Merge pull request #21 from pseyfert/dev-0.6

merge 0.6 into master

.gitlab-ci.yml

@@ -37,14 +37,12 @@ rootdocker-run:
     - sudo apt-get update
     - sudo apt-get upgrade -y
     - sudo apt-get install -y curl
-    - set +e
-    - source thisroot.sh
-    - set -e
     - sudo make install
     - mkdir -p test
-    - (cd test && root -l -b -q -n /usr/local/tutorials/tmva/TMVAClassification.C\(\"MLPBNN\"\) )
+    - (cd test && root -l -b -q -n /usr/local/share/doc/root/tutorials/tmva/TMVAClassification.C\(\"MLPBNN\"\) )
     - INPUTSFILE=$(find . -name tmva_class_example.root)
     - WEIGHTFILE=$(find . -name TMVAClassification_MLPBNN.weights.xml)
+    - echo "$INPUTSFILE" TreeS "$WEIGHTFILE" test/testoutput.root MLPBNN_from_branchadder
     - tmva-branch-adder "$INPUTSFILE" TreeS "$WEIGHTFILE" test/testoutput.root MLPBNN_from_branchadder
 
 

.travis.yml

@@ -1,46 +1,50 @@
-language: c++ # irrelevant afaiu
+sudo: required
+
+language: cpp
+
 services:
   - docker
-#before_install:
-#  - docker pull rootproject/root-ubuntu16
-#  - docker run -itd --name ROOTIMAGE -v $(pwd):/repo.git rootproject/root-ubuntu16
-#script:
-#  - docker exec ROOTIMAGE sudo make -C /repo.git/src
 
+# attempting to implement suggestion by
+# https://stackoverflow.com/a/50107380
 jobs:
   include:
     - stage: src-subdir
       script:
         - docker pull rootproject/root-ubuntu16
-        - docker run -itd --name ROOTIMAGE -v $(pwd):/repo.git rootproject/root-ubuntu16
+        - docker run -itd --name ROOTIMAGE -v ${TRAVIS_BUILD_DIR}:/repo.git rootproject/root-ubuntu16
         - docker exec ROOTIMAGE sudo make -C /repo.git/src
     - stage: install-test
       script:
         - docker pull rootproject/root-ubuntu16
-        - docker run -itd --name ROOTIMAGE -v $(pwd):/repo.git rootproject/root-ubuntu16
-        - docker exec ROOTIMAGE sudo apt-get update
-        - docker exec ROOTIMAGE sudo apt-get upgrade -y
-        - docker exec ROOTIMAGE sudo apt-get install -y ninja-build iwyu
-        - docker exec ROOTIMAGE mkdir -p /tmp/build
-        - docker exec ROOTIMAGE mkdir -p /tmp/install
-        - docker exec ROOTIMAGE cmake -B/tmp/build -H/repo.git -G Ninja -DCMAKE_BUILD_TYPE=RelWithDebInfo -DCMAKE_INSTALL_PREFIX=/tmp/install -DCMAKE_RULE_MESSAGES:BOOL=OFF -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON
-        - docker exec ROOTIMAGE cmake --build /tmp/build --target install
+        - docker run -it -v ${TRAVIS_BUILD_DIR}:/repo.git rootproject/root-ubuntu16 /bin/bash -c '
+          set -e
+          set -x
+          sudo apt-get update
+          sudo apt-get upgrade -y
+          sudo apt-get install -y ninja-build iwyu
+          cd $(mktemp -d)
+          cmake ${CI_PROJECT_DIR} -G Ninja -DCMAKE_BUILD_TYPE=RelWithDebInfo -DCMAKE_INSTALL_PREFIX=$(mktemp -d) -DCMAKE_RULE_MESSAGES:BOOL=OFF -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON
+          cmake --build . --target install'
     - stage: runtime-test
       script:
         - docker pull rootproject/root-ubuntu16
         - mkdir -p /tmp/test
-        - docker run -itd --name ROOTIMAGE -v $(pwd):/repo.git -v /tmp/test:/tmp/test rootproject/root-ubuntu16
-        - docker exec ROOTIMAGE sudo apt-get update
-        - docker exec ROOTIMAGE sudo apt-get upgrade -y
-        - docker exec ROOTIMAGE sudo apt-get install -y curl
-        - docker exec ROOTIMAGE sudo make -C /repo.git install
-        - docker exec ROOTIMAGE mkdir -p /tmp/test
-        - docker exec ROOTIMAGE /bin/bash -c 'cd /tmp/test \
-                                              root -l -b -q -n /usr/local/tutorials/tmva/TMVAClassification.C\(\"MLPBNN\"\) \
-                                              INPUTSFILE=$(find /tmp/test -name tmva_class_example.root) \
-                                              WEIGHTFILE=$(find /tmp/test -name TMVAClassification_MLPBNN.weights.xml) \
-                                              tmva-branch-adder "$INPUTSFILE" TreeS "$WEIGHTFILE" test/testoutput.root MLPBNN_from_branchadder'
-
+        - docker run -it -v ${TRAVIS_BUILD_DIR}:/repo.git -v /tmp/test:/tmp/test rootproject/root-ubuntu16 /bin/bash -c '
+          set -e
+          set -x
+          sudo apt-get update
+          sudo apt-get upgrade -y
+          sudo apt-get install -y curl
+          sudo make install
+          mkdir -p test
+          cd test
+          root -l -b -q -n /usr/local/share/doc/root/tutorials/tmva/TMVAClassification.C\(\"MLPBNN\"\)
+          cd ..
+          INPUTSFILE=$(find . -name tmva_class_example.root)
+          WEIGHTFILE=$(find . -name TMVAClassification_MLPBNN.weights.xml)
+          echo "$INPUTSFILE" TreeS "$WEIGHTFILE" test/testoutput.root MLPBNN_from_branchadder
+          tmva-branch-adder "$INPUTSFILE" TreeS "$WEIGHTFILE" test/testoutput.root MLPBNN_from_branchadder '
 
