Merge pull request #95 from rest-for-physics/lobis-pre-commit

Implement pre-commit checks and format files

.clang-format

@@ -0,0 +1,10 @@
+# Our style is based on the Google style
+# https://google.github.io/styleguide/cppguide.html
+BasedOnStyle: Google
+
+# we use left pointer alignment
+DerivePointerAlignment: false
+PointerAlignment: Left
+
+IndentWidth: 4
+ColumnLimit: 110

.cmake-format.yaml

@@ -0,0 +1,6 @@
+# https://cmake-format.readthedocs.io/en/latest/configuration.html
+
+format:
+  tab_size: 4
+  separate_ctrl_name_with_space: true
+  separate_fn_name_with_space: false

.github/workflows/validation.yml

@@ -70,6 +70,10 @@ jobs:
           ./scripts/checkoutRemoteBranch.sh ${{ env.BRANCH_NAME }}
           git log -1 --stat
       - uses: actions/checkout@v3
+      - name: Verify pre-commit config files match
+        run: |
+          cd $GITHUB_WORKSPACE
+          python ${{ env.REST_FRAMEWORK_SOURCE_DIR }}/scripts/validatePreCommitConfig.py
       - name: Setup, build and install
         run: |
           cd ${{ env.REST_FRAMEWORK_SOURCE_DIR }}

.pre-commit-config.yaml

@@ -0,0 +1,35 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: check-added-large-files
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: check-yaml
+      - id: check-xml
+      - id: requirements-txt-fixer
+      - id: end-of-file-fixer
+        exclude: external/.*$
+      - id: mixed-line-ending
+        exclude: external/.*$
+      - id: trailing-whitespace
+        exclude: external/.*$
+
+  - repo: https://github.com/pre-commit/mirrors-clang-format
+    rev: v15.0.6
+    hooks:
+      - id: clang-format
+        exclude: external/.*$
+
+  - repo: https://github.com/cheshirekow/cmake-format-precommit
+    rev: v0.6.13
+    hooks:
+      - id: cmake-format
+        additional_dependencies: [ pyyaml ]
+      # - id: cmake-lint
+
+  - repo: https://github.com/psf/black
+    rev: 22.12.0
+    hooks:
+      - id: black

CMakeLists.txt

@@ -2,23 +2,31 @@
 project(restG4)
 
 message("===============  ${PROJECT_NAME}  ==============")
-set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/../../cmake ${CMAKE_MODULE_PATH})
+set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/../../cmake
+                      ${CMAKE_MODULE_PATH})
 
 if (${CMAKE_PROJECT_NAME} STREQUAL ${PROJECT_NAME})
-    # this will only be accessed when build restG4 as a standalone package, not when building the framework
-    CMAKE_MINIMUM_REQUIRED(VERSION 3.16)
+    # this will only be accessed when build restG4 as a standalone package, not
+    # when building the framework
+    cmake_minimum_required(VERSION 3.16)
     find_package(REST REQUIRED)
     string(FIND ${REST_LIBRARIES} "RestGeant4" REST_GEANT4_FOUND)
-    If (${REST_GEANT4_FOUND} EQUAL -1)
-        message(SEND_ERROR "REST found but 'RestGeant4' library is not present. Please install REST with Geant4Lib")
+    if (${REST_GEANT4_FOUND} EQUAL -1)
+        message(
+            SEND_ERROR
+                "REST found but 'RestGeant4' library is not present. Please install REST with Geant4Lib"
+        )
     endif ()
 endif ()
 
 # Find ROOT
 find_package(ROOT REQUIRED COMPONENTS RIO Geom)
 execute_process(COMMAND root-config --cflags OUTPUT_VARIABLE ROOT_CFLAGS)
 string(STRIP ${ROOT_CFLAGS} ROOT_CFLAGS)
-message(STATUS "-- Found ROOT version: ${ROOT_VERSION} with compilation flags: ${ROOT_CFLAGS} and libraries: ${ROOT_LIBRARIES}")
+message(
+    STATUS
+        "-- Found ROOT version: ${ROOT_VERSION} with compilation flags: ${ROOT_CFLAGS} and libraries: ${ROOT_LIBRARIES}"
+)
 
