MinorEmbedding · keksklauer4 · Nov 7, 2021 · Feb 13, 2022 · Feb 16, 2022 · Mar 30, 2022
diff --git a/.gitignore b/.gitignore
@@ -1,12 +1,13 @@
 # Own stuff
 build/
 Makefile
-.vscode/
 external/lemon/
 external/lemon.tar.gz
 
 # Python
 __pycache__
+out/
+logs/
 
 # Prerequisites
 *.d
@@ -40,3 +41,5 @@ __pycache__
 *.exe
 *.out
 *.app
+
+.vscode/*
diff --git a/.gitmodules b/.gitmodules
@@ -4,3 +4,6 @@
 [submodule "external/eigen"]
 	path = external/eigen
 	url = https://gitlab.com/libeigen/eigen.git
+[submodule "external/thread-pool"]
+	path = external/thread-pool
+	url = https://github.com/bshoshany/thread-pool
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -0,0 +1,26 @@
+# .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 version of Python and other tools you might need
+# Python 3.9 problem: see https://github.com/readthedocs/readthedocs.org/issues/7554#issuecomment-785114155
+build:
+  os: ubuntu-20.04
+  tools:
+    python: "3.9"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   configuration: python/docs/source/conf.py
+
+# If using Sphinx, optionally build your docs in additional formats such as PDF
+formats:
+   - pdf
+
+# Optionally declare the Python requirements required to build your docs
+# python:
+#    install:
+#    - requirements: docs/requirements.txt
diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -0,0 +1,6 @@
+{
+    "python.formatting.autopep8Args": [
+        "--max-line-length",
+        "100"
+    ]
+}
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -6,24 +6,31 @@ option(MAJORMINER_BUILD_TESTS "Build majorminer test executable" ON)
 enable_language(C CXX)
 set(CMAKE_CXX_STANDARD 20)
 set(CXX_STANDARD_REQUIRED ON)
-set(CMAKE_BUILD_TYPE Debug)
-set(MM_INCLUDE_LIBS external/oneTBB/include external/eigen build/external/lemon/ external/lemon/ src/)
+set(CMAKE_BUILD_TYPE Release)
+set(MM_INCLUDE_LIBS external/oneTBB/include external/eigen build/external/lemon/ external/lemon/ external/ src/)
 set(MM_LINK_LIBS TBB::tbb lemon)
 
 # neither build tests nor tbbmalloc in oneTBB
 set(TBB_TEST CACHE BOOL OFF)
 set(TBBMALLOC_BUILD CACHE BOOL OFF)
+set(TBB_DISABLE_HWLOC_AUTOMATIC_SEARCH CACHE BOOL OFF)
+
+set(LEMON_ENABLE_GLPK CACHE BOOL OFF)
+set(LEMON_ENABLE_ILOG CACHE BOOL OFF)
+set(LEMON_ENABLE_ILOG CACHE BOOL OFF)
+set(LEMON_ENABLE_COIN CACHE BOOL OFF)
+set(LEMON_ENABLE_SOPLEX CACHE BOOL OFF)
+
 
 # build NetworkSimplex, gtest and oneTBB
 add_subdirectory(external)
 
 
-
 if ( CMAKE_COMPILER_IS_GNUCC )
-    set(CMAKE_CXX_FLAGS  "${CMAKE_CXX_FLAGS} -Wall -Wextra -fdiagnostics-color=always")
+    set(CMAKE_CXX_FLAGS  "${CMAKE_CXX_FLAGS} -Wall -Wextra -Wpedantic -Werror -fdiagnostics-color=always")
 endif()
 if ( MSVC )
-    set(CMAKE_CXX_FLAGS  "${CMAKE_CXX_FLAGS} /W4")
+    set(CMAKE_CXX_FLAGS  "${CMAKE_CXX_FLAGS} /W4 /WX")
 endif()
 
 add_library(majorminer)

diff --git a/README.md b/README.md
@@ -1,19 +1,24 @@
-# majorminer
+# graph-embedder
+[![Documentation Status](https://readthedocs.org/projects/majorminer/badge/?version=latest)](https://majorminer.readthedocs.io/en/latest/?badge=latest)
+
+
 Testing a bunch of graph minor embedding heuristics and related techniques to improve the embedding of QUBOs.
 
