Switch sphinx book theme

.gitignore

@@ -30,3 +30,14 @@ site/resources/_gen/*
 .idea
 ## vscode
 .vscode
+
+# Python
+*__pycache__*
+*egg-info/
+dist/
+build/
+.venv
+docs/_build
+
+# Mac
+.DS_Store

.readthedocs.yaml

@@ -0,0 +1,20 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+version: 2
+
+build:
+  os: ubuntu-20.04
+  tools:
+    python: "3.8"
+
+sphinx:
+  configuration: docs/conf.py
+
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs

README.md

@@ -1,64 +1,74 @@
 # Code Review During Development
 
-This repository is automatically built from [markdown](https://commonmark.org/) files by [Hugo](https://gohugo.io/) using [GitHub Actions](https://github.com/features/actions).
-This site uses the Hugo [LoveIt](https://hugoloveit.com/) theme.
+This repository is automatically built from [markdown](https://commonmark.org/) files by [Sphinx](https://www.sphinx-doc.org/) and the [MyST parser](https://myst-parser.readthedocs.io)
+using [ReadTheDocs](https://readthedocs.org/).
+This site uses the [Sphinx Book](https://sphinx-book-theme.readthedocs.io) theme.
 This site is available here: https://researchcodereviewcommunity.github.io/dev-review/
 
-The following branches in this repository are important: 
-- `main`: the markdown files corresponding to the current live version of the website
-- `gh-pages`: the static html site, automatically built by Hugo on new commits to `main` by [this script](.github/workflows/deploy.yml)
+The content of the website is contained in markdown files located in the `docs/` folder and are structured like so
+
+~~~text
+docs/
+├── flowcharts    <-- any mermaid flowcharts used in multiple locations
+│   └── high-level.md
+├── glossary.md    <-- a glossary of important terms for code review
+├── guidelines    <-- more general guidelines for code review apart from the more prescriptive recipes
+│   ├── approach.md
+│   └── points-to-check-for-reviewers.md
+├── index.md    <-- the landing page of the website
+├── recipes    <-- our suggested steps to follow during the code review process
+│   ├── explain_code_structure.md
+│   ├── find_a_reviewer.md
+│   ├── lonecoder.md
+│   ├── meet_and_agree_on_objectives.md
+│   ├── perform_code_review.md
+│   └── recipe_template.md
+└── refs-related.md    <-- references for material related to code review
+~~~
 
 ## Dependencies
-Install hugo extended dependency. 
-The "extended" hugo version is required to enable some features of [the LoveIt theme](https://hugoloveit.com/), such as mermaid diagrams.
-See commands to install hugo based on your Operating system.
-- macOS
+We use [`nox`](https://nox.thea.codes/en/stable/)
+as a task-runner to create development environments
+and to build the docs.
+There are many ways to install but we recommend the following:
+1. use a system package manager to install `pipx`
+2. use `pipx` to install `nox` so you can use it across projects
+3. finally ask `nox` to create a development environment
+
+- macOS/Linux
 ```
-brew install hugo
+brew install pipx  # or `python3 -m pip install --user pipx`
+pipx install nox
+nox -s dev
 ```
 - Windows
 ```
-choco install hugo -confirm
-```
-- GNU/Linux (Debian and Ubuntu)
+choco install pipx -confirm
+pipx install nox
+nox -s dev
 ```
-snap install hugo --channel=extended
-```
-
-See [documentation](https://gohugo.io/getting-started/installing/) for other options and furhter instructions. 
 
 ## Clone this repository
-After generating your SSH keys as suggested [here](https://docs.github.com/en/github/authenticating-to-github/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent). 
+After generating your SSH keys as suggested [here](https://docs.github.com/en/github/authenticating-to-github/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent).
 You can then clone the repository by typing (or copying) the following line in a terminal at your preferred path in your machine:
 ```
-git clone --recurse-submodules git@github.com:ResearchCodeReviewCommunity/dev-review.git
+git clone git@github.com:ResearchCodeReviewCommunity/dev-review.git
 ```
-If you've cloned this repo without the `--recurse-submodules` options, then you can initialise your local git submodule config with
 
-```
-git submodule init
-```
-and update it with
-```
-git submodule update
-```
+## Development
+To preview changes, you can build and serve the website locally.
 