 # Find Geant4
 find_package(Geant4 REQUIRED ui_all vis_all)
@@ -28,15 +36,19 @@ message("-- Found Geant4 version: ${Geant4_VERSION}")
 # Check Geant4 C++ standard is correct
 execute_process(COMMAND geant4-config --cxxstd OUTPUT_VARIABLE GEANT4_CXX_STD)
 if (NOT ${GEANT4_CXX_STD} MATCHES "17")
-    message(FATAL_ERROR "Geant4 installation was compiled with C++${GEANT4_CXX_STD} standard, but C++17 is required for REST")
+    message(
+        FATAL_ERROR
+            "Geant4 installation was compiled with C++${GEANT4_CXX_STD} standard, but C++17 is required for REST"
+    )
 endif ()
 
 # Fix for older Geant4 versions
 if (${Geant4_VERSION} VERSION_LESS 11.0.0)
     add_compile_definitions(GEANT4_VERSION_LESS_11_0_0)
 endif ()
 
-# Fix to allow compatibility with older Geant4 versions that don't have G4RunManagerFactory
+# Fix to allow compatibility with older Geant4 versions that don't have
+# G4RunManagerFactory
 if (NOT EXISTS "${Geant4_INCLUDE_DIRS}/G4RunManagerFactory.hh")
     add_compile_definitions(GEANT4_WITHOUT_G4RunManagerFactory)
 endif ()
@@ -45,62 +57,65 @@ if (NOT DEFINED CMAKE_INSTALL_PREFIX)
     set(CMAKE_INSTALL_PREFIX ${REST_PATH})
 endif ()
 
-message(STATUS "Package ${PROJECT_NAME} will be installed in ${CMAKE_INSTALL_PREFIX}")
+message(
+    STATUS
+        "Package ${PROJECT_NAME} will be installed in ${CMAKE_INSTALL_PREFIX}")
 
 if (NOT CMAKE_CXX_FLAGS)
     set(CMAKE_CXX_FLAGS " -std=c++1y")
 endif ()
 
 # Set include and lib
-set(INCLUDE_DIRS ${PROJECT_SOURCE_DIR}/include ${ROOT_INCLUDE_DIRS} ${Geant4_INCLUDE_DIR} ${REST_INCLUDE_DIRS})
+set(INCLUDE_DIRS ${PROJECT_SOURCE_DIR}/include ${ROOT_INCLUDE_DIRS}
+                 ${Geant4_INCLUDE_DIR} ${REST_INCLUDE_DIRS})
 
 if (NOT ${CMAKE_PROJECT_NAME} STREQUAL ${PROJECT_NAME})
     set(INCLUDE_DIRS ${INCLUDE_DIRS} ${rest_include_dirs})
 endif ()
 
-set(LINK_LIBRARIES ${Geant4_LIBRARIES} ${ROOT_LIBRARIES} RestFramework RestGeant4)
+set(LINK_LIBRARIES ${Geant4_LIBRARIES} ${ROOT_LIBRARIES} RestFramework
+                   RestGeant4)
 string(STRIP "${LINK_LIBRARIES}" LINK_LIBRARIES)
 
 file(GLOB sources ${PROJECT_SOURCE_DIR}/src/*.cxx)
 file(GLOB headers ${PROJECT_SOURCE_DIR}/include/*.h)
 
 # Create a library, necessary to enable testing
-set(LIBRARY RestRestG4) # this way the `ADD_LIBRARY_TEST` macro will pick the library name correctly
+set(LIBRARY RestRestG4) # this way the `ADD_LIBRARY_TEST` macro will pick the
+                        # library name correctly
 add_library(${LIBRARY} SHARED)
 
 target_sources(${LIBRARY} PUBLIC ${sources})
 target_link_libraries(${LIBRARY} ${LINK_LIBRARIES})
 target_include_directories(${LIBRARY} SYSTEM PUBLIC ${INCLUDE_DIRS})
 
 if (NOT ${CMAKE_PROJECT_NAME} STREQUAL ${PROJECT_NAME})
-    ADD_LIBRARY_TEST()
+    add_library_test()
 endif ()
 
 # Add the executable
 add_executable(${PROJECT_NAME} main.cxx)
-target_link_libraries(
-        ${PROJECT_NAME} PUBLIC
-        ${LIBRARY}
-)
+target_link_libraries(${PROJECT_NAME} PUBLIC ${LIBRARY})
 
 file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/examples
-        DESTINATION ${CMAKE_CURRENT_BINARY_DIR}
-        )
+     DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
 
