Release v2.3.1 (#200)

* Update README.rst

Adding more info about Av and clarifying the output of the enumeration strategies function

* Create dependabot.yml

* update testing and black formatting (#197)

* update testing and black formatting

* pylint fix

* pylint

* Bump automata-lib from 7.0.1 to 9.0.0 (#196)

Bumps [automata-lib](https://github.com/caleb531/automata) from 7.0.1 to 9.0.0.
- [Release notes](https://github.com/caleb531/automata/releases)
- [Commits](caleb531/automata@v7.0.1...v9.0.0)

---
updated-dependencies:
- dependency-name: automata-lib
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* mypy fix (#198)

* mypy fix

* more mypy

* ugh

* update build systems (#199)

* update build systems

* update readme

* update readme

* readme fix

* Create CITATION.cff

* Delete .zenodo.json

* Update README.rst

* Update CHANGELOG.md

* Bump version to 2.3.1 for release

---------

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: Henning Ulfarsson <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Author: 3 people

.github/dependabot.yml

@@ -0,0 +1,11 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+
+version: 2
+updates:
+  - package-ecosystem: "pip" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "weekly"

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

@@ -12,13 +12,13 @@ jobs:
     - uses: actions/checkout@v2
     - uses: actions/setup-python@v2
       with:
-        python-version: "3.10"
+        python-version: "3.13"
     - 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

@@ -9,25 +9,19 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - python: "3.11"
+          - python: "3.13"
             toxenv: flake8
             os: ubuntu-latest
-          - python: "3.11"
+          - python: "3.13"
             toxenv: mypy
             os: ubuntu-latest
-          - python: "3.11"
+          - python: "3.13"
             toxenv: pylint
             os: ubuntu-latest
-          - python: "3.11"
+          - python: "3.13"
             toxenv: black
             os: ubuntu-latest
 
-          - python: 3.8
-            toxenv: py38
-            os: ubuntu-latest
-          - python: 3.9
-            toxenv: py39
-            os: ubuntu-latest
           - python: "3.10"
             toxenv: py310
             os: ubuntu-latest
@@ -37,15 +31,22 @@ jobs:
           - python: "3.12"
             toxenv: py312
             os: ubuntu-latest
-          - python: 'pypy3.9'
-            toxenv: pypy39
+          - python: "3.13"
+            toxenv: py313
             os: ubuntu-latest
 
-          - python: "3.11"
-            toxenv: py311
+          - python: "pypy3.10"
+            toxenv: pypy310
+            os: ubuntu-latest
+          - python: "pypy3.11"
+            toxenv: pypy311
+            os: ubuntu-latest
+
+          - python: "3.13"
+            toxenv: py313
             os: macos-latest
-          - python: "3.11"
-            toxenv: py311
+          - python: "3.13"
+            toxenv: py313
             os: windows-latest
 
     runs-on: ${{ matrix.os }}
@@ -55,10 +56,10 @@ jobs:
         with:
           python-version: ${{  matrix.python }}
       - name: install dependencies
-        run: python -m pip install --upgrade pip tox setuptools wheel
+        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/

.pylintrc

@@ -6,12 +6,12 @@ ignore-patterns=test_.*?py,
                 bisc.py,
                 bisc_subfunctions.py
 ignore= tests
-init-hook="from pylint.config import find_pylintrc; import os, sys; sys.path.append(os.path.dirname(find_pylintrc())+'/permuta')"
+init-hook="import os, sys; sys.path.append(os.path.dirname(os.path.abspath('.')) + '/permuta')"
 disable=missing-module-docstring,
         fixme,
         unsubscriptable-object,
         unspecified-encoding
 good-names=i,j,n,k,x,y,_
 
 [SIMILARITIES]
-ignore-imports=yes
+ignore-imports=yes

.zenodo.json

@@ -4,7 +4,12 @@ All notable changes to this project will be documented in this file.
 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 
+## 2.3.1 - 2025-06-13 
+### 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

CHANGELOG.md

@@ -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"

CITATION.cff

@@ -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
 #############
@@ -65,7 +66,7 @@ interactive Python session, just like any other Python library:
 
     >>> from permuta import *
 
-Importing ``*`` from it supplies you with the 'Perm' and 'PermSet'
+Importing ``*`` supplies you with the 'Perm' and 'PermSet'
 classes along with the 'AvoidanceClass' class (with alias 'Av') for generating
 perms avoiding a set of patterns. It also gives you the 'MeshPatt' class
 and some other submodules which we will not discuss in this readme.
@@ -178,7 +179,7 @@ There are numerous practical methods available:
 Creating a perm class
 #####################
 
-Perm classes are specified with a basis:
+Perm classes are created by first specifying a basis and then calling the 'Av' class, to create the set of permutations avoiding the basis:
 
 .. code-block:: python
 
@@ -227,6 +228,8 @@ given class.
     Enumeration of Permutation Classes and Weighted Labelled Independent Sets: Corollary 4.6
     The class contains only finitely many simple permutations
 
+The output is the name of a paper, followed by the statement in the paper where the enumeration strategy is discussed or stated.
+
 Permutation statistics
 ######################
 
@@ -520,12 +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