latestdoi/121506164
 
@@ -54,7 +57,7 @@ development mode by cloning the repository, running
 
 .. code:: bash
 
-       ./setup.py develop
+       pip install -e .
 
 To verify that your installation is correct, you can try to get a specification for
 `Av(12)` by running in your terminal:

README.rst

@@ -1,12 +1,80 @@
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "tilings"
+dynamic = ["version"]
+authors = [
+    {name = "Permuta Triangle", email = "permutatriangle@gmail.com"},
+]
+description = "A Python library for gridded permutations and tilings."
+readme = "README.rst"
+license = {text = "BSD-3-Clause"}
+keywords = [
+    "permutation",
+    "perm",
+    "gridded",
+    "pattern",
+    "tiling",
+    "avoid",
+    "contain",
+    "occurrences",
+    "grid",
+    "class",
+]
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Intended Audience :: Education",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: BSD License",
+    "Programming Language :: Python :: 3",
+    "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 = [
+    "comb-spec-searcher>=4.2.1",
+    "permuta>=2.3.0",
+]
+
+[project.urls]
+Source = "https://github.com/PermutaTriangle/Tilings"
+Tracker = "https://github.com/PermutaTriangle/Tilings/issues"
+
+[project.scripts]
+tilescope = "tilings.cli:main"
+
+[tool.hatch.version]
+path = "tilings/__init__.py"
+
+[tool.hatchling.build.targets.wheel]
+packages = ["tilings"]
+
+[tool.hatchling.build.targets.sdist]
+include = [
+    "tilings",
+    "tests",
+    "README.rst",
+    "LICENSE",
+    "CHANGELOG.md",
+    "CITATION.cff",
+]
+
 [tool.black]
-target-version = ['py37']
+target-version = ['py310']
 include = '\.pyi?$'
 exclude = '''
-
 (
   /(
-      \.eggs         # exclude a few common directories in the
-    | \.git          # root of the project
+      \.eggs
+    | \.git
     | \.hg
     | \.mypy_cache
     | \.tox
@@ -16,7 +84,6 @@ exclude = '''
     | build
     | dist
   )/
-  | foo.py           # also separately exclude a file named foo.py in
-                     # the root of the project
+  | foo.py
 )
 '''