Merge pull request #2 from janbridley/admin/cleanup

Refactor project for demonstration and future development

.github/dependabot.yml

@@ -0,0 +1,24 @@
+version: 2
+updates:
+- package-ecosystem: "github-actions"
+  directory: "/"
+  target-branch: main
+  schedule:
+    interval: "monthly"
+    time: "07:00"
+    timezone: "EST5EDT"
+  pull-request-branch-name:
+    separator: "-"
+  open-pull-requests-limit: 2
+  reviewers:
+  - janbridley
+  groups:
+    actions-version:
+      applies-to: version-updates
+      patterns:
+      - '*'
+    actions-security:
+      applies-to: security-updates
+      patterns:
+      - '*'
+# Do not update pipfiles with dependabot - TODO: create custom action

.github/requirements.txt

@@ -0,0 +1 @@
+setuptools

.github/requirements3.10.txt

@@ -0,0 +1,47 @@
+# This file was autogenerated by uv via the following command:
+#    uv pip compile --python-version 3.10 requirements.txt tests/requirements.txt .github/requirements.txt
+attrs==24.2.0
+    # via hypothesis
+coxeter==0.9.0
+    # via -r tests/requirements.txt
+exceptiongroup==1.2.2
+    # via
+    #   hypothesis
+    #   pytest
+hypothesis==6.115.0
+    # via -r tests/requirements.txt
+iniconfig==2.0.0
+    # via pytest
+multipledispatch==1.0.0
+    # via pyrr
+numpy==2.1.2
+    # via
+    #   -r requirements.txt
+    #   coxeter
+    #   pyrr
+    #   rowan
+    #   scipy
+packaging==24.1
+    # via pytest
+pluggy==1.5.0
+    # via pytest
+pyrr==0.10.3
+    # via -r tests/requirements.txt
+pytest==8.3.3
+    # via -r tests/requirements.txt
+rowan==1.3.0.post1
+    # via
+    #   -r tests/requirements.txt
+    #   coxeter
+scipy==1.14.1
+    # via coxeter
+setuptools==75.1.0
+    # via -r .github/requirements.txt
+sortedcontainers==2.4.0
+    # via hypothesis
+svgwrite==1.4.3
+    # via -r requirements.txt
+tomli==2.0.2
+    # via pytest
+tqdm==4.66.5
+    # via -r requirements.txt

.github/requirements3.11.txt

@@ -0,0 +1,41 @@
+# This file was autogenerated by uv via the following command:
+#    uv pip compile --python-version 3.11 requirements.txt tests/requirements.txt .github/requirements.txt
+attrs==24.2.0
+    # via hypothesis
+coxeter==0.9.0
+    # via -r tests/requirements.txt
+hypothesis==6.115.0
+    # via -r tests/requirements.txt
+iniconfig==2.0.0
+    # via pytest
+multipledispatch==1.0.0
+    # via pyrr
+numpy==2.1.2
+    # via
+    #   -r requirements.txt
+    #   coxeter
+    #   pyrr
+    #   rowan
+    #   scipy
+packaging==24.1
+    # via pytest
+pluggy==1.5.0
+    # via pytest
+pyrr==0.10.3
+    # via -r tests/requirements.txt
+pytest==8.3.3
+    # via -r tests/requirements.txt
+rowan==1.3.0.post1
+    # via
+    #   -r tests/requirements.txt
+    #   coxeter
+scipy==1.14.1
+    # via coxeter
+setuptools==75.1.0
+    # via -r .github/requirements.txt
+sortedcontainers==2.4.0
+    # via hypothesis
+svgwrite==1.4.3
+    # via -r requirements.txt
+tqdm==4.66.5
+    # via -r requirements.txt

.github/requirements3.12.txt

@@ -0,0 +1,41 @@
+# This file was autogenerated by uv via the following command:
+#    uv pip compile --python-version 3.12 requirements.txt tests/requirements.txt .github/requirements.txt
+attrs==24.2.0
+    # via hypothesis
+coxeter==0.9.0
+    # via -r tests/requirements.txt
+hypothesis==6.115.0
+    # via -r tests/requirements.txt
+iniconfig==2.0.0
+    # via pytest
+multipledispatch==1.0.0
+    # via pyrr
+numpy==2.1.2
+    # via
+    #   -r requirements.txt
+    #   coxeter
+    #   pyrr
+    #   rowan
+    #   scipy
+packaging==24.1
+    # via pytest
+pluggy==1.5.0
+    # via pytest
+pyrr==0.10.3
+    # via -r tests/requirements.txt
+pytest==8.3.3
+    # via -r tests/requirements.txt
+rowan==1.3.0.post1
+    # via
+    #   -r tests/requirements.txt
+    #   coxeter
+scipy==1.14.1
+    # via coxeter
+setuptools==75.1.0
+    # via -r .github/requirements.txt
+sortedcontainers==2.4.0
+    # via hypothesis
+svgwrite==1.4.3
+    # via -r requirements.txt
+tqdm==4.66.5
+    # via -r requirements.txt