-install(DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/examples/
-        DESTINATION ./examples/restG4/
-        COMPONENT install
-        )
+install(
+    DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/examples/
+    DESTINATION ./examples/restG4/
+    COMPONENT install)
 
-install(DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/mac
-        DESTINATION macros
-        COMPONENT install
-        )
+install(
+    DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/mac
+    DESTINATION macros
+    COMPONENT install)
 
 install(TARGETS ${PROJECT_NAME} DESTINATION bin)
 install(TARGETS ${LIBRARY} DESTINATION lib)
 
 if (NOT ${CMAKE_PROJECT_NAME} STREQUAL ${PROJECT_NAME})
     set(package_added "${PROJECT_NAME} ")
-    set(package_added ${package_added} PARENT_SCOPE)
+    set(package_added
+        ${package_added}
+        PARENT_SCOPE)
 endif ()

examples/01.NLDBD/NLDBD.rml

@@ -5,7 +5,7 @@
      First concept author J. Galan (26-Apr-2015)
  -->
 
-<!-- 
+<!--
 By default REST units are mm, keV and degrees
 -->
 

examples/01.NLDBD/geometry/myGeometryTemplate.gdml

@@ -62,4 +62,4 @@
 </volume>
 <!-- }}} -->
 
-</structure>
+</structure>

examples/01.NLDBD/geometry/mySetupTemplate.gdml

@@ -9,7 +9,7 @@
 <gdml xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
       xsi:noNamespaceSchemaLocation="http://service-spi.web.cern.ch/service-spi/app/releases/GDML/schema/gdml.xsd">
 
-    <!-- Just an example of main geometry file : myGeometryTemplate.gdml 
+    <!-- Just an example of main geometry file : myGeometryTemplate.gdml
          This file just defines de parameters of the geometry.
          The geometry it is defined in geometry/myGeometryDefinition.gdml
          The materials are defined in geometry/materials.xml

examples/02.TREXDM/g4Analysis.rml

@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no" ?>
 
-<!--This file is an example of REST simulation functionality. We process the output root file 
-from restG4, converting its TRestGeant4Event to TRestDetectorSignalEvent. Observables and processes's 
+<!--This file is an example of REST simulation functionality. We process the output root file
+from restG4, converting its TRestGeant4Event to TRestDetectorSignalEvent. Observables and processes's
 internal values are saved.
 -->
 
@@ -47,4 +47,3 @@ internal values are saved.
     <addTask type="processEvents" value="ON"/>
 
 </TRestManager>
-

examples/02.TREXDM/geometry/README.md

@@ -1,8 +1,8 @@
 This geometry was extracted from the [trexdm-geometry](https://lfna.unizar.es/gifna/trexdm-geometry) project. Check there for the most official and updated TREX-DM geometries.
 
-These files define a very basic geometry without great detail but integrating the most important components. 
+These files define a very basic geometry without great detail but integrating the most important components.
 
-- Complete enclosing vessel 
+- Complete enclosing vessel
 
 - Mylar cathode
 

examples/03.Fluorescence/electron.rml

@@ -5,7 +5,7 @@
      First concept author J. Galan (26-Apr-2015)
  -->
 
-<!-- 
+<!--
 By default REST units are mm, keV and degrees
 -->
 

examples/03.Fluorescence/g4Analysis.rml

@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no" ?>
 
-<!--This file is an example of REST simulation functionality. We process the output root file 
-from restG4, converting its TRestGeant4Event to TRestDetectorSignalEvent. Observables and processes's 
+<!--This file is an example of REST simulation functionality. We process the output root file
+from restG4, converting its TRestGeant4Event to TRestDetectorSignalEvent. Observables and processes's
 internal values are saved.
 -->
 
@@ -46,4 +46,3 @@ internal values are saved.
     <addTask type="processEvents" value="ON"/>
 
 </TRestManager>
-

examples/03.Fluorescence/gamma.rml

@@ -5,7 +5,7 @@
      First concept author J. Galan (26-Apr-2015)
  -->
 
-<!-- 
+<!--
 By default REST units are mm, keV and degrees
 -->
 

examples/03.Fluorescence/geometry/setup.gdml

@@ -9,7 +9,7 @@
 <gdml xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
       xsi:noNamespaceSchemaLocation="http://service-spi.web.cern.ch/service-spi/app/releases/GDML/schema/gdml.xsd">
 
