Merge branch 'master' into feature/migrate_views_to_basetreemodel

.github/workflows/macOS.yml

@@ -89,12 +89,18 @@ jobs:
         run: |
           mkdir -p build
           cd build
-          export PATH="/usr/local/opt/qt@5/bin:$PATH"
-          ls ..
-          cmake -G Ninja .. -DQt5_DIR=/usr/local/opt/qt@5/lib/cmake -DCMAKE_BUILD_TYPE=Debug -DBUILD_ALL_PLUGINS=ON -DBUILD_TESTS=ON -DPL_GUI=ON -DCMAKE_C_COMPILER=/usr/local/opt/llvm@14/bin/clang -DCMAKE_CXX_COMPILER=/usr/local/opt/llvm@14/bin/clang++
+          export PATH="$(brew --prefix qt@5)/bin:$PATH"
+          brew ls llvm@14
+          brew --prefix llvm@14
+          ls -l /usr/local
+          ls -l /opt/homebrew/opt
+          ls -l /opt/homebrew/opt/llvm@14
+          ls -l /opt/homebrew/opt/llvm@14/bin
+          ls -l /opt/homebrew/opt/llvm@14/bin/clang
+          cmake -G Ninja .. -DQt5_DIR="$(brew --prefix qt@5)/lib/cmake" -DCMAKE_BUILD_TYPE=Debug -DBUILD_ALL_PLUGINS=ON -DBUILD_TESTS=ON -DPL_GUI=ON -DCMAKE_C_COMPILER=$(brew --prefix llvm@14)/bin/clang -DCMAKE_CXX_COMPILER=$(brew --prefix llvm@14)/bin/clang++
         env:
-          LDFLAGS: "-L/usr/local/opt/qt@5/lib -L/usr/local/opt/llvm@14/lib -Wl,-rpath,/usr/local/opt/llvm@14/lib"
-          CPPFLAGS: "-I/usr/local/opt/llvm@14/include"
+          LDFLAGS: "-L$(brew --prefix qt@5)/lib -L$(brew --prefix llvm@14)/lib -Wl,-rpath,$(brew --prefix llvm@14)/lib"
+          CPPFLAGS: "-I$(brew --prefix llvm@14)/include"
           HAL_BASE_PATH: ${{runner.workspace}}/hal/build
           CCACHE_DIR: ${{runner.workspace}}/.ccache
           CCACHE_COMPRESS: true
@@ -107,12 +113,12 @@ jobs:
         # Execute the build.  You can specify a specific target with "--target <NAME>"
         run: |
           cd build
-          export PATH="/usr/local/opt/qt/bin:$PATH"
+          export PATH="$(brew --prefix qt@5)/bin:$PATH"
           export BUILD_TYPE=Debug
           cmake --build . --target all --clean-first --config $BUILD_TYPE
         env:
-          LDFLAGS: "-L/usr/local/opt/qt@5/lib -L/usr/local/opt/llvm@14/lib -Wl,-rpath,/usr/local/opt/llvm@14/lib"
-          CPPFLAGS: "-I/usr/local/opt/llvm@14/include"
+          LDFLAGS: "-L$(brew --prefix qt@5)/lib -L$(brew --prefix llvm@14)/lib -Wl,-rpath,$(brew --prefix llvm@14)/lib"
+          CPPFLAGS: "-I$(brew --prefix llvm@14)/include"
           HAL_BASE_PATH: ${{runner.workspace}}/hal/build
           CCACHE_DIR: ${{runner.workspace}}/.ccache
           CCACHE_COMPRESS: true
@@ -133,8 +139,8 @@ jobs:
         #  ninja -v hal_coverage
         # bash <(curl -s https://codecov.io/bash) -f hal_coverage.info.cleaned || echo "Codecov did not collect coverage reports"
         env:
-          LDFLAGS: "-L/usr/local/opt/qt@5/lib -L/usr/local/opt/llvm@14/lib -Wl,-rpath,/usr/local/opt/llvm@14/lib"
-          CPPFLAGS: "-I/usr/local/opt/llvm@14/include"
+          LDFLAGS: "-L$(brew --prefix qt@5)/lib -L$(brew --prefix llvm@14)/lib -Wl,-rpath,$(brew --prefix llvm@14)/lib"
+          CPPFLAGS: "-I$(brew --prefix llvm@14)/include"
           HAL_BASE_PATH: ${{runner.workspace}}/hal/build
           CCACHE_DIR: ${{runner.workspace}}/.ccache
           CCACHE_COMPRESS: true

