basic sphinx docs

man/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     = .
+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)

man/conf.py

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+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+# import os
+import sys
+sys.path.insert(0, "../plot_phylo")
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'plot_phylo'
+copyright = '2024 Katy Brown, Duncan Cross'
+author = 'Katy Brown, Duncan Cross'
+
+# The full version, including alpha/beta/rc tags
+release = '0.1.6'
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = ['recommonmark', 'sphinx_markdown_tables', 'sphinx.ext.autodoc']
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+root_doc = 'contents'
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+import sphinx_rtd_theme
+html_theme = "sphinx_rtd_theme"
+html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
+
+# 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']

man/contents.rst

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+plot_phylo
+==========
+
+.. toctree::
+   :maxdepth: 3
+
+   pages/introduction.md
+   pages/installation.md
+   pages/quickstart.md
+   pages/parameters.md
+   pages/functions.rst
+   pages/detailed.md

man/pages/detailed.md

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+# Detailed Example

man/pages/functions.rst

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+Functions
+======================
+
+.. automodule:: plot_phylo
+   :members:
+   :undoc-members:
+   :show-inheritance:

man/pages/installation.md

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+## Installation
+
+**Requirements**
+
+* python >= 3.6
+* matplotlib >= 2.1.1
+* ete3 >= 3.1.0
+
+## Installation
+The module can be installed using pip
+
+`pip install plot_phylo`
+
+You can also download the latest release [here](https://github.com/KatyBrown/plot_phylo/releases/latest)
+
+Or clone the GitHub repository directly.
+
+`git clone [email protected]:KatyBrown/plot_phylo.git`

man/pages/introduction.md

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+# Introduction
+
+This module allows the user to plot a phylogenetic tree on an existing matplotlib axis.
+
+This means that:
+* Phylogenies can be incorporated into existing plots.
+* Annotations can be added using standard matplotlib functionality.
+* Plots can be output in png, pdf, svg or tiff formats.
+* Automatically generated and updated figures can include phylogenies
+
+1. [Installation](installation.md)
+2. [Quick Start](quickstart.md)
+3. [Incorporating Matplotlib Parameters](matplotlib.md)
+4. [Parameters](parameters.md)
+5. [Functions](functions.md)
+6. [Detailed Example](detailed.md)
+
+![Illustration](examples/layered.png "Illustration")

man/pages/matplotlib.md

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+# Incorporating Matplotlib Parameters

man/pages/parameters.md

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+# Parameters

man/pages/quickstart.md

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+# Quick Start