Added basic sphinx documentation

.github/workflows/docs.yml

@@ -0,0 +1,39 @@
+name: "Build documentation"
+on:
+  pull_request:
+    branches:
+      - main
+  push:
+    branches:
+      - main
+  workflow_dispatch:
+jobs:
+  build:
+    timeout-minutes: 5
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
+      with:
+        python-version: "3.12"
+        cache: "pip"
+        cache-dependency-path: "requirements-dev.txt"
+    - name: Gather dependencies
+      run: |
+        pip install -U pip
+        pip install -r requirements-dev.txt
+    - name: Build HTML
+      run: sphinx-build -b html docs/source docs/build/html
+    - name: Upload artifacts
+      uses: actions/upload-artifact@v4
+      with:
+        name: html-docs
+        path: docs/build/html/
+    - name: Deploy
+      uses: peaceiris/actions-gh-pages@v3
+      if: github.ref == 'refs/heads/main'
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: docs/build/html

README.md

@@ -15,6 +15,8 @@ Fargonaut is a package for post-processing and visualising outputs of [FARGO3D](
 
 ![Gas surface density output 50](docs/images/fargo_gasdens50.png)
 
+See the documentation for installation instructions, example usage and the API reference.
+
 ## Contributing to Fargonaut
 
 Contributions to Fargonaut are welcome. Please see the [contributing guidelines](CONTRIBUTING.md).

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/api_ref.rst

@@ -0,0 +1,8 @@
+API Reference
+=============
+
+.. toctree::
+   :maxdepth: 2
+
+   fargonaut
+

docs/source/conf.py

@@ -0,0 +1,27 @@
+"""Configuration file for the Sphinx documentation builder."""
+
+import os
+import sys
+
+sys.path.insert(0, os.path.abspath("../.."))
+
+
+# -- Project information -----------------------------------------------------
+
+project = "Fargonaut"
+copyright = "2024, Dan Cummins"
+author = "Dan Cummins"
+
+
+# -- General configuration ---------------------------------------------------
+
+extensions = ["sphinx.ext.autodoc", "sphinx.ext.napoleon", "sphinx_rtd_theme"]
+
+templates_path = ["_templates"]
+exclude_patterns = []
+
+
+# -- Options for HTML output -------------------------------------------------
+
+html_theme = "sphinx_rtd_theme"
+html_static_path = ["_static"]

docs/source/fargonaut.fields.rst

@@ -0,0 +1,45 @@
+fargonaut.fields package
+========================
+
+Submodules
+----------
+
+fargonaut.fields.density module
+-------------------------------
+
+.. automodule:: fargonaut.fields.density
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+fargonaut.fields.energy module
+------------------------------
+
+.. automodule:: fargonaut.fields.energy
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+fargonaut.fields.magnetic\_field module
+---------------------------------------
+
+.. automodule:: fargonaut.fields.magnetic_field
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+fargonaut.fields.velocity module
+--------------------------------
+
+.. automodule:: fargonaut.fields.velocity
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: fargonaut.fields
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/fargonaut.rst

@@ -0,0 +1,37 @@
+fargonaut package
+=================
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   fargonaut.fields
+
+Submodules
+----------
+
+fargonaut.field module
+----------------------
+
+.. automodule:: fargonaut.field
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+fargonaut.output module
+-----------------------
+
+.. automodule:: fargonaut.output
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: fargonaut
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/index.rst

@@ -0,0 +1,14 @@
+Fargonaut documentation
+=======================
+
+Fargonaut is an object-oriented toolkit for post-processing and visualising outputs of FARGO3D_, written in Python.
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   User Documentation <user_docs>
+   API Reference <api_ref>
+
+
+.. _fargo3d: https://github.com/FARGO3D/fargo3d

docs/source/user_docs.rst

@@ -0,0 +1,9 @@
+User Documentation
+==================
+
+.. toctree::
+   :maxdepth: 2
+
+   user_docs/installation
+   user_docs/basic_usage
+   user_docs/contrib_guide

docs/source/user_docs/basic_usage.rst

@@ -0,0 +1,41 @@
+Basic Usage
+===========
+
+Locate the directory containing the FARGO3D output you want to open. For demonstrative purposes, we will use "/path/to/fargo3d/outputs", and use the "fargo" output, created when running the example "fargo" setup.
+
+Open the Python interpreter::
+
+  $ python
+
+Import the top-level ``Output`` class::
+
+  >>> from fargonaut.output import Output
+
+Use this class to create an object for handling your output::
+
+  >>> output = Output("/path/to/fargo3d/outputs/fargo")
+
+Using the ``Output`` class::
+
+  >>> help(output)
+
+Retrieve variables defined in the variables.par file using the ``get_var`` method, e.g.::
+
+  >>> output.get_var("FRAME")
+  'G'
+
+Some commonly used variables are stored as properties, in particular those related to the grid, e.g.::
+
+  >>> output.ny
+  128
+  >>> output.nghy
+  3
+  >>> len(output.ydomain)
+  135
+  >>> output.xdomain
+  array([-3.14159265, -3.12523019, -3.10886773, ..., 0, ... 3.14159265])
+
+Use the ``get_field`` method to retrieve a field at a given output time. The names of the fields are those of the corresponding output files, e.g. to retrieve the gas density::
+
+  >>> gasdens50 = output.get_field("gasdens", 50)
+

docs/source/user_docs/contrib_guide.rst

@@ -0,0 +1,24 @@
+Contributing Guidelines
+=======================
+
+Install the development requirements::
+
+  $ pip install -r requirements-dev.txt
+
+Install the pre-commit hooks::
+
+  $ pre-commit install
+
+Run the tests::
+
+  $ python -m unittest discover tests
+
+Check test coverage::
+
+  $ coverage run --omit=tests/* -m unittest discover tests
+  $ coverage report -m
+
+Build the documentation::
+
+  $ cd docs
+  $ make html

docs/source/user_docs/installation.rst

@@ -0,0 +1,20 @@
+Installation
+============
+
+The only requirements for installing Fargonaut are Git and Python.
+
+First, clone the repository::
+
+  $ git clone https://github.com/dc2917/Fargonaut
+
+Create a virtual environment to keep the Python packages separate from system packages and other local environments::
+
+  $ python -m venv .venv
+
+Activate the environment::
+
+  $ source .venv/bin/activate
+
+Install the dependencies::
+
+  $ pip install -r requirements.txt