.github/requirements3.13.txt

@@ -0,0 +1,41 @@
+# This file was autogenerated by uv via the following command:
+#    uv pip compile --python-version 3.13 requirements.txt tests/requirements.txt .github/requirements.txt
+attrs==24.2.0
+    # via hypothesis
+coxeter==0.9.0
+    # via -r tests/requirements.txt
+hypothesis==6.115.0
+    # via -r tests/requirements.txt
+iniconfig==2.0.0
+    # via pytest
+multipledispatch==1.0.0
+    # via pyrr
+numpy==2.1.2
+    # via
+    #   -r requirements.txt
+    #   coxeter
+    #   pyrr
+    #   rowan
+    #   scipy
+packaging==24.1
+    # via pytest
+pluggy==1.5.0
+    # via pytest
+pyrr==0.10.3
+    # via -r tests/requirements.txt
+pytest==8.3.3
+    # via -r tests/requirements.txt
+rowan==1.3.0.post1
+    # via
+    #   -r tests/requirements.txt
+    #   coxeter
+scipy==1.14.1
+    # via coxeter
+setuptools==75.1.0
+    # via -r .github/requirements.txt
+sortedcontainers==2.4.0
+    # via hypothesis
+svgwrite==1.4.3
+    # via -r requirements.txt
+tqdm==4.66.5
+    # via -r requirements.txt

.github/requirements3.9.txt

@@ -0,0 +1,47 @@
+# This file was autogenerated by uv via the following command:
+#    uv pip compile --python-version 3.9 requirements.txt tests/requirements.txt .github/requirements.txt
+attrs==24.2.0
+    # via hypothesis
+coxeter==0.9.0
+    # via -r tests/requirements.txt
+exceptiongroup==1.2.2
+    # via
+    #   hypothesis
+    #   pytest
+hypothesis==6.115.0
+    # via -r tests/requirements.txt
+iniconfig==2.0.0
+    # via pytest
+multipledispatch==1.0.0
+    # via pyrr
+numpy==2.0.2
+    # via
+    #   -r requirements.txt
+    #   coxeter
+    #   pyrr
+    #   rowan
+    #   scipy
+packaging==24.1
+    # via pytest
+pluggy==1.5.0
+    # via pytest
+pyrr==0.10.3
+    # via -r tests/requirements.txt
+pytest==8.3.3
+    # via -r tests/requirements.txt
+rowan==1.3.0.post1
+    # via
+    #   -r tests/requirements.txt
+    #   coxeter
+scipy==1.13.1
+    # via coxeter
+setuptools==75.1.0
+    # via -r .github/requirements.txt
+sortedcontainers==2.4.0
+    # via hypothesis
+svgwrite==1.4.3
+    # via -r requirements.txt
+tomli==2.0.2
+    # via pytest
+tqdm==4.66.5
+    # via -r requirements.txt

.github/update-pipfiles.sh

@@ -0,0 +1,5 @@
+#!/bin/bash
+
+for v in "3.9" "3.10" "3.11" "3.12" "3.13"; do
+  uv pip compile --python-version $v requirements.txt tests/requirements.txt .github/requirements.txt > .github/requirements$v.txt
+done

.github/workflows/run-pytest.yml

@@ -0,0 +1,50 @@
+name: Run Unit Tests
+
+on:
+  # trigger on pull requests
+  pull_request:
+
+  # trigger on all commits to main
+  push:
+    branches:
+      - 'main'
+
+  # trigger on request
+  workflow_dispatch:
+concurrency:
+  group: "${{ github.workflow }}-${{ github.ref }}"
+  cancel-in-progress: true
+jobs:
+  test:
+    name: test (${{ matrix.os }}, ${{ matrix.python }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: true
+      matrix:
+        os: [ubuntu-latest]
+        python: ['3.10', '3.11', '3.12', '3.13']
+        include:
+          # Other tests
+          - os: 'macos-latest'
+            python: '3.10'
+          - os: 'macos-latest'
+            python: '3.13'
+    steps:
+    - name: Checkout
+      uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29  # v4.2.1
+    - name: Set up Python ${{ matrix.python }}
+      uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
+      with:
+        python-version: ${{ matrix.python }}
+    - name: Set up Python environment
+      uses: glotzerlab/workflows/setup-uv@3573ddaebf3290e00bfb150b82a46412192a61d3
+      with:
+        # only-binary: ":none:"
+        lockfile: ".github/requirements${{ matrix.python }}.txt"
+    - name: Install package
+      run: |
+        python --version
+        uv pip install . --no-build-isolation --no-deps --system -v
+    - name: Test with pytest
+      run: |
+        python -m pytest

.gitignore

@@ -1,4 +1,20 @@
-*.svg
-*.png
-*.pxd
-__pycache__
+# Packaging and distribution
+*.egg
+*.egg-info*
+*.whl
+dist
+build
+
+# Compiled files
+__pycache__/
+*.pyc
+*.out
+
+# Development tooling
+.hypothesis/
+.ipynb_checkpoints/
+.pytest_cache/
+.ruff_cache/
+
+# Example files (not distributed for copyright reasons)
+*.obj

.pre-commit-config.yaml

@@ -0,0 +1,26 @@
+ci:
+  autoupdate_schedule: quarterly
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: 'v4.4.0'
+    hooks:
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+      - id: check-builtin-literals
+      - id: check-executables-have-shebangs
+      - id: check-json
+      - id: check-yaml
+      - id: debug-statements
+      - id: requirements-txt-fixer
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.6.8
+    hooks:
+      # Run the linter.
+      - id: ruff
+        types_or: [ python, pyi, jupyter ]
+        args: [ --fix ]
+      # Run the formatter.
+      - id: ruff-format
+        types_or: [ python, pyi, jupyter ]

LICENSE

@@ -1,5 +1,6 @@
 MIT License
 
+Copyright (c) 2024 Jenna Bradley
 Copyright (c) 2018 Philip Rideout
 
 Permission is hereby granted, free of charge, to any person obtaining a copy