-    <!-- Just an example of main geometry file : myGeometryTemplate.gdml 
+    <!-- Just an example of main geometry file : myGeometryTemplate.gdml
          This file just defines de parameters of the geometry.
          The geometry it is defined in geometry/myGeometryDefinition.gdml
          The materials are defined in geometry/materials.xml

examples/05.PandaXIII/README.md

@@ -1,7 +1,6 @@
-The following example has been extracted from the pipeline validation at the main framework, where 
+The following example has been extracted from the pipeline validation at the main framework, where
 the full data processing Montecarlo chain is validated.
 
-We use Xe136bb0n.rml to run restG4 for Geant4 simulation. Use ValidateG4.C to check if the simulation 
-goes smoothly. i.e. all 500 events are simulated and metadata is correctly recorded. The output file will 
+We use Xe136bb0n.rml to run restG4 for Geant4 simulation. Use ValidateG4.C to check if the simulation
+goes smoothly. i.e. all 500 events are simulated and metadata is correctly recorded. The output file will
 be used later on
-

examples/05.PandaXIII/geometry/AcrylicPart.gdml

@@ -371,4 +371,3 @@
     <second ref="AcrylicCoverSolid" />
     <positionref ref="AcrylicCoverPosition" />
 </union>
-

examples/05.PandaXIII/geometry/CopperRings.gdml

@@ -346,4 +346,4 @@
     <first ref="CopperRing_57" />
     <second ref="CopperRing" />
     <positionref ref="ringPositionBottom_29" />
-</union>
+</union>

examples/05.PandaXIII/geometry/LeadShelding.gdml

@@ -30,4 +30,3 @@
     <second ref="LeadSheldingCap" />
     <position name="Position_guagua3" x="0" y="0" z="-0.5*(LeadSheldingLength+LeadSheldingCapLength)" />
 </union>
-

examples/05.PandaXIII/geometry/OtherXeTMAGas.gdml

@@ -32,4 +32,3 @@
     <second ref="ResistanceSolid"/>
     <positionref ref="ResistancePosition" />
 </subtraction>
-

examples/05.PandaXIII/geometry/Resistance.gdml

@@ -340,4 +340,4 @@
     <first ref="Resistance_56" />
     <second ref="Resistance" />
     <positionref ref="ringPositionBottom_29" />
-</union>
+</union>

examples/05.PandaXIII/geometry/Th232_SS_01.rml

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no" ?>
 
-<!-- 
+<!--
      File   : isotopeFromVolume.rml
      Authors : J. Galan / H.Liang
      Date   :  9th-Apr-2016
@@ -77,5 +77,5 @@
     <physicsList name="G4EmExtraPhysics"> </physicsList>
 
   </TRestGeant4PhysicsLists>
-  
+
 </restG4>

examples/05.PandaXIII/geometry/XeTMAGas_new.gdml

@@ -5,4 +5,3 @@
     <second ref="ResistanceSolid"/>
     <positionref ref="ResistancePosition" />
 </subtraction>
-

examples/06.IonRecoils/README.md

@@ -25,4 +25,3 @@ restG4 recoils.rml
 ```
 
 See also `Validation.C` for validation routines executed in the pipeline.
-

examples/06.IonRecoils/geometry/setup.gdml

@@ -9,7 +9,7 @@
 <gdml xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
       xsi:noNamespaceSchemaLocation="http://service-spi.web.cern.ch/service-spi/app/releases/GDML/schema/gdml.xsd">
 
-    <!-- Just an example of main geometry file : myGeometryTemplate.gdml 
+    <!-- Just an example of main geometry file : myGeometryTemplate.gdml
          This file just defines de parameters of the geometry.
          The geometry it is defined in geometry/myGeometryDefinition.gdml
          The materials are defined in geometry/materials.xml

examples/06.IonRecoils/recoils.rml

@@ -5,7 +5,7 @@
      First concept author J. Galan (26-Apr-2015)
  -->
 
-<!-- 
+<!--
 By default REST units are mm, keV and degrees
 -->
 

examples/07.FullChainDecay/README.md

@@ -25,4 +25,3 @@ restG4 singleDecay.rml
 ```
 
 See also `Validation.C` for validation routines executed in the pipeline.
-