Add files for readthedocs

.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: "3.8"
+    # 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/source/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     = 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 +1,4 @@
+problog
+torchvision
+torch
+furo

docs/source/conf.py

@@ -0,0 +1,55 @@
+# 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
+
+# -- Path setup --------------------------------------------------------------
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here.
+#import pathlib
+#import sys
+#sys.path.insert(0, pathlib.Path(__file__).parents[2].resolve().as_posix())
+
+import sys
+import os
+
+# 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.
+# sys.path.insert(0, os.path.abspath('.'))
+
+sys.path.insert(0, os.path.abspath("../../"))
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = 'DeepStochLog'
+copyright = '2023, KU Leuven, DTAI Research Group'
+author = 'KU Leuven, DTAI Research Group'
+# release = '1.0'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.todo",
+    "sphinx.ext.coverage",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.graphviz",
+    "sphinx.ext.ifconfig",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.inheritance_diagram",
+]
+
+templates_path = ['_templates']
+exclude_patterns = []
+
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'furo'
+html_static_path = ['_static']

docs/source/deepstochlog_api.rst

@@ -0,0 +1,103 @@
+API Documentation
+=================
+
+context
+----------
+.. automodule:: deepstochlog.context
+    :members:
+
+
+dataloader
+----------
+.. autoclass:: deepstochlog.dataloader.DataLoader
+    :members:
+
+
+dataset
+----------
+.. automodule:: deepstochlog.dataset
+    :members:
+
+
+inferences
+----------
+.. automodule:: deepstochlog.inferences
+    :members:
+
+
+logic
+----------
+.. automodule:: deepstochlog.logic
+    :members:
+
+
+model
+----------
+.. autoclass:: deepstochlog.model.DeepStochLogModel
+    :members:
+
+
+network
+----------
+.. autoclass:: deepstochlog.network.Network
+    :members:
+
+.. autoclass:: deepstochlog.network.NetworkStore
+    :members:
+
+
+networkevaluation
+-----------------
+.. autoclass:: deepstochlog.networkevaluation.RequiredEvaluation
+    :members:
+
+.. autoclass:: deepstochlog.networkevaluation.PreparedEvaluation
+    :members:
+
+
+nn_models
+-----------------
+.. autoclass:: deepstochlog.nn_models.TrainableProbability
+    :members:
+
+
+parser
+----------
+.. automodule:: deepstochlog.parser
+    :members:
+
+
+rule
+----------
+.. automodule:: deepstochlog.rule
+    :members:
+
+
+tabled_and_or_trees
+-------------------
+.. automodule:: deepstochlog.tabled_and_or_trees
+    :members:
+
+
+tabled_tree_builder
+-------------------
+.. automodule:: deepstochlog.tabled_tree_builder
+    :members:
+
+
+term
+-------------------
+.. automodule:: deepstochlog.term
+    :members:
+
+
+trainer
+-------------------
+.. automodule:: deepstochlog.trainer
+    :members:
+
+
+utils
+-------------------
+.. automodule:: deepstochlog.utils
+    :members:

docs/source/deepstochlog_download.rst

@@ -0,0 +1,46 @@
+Download
+===============================================
+
+Installation
+------------
+DeepStochLog requires SWI Prolog to run. Run the following commands to install:
+
+.. code-block:: bash
+
+    sudo apt-add-repository ppa:swi-prolog/stable
+    sudo apt-get update
+    sudo apt-get install swi-prolog
+
+To install DeepStochLog itself, run the following command:
+
+.. code-block:: bash
+
+    pip install deepstochlog
+
+
+Requirements
+------------
+
+DeepStochLog has the following requirements:
+
+* torch~=1.5.1
+* torchvision~=0.6.1
+* numpy~=1.18.1
+* pandas~=1.2.4
+* pyparsing~=2.4.7
+* dgl~=0.6.1
+
+
+Running the examples
+--------------------
+**Local dependencies**
+To see DeepStochLog in action, please first install SWI Prolog (as explained about), as well as all requirements.
+
+**Datasets**
+The datasets used in the tasks used to evaluate DeepStochLog can be found `here <https://github.com/ML-KULeuven/deepstochlog/releases/tag/0.0.1>`_.
+
+**Addition example**
+To see DeepStochLog in action, navigate to ``examples/addition`` and run ``addition.py`` in the `github repo <https://github.com/ML-KULeuven/deepstochlog/tree/main>`_.
+The neural definite clause grammar specification is provided in ``addition.pl``.
+The ``addition(N)`` predicate specifies/recognises that two handwritten digits *N1* and *N2* sum to *N*.
+The neural probability ``nn(number, [X], Y, digit)`` makes the neural network with name ``number`` (a MNIST classifier) label input image X with the digit Y.

docs/source/index.rst

@@ -0,0 +1,26 @@
+.. DeepStochLog documentation master file, created by
+   sphinx-quickstart on Tue Aug  8 11:25:48 2023.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+DeepStochLog
+=======================================
+Welcome to DeepStochLog's documentation.
+
+DeepStochLog is a neuro-symbolic framework that combines grammars, logic, probabilities and neural networks. By writing a DeepStochLog program, one can train a neural network with the given background knowledge. One can express symbolic information about subsymbolic data in DeepStochLog and help train neural networks more efficiently this way.
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   Install <deepstochlog_download>
+   Api <deepstochlog_api>
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`