 stages:
   - src-subdir

CMakeLists.txt

@@ -1,10 +1,125 @@
 cmake_minimum_required(VERSION 3.3)
-project(tmva-branch-adder VERSION 0.5)
-set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra -Wshadow")
+project(tmva-branch-adder VERSION 0.6 LANGUAGES CXX)
+
+#### cmake features
+
+include(CMakePackageConfigHelpers)
+include(GNUInstallDirs)
+
+
+#### general compilation
+
+# https://cmake.org/pipermail/cmake/2015-October/061886.html
+include(CheckCXXCompilerFlag)
+macro(AddCXXFlagIfSupported flag test)
+  CHECK_CXX_COMPILER_FLAG(${flag} ${test})
+  if( ${${test}} )
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${flag}")
+  endif()
+endmacro()
+
+AddCXXFlagIfSupported(-Wall COMPILER_SUPPORTS_Wall)
+AddCXXFlagIfSupported(-Wextra COMPILER_SUPPORTS_Wextra)
+AddCXXFlagIfSupported(-Wshadow COMPILER_SUPPORTS_Wshadow)
+AddCXXFlagIfSupported(-Wpedantic COMPILER_SUPPORTS_Wpedantic)
+
+## NB: colorization is a bit of a mess with make vs. ninja vs -v
+AddCXXFlagIfSupported(-fcolor-diagnostics COMPILER_SUPPORTS_fcolor-diagnostics) # e.g. clang 3.9
+AddCXXFlagIfSupported(--fdiagnostics-color=always COMPILER_SUPPORTS_fdiagnostics-color-always) # e.g. gcc
+
 find_program(iwyu_path NAMES include-what-you-use iwyu)
 if(NOT iwyu_path)
   message(STATUS "Could not find the program include-what-you-use")
 endif()
-add_subdirectory(src)
 
