Merge branch 'WIP-doc' into WIP-update_deps

.gitignore

@@ -5,6 +5,7 @@ __pycache__/
 *.egg-info
 dist/
 build/
+docs/_build/
 # mac
 *DS_Store
 # dev

.readthedocs.yaml

@@ -0,0 +1,32 @@
+# .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: "3.12"
+    # 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:
+   - requirements: docs/requirements.txt

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 +1,74 @@
+# 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
+
+project = 'viASP'
+copyright = '2023, Stephan Zwicknagl, Luis Glaser'
+author = 'Stephan Zwicknagl, Luis Glaser'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    'nbsphinx',
+    'sphinx_rtd_theme',
+    # 'sphinx.ext.autodoc',
+    'sphinx.ext.napoleon',
+    'sphinx.ext.autosectionlabel',
+    'sphinx.ext.intersphinx'
+]
+# intersphinx_mapping = {'clorm': ('https://clorm.readthedocs.io/en/latest/', None)}
+
+# napoleon_google_docstring = False
+# napoleon_use_ivar = True
+napoleon_include_init_with_doc = False
+napoleon_use_admonition_for_examples = False
+napoleon_use_admonition_for_references = True
+
+# napoleon_use_param = True
+# napoleon_type_aliases = {
+#     "Factbase": "clingraph.orm.Factbase",
+#     "dict-like": ":term:`array-like`",
+# }
+
+# 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']
+
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#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_rtd_theme'
+
+html_theme_options = {
+    'canonical_url': '',
+#    'analytics_id': 'UA-XXXXXXX-1',  #  Provided by Google in your dashboard
+    'logo_only': False,
+    'display_version': True,
+    'display_version': True,
+    'prev_next_buttons_location': 'bottom',
+    'style_external_links': False,
+    # Toc options
+    'collapse_navigation': True,
+    'sticky_navigation': False,
+    'navigation_depth': 4,
+    'includehidden': True,
+    'titles_only': 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']

docs/index.rst

@@ -0,0 +1,33 @@
+=======================================
+viASP: An interactive ASP visualizer
+=======================================
+
+viASP generates interactive explanations of ASP programs and their stable models. A step-by-step break-down shows how the atoms of the stable models are derived.
+
+To use viASP the programs have to executed them using the clingo python API.
+
+..
+   comment viASP uses the clingo python API, a Flask server and a Dash frontend to generate the visualizations.
+
+.. image:: ./img/header.png
+
+viASP allows you to explore the visualization in a variety of ways:
+
+* Inspect iterations of recursive rules individually
+* Explain the derivation of symbols with arrows
+* Relax the constraints of unsatisfiable programs
+* Toggle parts of the program
+* Show the added symbols or all of them
+* Inspect a single model
+* Add #show statements on the fly
+* Search models, signatures and rules.
+
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   viasp/installation
+   viasp/usage
+   viasp/api
+   viasp/contributing

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 @@
+clingo>=5.5.2
+sphinx>=4.5.0
+sphinx-rtd-theme==0.5.2
+nbsphinx>=0.8.8
+jinja2>=3.0.3

docs/viasp/api.rst

@@ -0,0 +1,4 @@
+=================
+API Documentation
+=================
+

docs/viasp/contributing.rst

@@ -0,0 +1,35 @@
+=================
+Contributing
+=================
+
+Requirements
+============
+
+- `Git <https://git-scm.com>`_
+- `Node.JS <https://nodejs.org>`_
+- `Python <https://www.python.org>`_
+- A suitable browser
+
+
+Getting started
+===============
+
+1. Clone the repository using :code:`git clone https://github.com/stephanzwicknagl/viasp.git`
+2. Create and activate a conda environment
+3. Install pip :code:`conda install pip`
+4. Install viASP in editable mode :code:`pip install -e viasp -e viasp/backend -e viasp/frontend`
+
+Developing the backend
+======================
+
+1. Simply edit the code in the backend folder :code:`viasp/backend/src`
+2. Run viASP with a clingo program :code:`viasp encoding.lp`
+
+Developing the frontend
+=======================
+
+1. Move to frontend folder :code:`cd viasp/frontend`
+2. Run :code:`npm i` to install all needed dependencies
+3. Run :code:`npx webpack` to pack the javascript
+4. Run viASP with a clingo program :code:`viasp encoding.lp`
+

docs/viasp/installation.rst

@@ -0,0 +1,40 @@
+============
+Installation
+============
+
+Installing with pip 
+===================
+
+The python viasp package can be found `here <https://pypi.org/project/viasp/>`_.
+
+.. warning:: 
+    The latest version is currently not available on PyPI. Please install from source.
+
+.. code-block:: bash
+
+    $ pip install viasp
+
+
+Installing from source
+======================
+
+The project can currently only be installed from source. To do so, clone the repository at https://github.com/stephanzwicknagl/viasp and run the following commands in the root directory of the project:
+
+1. create a virtual environment
+
+.. code-block:: bash
+    
+    $ conda create -n viasp_env
+    $ conda activate viasp_env
+
+2. install pip
+
+.. code-block:: bash
+
+    $ conda install pip
+
+3. use pip to install the project
+
+.. code-block:: bash
+
+    $ pip install -q viasp viasp/backend viasp/frontend