-## Development 
-To preview changes locally, you can build and serve the website locally. 
-The `disableFastRender` option is required to render some features brought by the LoveIt theme, such as mermaid diagrams. 
 ```
-cd site/ && hugo serve --disableFastRender
+nox -s docs -- serve
 ```
 
 Open your favorite web-browser using the following url:
 ```
-Web Server is available at http://localhost:1313/dev-review/ (bind address 127.0.0.1)
-Press Ctrl+C to stop
+Serving HTTP on 0.0.0.0 port 8000 (http://0.0.0.0:8000/) ...
 ```
-See [Launching the website locally (hugoloveit.com)](https://hugoloveit.com/theme-documentation-basics/#25-launching-the-website-locally) for further information. 
 
 ## Contributing
-Commit changes to any other branch than `main` or `gh-pages`, open a pull request and request for reviews as common practice following the [pull request workflow with git](https://medium.com/@urna.hybesis/pull-request-workflow-with-git-6-steps-guide-3858e30b5fa4).  
-Once your changes are merged into `main` branch, the site will be automatically built and deployed and will be live roughly 1 minute later. 
+Commit changes to any other branch than `main`, open a pull request and request for reviews as common practice following the [pull request workflow with git](https://medium.com/@urna.hybesis/pull-request-workflow-with-git-6-steps-guide-3858e30b5fa4).  
+Once your changes are merged into `main` branch, the site will be automatically built and deployed and will be live roughly 1 minute later.
 
-:warning: **Do not commit directly to `main` or `gh-pages`.** :warning:
+:warning: **Do not commit directly to `main`.** :warning:

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     = .
+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/conf.py

@@ -0,0 +1,72 @@
+# 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, os.path.abspath('.'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'Code Review During Research'
+copyright = '2022, Research Code Review Community'
+author = 'Research Code Review Community'
+
+# The full version, including alpha/beta/rc tags
+release = '0.1.0'
+
+
+# -- 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 = [
+    'myst_parser',
+    'sphinxcontrib.mermaid',
+    'sphinx.ext.autodoc',
+    'sphinx.ext.coverage',
+    'sphinx_copybutton',
+    'sphinx.ext.doctest',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.todo',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.napoleon',
+    'sphinxext.opengraph',
+    'sphinx.ext.ifconfig',
+    'sphinx.ext.viewcode',
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+source_suffix = ['.rst', '.md']
+
+master_doc = 'index'
+
+# 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']
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'sphinx_book_theme'
+
+# 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']

site/content/flowcharts/high-level.md → docs/flowcharts/high-level.md

@@ -3,7 +3,7 @@
 Here's a high-level view of a workflow researchers can follow to make code
 review part of their development process.
 
-{{< mermaid >}}
+```{mermaid}
 %% codereview mermaid
 graph TD;
   Link(Click on orange boxes for more detail)
@@ -17,15 +17,15 @@ graph TD;
   H -- Yes --> D
   H -- No --> I([Finish])
 
-  click B "./#find-a-reviewer" "Find a reviewer"
-  click C "./#meet-and-agree-on-objectives" "Meet and agree on objectives"
-  click D,E,F,G "./#perform-code-review" "Perform Code Review"
-  click I "./#finish" "Finish"
+  click B "#find-a-reviewer" "Find a reviewer"
+  click C "#meet-and-agree-on-objectives" "Meet and agree on objectives"
+  click D,E,F,G "#perform-code-review" "Perform Code Review"
+  click I "#finish" "Finish"
 
   classDef default fill:#8EB6DE,stroke:#162D4D,stroke-width:2px,color:#162D4D;
   classDef linkedBox fill:#FABB00,stroke:#000,stroke-width:2px,color:#000;
   class Link,B,C,D,E,F,G,I linkedBox
-{{< /mermaid >}}
+```
 
 ### Find a reviewer
 

site/content/_index.md → docs/index.md

@@ -20,14 +20,14 @@ accessible by researchers at all levels, from research students to
 senior professors, whether they are new to programming or software
 engineering experts.**
 
-{{< mermaid >}}
+```{mermaid}
 graph TD;
   A(Initial reviewer-author meeting) --> B(Reviewer examines code)
   B --> C(Reviewer compiles suggestions)
   C --> D(Author and reviewer go over code)
   D --> E(Author improves code)
   E --> B
-{{< /mermaid >}}
+```
 
 ## Getting Started
 Please see [this page](flowcharts/high-level)

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