Create python-publish.yml

.github/workflows/python-package.yml

@@ -0,0 +1,58 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Python package
+
+on:
+  push:
+      branches:
+        - main
+  pull_request:
+      branches:
+        - main
+        - devel
+        - packaging-updates
+      types:
+        - opened
+        - reopened
+        - synchronize
+        - ready_for_review
+
+
+concurrency:
+  group: ${{ github.event_name }}-${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ github.event_name == 'pull_request'}}
+
+jobs:
+  build-lint-pytest:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install uv
+        python -m pip install flake8 pytest
+        uv pip compile pyproject.toml -o requirements.txt
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Install package
+      run: pip install -e .
+    - name: Test with pytest
+      run: |
+        pytest

.github/workflows/python-publish.yml

@@ -0,0 +1,71 @@
+name: Publish Python Package
+
+on:
+  push:
+    tags:
+      - '[0-9]*.[0-9]*.[0-9]*'
+      - 'v[0-9]*.[0-9]*.[0-9]*'
+
+permissions:
+  contents: write  # Required for creating a GitHub release
+  id-token: write  # Required for trusted publishing to PyPI
+
+jobs:
+  create-release:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Create GitHub Release
+        id: create_release
+        uses: actions/create-release@v1
+        with:
+          tag_name: ${{ github.ref_name }}
+          release_name: Release ${{ github.ref_name }}
+          body: |
+            This is an automated release for version ${{ github.ref_name }}.
+          draft: false
+          prerelease: false
+
+  release-build:
+    runs-on: ubuntu-latest
+    needs: create-release
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+
+      - name: Build release distributions
+        run: |
+          python -m pip install build
+          python -m build
+
+      - name: Upload distributions
+        uses: actions/upload-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+  pypi-publish:
+    runs-on: ubuntu-latest
+    needs: release-build
+    environment:
+      name: release
+      url: https://pypi.org/project/ammber
+
+    steps:
+      - name: Retrieve release distributions
+        uses: actions/download-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+      - name: Publish release distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: dist/

.gitignore

@@ -7,4 +7,7 @@ __pycache__
 ../build
 dist
 *egg-info
-*.pyc
+*.pyc
+
+*.DS_Store
+*.vscode

pyproject.toml

@@ -36,7 +36,8 @@ authors = [
     { name = "Xander Mensah", email = "xmen@umich.edu" },
     { name = "Katsuyo Thornton", email = "kthorn@umich.edu" }
 ]
-license = { file = "LICENSE.md" }
+license = "MIT"
+license-files = ["LICENSE.md"]
 readme = "README.md"
 
 requires-python = ">=2.7, <4"
@@ -50,13 +51,13 @@ dependencies = [
 classifiers=[
     'Development Status :: 1 - Planning',
     'Intended Audience :: Science/Research',
-    'License :: OSI Approved :: MIT License',
-    'Programming Language :: Python :: 2',
-    'Programming Language :: Python :: 2.7',
     'Programming Language :: Python :: 3',
     'Programming Language :: Python :: 3.4',
     'Programming Language :: Python :: 3.5',
 ]
 
+[tool.setuptools.packages.find]
+include = ["ammber"]
+
 [project.urls]
 Homepage = "https://github.com/UMThorntongroup/"

requirements.txt

@@ -0,0 +1,89 @@
+# This file was autogenerated by uv via the following command:
+#    uv pip compile pyproject.toml -o requirements.txt
+contourpy==1.3.0
+    # via matplotlib
+coverage==7.8.0
+    # via pytest-cov
+cycler==0.12.1
+    # via matplotlib
+flexcache==0.3
+    # via pint
+flexparser==0.4
+    # via pint
+fonttools==4.57.0
+    # via matplotlib
+iniconfig==2.1.0
+    # via pytest
+kiwisolver==1.4.8
+    # via matplotlib
+matplotlib==3.10.1
+    # via pycalphad
+numpy==1.26.4
+    # via
+    #   ammber (pyproject.toml)
+    #   contourpy
+    #   matplotlib
+    #   pandas
+    #   pycalphad
+    #   scipy
+    #   xarray
+packaging==24.2
+    # via
+    #   matplotlib
+    #   pytest
+    #   setuptools-scm
+    #   xarray
+pandas==2.2.3
+    # via xarray
+pillow==11.2.1
+    # via matplotlib
+pint==0.24.4
+    # via pycalphad
+platformdirs==4.3.7
+    # via pint
+pluggy==1.5.0
+    # via pytest
+pycalphad==0.11.0
+    # via ammber (pyproject.toml)
+pyparsing==3.2.3
+    # via
+    #   matplotlib
+    #   pycalphad
+pytest==8.3.5
+    # via
+    #   pycalphad
+    #   pytest-cov
+pytest-cov==6.1.1
+    # via pycalphad
+python-dateutil==2.9.0.post0
+    # via
+    #   matplotlib
+    #   pandas
+pytz==2025.2
+    # via pandas
+runtype==0.5.3
+    # via pycalphad
+scipy==1.15.2
+    # via
+    #   ammber (pyproject.toml)
+    #   pycalphad
+setuptools==78.1.0
+    # via setuptools-scm
+setuptools-scm==8.2.0
+    # via pycalphad
+six==1.17.0
+    # via python-dateutil
+symengine==0.14.0
+    # via pycalphad
+tinydb==4.8.2
+    # via pycalphad
+typing-extensions==4.13.2
+    # via
+    #   flexcache
+    #   flexparser
+    #   pint
+    #   pycalphad
+tzdata==2025.2
+    # via pandas
+xarray==2025.3.1
+    # via pycalphad