.github/workflows/ubuntu20.04.yml → .github/workflows/ubuntu24.04.yml

@@ -1,4 +1,4 @@
-name: Ubuntu 20.04
+name: Ubuntu 24.04
 
 on:
   push:
@@ -7,13 +7,13 @@ on:
 #      - v*
 
 jobs:
-  build_ubuntu_20_04:
-    name:  Build and Test on Ubuntu 20.04
+  build_ubuntu_24_04:
+    name: Build and Test on Ubuntu 24.04
 
     strategy:
       matrix:
-        #        runs-on: [ ubuntu-20.04, macOS-latest]
-        runs-on: [ ubuntu-20.04 ]
+        #        runs-on: [ ubuntu-22.04, macOS-latest]
+        runs-on: [ ubuntu-24.04 ]
       fail-fast: false
 
     runs-on: ${{ matrix.runs-on }}

CHANGELOG.md

@@ -2,6 +2,7 @@
 All notable changes to this project will be documented in this file.
 
 ## [Unreleased]
+* **WARNING:** this release breaks the API of the `graph_algorithm` plugin
 * refactored module widget
   * added option to show gate content for each module
   * added option to show interior nets for each module
@@ -19,6 +20,11 @@ All notable changes to this project will be documented in this file.
   * boosted performance by using classes with faster memory access
   * removed layouter code used prior to version 3.1.0 - thus removing the setting option to use that code
   * added setting option to dump junction layout input data for experts to debug in case of layout errors
+* refactored `graph_algorithm` plugin
+  * updated the igraph dependency shipped with HAL
+  * changed the API and made everything accessible via Python
+  * graph corresponding to a netlist is now encapsulated within an `NetlistGraph` object that allows easy interaction with the graph
+  * added new functions for computing neighborhoods, shortest paths, subgraphs, and (strongly) connected components
 * module pins
   * added qualifier for `pin_changed` core events telling receiver details about the recent modification
   * added event scope and stacking classes so that `pin_changed` events can be collected and prioritized

CMakeLists.txt

@@ -62,6 +62,10 @@ option(HAL_VERSION_MAJOR "Pass major version via cmake options" "")
 option(HAL_VERSION_MINOR "Pass minor version via cmake options" "")
 option(HAL_VERSION_PATCH "Pass patch version via cmake options" "")
 option(USE_LIBCXX "Force the use of LIBCXX for e.g. gcc" FALSE)
+option(USE_VENDORED_PYBIND11 "Use vendored 'pybind11' Python library" ON)
+option(USE_VENDORED_SPDLOG "Use vendored 'spdlog' library" ON)
+option(USE_VENDORED_QUAZIP "Use vendored 'quazip' library" ON)
+option(USE_VENDORED_IGRAPH "Use vendored 'igraph' library" ON)
 option(BUILD_ALL_PLUGINS "Build all available plugins" OFF)
 option(BUILD_TESTS "Enable test builds" OFF)
 option(BUILD_COVERAGE "Enable code coverage build" OFF)
@@ -325,8 +329,12 @@ install(FILES tools/genversion.py
     GROUP_EXECUTE
     WORLD_READ
     WORLD_EXECUTE)
-install(DIRECTORY ${CMAKE_SOURCE_DIR}/deps/pybind11 DESTINATION ${HAL_CMAKECONFIG_INSTALL_DIR})
-install(DIRECTORY ${CMAKE_SOURCE_DIR}/deps/spdlog-${spdlog_VERSION} DESTINATION ${HAL_CMAKECONFIG_INSTALL_DIR})
+if(USE_VENDORED_PYBIND11)
+    install(DIRECTORY ${CMAKE_SOURCE_DIR}/deps/pybind11 DESTINATION ${HAL_CMAKECONFIG_INSTALL_DIR})
+endif()
+if(USE_VENDORED_SPDLOG)
+    install(DIRECTORY ${CMAKE_SOURCE_DIR}/deps/spdlog-${spdlog_VERSION} DESTINATION ${HAL_CMAKECONFIG_INSTALL_DIR})
+endif()
 install(DIRECTORY ${CMAKE_SOURCE_DIR}/deps/subprocess DESTINATION ${HAL_CMAKECONFIG_INSTALL_DIR})
 
 