+Our final results for the project can be found [here](doc/Studienarbeit.pdf).
+
 
-| :warning:    | This is a research repo, so APIs and algorithms might change frequently as were are trying out different ideas. Moreover, this means that the code is not production-ready. |
+
+| :warning:    | This is a research repo, so APIs and algorithms might change frequently as we are trying out different ideas. Moreover, this means that the code is not production-ready. |
 |---------------|:------------------------|
 
 | :point_up:    | We currently do not implement the same approaches in C++ and Python, but try out different ideas in different programming languages. Make sure to check out both the C++ and Python implementation. |
 |---------------|:------------------------|
 
+# Python
+All Python-related code and documentation can be found [in the Python folder](python/).
 
-
-<details>
-  <summary>C++</summary>
-
-# Build C++ library
+# C++
+## Build C++ library
 Note that in order to build, you have to clone the submodules as well. That is,
 if you have already cloned this repository, you should run ```git submodule update --init --recursive``` and find the submodules in ```external/```.
 In the case, you are about to clone the repository, just run ```git clone --recursive https://github.com/MinorEmbedding/majorminer.git```.
@@ -27,17 +32,10 @@ cmake .. -DMAJORMINER_BUILD_TESTS=[ON|OFF] # depending on whether you want to ru
 make
 ```
 
-# Libraries used in the C++-Project
+## Libraries used in the C++-Project
 #### [oneTBB](https://github.com/oneapi-src/oneTBB) (License: [Apache 2.0](https://choosealicense.com/licenses/apache-2.0/))
 #### [GoogleTest](https://github.com/google/googletest) (License: [BSD 3-Clause "New" or "Revised"](https://choosealicense.com/licenses/bsd-3-clause/))
 #### [LEMON](https://lemon.cs.elte.hu/trac/lemon) (License: [Boost Software License 1.0](https://choosealicense.com/licenses/bsl-1.0/))
 #### [Eigen](https://eigen.tuxfamily.org/index.php?title=Main_Page) (License: [MPL2](https://choosealicense.com/licenses/mpl-2.0/), disabled LGPL features.)
-</details>
-
+#### [thread-pool](https://github.com/bshoshany/thread-pool) (License: [MIT](https://choosealicense.com/licenses/mit/))
 
-
-<details>
-<summary>Python</summary>
-
-All Python-related code and documentation can be found [in the Python folder](python/).
-</details>
diff --git a/doc/Studienarbeit.pdf b/doc/Studienarbeit.pdf
diff --git a/external/thread-pool b/external/thread-pool
diff --git a/img/chimera_clique_12_95.svg b/img/chimera_clique_12_95.svg
diff --git a/img/chimera_clique_15_170.svg b/img/chimera_clique_15_170.svg
diff --git a/img/chimera_clique_18_211.svg b/img/chimera_clique_18_211.svg
diff --git a/img/chimera_clique_21_302.svg b/img/chimera_clique_21_302.svg
diff --git a/img/chimera_clique_25_421.svg b/img/chimera_clique_25_421.svg
diff --git a/img/chimera_clique_28_543.svg b/img/chimera_clique_28_543.svg
diff --git a/img/chimera_clique_31_653.svg b/img/chimera_clique_31_653.svg
diff --git a/img/chimera_clique_33_767.svg b/img/chimera_clique_33_767.svg
diff --git a/img/chimera_clique_34_799.svg b/img/chimera_clique_34_799.svg
diff --git a/img/chimera_clique_8_19.svg → img/chimera_clique_8_52.svg b/img/chimera_clique_8_19.svg → img/chimera_clique_8_52.svg
diff --git a/include/majorminer_lib.hpp b/include/majorminer_lib.hpp
@@ -0,0 +1,15 @@
+#ifndef __MAJORMINER_MAJORMINER_LIB_HPP_
+#define __MAJORMINER_MAJORMINER_LIB_HPP_
+
+#include <majorminer_types.hpp>
+
+#include <src/majorminer.hpp>
+
+#include <src/common/embedding_analyzer.hpp>
+#include <src/common/graph_info.hpp>
+#include <src/common/embedding_validator.hpp>
+#include <src/common/embedding_visualizer.hpp>
+#include <src/lmrp/lmrp_king_subgraph.hpp>
+#include <src/lmrp/lmrp_chimera_subgraph.hpp>
+
+#endif
diff --git a/python/Dockerfile b/python/Dockerfile
@@ -0,0 +1,12 @@
+FROM python:3.9.10
+WORKDIR /app
+
+RUN mkdir /app/out
+RUN mkdir /app/logs
+
+COPY requirements.txt .
+RUN pip install -r requirements.txt
+
+COPY ./src /app/src
+
+ENTRYPOINT [ "python", "-m", "src.solver.evolution" ]
diff --git a/python/README.md b/python/README.md
@@ -1,5 +1,8 @@
 # Python evolutionary embedding
 
+| :warning:    | This Readme is currently outdated. You can find the [documentation here](https://majorminer.readthedocs.io/)|
+|---------------|:------------------------|
+
 ## Usage
 Execute (from within the python folder):
 
@@ -16,4 +19,4 @@ In order to get **144 unique K4 embeddings on a single chimera cell**, execute (
 python -m src.solver.k4_results
 ```
 
