Add Sphinx docs generation (TopoToolbox#33)

This adds a basic framework for documentation using Sphinx. API documentation is automatically generated from the Python docstrings. A GitHub Actions workflow builds the documentation and pushes it to the repository's GitHub Pages site.

.github/workflows/docs.yaml

@@ -0,0 +1,47 @@
+name: docs
+
+on:
+  push:
+    branches: ["main"]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Install Pandoc
+        run: sudo apt-get install -y pandoc
+
+      - name: Install Python build dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r ${{ github.workspace }}/docs/requirements.txt
+          python3 -m pip install .[opensimplex]
+
+      - name: Build Sphinx documentation
+        working-directory: ${{ github.workspace }}/docs
+        run: |
+          make clean
+          make html
+
+      - name: Package artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: ${{ github.workspace }}/docs/_build/html
+
+  deploy:
+    needs: build
+    permissions:
+      pages: write
+      id-token: write
+
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

.gitignore

@@ -1,14 +1,14 @@
 # ignore .vscode settings:
 .vscode/
 
-# ignore example directory
-examples/perfectworld.tif
-
 # ignore dist directory
 dist/
 
-# ignore C++/C library
-src/topotoolbox/libtopotoolbox.so
-
 # ingnore tests pycache
-tests/__pycache__ 
+tests/__pycache__ 
+
+# ignore build docs
+docs/_build/*
+
+# ignore _autosummary
+docs/_autosummary/*

docs/Makefile

@@ -0,0 +1,31 @@
+# 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
+
+EXAMPLEDIR    = ../examples
+DOCEXAMPLEDIR = $(SOURCEDIR)/_examples
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Target to build HTML documentation, including copying/removing examples
+html: 
+	@echo "Copying examples directory..."
+	@cp -r $(EXAMPLEDIR) $(DOCEXAMPLEDIR)
+	@$(SPHINXBUILD) -M html "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@echo "Cleaning up examples directory..."
+	@rm -rf $(DOCEXAMPLEDIR)
+
+# 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/README.md

@@ -0,0 +1,11 @@
+# Generation Sphinx Documentation
+
+Before being able to generate the Docs, make sure to install all the python dependencies: `pip install -r requirements.txt` and pandoc. However, they can be ignored since they don't lead to any actual issues. To generate the Sphinx documentation HTML page, run the following commands (Linux):
+
+```bash
+cd /path/to/topotoolbox/docs/
+make clean
+make html
+```
+
+then open the `pytopotoolbox/docs/_build/html/index.html` file in your browser.

docs/api.rst

@@ -0,0 +1,8 @@
+API Documentation
+=================
+
+.. autosummary::
+   :toctree: _autosummary
+   :recursive:
+
+   topotoolbox

docs/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 -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+import os
+import sys
+
+import sphinx_book_theme
+
+import topotoolbox
+
+
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.autosummary',
+    'sphinx.ext.napoleon',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.todo',
+    'nbsphinx',
+]
+
+project = 'TopoToolbox'
+copyright = '2024, TopoToolbox Team'
+author = 'TopoToolbox Team'
+release = '3.0.1'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+templates_path = ['_templates']
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'sphinx_book_theme'
+html_static_path = ['_static']
+html_logo = 'logo.png'
+
+html_context = {
+    "default_mode": "light",
+}
+
+# -- Options for nbsphinx ----------------------------------------------------
+
+nbsphinx_allow_errors = True
+
+# -- Options for autodoc -----------------------------------------------------
+
+autodoc_default_options = {
+    'members': True,
+    'undoc-members': True,
+    'private-members': False,
+    'special-members': '__init__',
+    'inherited-members': True,
+    'show-inheritance': True,
+}
+
+autosummary_generate = True  # Enable autosummary to generate stub files

docs/examples.rst

@@ -0,0 +1,8 @@
+Examples
+========
+
+.. nbgallery::
+   /_examples/test_genGrid
+   /_examples/test_GridObject
+   /_examples/test_load_dem
+   /_examples/example_magic_funcs

docs/index.rst

@@ -0,0 +1,20 @@
+Welcome to TopoToolbox's python documentation!
+==============================================
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Contents:
+
+   Installing <installing>
+   Tutorial <tutorial>
+   Examples <examples>
+   API <api>
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/installing.rst

@@ -0,0 +1,80 @@
+How to install
+==============
+
+Generating/Installing distribution archives
+-------------------------------------------
+
+For any operating system, install the following:
+
+- **Python**
+- **pip**
+- **Git** (only when *building* the package yourself)
+
+Linux
+~~~~~
+
+**Installing from .whl file**
+
+Make sure to choose the appropriate file for your OS. For Linux, the file name should contain something like: `linux_x86_64`
+
+.. code-block:: bash
+
+    pip install dist_name.whl
+
+**Installing directly from the repository:**
+
+.. code-block:: bash
+
+    cd path/to/pytopotoolbox
+    pip install .
+
+**Generating distribution archives**
+
+.. code-block:: bash
+
+    cd path/to/pytopotoolbox
+    python3 -m pip install --upgrade build
+    python3 -m build
+
+Windows
+~~~~~~~
+
+**Installing from .whl file**
+
+Make sure to choose the appropriate file for your OS. For Windows, the file name should contain something like: `win_amd64`.
+
+.. code-block:: bash
+
+    pip install dist_name.whl
+
+**Installing directly from the repository:**
+
+Since there are C/C++ files that need to be compiled in order to build the package, there are a few extra steps to take.
+
+1. Install the `Developer Command Prompt for VS 2022 <https://visualstudio.microsoft.com/downloads/>`_.
+    - Scroll down to '*All Downloads*'
+    - Open '*Tools for Visual Studio*'
+    - Download '*Build Tools for Visual Studio 2022*'
+    - Install it while including the '*Desktop development with C++*' workload
+2. To ensure the compiler is working with 64-bit architecture, that is necessary for python, **open 'x64 Native Tools Command Prompt for VS 2022'** instead of the '*Developer Command Prompt*' that defaults to 32-bit architecture.
+3. In the newly opened terminal, run:
+
+    .. code-block:: bash
+
+        cd path\to\pytopotoolbox
+        pip install .
+
+**Generating distribution archives**
+
+Open the 'x64 Native Tools Command Prompt for VS 2022' Terminal and run:
+
+.. code-block:: bash
+
+    cd path\to\pytopotoolbox
+    py -m pip install --upgrade build
+    py -m build
+
+Mac
+~~~
+
+*work in progress*

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=.
+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/requirements.txt

@@ -0,0 +1,5 @@
+Sphinx==7.3.7
+sphinx-book-theme==1.1.2
+nbsphinx==0.9.4
+notebook==7.0.5
+jupyter==1.0.0

docs/tutorial.rst

@@ -0,0 +1,18 @@
+Tutorial
+========
+
+Introduction
+------------
+
+Installing
+----------
+
+First steps
+-----------
+
+Using the provided examples
+---------------------------
+
+Using API documentation
+-----------------------
+

examples/example_magic_funcs.ipynb

@@ -1,5 +1,12 @@
 {
  "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## example magic functions"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,

examples/test_GridObject.ipynb

@@ -1,5 +1,12 @@
 {
  "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## test GridObject"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,