Dockerfile

@@ -14,7 +14,7 @@ RUN apt-get update -y && \
     apt-get install -y lsb-release
 
 COPY . .
-RUN ./install_dependencies.sh
+RUN HAL_DOCKER=1 ./install_dependencies.sh
 
 RUN mkdir build
 WORKDIR ${hal_path}/build/

README.md

@@ -30,7 +30,7 @@ We want HAL to enable a common baseline for researchers and analysts to improve
 - **Stability** is ensured via a rich test suite
 
 HAL is actively developed by the Embedded Security group of the [Max Planck Institute for Security and Privacy](https://www.mpi-sp.org).
-Apart from multiple research projects, it is also used in our university lecture [Introduction to Hardware Reverse Engineering](https://www.ei.ruhr-uni-bochum.de/studium/lehrveranstaltungen/832/).
+Apart from multiple research projects, it is also used in our university lecture "Einführung ins Hardware Reverse Engineering" (Introduction to Hardware Reverse Engineering) at Ruhr University Bochum (RUB).
 
 Note that we also have a set of **modern** state-of-the-art benchmark circuits for the evaluation of netlist reverse engineering techniques available in a seperate [repository](https://github.com/emsec/hal-benchmarks).
 
@@ -54,9 +54,6 @@ This repository contains a selection of curated plugins:
 ## Documentation
 A comprehensive documentation of HAL's features from a user perspective is available in our [Wiki](https://github.com/emsec/hal/wiki). In addition, we provide a full [C++ API](https://emsec.github.io/hal/doc/) and [Python API](https://emsec.github.io/hal/pydoc/) documentation.
 
-## Slack, Contact and Support
-For all kinds of inquiries, please contact us using our dedicated e-mail address: [[email protected]](mailto:[email protected]).
-
 <a name="build-instructions"></a>
 # Build Instructions 
 

cmake/detect_dependencies.cmake

@@ -153,20 +153,33 @@ find_package(pybind11 2.7 CONFIG)
 if(${pybind11_FOUND})
     message(VERBOSE "Found pybind11 v${pybind11_VERSION}: ${pybind11_INCLUDE_DIRS}")
     message(VERBOSE "Found pybind11 >= 2.7")
-else()
+elseif(USE_VENDORED_PYBIND11)
     message(STATUS "pybind11 >= 2.7 not found, will build our provided version")
     add_subdirectory(deps/pybind11)
+else()
+    message(FATAL_ERROR "pybind11 >= 2.7 not found and USE_VENDORED_PYBIND11 is OFF")
 endif()
 
 # ###############################
 # ####   spdlog
 # ###############################
-message(STATUS "using spdlog from deps")
-set(spdlog_VERSION 1.9.2)
-add_library(spdlog::spdlog INTERFACE IMPORTED)
-set_target_properties(spdlog::spdlog PROPERTIES
-    INTERFACE_INCLUDE_DIRECTORIES "${CMAKE_SOURCE_DIR}/deps/spdlog-${spdlog_VERSION}/include"
-)
+
+if(USE_VENDORED_SPDLOG)
+    message(STATUS "using spdlog from deps")
+    set(spdlog_VERSION 1.9.2)
+    add_library(spdlog::spdlog INTERFACE IMPORTED)
+    set_target_properties(spdlog::spdlog PROPERTIES
+        INTERFACE_INCLUDE_DIRECTORIES "${CMAKE_SOURCE_DIR}/deps/spdlog-${spdlog_VERSION}/include"
+    )
+else()
+    find_package(spdlog REQUIRED)
+    if(spdlog_FOUND)
+        get_target_property(SPDLOG_HEADERS_DIR spdlog::spdlog INTERFACE_INCLUDE_DIRECTORIES)
+        message(STATUS "Using system's spdlog headers at ${SPDLOG_HEADERS_DIR}")
+    else()
+        message(FATAL_ERROR "spdlog was not found and USE_VENDORED_SPDLOG is OFF")
+    endif()
+endif()
 
