Merge pull request #3 from RasmussenLab/docs

Add Sphinx template

.gitignore

@@ -15,6 +15,12 @@ build/
 dist/
 **.egg-info
 
+# Sphinx documenter creates these
+_build
+_static
+_templates
+/docs/reference
+
 # MacOS automatically creates these files
 .DS_Store
 

.readthedocs.yaml

@@ -0,0 +1,35 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+    # You can also specify other tool versions:
+    # nodejs: "19"
+    # rust: "1.64"
+    # golang: "1.19"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+
+# Optionally build your docs in additional formats such as PDF and ePub
+# formats:
+#    - pdf
+#    - epub
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs

README.md

@@ -8,3 +8,20 @@ Install package so that new code is picked up in a restared python interpreter:
 pip install -e .
 ```
 
+## TestPyPI
+
+Install vom [TestPyPI](https://test.pypi.org/project/rasmussenlab-mockup):
+
+```
+pip install -i https://test.pypi.org/simple/ rasmussenlab-mockup
+```
+
+> The package on PyPI is call `rasmussenlab-mockup` and not `mockup` as the package name is already taken. The import is still `import mockup`.
+
+## Readthedocs
+
+The documentation is build using readthedocs automatically. See 
+[project on Readthedocs](https://readthedocs.org/projects/rasmussenlab-python-package/).
+
+- make sure to enable build from PRs in the settings (advanded settings)
+- checkout configuration file: [`.readthedocs.yaml`](.readthedocs.yaml)

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/README.md

@@ -0,0 +1,31 @@
+# Docs creation
+
+In order to build the docs you need to 
+
+  1. install sphinx and additional support packages
+  2. build the package reference files
+  3. run sphinx to create a local html version
+
+The documentation is build using readthedocs automatically.
+
+Install the docs dependencies of the package (as speciefied in toml):
+
+```bash
+# in main folder
+pip install .[docs]
+```
+
+## Build docs using Sphinx command line tools
+
+Command to be run from `path/to/docs`, i.e. from within the `docs` package folder: 
+
+Options:
+  - `--separate` to build separate pages for each (sub-)module
+
+```bash	
+# pwd: docs
+# apidoc
+sphinx-apidoc --force --implicit-namespaces --module-first -o reference ../src/mockup
+# build docs
+sphinx-build -n -W --keep-going -b html ./ ./_build/
+```

docs/conf.py

@@ -0,0 +1,140 @@
+# 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
+from importlib import metadata
+
+
+# -- Project information -----------------------------------------------------
+
+project = "mockup"
+copyright = "2024, Jakob Nybo Nissen, Henry Webel"
+author = "Jakob Nybo Nissen, Henry Webel"
+PACKAGE_VERSION = metadata.version("rasmussenlab-mockup")
+version = PACKAGE_VERSION
+release = PACKAGE_VERSION
+
+
+# -- 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 = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autodoc.typehints",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.intersphinx",
+    "sphinx_new_tab_link",
+    "myst_nb",
+]
+
+#  https://myst-nb.readthedocs.io/en/latest/computation/execute.html
+nb_execution_mode = "auto"
+
+myst_enable_extensions = ["dollarmath", "amsmath"]
+
+# Plolty support through require javascript library
+# https://myst-nb.readthedocs.io/en/latest/render/interactive.html#plotly
+html_js_files = [
+    "https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"
+]
+
+# https://myst-nb.readthedocs.io/en/latest/configuration.html
+# Execution
+nb_execution_raise_on_error = True
+# Rendering
+nb_merge_streams = True
+
+# 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"]
+
+
+# Intersphinx options
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/3", None),
+    # "pandas": ("https://pandas.pydata.org/pandas-docs/stable/", None),
+    # "scikit-learn": ("https://scikit-learn.org/stable/", None),
+    # "matplotlib": ("https://matplotlib.org/stable/", None),
+}
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+# See:
+# https://github.com/executablebooks/MyST-NB/blob/master/docs/conf.py
+# html_title = ""
+html_theme = "sphinx_book_theme"
+# html_logo = "_static/logo-wide.svg"
+# html_favicon = "_static/logo-square.svg"
+html_theme_options = {
+    "github_url": "https://github.com/RasmussenLab/python_package",
+    "repository_url": "https://github.com/RasmussenLab/python_package",
+    "repository_branch": "main",
+    "home_page_in_toc": True,
+    "path_to_docs": "docs",
+    "show_navbar_depth": 1,
+    "use_edit_page_button": True,
+    "use_repository_button": True,
+    "use_download_button": True,
+    "launch_buttons": {
+        "colab_url": "https://colab.research.google.com"
+        #     "binderhub_url": "https://mybinder.org",
+        #     "notebook_interface": "jupyterlab",
+    },
+    "navigation_with_keys": 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"]
+
+
+# -- Setup for sphinx-apidoc -------------------------------------------------
+
+# Read the Docs doesn't support running arbitrary commands like tox.
+# sphinx-apidoc needs to be called manually if Sphinx is running there.
+# https://github.com/readthedocs/readthedocs.org/issues/1139
+
+if os.environ.get("READTHEDOCS") == "True":
+    from pathlib import Path
+
+    PROJECT_ROOT = Path(__file__).parent.parent
+    PACKAGE_ROOT = PROJECT_ROOT / "src" / "mockup"
+
+    def run_apidoc(_):
+        from sphinx.ext import apidoc
+
+        apidoc.main(
+            [
+                "--force",
+                "--implicit-namespaces",
+                "--module-first",
+                "--separate",
+                "-o",
+                str(PROJECT_ROOT / "docs" / "reference"),
+                str(PACKAGE_ROOT),
+                str(PACKAGE_ROOT / "*.c"),
+                str(PACKAGE_ROOT / "*.so"),
+            ]
+        )
+
+    def setup(app):
+        app.connect("builder-inited", run_apidoc)

docs/index.rst

@@ -0,0 +1,39 @@
+.. mockup documentation master file, created by
+   sphinx-quickstart on Mon Aug 28 14:09:15 2023.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+The mockup package
+==================================
+
+Mockup is a Python package with some simple example code.
+To get started, explore the :class:`mockup.Circle` class.
+
+
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Tutorial
+
+   tutorial/tutorial
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   reference/modules
+
+.. toctree::
+   :hidden:
+   :caption: Technical notes
+
+   README.md
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/tutorial/tutorial.ipynb

@@ -0,0 +1,83 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Mockup tutorial"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from mockup import mockup"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "mockup.add_one(-11)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "list(mockup.flatten_ints([[9, 11], [12], [4, 5]]))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "c2 = mockup.Circle.from_circumference(100)\n",
+    "round(c2.radius, 3)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "c2  # repr"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "pathways",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.11.4"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}