 
+#### dependencies
+
+if(EXISTS $ENV{ROOTSYS}/cmake/ROOTConfig.cmake)
+  list(APPEND CMAKE_PREFIX_PATH $ENV{ROOTSYS})
+else()
+  list(APPEND CMAKE_MODULE_PATH $ENV{ROOTSYS}/etc/cmake)
+endif()
+find_package(ROOT REQUIRED COMPONENTS TMVA XMLIO TreePlayer MathMore Foam)
+include(${ROOT_USE_FILE})
+
+
+#### build exe
+
+add_executable(tmva-branch-adder src/blacklist.cpp src/main.cpp src/reader_wrapper.cpp)
+target_link_libraries(tmva-branch-adder TMVA XMLIO TreePlayer Tree RIO Core)
+target_include_directories(tmva-branch-adder
+    PUBLIC
+        $<INSTALL_INTERFACE:include>
+        $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/src>
+)
+
+if(iwyu_path)
+  set_property(TARGET tmva-branch-adder PROPERTY CXX_INCLUDE_WHAT_YOU_USE ${iwyu_path})
+endif()
+
+
+#### build lib
+
+add_library(BranchAdder SHARED src/reader_wrapper.cpp src/blacklist.cpp)
+set_target_properties(BranchAdder PROPERTIES VERSION ${PROJECT_VERSION})
+set_target_properties(BranchAdder PROPERTIES PUBLIC_HEADER src/reader_wrapper.h)
+# semi redundant due to ROOT_USE_FILE
+target_include_directories(BranchAdder
+  SYSTEM PUBLIC
+  ${ROOT_INCLUDE_DIRS}
+  )
+target_include_directories(BranchAdder
+    PUBLIC
+        $<INSTALL_INTERFACE:include>
+        $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/src>
+)
+target_link_libraries(BranchAdder
+  INTERFACE
+  TMVA XMLIO TreePlayer Tree RIO Core)
+
+
+#### install exe
+install(TARGETS tmva-branch-adder DESTINATION ${CMAKE_INSTALL_BINDIR})
+
+#### install lib
+install(TARGETS BranchAdder
+        EXPORT tmva-branch-adder-targets
+        LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
+        PUBLIC_HEADER DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
+
+#### install header
+install(FILES src/blacklist.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
+
+#### configure cmake modules
+# configure tmva-branch-adder-config.cmake
+set(INSTALL_CONFIGDIR ${CMAKE_INSTALL_LIBDIR}/cmake)
+configure_package_config_file(${CMAKE_CURRENT_LIST_DIR}/cmake/tmva-branch-adder-config.cmake.in
+  ${CMAKE_CURRENT_BINARY_DIR}/tmva-branch-adder-config.cmake
+  INSTALL_DESTINATION ${INSTALL_CONFIGDIR}
+)
+
+# configure tmva-branch-adder-targets.cmake
+install(EXPORT tmva-branch-adder-targets
+  FILE tmva-branch-adder-targets.cmake
+  DESTINATION ${INSTALL_CONFIGDIR}
+  )
+
+# configure tmva-branch-adder-config-version.cmake
+write_basic_package_version_file(
+  ${CMAKE_CURRENT_BINARY_DIR}/tmva-branch-adder-config-version.cmake
+  VERSION ${PROJECT_VERSION}
+  COMPATIBILITY ExactVersion
+  )
+
+
+#### install cmake modules
+# install tmva-branch-adder-config-version.cmake
+install(FILES
+  ${CMAKE_CURRENT_BINARY_DIR}/tmva-branch-adder-config-version.cmake
+  DESTINATION ${INSTALL_CONFIGDIR})
+# install tmva-branch-adder-config.cmake
+install(FILES
+  ${CMAKE_CURRENT_BINARY_DIR}/tmva-branch-adder-config.cmake
+  DESTINATION ${INSTALL_CONFIGDIR})
+# install tmva-branch-adder-targets.cmake already done at configuration!

README.md

@@ -1,4 +1,5 @@
 # tmva-branch-adder
+[![DOI](https://zenodo.org/badge/54739571.svg)](https://zenodo.org/badge/latestdoi/54739571)
 [![Licence: GPL v3](https://img.shields.io/github/license/pseyfert/tmva-branch-adder.svg)](LICENSE)
 [![gitlab CI status](https://gitlab.cern.ch/pseyfert/tmva-branch-adder/badges/master/pipeline.svg)](https://gitlab.cern.ch/pseyfert/tmva-branch-adder/commits/master)
 [![travis Status](https://travis-ci.org/pseyfert/tmva-branch-adder.svg?branch=master)](https://travis-ci.org/pseyfert/tmva-branch-adder)

cmake/tmva-branch-adder-config.cmake.in

@@ -0,0 +1,14 @@
+include(CMakeFindDependencyMacro)
+if(EXISTS $ENV{ROOTSYS}/cmake/ROOTConfig.cmake)
+  list(APPEND CMAKE_PREFIX_PATH $ENV{ROOTSYS})
+else()
+  list(APPEND CMAKE_MODULE_PATH $ENV{ROOTSYS}/etc/cmake)
+endif()
+find_package(ROOT @ROOT_VERSION@ EXACT REQUIRED COMPONENTS TMVA XMLIO TreePlayer MathMore Foam)
+include(${ROOT_USE_FILE})
+
+get_filename_component(TMVABRANCHADDER_CMAKE_DIR "${CMAKE_CURRENT_LIST_FILE}" PATH)
+if(NOT TARGET BranchAdder)
+  include("${TMVABRANCHADDER_CMAKE_DIR}/tmva-branch-adder-targets.cmake")
+endif()
+