 # ###############################
 # ####   subprocess
@@ -259,7 +272,15 @@ endif(Z3_FOUND)
 # ###############################
 # ####   igraph
 # ###############################
-set(IGRAPH_SUBDIR "${CMAKE_SOURCE_DIR}/deps/igraph-0.9.10")
-add_subdirectory(${IGRAPH_SUBDIR})
-get_directory_property(IGRAPH_INCLUDES DIRECTORY ${IGRAPH_SUBDIR} DEFINITION IGRAPH_INCLUDES)
-get_directory_property(IGRAPH_LIB DIRECTORY ${IGRAPH_SUBDIR} DEFINITION IGRAPH_LIB)
+if(USE_VENDORED_IGRAPH)
+    set(IGRAPH_SUBDIR "${CMAKE_SOURCE_DIR}/deps/igraph-0.10.x")
+    add_subdirectory(${IGRAPH_SUBDIR})
+    get_directory_property(igraph_INCLUDES DIRECTORY ${IGRAPH_SUBDIR} DEFINITION IGRAPH_INCLUDES)
+    get_directory_property(igraph_LIBRARIES      DIRECTORY ${IGRAPH_SUBDIR} DEFINITION IGRAPH_LIB)
+    message(STATUS "Using igraph from ${IGRAPH_SUBDIR}")
+else()
+    find_package(igraph REQUIRED)
+    get_target_property(igraph_LIBRARIES igraph::igraph IMPORTED_LOCATION_RELEASE)
+    get_target_property(igraph_INCLUDES igraph::igraph INTERFACE_INCLUDE_DIRECTORIES)
+    message(STATUS "Using system's igraph from ${igraph_LIBRARIES}")
+endif()

deps/igraph-0.9.10/CMakeLists.txt → deps/igraph-0.10.x/CMakeLists.txt

@@ -8,15 +8,20 @@ set (IGRAPH_INCLUDES  "${IGRAPH_INSTALL}/include")
 set (IGRAPH_LIB       "${IGRAPH_INSTALL}/lib/libigraph${CMAKE_SHARED_LIBRARY_SUFFIX}")
 set (HAVE_IGRAPH TRUE)
 
-message("-- IGRAPH version 0.9.10 : download and build libigraph${CMAKE_SHARED_LIBRARY_SUFFIX} in ${IGRAPH_BASE}")
+message("-- IGRAPH version 0.10.12 : download and build libigraph${CMAKE_SHARED_LIBRARY_SUFFIX} in ${IGRAPH_BASE}")
 
-ExternalProject_Add(igraph_0_9
+#Avoid warning about DOWNLOAD_EXTRACT_TIMESTAMP in CMake 3.24
+if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.24.0")
+    cmake_policy(SET CMP0135 NEW)
+endif()
+
+ExternalProject_Add(igraph_0_10
   PREFIX "${IGRAPH_INSTALL}"
-  URL "https://github.com/igraph/igraph/releases/download/0.9.10/igraph-0.9.10.tar.gz"
+  URL "https://github.com/igraph/igraph/releases/download/0.10.12/igraph-0.10.12.tar.gz"
   SOURCE_DIR "${IGRAPH_DOWNLOAD}"
-  CMAKE_ARGS "-DCMAKE_INSTALL_PREFIX=${IGRAPH_INSTALL}" "-DBUILD_SHARED_LIBS=ON" "-DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}" "-Wno-deprecated" "-DIGRAPH_VERSION=0.9.10"
+  CMAKE_ARGS "-DCMAKE_INSTALL_PREFIX=${IGRAPH_INSTALL}" "-DBUILD_SHARED_LIBS=ON" "-DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}" "-Wno-deprecated" "-DIGRAPH_VERSION=0.10.12"
   BINARY_DIR "${IGRAPH_BUILD}"
-  PATCH_COMMAND patch -p2 -u -i ${CMAKE_CURRENT_SOURCE_DIR}/patch.txt
+  PATCH_COMMAND echo "No patch for igraph-0.10.x required"
   INSTALL_DIR "${IGRAPH_INSTALL}"
   BUILD_BYPRODUCTS "${IGRAPH_LIB}"
   )
@@ -29,7 +34,7 @@ set_target_properties ( igraph::igraph PROPERTIES
   INTERFACE_INCLUDE_DIRECTORIES ${IGRAPH_INCLUDES}
 )
 
