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Merge pull request #8 from dc2917/add_docs
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Added basic sphinx documentation
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dc2917 authored Sep 29, 2024
2 parents 8f464e8 + 36328ae commit a673553
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39 changes: 39 additions & 0 deletions .github/workflows/docs.yml
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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
2 changes: 2 additions & 0 deletions README.md
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Expand Up @@ -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).
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20 changes: 20 additions & 0 deletions docs/Makefile
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# 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)
35 changes: 35 additions & 0 deletions docs/make.bat
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@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
8 changes: 8 additions & 0 deletions docs/source/api_ref.rst
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API Reference
=============

.. toctree::
:maxdepth: 2

fargonaut

27 changes: 27 additions & 0 deletions docs/source/conf.py
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"""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"]
45 changes: 45 additions & 0 deletions docs/source/fargonaut.fields.rst
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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:
37 changes: 37 additions & 0 deletions docs/source/fargonaut.rst
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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:
14 changes: 14 additions & 0 deletions docs/source/index.rst
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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
9 changes: 9 additions & 0 deletions docs/source/user_docs.rst
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User Documentation
==================

.. toctree::
:maxdepth: 2

user_docs/installation
user_docs/basic_usage
user_docs/contrib_guide
41 changes: 41 additions & 0 deletions docs/source/user_docs/basic_usage.rst
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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)

24 changes: 24 additions & 0 deletions docs/source/user_docs/contrib_guide.rst
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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
20 changes: 20 additions & 0 deletions docs/source/user_docs/installation.rst
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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

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