Add basic website structure (#114)

* Add basic website structure

* Exclude built docs

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.github/workflows/docs_build_and_deploy.yml

@@ -0,0 +1,42 @@
+name: Build Sphinx docs and deploy to GitHub Pages
+
+# Generate the documentation on all merges to main, all pull requests, or by
+# manual workflow dispatch. The build job can be used as a CI check that the
+# docs still build successfully. The deploy job only runs when a tag is
+# pushed and actually moves the generated html to the gh-pages branch
+# (which triggers a GitHub pages deployment).
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - '*'
+  pull_request:
+  workflow_dispatch:
+
+
+jobs:
+  linting:
+    # scheduled workflows should not run on forks
+    if: (${{ github.event_name == 'schedule' }} && ${{ github.repository_owner == 'SainsburyWellcomeCentre' }} && ${{ github.ref == 'refs/heads/main' }}) || (${{ github.event_name != 'schedule' }})
+    runs-on: ubuntu-latest
+    steps:
+      - uses: neuroinformatics-unit/actions/lint@v2
+
+  build_sphinx_docs:
+    name: Build Sphinx Docs
+    runs-on: ubuntu-latest
+    steps:
+      - uses: neuroinformatics-unit/actions/build_sphinx_docs@v2
+
+  deploy_sphinx_docs:
+    name: Deploy Sphinx Docs
+    needs: build_sphinx_docs
+    permissions:
+      contents: write
+    if: github.event_name == 'push' && github.ref_type == 'tag'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: neuroinformatics-unit/actions/deploy_sphinx_docs@v2
+        with:
+          secret_input: ${{ secrets.GITHUB_TOKEN }}

.gitignore

@@ -62,3 +62,6 @@ coverage.xml
 
 # PyPI distribution / packages
 dist/
+
+# Sphinx documentation
+docs/build/

MANIFEST.in

@@ -10,3 +10,5 @@ recursive-include images *
 recursive-include documents *.cff
 recursive-include documents *.md
 recursive-include neuralplayground *.md
+
+recursive-exclude docs *

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/requirements.txt

@@ -0,0 +1,8 @@
+linkify-it-py
+myst-parser
+nbsphinx
+pydata-sphinx-theme
+setuptools-scm
+sphinx
+sphinx-autodoc-typehints
+sphinx-sitemap

docs/source/conf.py

@@ -0,0 +1,122 @@
+# 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 setuptools_scm
+
+# Used when building API docs, put the dependencies
+# of any class you are documenting here
+autodoc_mock_imports = []
+
+# Add the module path to sys.path here.
+# If the directory is relative to the documentation root,
+# use os.path.abspath to make it absolute, like shown here.
+sys.path.insert(0, os.path.abspath("../.."))
+
+project = "NeuralPlayground"
+copyright = "2024, University College London"
+author = "University College London"
+try:
+    release = setuptools_scm.get_version(root="../..", relative_to=__file__)
+except LookupError:
+    # if git is not initialised, still allow local build
+    # with a dummy version
+    release = "0.0.0"
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    "sphinx.ext.napoleon",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.githubpages",
+    "sphinx_autodoc_typehints",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.intersphinx",
+    "sphinx_sitemap",
+    "myst_parser",
+    "nbsphinx",
+]
+
+# Configure the myst parser to enable cool markdown features
+# See https://sphinx-design.readthedocs.io
+myst_enable_extensions = [
+    "amsmath",
+    "colon_fence",
+    "deflist",
+    "dollarmath",
+    "fieldlist",
+    "html_admonition",
+    "html_image",
+    "linkify",
+    "replacements",
+    "smartquotes",
+    "strikethrough",
+    "substitution",
+    "tasklist",
+]
+# Automatically add anchors to markdown headings
+myst_heading_anchors = 3
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ["_templates"]
+
+# Automatically generate stub pages for API
+autosummary_generate = True
+autodoc_default_flags = ["members", "inherited-members"]
+
+# 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 = [
+    "**.ipynb_checkpoints",
+    # to ensure that include files (partial pages) aren't built, exclude them
+    # https://github.com/sphinx-doc/sphinx/issues/1965#issuecomment-124732907
+    "**/includes/**",
+]
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+html_theme = "pydata_sphinx_theme"
+html_title = "NeuralPlayground"
+
+# Customize the theme
+html_theme_options = {
+    "icon_links": [
+        {
+            # Label for this link
+            "name": "GitHub",
+            # URL where the link will redirect
+            "url": "https://github.com/SainsburyWellcomeCentre/NeuralPlayground",  # required
+            # Icon class (if "type": "fontawesome"),
+            # or path to local image (if "type": "local")
+            "icon": "fa-brands fa-github",
+            # The type of image to be used (see below for details)
+            "type": "fontawesome",
+        }
+    ],
+    "logo": {
+        "text": f"{project} v{release}",
+    },
+}
+
+# Redirect the webpage to another URL
+# Sphinx will create the appropriate CNAME file in the build directory
+# The default is the URL of the GitHub pages
+# https://www.sphinx-doc.org/en/master/usage/extensions/githubpages.html
+github_user = "SainsburyWellcomeCentre"
+html_baseurl = f"https://{github_user}.github.io/{project}"
+sitemap_url_scheme = "{link}"
+
+# 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']

docs/source/getting_started.md

@@ -0,0 +1,11 @@
+# Getting started
+
+Here you may demonstrate the basic functionalities your package.
+
+You can include code snippets using the usual Markdown syntax:
+
+```python
+from my_package import my_function
+
+result = my_function()
+```

docs/source/index.rst

@@ -0,0 +1,46 @@
+.. NeuralPlayground documentation master file, created by
+   sphinx-quickstart on Fri Dec  9 14:12:42 2022.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to NeuralPlayground's documentation!
+=========================================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   getting_started
+   api_index
+
+By default the documentation includes the following sections:
+
+* Getting started. Here you could describe the basic functionalities of your package. To modify this page, edit the file ``docs/source/getting_started.md``.
+* API: here you can find the auto-generated documentation of your package, which is based on the docstrings in your code. To modify which modules/classes/functions are included in the API documentation, edit the file ``docs/source/api_index.rst``.
+
+You can create additional sections with narrative documentation,
+by adding new ``.md`` or ``.rst`` files to the ``docs/source`` folder.
+These files should start with a level-1 (H1) header,
+which will be used as the section title. Sub-sections can be created
+with lower-level headers (H2, H3, etc.) within the same file.
+
+To include a section in the rendered documentation,
+add it to the ``toctree`` directive in this (``docs/source/index.rst``) file.
+
+For example, you could create a ``docs/source/installation.md`` file
+and add it to the ``toctree`` like this:
+
+.. code-block:: rst
+
+   .. toctree::
+      :maxdepth: 2
+      :caption: Contents:
+
+      getting_started
+      installation
+      api_index
+
+Index & Search
+--------------
+* :ref:`genindex`
+* :ref:`search`