🔀 Resolve merge conflicts

.codecov.yml

@@ -0,0 +1,28 @@
+codecov:
+  require_ci_to_pass: true
+comment:
+  behavior: default
+  layout: reach,diff,flags,files,footer
+  require_changes: false
+coverage:
+  precision: 2
+  range: 70..100
+  round: down
+  status:
+    patch:
+      default:
+        base: auto
+        target: 95%
+        threshold: 0.5%
+    project:
+      default:
+        base: auto
+        target: 95%
+        threshold: 0.5%
+parsers:
+  gcov:
+    branch_detection:
+      conditional: true
+      loop: true
+      macro: false
+      method: false

.github/release-drafter.yml

@@ -49,7 +49,7 @@ footer: |
 
 template: |
   ## 👀 What's Changed
-  
+
   $CHANGES
-  
+
   **Full [CHANGELOG](https://fiction.readthedocs.io/en/latest/changelog.html)**: https://github.com/$OWNER/$REPOSITORY/compare/$PREVIOUS_TAG...v$RESOLVED_VERSION

.github/workflows/codeql-analysis.yml

@@ -59,7 +59,7 @@ jobs:
           large-packages: false
           docker-images: false
           swap-storage: false
-          
+
       - name: Install libraries and the respective compiler
         run: sudo apt-get update && sudo apt-get install -yq libtbb-dev ${{matrix.compiler}}
 

.pre-commit-config.yaml

@@ -0,0 +1,53 @@
+# To run all pre-commit checks, use:
+#
+#     pre-commit run -a
+#
+# To install pre-commit hooks that run every time you commit:
+#
+#     pre-commit install
+#
+
+ci:
+  autoupdate_commit_msg: "⬆️ Bump pre-commit hooks"
+  autofix_commit_msg: "🎨 Incorporated pre-commit fixes"
+
+exclude: "^libs/|^benchmarks/"
+
+repos:
+  # Standard hooks
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: check-added-large-files
+      - id: check-case-conflict
+      - id: check-docstring-first
+      - id: check-merge-conflict
+      - id: check-toml
+      - id: check-yaml
+      - id: debug-statements
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+      - id: trailing-whitespace
+
+  # Handle unwanted unicode characters
+  - repo: https://github.com/sirosen/texthooks
+    rev: 0.6.2
+    hooks:
+      - id: fix-ligatures
+      - id: fix-smartquotes
+
+  # Check for common RST mistakes
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: v1.10.0
+    hooks:
+      - id: rst-backticks
+      - id: rst-directive-colons
+      - id: rst-inline-touching-normal
+
+  # clang-format the C++ part of the code base
+  - repo: https://github.com/pre-commit/mirrors-clang-format
+    rev: v17.0.4
+    hooks:
+      - id: clang-format
+        types_or: [ c++, c ]
+        args: [ "-style=file" ]

.readthedocs.yml

@@ -1,16 +1,11 @@
 version: 2
 
-build:
-  os: ubuntu-22.04
-  tools:
-    python: "3.9"
-
 submodules:
   include: all
   recursive: true
 
 build:
-  os: ubuntu-20.04
+  os: ubuntu-22.04
   tools:
     python: "3.9"
   apt_packages:

CMakeLists.txt

@@ -1,26 +1,28 @@
-# Large parts of this build system are based on Jason Turner's
-# C++ Starter Project (https://github.com/lefticus/cpp_starter_project) and
-# CMake Template (https://github.com/cpp-best-practices/cmake_template)
+# Large parts of this build system are based on Jason Turner's C++ Starter
+# Project (https://github.com/lefticus/cpp_starter_project) and CMake Template
+# (https://github.com/cpp-best-practices/cmake_template)
 
 cmake_minimum_required(VERSION 3.21)
 
 # Only set the CMAKE_CXX_STANDARD if it is not set by someone else
-if (NOT DEFINED CMAKE_CXX_STANDARD)
-    # Set C++ standard; at least C++17 is required
-    set(CMAKE_CXX_STANDARD 17)
-endif ()
+if(NOT DEFINED CMAKE_CXX_STANDARD)
+  # Set C++ standard; at least C++17 is required
+  set(CMAKE_CXX_STANDARD 17)
+endif()
 
