Lots of little polishing updates in preparation for v0.5.0

.github/dependabot.yml

@@ -0,0 +1,11 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    target-branch: "develop"
+    schedule:
+      interval: "monthly"
+    groups:
+      github-actions:
+        patterns:
+          - "*"

.github/workflows/publish-to-pypi.yml

@@ -0,0 +1,150 @@
+name: Build, test, and deploy
+
+on:
+  push:
+    branches: [develop, main]
+  pull_request:
+    branches: [develop, main]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  lint:
+    name: Lint and check formatting
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v7
+        with:
+          persist-credentials: false
+
+      - name: Check code with ruff
+        uses: astral-sh/ruff-action@v3
+        with:
+          version: "0.16.9"
+          args: check
+
+      - name: Check formatting with ruff
+        uses: astral-sh/ruff-action@v3
+        with:
+          version: "0.16.9"
+          args: format --check
+
+  build:
+    name: Build distributions
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v7
+        with:
+          persist-credentials: false
+
+      - uses: actions/setup-python@v7
+        with:
+          python-version: "3.14"
+
+      - name: Check release tag matches package version
+        if: github.event_name == 'release'
+        shell: bash
+        run: |
+          version=$(python -c "import tomllib; print(tomllib.load(open('pyproject.toml', 'rb'))['project']['version'])")
+          tag="${GITHUB_REF_NAME#v}"
+          if [ "$tag" != "$version" ]; then
+            echo "::error::Release tag ($GITHUB_REF_NAME) does not match version in pyproject.toml ($version)"
+            exit 1
+          fi
+
+      - name: Build sdist and wheel
+        run: pipx run build
+
+      - name: Check distribution metadata
+        run: pipx run twine check --strict dist/*
+
+      - uses: actions/upload-artifact@v7
+        with:
+          name: dist
+          path: dist/
+
+  test:
+    name: Test on ${{ matrix.os }} with Python ${{ matrix.python-version }}
+    needs: build
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        # macos-15-intel is an Intel runner, macos-15 is Apple silicon
+        os: [ubuntu-latest, ubuntu-24.04-arm, windows-latest, windows-11-arm, macos-15-intel, macos-15]
+        python-version: ["3.10", "3.15"]
+        exclude:
+          # NumPy and SciPy do not provide Windows ARM64 packages for Python 3.10
+          - os: windows-11-arm
+            python-version: "3.10"
+        include:
+          # Test the intermediate Python versions on Linux only
+          - os: ubuntu-latest
+            python-version: "3.11"
+          - os: ubuntu-latest
+            python-version: "3.12"
+          - os: ubuntu-latest
+            python-version: "3.13"
+          - os: ubuntu-latest
+            python-version: "3.14"
+
+    steps:
+      # Checkout is only needed for the tests and sample data; the package is
+      # installed from the built wheel so the tests check what gets published
+      - uses: actions/checkout@v7
+        with:
+          persist-credentials: false
+
+      - uses: actions/setup-python@v7
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - uses: actions/download-artifact@v8
+        with:
+          name: dist
+          path: dist
+
+      - name: Install tcplotter wheel and test dependencies
+        shell: bash
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install dist/*.whl pytest
+
+      - name: Run tests
+        run: python -m pytest -v
+
+  upload_testpypi:
+    name: Publish to TestPyPI
+    needs: [lint, build, test]
+    runs-on: ubuntu-latest
+    environment: testpypi
+    permissions:
+      id-token: write
+    if: github.event_name == 'workflow_dispatch'
+    steps:
+      - uses: actions/download-artifact@v8
+        with:
+          name: dist
+          path: dist
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/
+
+  upload_pypi:
+    name: Publish to PyPI
+    needs: [lint, build, test]
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      id-token: write
+    if: github.event_name == 'release' && github.event.action == 'published'
+    steps:
+      - uses: actions/download-artifact@v8
+        with:
+          name: dist
+          path: dist
+      - uses: pypa/gh-action-pypi-publish@release/v1

.gitignore

@@ -4,3 +4,9 @@ __pycache__
 .pixi/*
 !.pixi/config.toml
 .DS_Store
+
+# Build and test output
+build/
+dist/
+*.egg-info/
+.pytest_cache/

.readthedocs.yaml

@@ -6,7 +6,7 @@ version: 2
 
 # Set the OS, Python version and other tools you might need
 build:
-  os: ubuntu-22.04
+  os: ubuntu-24.04
   tools:
     python: "3.12"
 

CITATION.cff

@@ -0,0 +1,38 @@
+cff-version: 1.2.0
+message: "If you use tcplotter in your work, please cite it as below."
+type: software
+title: "tcplotter: a Python package for creating and customizing thermochronometer age and closure temperature plots"
+authors:
+  - family-names: Whipp
+    given-names: David M.
+    affiliation: University of Helsinki, Finland
+  - family-names: Ketcham
+    given-names: Richard A.
+    affiliation: University of Texas at Austin, USA
+version: 0.5.0
+doi: 10.5281/zenodo.5958939
+license: GPL-3.0-or-later
+repository-code: "https://github.com/HUGG/tcplotter"
+url: "https://tcplotter.readthedocs.io/"
+keywords:
+  - thermochronology
+  - geology
+  - geophysics
+references:
+  - type: article
+    title: "Short communication: Modeling competing effects of cooling rate, grain size, and radiation damage in low-temperature thermochronometers"
+    authors:
+      - family-names: Whipp
+        given-names: David M.
+      - family-names: Kellett
+        given-names: Dawn A.
+      - family-names: Coutand
+        given-names: Isabelle
+      - family-names: Ketcham
+        given-names: Richard A.
+    journal: Geochronology
+    volume: 4
+    start: 143
+    end: 152
+    year: 2022
+    doi: 10.5194/gchron-4-143-2022