-add_dependencies ( igraph::igraph igraph_0_9 )
+add_dependencies ( igraph::igraph igraph_0_10 )
 
 mark_as_advanced (
   HAVE_IGRAPH

include/hal_core/netlist/pins/pin_group.h

@@ -252,7 +252,7 @@ namespace hal
          * @param[in] pin - The pin.
          * @returns The index of the pin on success, an error message otherwise.
          */
-        Result<u32> get_index(const T* pin) const
+        Result<i32> get_index(const T* pin) const
         {
             if (pin == nullptr)
             {

install_dependencies.sh

@@ -4,7 +4,7 @@ platform='unknown'
 unamestr=$(uname)
 distribution='unknown'
 release='unknown'
-if [[ -f "/.dockerenv" ]]; then
+if [[ "${HAL_DOCKER:-0}" == "1" ]]; then
    platform='docker'
    distribution=$(lsb_release -is)
    release=$(lsb_release -rs)

plugins/graph_algorithm/CMakeLists.txt

@@ -1,4 +1,4 @@
-option(PL_GRAPH_ALGORITHM "PL_GRAPH_ALGORITHM" OFF)
+option(PL_GRAPH_ALGORITHM "PL_GRAPH_ALGORITHM" ON)
 
 if(PL_GRAPH_ALGORITHM OR BUILD_ALL_PLUGINS)
     file(GLOB_RECURSE GRAPH_ALGORITHM_INC ${CMAKE_CURRENT_SOURCE_DIR}/include/*.h)
@@ -10,8 +10,10 @@ if(PL_GRAPH_ALGORITHM OR BUILD_ALL_PLUGINS)
         PYDOC SPHINX_DOC_INDEX_FILE ${CMAKE_CURRENT_SOURCE_DIR}/documentation/graph_algorithm.rst
         HEADER ${GRAPH_ALGORITHM_INC}
         SOURCES ${GRAPH_ALGORITHM_SRC} ${GRAPH_ALGORITHM_PYTHON_SRC}
-        INCLUDES PUBLIC $<BUILD_INTERFACE:${IGRAPH_INCLUDES}>
-        LINK_LIBRARIES PUBLIC ${IGRAPH_LIB}
+        INCLUDES PUBLIC $<BUILD_INTERFACE:${igraph_INCLUDES}>
+        LINK_LIBRARIES PUBLIC ${igraph_LIBRARIES}
     )
 
+add_dependencies(graph_algorithm igraph_0_10)
+
 endif()

plugins/graph_algorithm/documentation/graph_algorithm.rst

@@ -1,5 +1,5 @@
 Graph Algorithms
 ==========================
 
-.. autoclass:: graph_algorithm.GraphAlgorithmPlugin
-   :members:
+.. automodule:: graph_algorithm
+    :members:

plugins/graph_algorithm/include/graph_algorithm/algorithms/components.h

@@ -0,0 +1,51 @@
+// MIT License
+//
+// Copyright (c) 2019 Ruhr University Bochum, Chair for Embedded Security. All Rights reserved.
+// Copyright (c) 2019 Marc Fyrbiak, Sebastian Wallat, Max Hoffmann ("ORIGINAL AUTHORS"). All rights reserved.
+// Copyright (c) 2021 Max Planck Institute for Security and Privacy. All Rights reserved.
+// Copyright (c) 2021 Jörn Langheinrich, Julian Speith, Nils Albartus, René Walendy, Simon Klix ("ORIGINAL AUTHORS"). All Rights reserved.
+//
+// Permission is hereby granted, free of charge, to any person obtaining a copy
+// of this software and associated documentation files (the "Software"), to deal
+// in the Software without restriction, including without limitation the rights
+// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+// copies of the Software, and to permit persons to whom the Software is
+// furnished to do so, subject to the following conditions:
+//
+// The above copyright notice and this permission notice shall be included in all
+// copies or substantial portions of the Software.
+//
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+// SOFTWARE.
+
+#pragma once
+
+#include "hal_core/defines.h"
+#include "hal_core/utilities/result.h"
+
+#include <igraph/igraph.h>
+#include <set>
+
+namespace hal
+{
+    namespace graph_algorithm
+    {
+        class NetlistGraph;
+
+        /** 
+         * Compute the (strongly) connected components of the specified graph.
+         * Returns each connected component as a vector of vertices in the netlist graph.
+         * 
+         * @param[in] graph - The netlist graph.
+         * @param[in] strong - Set `true` to compute strongly connected components, `false` otherwise.
+         * @param[in] min_size - Minimal size of a connected component to be part of the result. Set to `0` to include all components. Defaults to `0`.
+         * @returns A vector of strongly connected components on success, an error otherwise.
+         */
+        Result<std::vector<std::vector<u32>>> get_connected_components(NetlistGraph* graph, bool strong, u32 min_size = 0);
+    }    // namespace graph_algorithm
+}    // namespace hal