Merge branch '6-add-docs' into 'main'

Resolve "Add docs"

Closes #6

See merge request !16

.gitignore

@@ -71,6 +71,8 @@ instance/
 
 # Sphinx documentation
 docs/_build/
+docs/_static/
+docs/_templates/
 
 # PyBuilder
 .pybuilder/

GeoSpatialTools/distance_metrics.py

 """
+Distance Metrics
+----------------
 Functions for computing navigational information. Can be used to add
 navigational information to DataFrames.
 """

GeoSpatialTools/great_circle.py

-"""Class for a Great Circle object."""
+"""
+GreatCircle
+-----------
+Constructors and methods for interacting with GreatCircle objects, including
+comparisons between GreatCircle objects.
+"""
 
 import numpy as np
 

GeoSpatialTools/kdtree.py

 """
+KDTree
+------
 An implementation of KDTree using Haversine Distance for GeoSpatial analysis.
-Useful tool for quickly searching for nearest neighbours.
+Useful tool for quickly searching for nearest neighbours. The implementation is
+a K=2 or 2DTree as only 2 dimensions (longitude and latitude) are used.
+
+Haversine distances are used for comparisons, so that the spherical geometry
+of the earth is accounted for.
 """
 
 from . import Record

GeoSpatialTools/neighbours.py

-"""Functions for finding nearest neighbours using bisection."""
+"""
+Neighbours
+----------
+Functions for finding nearest neighbours using bisection.
+"""
 
 from numpy import argmin
 from bisect import bisect

GeoSpatialTools/octtree.py

+"""
+OctTree
+-------
+Constuctors for OctTree classes that can decrease the number of comparisons
+for detecting nearby records for example. This is an implementation that uses
+Haversine distances for comparisons between records for identification of
+neighbours.
+"""
+
 from dataclasses import dataclass
 from typing import List, Optional
 import datetime

GeoSpatialTools/quadtree.py

 """
+QuadTree
+--------
 Constuctors for QuadTree classes that can decrease the number of comparisons
-for detecting nearby records for example
+for detecting nearby records for example. This is an implementation that uses
+Haversine distances for comparisons between records for identification of
+neighbours.
 """
 
 from dataclasses import dataclass

docs/Makefile

+# 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)

docs/authors.rst

+=======
+Credits
+=======
+
+Development Lead
+----------------
+
+* Joseph T. Siddons <josidd@noc.ac.uk> `@josidd <git.noc.ac.uk/josidd>`_
+
+Contributoring Developers
+-------------------------
+
+* Richard C. Cornes <rcornes@noc.ac.uk> `@ricorne <git.noc.ac.uk/ricorne>`_

docs/conf.py

+"""Conf file for documentation builder"""
+# 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 -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+import os
+import sys
+
+sys.path.insert(0, os.path.abspath("../"))
+
+project = "GeoSpatialTools"
+copyright = "2024, National Oceanography Centre"
+author = "NOC Surface Processes"
+release = "0.10.0"
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.doctest",
+    "sphinx.ext.todo",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.ifconfig",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.githubpages",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.autosummary",
+    "sphinx_autodoc_typehints",
+]  # 'autoapi.extension',
+
+# autoapi_type = 'python'
+# autoapi_dirs = ['../../']
+# add_module_names = False
+# autoapi_keep_files = False
+# autodoc_typehints = "description"
+
+# autoapi_options = ['members', 'undoc-members', 'private-members']
+# autoapi_options = ['members', 'undoc-members', 'private-members',
+#                    'show-inheritance', 'show-module-summary',
+#                    'special-members', 'imported-members']
+# autoapi_ignore = ['*mymodel*', '*conf*', '*gather_stats_c99.py*']
+
+# 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"]
+
+pygments_style = "gruvbox-light"
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+# "sphinxawesome_theme" # 'sphinx_rtd_theme' # 'alabaster'
+html_theme = "sphinx_rtd_theme"
+# html_theme_options = {
+#     "rightsidebar": "true",
+#     "relbarbgcolor": "black"
+# }
+# 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 = {
+    "style_nav_header_background": "white",
+    "display_version": True,
+    "logo_only": False,
+    "collapse_navigation": False,
+}
+
+# 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']
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# The default sidebars (for documents that don't match any pattern) are
+# defined by theme itself.  Builtin themes are using these templates by
+# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
+# 'searchbox.html']``.
+#
+html_sidebars = {
+    "**": ["logo-text.html", "globaltoc.html", "searchbox.html"]
+    # '**': ['logo-text.html', 'globaltoc.html', 'localtoc.html',
+    #        'searchbox.html']
+}
+
+numfig = True
+math_numfig = True
+numfig_secnum_depth = 2
+math_eqref_format = "Eq. {number}"

docs/getting_started.rst

+===============
+Getting Started
+===============
+
+Installation
+============
+
+Via Pip
+-------
+
+GeoSpatialTools is not available on PyPI, however it can be installed via pip with the following command:
+
+.. code-block:: console
+
+   pip install git+ssh://git@git.noc.ac.uk/nocsurfaceprocesses/geospatialtools.git
+
+From Source
+-----------
+
+Alternatively, you can clone the repository and install using pip (or conda if preferred).
+
+.. code-block:: console
+
+   git clone git@git.noc.ac.uk/nocsurfaceprocesses/geospatialtools.git
+   cd geospatialtools
+   python -m venv venv
+   source venv/bin/activate
+   pip install -e .

docs/index.rst

+.. PyCOADS documentation master file, created by
+   sphinx-quickstart on Fri Jul  5 11:49:36 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to GeoSpatialTool's documentation!
+==========================================
+
+.. toctree::
+   :maxdepth: 4
+   :caption: Contents:
+    
+   introduction 
+   getting_started
+   authors
+   users_guide
+
+..
+.. Indices and tables
+.. ==================
+..
+.. * :ref:`genindex`
+.. * :ref:`modindex`
+.. * :ref:`search`

docs/introduction.rst

+============
+Introduction
+============
+
+Python library containing useful functions and classes for Spatial Analysis.
+
+Tested on Python versions 3.9 to 3.13.

docs/make.bat

+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+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/users_guide.rst

+===========
+Users Guide
+===========
+
+.. automodule:: GeoSpatialTools.neighbours
+   :members:
+
+.. automodule:: GeoSpatialTools.quadtree
+   :members:
+
+.. automodule:: GeoSpatialTools.octtree
+   :members:
+
+.. automodule:: GeoSpatialTools.kdtree
+   :members:
+
+.. automodule:: GeoSpatialTools.great_circle
+   :members:
+
+.. automodule:: GeoSpatialTools.distance_metrics
+   :members:

pyproject.toml

@@ -12,7 +12,7 @@ packages = ["GeoSpatialTools"]
 
 [project]
 name = "GeoSpatialTools"
-version = "0.9.0"
+version = "0.10.0"
 dependencies = [
     "numpy",
 ]
@@ -45,10 +45,18 @@ notebooks = [
 test = [
     "pytest",
 ]
+docs = [
+    "sphinx>=7.4.7",
+    "sphinx-autodoc-typehints>=2.3.0",
+    "sphinx-rtd-theme>=3.0.2",
+]
 all = [
     "ipykernel",
     "polars",
     "pytest",
+    "sphinx>=7.4.7",
+    "sphinx-autodoc-typehints>=2.3.0",
+    "sphinx-rtd-theme>=3.0.2",
 ]
 
 [tool.ruff]