Refactor package towards 1.0.0 release

.github/workflows/ci.yaml

@@ -4,7 +4,6 @@ on:
   push:
     branches: [master]
   pull_request:
-    branches: [master]
 
 jobs:
   build:
@@ -15,9 +14,10 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - {python-version: "3.8", os: ubuntu-latest, documentation: True}
-          - {python-version: "3.9", os: ubuntu-latest, documentation: False}
-          - {python-version: "3.10", os: ubuntu-latest, documentation: False}
+          - {python-version: "3.10", os: ubuntu-latest}
+          - {python-version: "3.11", os: ubuntu-latest}
+          - {python-version: "3.12", os: ubuntu-latest}
+          - {python-version: "3.12", os: macos-latest}
 
     steps:
       - uses: actions/checkout@v2
@@ -34,12 +34,17 @@ jobs:
           python -m pip install .[dev]
       - name: Linting
         run: |
-          python -m black dyson/ --diff --check --verbose
-          python -m isort dyson/ --diff --check-only --verbose
+          ruff check
+          ruff format --check
+          mypy dyson/ tests/
       - name: Run unit tests
         run: |
-          python -m pip install pytest pytest-cov
-          pytest --cov dyson/
+          OMP_NUM_THREADS=1 pytest
+      - name: Run examples
+        env:
+          MPLBACKEND: Agg
+        run: |
+          find examples -name "*.py" -print0 | xargs -0 -n1 python
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v3
         with:

.github/workflows/docs.yaml

@@ -0,0 +1,21 @@
+name: Documentation
+
+on:
+  push:
+    branches: [refactor]
+
+jobs:
+  pages:
+    runs-on: ubuntu-latest
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    permissions:
+      pages: write
+      id-token: write
+    steps:
+    - id: deployment
+      uses: sphinx-notes/pages@v3
+      with:
+        documentation_path: docs/source
+        pyproject_extras: dev

README.md

@@ -1,9 +1,11 @@
-# dyson: Dyson equation solvers for electron propagator methods
+# `dyson`: Dyson equation solvers for Green's function methods
 
-The `dyson` package implements various Dyson equation solvers, with a focus on those avoiding explicitly grid-resolved numerical procedures such as Fourier transforms and analytical continutation.
+[![CI](https://github.com/BoothGroup/dyson/workflows/CI/badge.svg)](https://github.com/BoothGroup/dyson/actions?query=workflow%3ACI+branch%3Amaster)  
+
+The `dyson` package implements various Dyson equation solvers, including novel approaches that avoiding explicitly grid-resolved numerical procedures such as Fourier transforms and analytical continuation.
 These include the moment-resolved block Lanczos methods for moments of the Green's function or self-energy.
 
-### Installation:
+## Installation
 
 From source:
 
@@ -12,6 +14,6 @@ git clone https://github.com/BoothGroup/dyson
 pip install .
 ```
 
-### Usage
+## Usage
 
 Examples are available in the `examples` directory.

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/source/conf.py

@@ -0,0 +1,64 @@
+"""Configuration file for the Sphinx documentation builder.
+
+For the full list of built-in configuration values, see the documentation:
+https://www.sphinx-doc.org/en/master/usage/configuration.html
+"""
+
+
+# Project information
+
+project = "dyson"
+copyright = "2025, Booth Group, King's College London"
+author = "Oliver J. Backhouse, Basil Ibrahim, Marcus K. Allen, George H. Booth"
+
+
+# General configuration
+
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.coverage",
+    "sphinx.ext.doctest",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.viewcode",
+    "sphinx_mdinclude",
+]
+
+templates_path = ["_templates"]
+exclude_patterns = []
+
+
+# Options for HTML output
+
+html_theme = "sphinx_book_theme"
+html_static_path = ["_static"]
+default_role = "autolink"
+
+
+# Options for autosummary
+
+autosummary_generate = True
+autodoc_default_options = {
+    "members": True,
+    "undoc-members": True,
+    "inherited-members": False,
+    "show-inheritance": True,
+    "member-order": "bysource",
+}
+
+
+# Options for intersphinx
+
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/3/", None),
+    "numpy": ("https://numpy.org/doc/stable/", None),
+    "scipy": ("https://docs.scipy.org/doc/scipy/", None),
+    "pyscf": ("https://pyscf.org/", None),
+    "rich": ("https://rich.readthedocs.io/en/stable/", None),
+}
+
+
+# Options for napoleon
+
+napoleon_google_docstring = True

docs/source/dyson.rst

@@ -0,0 +1,4 @@
+dyson
+=====
+
+.. automodule:: dyson

docs/source/index.rst

@@ -0,0 +1,17 @@
+.. dyson documentation master file, created by
+   sphinx-quickstart on Sat Jul 19 19:21:09 2025.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+.. mdinclude:: ../../README.md
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+.. toctree::
+   :maxdepth: 1
+   :hidden:
+   :caption: API Reference
+
+   dyson