Adding github workflows to check and auto-publish code to pypi

.github/workflows/publish-package.yml

@@ -0,0 +1,72 @@
+# This workflow will upload a Python Package to PyPI when a release is created
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  release-build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+
+      - name: Build release distributions
+        run: |
+          # NOTE: put your own distribution build steps here.
+          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
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write
+
+    # Dedicated environments with protections for publishing are strongly recommended.
+    # For more information, see: https://docs.github.com/en/actions/deployment/targeting-different-environments/using-environments-for-deployment#deployment-protection-rules
+    environment:
+      name: pypi
+      # OPTIONAL: uncomment and update to include your PyPI project URL in the deployment status:
+      url: https://pypi.org/p/mesa-reader
+      #
+      # ALTERNATIVE: if your GitHub Release name is the PyPI project version string
+      # ALTERNATIVE: exactly, uncomment the following line instead:
+      # url: https://pypi.org/project/YOURPROJECT/${{ github.event.release.name }}
+
+    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:
+          user: __token__
+          password: ${{ secrets.PYPI_API_TOKEN }}
+          packages-dir: dist/

.github/workflows/test-package.yml

@@ -0,0 +1,40 @@
+# 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: tests
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["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 -r requirements-dev.txt
+        # if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        pip install .
+    - name: Lint with ruff
+      run: |
+        cd ${{ github.workspace }}
+        ruff format --check
+        ruff check
+    - name: Test with pytest
+      run: |
+        pytest

README.md

@@ -1,28 +1,64 @@
-mesa_reader
-===========
+[![Repo Status][status-badge]][status-link]
+[![PyPI Version Status][pypi-badge]][pypi-link]
+[![Test Status][workflow-test-badge]][workflow-test-link]
+[![Readthedocs Status][docs-badge]][docs-link]
+[![License][license-badge]][license-link]
+
+[status-link]:         https://www.repostatus.org/#active
+[status-badge]:        https://www.repostatus.org/badges/latest/active.svg
+[pypi-link]:           https://pypi.org/project/mesa-reader
+[pypi-badge]:          https://img.shields.io/pypi/v/mesa-reader?label=PyPI&logo=pypi
+[workflow-test-link]:  https://github.com/wmwolf/py_mesa_reader/actions/workflows/test-package.yml
+[workflow-test-badge]: https://github.com/wmwolf/py_mesa_reader/actions/workflows/test-package.yml/badge.svg?event=push
+[docs-link]:           https://wmwolf.github.io/py_mesa_reader
+[docs-badge]:          https://github.com/wmwolf/py_mesa_reader/actions/workflows/pages/pages-build-deployment/badge.svg
+[license-link]:        https://opensource.org/license/gpl-3-0
+[license-badge]:       https://img.shields.io/badge/license-GPLv3-blue.svg
+
+# mesa_reader
+
+A Python package for easily accessing and manipulating output of the [Modules for Experiments in Stellar Astrophysics (MESA)](https://mesastar.org/) code.
 
-Tools for easily accessing and manipulating data from `MESA star` and `MESA binary` in python.
 
 ## Installation
-The easiest way to install is via `pip`:
 
-    pip install mesa_reader
+The easiest way to install the package is via `pip`:
 
-You can also install by cloning or downloading the repository at github.com/wmwolf/py_mesa_reader, `cd` into it and then execute
+```console
+pip install mesa_reader
+```
 
-    python setup.py install
+You can also install by cloning or downloading this repository, `cd` into it and then execute
+
+```console
+python setup.py install
+```
 
 or
 
-    pip install .
+```console
+pip install .
+```
 
 to install the package on your system.
 
+
 ## Uninstallation
-Uninstall by executing
 
-    pip uninstall mesa_reader
+Uninstall the package by executing
+
+```console
+pip uninstall mesa_reader
+```
+
 
 ## Usage
+
+Start using the package in your Python scripts by first importing it:
+
+```python
+import mesa_reader as mr
+```
+
 Complete documentation on the `mesa_reader` module found
-[here](https://wmwolf.github.io/py_mesa_reader).
+[here](https://wmwolf.github.io/py_mesa_reader).

docs_source/conf.py

@@ -18,11 +18,9 @@
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
 import os
-from os.path import join
 import sys
-import sphinx_rtd_theme
-sys.path.insert(0, os.path.abspath(join('..')))
 
+sys.path.insert(0, os.path.abspath(".."))
 
 # -- General configuration ------------------------------------------------
 
@@ -33,37 +31,40 @@
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = ['sphinx.ext.autodoc',
-              'sphinx.ext.mathjax',
-              'sphinx.ext.viewcode',
-              'sphinx.ext.githubpages',
-              'sphinx.ext.napoleon']
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.githubpages",
+    "sphinx.ext.napoleon",
+    "sphinx_copybutton",
+]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
 #
 # source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
+source_suffix = ".rst"
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # General information about the project.
-project = 'PyMesaReader'
-copyright = '2017, William Wolf and Josiah Schwab'
-author = 'William Wolf and Josiah Schwab'
+project = "PyMesaReader"
+copyright = "2017, William Wolf and Josiah Schwab"
+author = "William Wolf and Josiah Schwab"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
-version = '3.1'
+version = "3.5"
 # The full version, including alpha/beta/rc tags.
-release = '3.1.0'
+release = "3.5.0"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -78,7 +79,7 @@
 exclude_patterns = []
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = False
@@ -89,28 +90,28 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'sphinx_rtd_theme'
+html_theme = "sphinx_rtd_theme"
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
 #
 # html_theme_options = {}
 html_theme_options = {
-    'collapse_navigation': False,
-    'display_version': False,
-    'navigation_depth': 3,
+    "collapse_navigation": False,
+    "display_version": False,
+    "navigation_depth": 3,
 }
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]
 
 
 # -- Options for HTMLHelp output ------------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'PyMesaReaderdoc'
+htmlhelp_basename = "PyMesaReaderdoc"
 
 
 # -- Options for LaTeX output ---------------------------------------------
@@ -119,15 +120,12 @@
     # The paper size ('letterpaper' or 'a4paper').
     #
     # 'papersize': 'letterpaper',
-
     # The font size ('10pt', '11pt' or '12pt').
     #
     # 'pointsize': '10pt',
-
     # Additional stuff for the LaTeX preamble.
     #
     # 'preamble': '',
-
     # Latex figure (float) alignment
     #
     # 'figure_align': 'htbp',
@@ -137,19 +135,21 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'PyMesaReader.tex', 'PyMesaReader Documentation',
-     'William Wolf and Josiah Schwab', 'manual'),
+    (
+        master_doc,
+        "PyMesaReader.tex",
+        "PyMesaReader Documentation",
+        "William Wolf and Josiah Schwab",
+        "manual",
+    ),
 ]
 
 
 # -- Options for manual page output ---------------------------------------
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [
-    (master_doc, 'pymesareader', 'PyMesaReader Documentation',
-     [author], 1)
-]
+man_pages = [(master_doc, "pymesareader", "PyMesaReader Documentation", [author], 1)]
 
 
 # -- Options for Texinfo output -------------------------------------------
@@ -158,7 +158,13 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'PyMesaReader', 'PyMesaReader Documentation',
-     author, 'PyMesaReader', 'One line description of project.',
-     'Miscellaneous'),
+    (
+        master_doc,
+        "PyMesaReader",
+        "PyMesaReader Documentation",
+        author,
+        "PyMesaReader",
+        "One line description of project.",
+        "Miscellaneous",
+    ),
 ]

requirements-dev.txt

@@ -0,0 +1,2 @@
+ruff
+pytest