-![144 unique K4 embeddings on a single chimera cell](./images/k4_embedding.svg)
+![144 unique K4 embeddings on a single chimera cell](./images/k4_embedding.svg)
diff --git a/python/docs/Majorminer Python class diagram.drawio b/python/docs/Majorminer Python class diagram.drawio
@@ -0,0 +1 @@
+<mxfile host="Electron" modified="2021-11-17T06:44:44.188Z" agent="5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) draw.io/14.5.1 Chrome/89.0.4389.82 Electron/12.0.1 Safari/537.36" etag="YLhbU3H9Y_1-47_qsndC" version="14.5.1" type="device"><diagram id="C5RBs43oDa-KdzZeNtuy" name="Page-1">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</diagram></mxfile>
diff --git a/python/docs/make.bat b/python/docs/make.bat
@@ -0,0 +1,37 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+if "%1" == "" goto help
+
+%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
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd
+
+pause
diff --git a/python/src/graphs/__init__.py → python/docs/source/_static/.gitkeep b/python/src/graphs/__init__.py → python/docs/source/_static/.gitkeep
diff --git a/python/docs/source/_static/embedding_solver_principle.png b/python/docs/source/_static/embedding_solver_principle.png
diff --git a/python/docs/source/_static/python_architecture.png b/python/docs/source/_static/python_architecture.png
diff --git a/python/docs/source/_templates/.gitkeep b/python/docs/source/_templates/.gitkeep
diff --git a/python/docs/source/api.rst b/python/docs/source/api.rst
@@ -0,0 +1,31 @@
+.. _api:
+
+API Reference
+=============
+
+
+Graph Module
+------------
+
+.. automodule:: src.graph.undirected_graph
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+.. automodule:: src.graph.embedding_graph
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+.. automodule:: src.graph.chimera_graph
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+More Modules
+------------
+
+.. note::
+
+   To come soon...
diff --git a/python/docs/source/conf.py b/python/docs/source/conf.py
@@ -0,0 +1,82 @@
+# Great tutorial for this setup
+# https://samnicholls.net/2016/06/15/how-to-sphinx-readthedocs/#fn-841-5
+
+# In order to build run the following commands:
+# luckily ReadTheDocs is doing this automatically for us
+
+# https://stackoverflow.com/a/46349694
+# cd docs/
+# sphinx-apidoc -o source/ ../src -f
+# and after that run:
+# ./make.bat html
+
+
+# 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
+
+# https://stackoverflow.com/a/44980548
+sys.path.insert(0, os.path.abspath('../..'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'majorminer'
+copyright = '2021, Dominic Plein, Julien Meier'
+author = 'Dominic Plein, Julien Meier'
+
+
+# -- 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.napoleon",
+    "sphinx.ext.autosummary"
+]
+
+# Napoleon setup
+napoleon_google_docstring = True  # defaults to True
+napoleon_use_ivar = True
+
+# Inheritance Diagram
+# https://www.sphinx-doc.org/en/master/usage/extensions/inheritance.html
+# inheritance_graph_attrs = dict(
+#     rankdir="TB",
+#     size='""'
+# )
+
+# 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 = []
+
+
+# -- 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'
+
+# 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']
diff --git a/python/docs/source/index.rst b/python/docs/source/index.rst
@@ -0,0 +1,25 @@
+.. majorminer documentation master file
+
+
+Welcome to the documentation of the majorminer research project realized by two students of the DHBW Karlsruhe. This documentation only includes the API for the Python code, NOT the C++ code.
+
+* :ref:`genindex`
+* :ref:`modindex`
+
+
+Overview
+========
+
+.. toctree::
+   :maxdepth: 2
+
+   overview
+
+
+API Reference
+=============
+
+.. toctree::
+   :maxdepth: 2
+
+   api
diff --git a/python/docs/source/modules.rst b/python/docs/source/modules.rst
@@ -0,0 +1,7 @@
+src
+===
+
+.. toctree::
+   :maxdepth: 4
+
+   src
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