 # strongly encouraged to enable this globally to avoid conflicts between
-# -Wpedantic being enabled and -std=c++20 and -std=gnu++20 for example
-# when compiling with PCH enabled
+# -Wpedantic being enabled and -std=c++20 and -std=gnu++20 for example when
+# compiling with PCH enabled
 set(CMAKE_CXX_EXTENSIONS OFF)
 
 # Set the project name and version
-project(fiction
-        VERSION 0.5.0
-        DESCRIPTION "An open-source design automation framework for Field-coupled Nanotechnologies"
-        HOMEPAGE_URL "https://github.com/cda-tum/fiction"
-        LANGUAGES CXX C)
+project(
+  fiction
+  VERSION 0.5.0
+  DESCRIPTION
+    "An open-source design automation framework for Field-coupled Nanotechnologies"
+  HOMEPAGE_URL "https://github.com/cda-tum/fiction"
+  LANGUAGES CXX C)
 
 include(cmake/PreventInSourceBuilds.cmake)
 include(cmake/ProjectOptions.cmake)
@@ -30,18 +32,13 @@ fiction_setup_options()
 fiction_global_options()
 fiction_local_options()
 
-
 # don't know if this should be set globally from here or not...
 set(CMAKE_CXX_VISIBILITY_PRESET hidden)
 
 set(GIT_SHA
-        "Unknown"
-        CACHE STRING "SHA this build was generated from")
-string(
-        SUBSTRING "${GIT_SHA}"
-        0
-        8
-        GIT_SHORT_SHA)
+    "Unknown"
+    CACHE STRING "SHA this build was generated from")
+string(SUBSTRING "${GIT_SHA}" 0 8 GIT_SHORT_SHA)
 
 target_compile_features(fiction_options INTERFACE cxx_std_${CMAKE_CXX_STANDARD})
 
@@ -57,53 +54,57 @@ add_subdirectory(include)
 add_subdirectory(libs)
 
 # Enable progress bars
-if (NOT WIN32)
-    option(FICTION_PROGRESS_BARS "Enable animated progress bars in command line" ON)
-    if (FICTION_PROGRESS_BARS)
-        target_compile_definitions(fiction_options INTERFACE PROGRESS_BARS)
-    endif ()
-endif ()
+if(NOT WIN32)
+  option(FICTION_PROGRESS_BARS "Enable animated progress bars in command line"
+         ON)
+  if(FICTION_PROGRESS_BARS)
+    target_compile_definitions(fiction_options INTERFACE PROGRESS_BARS)
+  endif()
+endif()
 
 # CLI
 option(FICTION_CLI "Build fiction CLI" ON)
-if (FICTION_CLI)
-    message(STATUS "Building fiction CLI")
-    add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/cli)
-endif ()
+if(FICTION_CLI)
+  message(STATUS "Building fiction CLI")
+  add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/cli)
+endif()
 
 # Experiments
 option(FICTION_EXPERIMENTS "Build fiction experiments" OFF)
-if (FICTION_EXPERIMENTS)
-    message(STATUS "Building fiction experiments")
-    add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/experiments)
-endif ()
+if(FICTION_EXPERIMENTS)
+  message(STATUS "Building fiction experiments")
+  add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/experiments)
+endif()
 
 # Python Bindings
 option(FICTION_PYTHON_BINDINGS "Build fiction Python bindings" OFF)
-if (FICTION_PYTHON_BINDINGS)
-    message(STATUS "Building fiction Python bindings")
-    add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/bindings/)
-endif ()
+if(FICTION_PYTHON_BINDINGS)
+  message(STATUS "Building fiction Python bindings")
+  add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/bindings/)
+endif()
 
 # Testing
 option(FICTION_TEST "Build fiction tests" OFF)
-if (FICTION_TEST)
-    enable_testing()
-    message(STATUS "Building fiction tests")
-    add_subdirectory(test)
-endif ()
-
-# If MSVC is being used, and ASAN is enabled, we need to set the debugger environment
-# so that it behaves well with MSVC's debugger, and we can run the target from visual studio
-if (MSVC)
-    get_all_installable_targets(all_targets)
-    message("all_targets=${all_targets}")
-    set_target_properties(${all_targets} PROPERTIES VS_DEBUGGER_ENVIRONMENT "PATH=$(VC_ExecutablePath_x64);%PATH%")
-endif ()
+if(FICTION_TEST)
+  enable_testing()
+  message(STATUS "Building fiction tests")
+  add_subdirectory(test)
+endif()
+
+# If MSVC is being used, and ASAN is enabled, we need to set the debugger
+# environment so that it behaves well with MSVC's debugger, and we can run the
+# target from visual studio
+if(MSVC)
+  get_all_installable_targets(all_targets)
+  message("all_targets=${all_targets}")
+  set_target_properties(
+    ${all_targets} PROPERTIES VS_DEBUGGER_ENVIRONMENT
+                              "PATH=$(VC_ExecutablePath_x64);%PATH%")
+endif()
 