module/example.py

@@ -1,14 +1,14 @@
 from ROOT import TString
 from ROOT import TFile
 from ROOT import TTree
-from tmva_branch_adder import *
+from tmva_branch_adder import reader_wrapper
 
 if __name__ == "__main__":
     from sys import argv
     import sys
     argc = len(argv)
-    if ("-h" in argv) or (argc not in [5,6]):
-        print "USAGE: ", argv[0], " <root file> <tree name> <xml file> <output file> [<target branch>]"
+    if ("-h" in argv) or (argc not in [5, 6]):
+        print("USAGE: ", argv[0], " <root file> <tree name> <xml file> <output file> [<target branch>]")
         sys.exit(1)
     xmlfile  = TString(argv[3])
     infile   = TString(argv[1])
@@ -17,25 +17,24 @@
 
     errorcode = int(0)
     wrapper = reader_wrapper()
-    of = TFile.Open(outfile.Data(),"create")
+    of = TFile.Open(outfile.Data(), "create")
     errorcode |= wrapper.SetTargetFile(of)
     if errorcode:
         sys.exit(errorcode)
-    if 6==argc:
+    if 6 == argc:
         errorcode |= wrapper.SetTargetBranch(argv[5])
     if errorcode:
         sys.exit(errorcode)
     errorcode |= wrapper.SetXMLFile(xmlfile)
     if errorcode:
         sys.exit(errorcode)
 
-    if_ = TFile.Open(infile.Data(),"read")
+    if_ = TFile.Open(infile.Data(), "read")
     intree = if_.Get(treename.Data())
     errorcode |= wrapper.SetTree(intree)
     if errorcode:
         sys.exit(errorcode)
 
-
     errorcode |= wrapper.Process()
     if errorcode:
         sys.exit(errorcode)

module/tmva_branch_adder.py

@@ -1,21 +1,30 @@
 from ROOT import gInterpreter
+
+
 def hack_compilation():
     from ROOT import gSystem
     cmd = gSystem.GetMakeSharedLib()
     import subprocess
-    compiler = subprocess.check_output(["root-config","--cxx"])
-    compiler=compiler[:-1] # remove trailing line feed
+    # modern way for python3 to avoid byte vs. string mess
+    # fallback to python2
+    try:
+        compiler = subprocess.getoutput("root-config --cxx")
+    except AttributeError:
+        compiler = subprocess.check_output(["root-config", "--cxx"])
+        compiler = compiler[:-1]  # remove trailing line feed
+    # FIXME: no idea what this if statement was meant to do
     if compiler.find(" "):
-        print "WILL NEED TO FIX BUILD COMMAND"
-        print "old command:"
-        print cmd
+        print("WILL NEED TO FIX BUILD COMMAND")
+        print("old command:")
+        print(cmd)
         # the GetMakeSharedLib is broken on one of my systems because the
         # compiler command contains a white space "ccache g++"
         # gInterpreter then uses only the first word "ccache"
-        cmd = cmd.replace("ccache",compiler)
+        cmd = cmd.replace("ccache", compiler)
         gSystem.SetMakeSharedLib(cmd)
-        print "new command:"
-        print cmd
+        print("new command:")
+        print(cmd)
+
 
 hack_compilation()
 gInterpreter.LoadMacro("../src/blacklist.cpp+")

src/_tmva-branch-adder

@@ -11,7 +11,7 @@ _rootfile() {
 }
 
 _listtrees() {
-  _wanted arguments expl "input ttree name" compadd $(python -c "from root_numpy import list_trees;exec '''for t in list_trees('$words[$CURRENT-1]'):\n print t'''")
+  _wanted arguments expl "input ttree name" compadd $(python -c "from root_numpy import list_trees;exec('''for t in list_trees('$words[$CURRENT-1]'):\n print(t)''')" 2> /dev/null)
 }
 
 _arguments "1:input file:_rootfile" "2:input ttree name:_listtrees" "3:xml file:_files -g '*.xml'" "4:output file:_rootfile" "5:output branch name:"