Merge pull request #9 from Quinten-D/add_documentation

Add documentation

src/.gitignore

@@ -23,3 +23,5 @@ deepproblog/examples/CLUTRR/data/data_d83ecc3e/
 deepproblog/examples/CLUTRR/data/data_7c5b0e70/
 
 deepproblog/examples/MNIST/log/
+
+docs/source/.DS_Store

src/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)

src/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

src/docs/source/api.rst

@@ -0,0 +1,79 @@
+API Documentation
+=================
+
+embeddings
+----------
+.. automodule:: deepproblog.embeddings
+    :members:
+    :show-inheritance:
+
+tensor
+------
+.. automodule:: deepproblog.tensor
+    :members:
+    :show-inheritance:
+
+query
+-----
+.. automodule:: deepproblog.query
+    :members:
+    :show-inheritance:
+
+dataset
+-------
+.. automodule:: deepproblog.dataset
+    :members:
+    :show-inheritance:
+
+
+network
+-------
+.. automodule:: deepproblog.network
+    :members:
+    :show-inheritance:
+
+optimizer
+---------
+.. automodule:: deepproblog.optimizer
+    :members:
+    :show-inheritance:
+
+model
+-----
+.. autoclass:: deepproblog.model.Model
+    :members:
+
+train
+-----
+.. automodule:: deepproblog.train
+    :members:
+    :show-inheritance:
+
+evaluate
+--------
+.. automodule:: deepproblog.evaluate
+    :members:
+    :show-inheritance:
+
+solver
+-------
+.. automodule:: deepproblog.solver
+    :members:
+    :show-inheritance:
+
+engine
+------
+.. automodule:: deepproblog.engines.engine
+    :members:
+    :show-inheritance:
+
+semiring
+--------
+.. automodule:: deepproblog.semiring
+    :members:
+    :show-inheritance:
+
+arithmetic circuit
+------------------
+.. autoclass:: deepproblog.arithmetic_circuit.ArithmeticCircuit
+    :members:

src/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 = 'DeepProbLog'
+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']

src/docs/source/index.rst

@@ -0,0 +1,32 @@
+.. DeepProbLog 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.
+
+DeepProbLog
+=======================================
+Welcome to DeepProbLog's documentation.
+
+DeepProbLog is an extension of ProbLog that integrates Probabilistic Logic Programming with deep learning by introducing the neural predicate. The neural predicate represents probabilistic facts whose probabilites are parameterized by neural networks.
+
+.. raw:: html
+
+  <br />
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   install
+   problog
+   neural_predicate
+   api
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

src/docs/source/install.rst

@@ -0,0 +1,56 @@
+Installing DeepProbLog
+======================
+
+Installation
+------------
+DeepProbLog can easily be installed using the following command:
+Make sure the following packages are installed:
+
+.. code-block:: bash
+
+    pip install deepproblog
+
+Test
+----
+To make sure your installation works, install pytest
+
+.. code-block:: bash
+
+    pip install pytest
+
+and run
+
+.. code-block:: bash
+
+    python -m deepproblog test
+
+
+Requirements
+------------
+
+DeepProbLog has the following requirements:
+
+* Python > 3.9
+* [ProbLog](https://dtai.cs.kuleuven.be/problog/)
+* [PySDD](https://pysdd.readthedocs.io/en/latest/)
+* [PyTorch](https://pytorch.org/)
+* [TorchVision](https://pytorch.org/vision/stable/index.html)
+
+Approximate Inference
+---------------------
+To use Approximate Inference, we have the followign additional requirements
+
+* [PySwip](https://github.com/ML-KULeuven/pyswip)
+
+.. code-block::
+
+    pip install git+https://github.com/ML-KULeuven/pyswip
+
+* [SWI-Prolog < 9.0.0](https://www.swi-prolog.org/)
+
+The latter can be installed on Ubuntu with the following commands:
+
+.. code-block:: bash
+
+  sudo apt-add-repository ppa:swi-prolog/stable
+  sudo apt install swi-prolog=8.4* swi-prolog-nox=8.4* swi-prolog-x=8.4*

src/docs/source/neural_predicate.rst

@@ -0,0 +1,4 @@
+DeepProbLog and the Neural Predicate
+====================================
+
+Information about the neural predicate is available `here <https://dtai.cs.kuleuven.be/stories/post/robin-manhaeve/deepproblog/>`_.

src/docs/source/problog.rst

@@ -0,0 +1,4 @@
+ProbLog
+=======
+
+ProbLog documentation and tutorials are available `here <https://dtai.cs.kuleuven.be/problog/>`_.