 # set the startup project for the "play" button in MSVC
 set_property(DIRECTORY PROPERTY VS_STARTUP_PROJECT intro)
 
-if (CMAKE_SKIP_INSTALL_RULES)
-    return()
-endif ()
+if(CMAKE_SKIP_INSTALL_RULES)
+  return()
+endif()

bindings/pyfiction/CMakeLists.txt

@@ -1,4 +1,5 @@
 pybind11_add_module(pyfiction pyfiction.cpp)
 target_link_libraries(pyfiction PRIVATE libfiction)
-target_include_directories(pyfiction PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/include)
+target_include_directories(pyfiction
+                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/include)
 set_property(TARGET pyfiction PROPERTY POSITION_INDEPENDENT_CODE ON)

bindings/pyfiction/include/pyfiction/algorithms/physical_design/apply_gate_library.hpp

@@ -16,11 +16,12 @@
 #include <fiction/types.hpp>
 
 #include <fmt/format.h>
-#include <pybind11/pybind11.h>
-#include <pybind11/stl.h>
 
 #include <string>
 
+#include <pybind11/pybind11.h>
+#include <pybind11/stl.h>
+
 namespace pyfiction
 {
 

bindings/pyfiction/include/pyfiction/algorithms/physical_design/exact.hpp

@@ -12,11 +12,11 @@
 
 #include <fiction/algorithms/physical_design/exact.hpp>
 
+#include <sstream>
+
 #include <pybind11/pybind11.h>
 #include <pybind11/stl.h>
 
-#include <sstream>
-
 namespace pyfiction
 {
 

bindings/pyfiction/include/pyfiction/algorithms/physical_design/orthogonal.hpp

@@ -10,11 +10,11 @@
 
 #include <fiction/algorithms/physical_design/orthogonal.hpp>
 
+#include <sstream>
+
 #include <pybind11/pybind11.h>
 #include <pybind11/stl.h>
 
-#include <sstream>
-
 namespace pyfiction
 {
 

bindings/pyfiction/include/pyfiction/algorithms/simulation/logic_simulation.hpp

@@ -13,13 +13,14 @@
 #include <fmt/format.h>
 #include <kitty/print.hpp>
 #include <mockturtle/algorithms/simulation.hpp>
-#include <pybind11/pybind11.h>
-#include <pybind11/stl.h>
 
 #include <string>
 #include <unordered_map>
 #include <vector>
 
+#include <pybind11/pybind11.h>
+#include <pybind11/stl.h>
+
 namespace pyfiction
 {
 

bindings/pyfiction/include/pyfiction/inout/read_sqd_layout.hpp

@@ -10,10 +10,10 @@
 
 #include <fiction/io/read_sqd_layout.hpp>
 
-#include <pybind11/pybind11.h>
-
 #include <string_view>
 
+#include <pybind11/pybind11.h>
+
 namespace pyfiction
 {
 

bindings/pyfiction/include/pyfiction/inout/write_fqca_layout.hpp

@@ -10,10 +10,10 @@
 
 #include <fiction/io/write_fqca_layout.hpp>
 
-#include <pybind11/pybind11.h>
-
 #include <string_view>
 
+#include <pybind11/pybind11.h>
+
 namespace pyfiction
 {
 

bindings/pyfiction/include/pyfiction/inout/write_qca_layout.hpp

@@ -10,10 +10,10 @@
 
 #include <fiction/io/write_qca_layout.hpp>
 
-#include <pybind11/pybind11.h>
-
 #include <string_view>
 
+#include <pybind11/pybind11.h>
+
 namespace pyfiction
 {
 

bindings/pyfiction/include/pyfiction/inout/write_qcc_layout.hpp

@@ -10,10 +10,10 @@
 
 #include <fiction/io/write_qcc_layout.hpp>
 
-#include <pybind11/pybind11.h>
-
 #include <string_view>
 
+#include <pybind11/pybind11.h>
+
 namespace pyfiction
 {