Merge branch 'preprod' into 'master'

Merge preprod to master

See merge request !66

.gitlab-ci.yml

-image: gitlab-registry.in2p3.fr/ipnl_gamma/docker_gamma:latest
+image: gitlab-registry.in2p3.fr/ipnl_gamma/docker_gamma:ubuntu18
 
 stages:
     - build

CMakeLists.txt

@@ -43,10 +43,15 @@ set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib_)
 set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib_)
 set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin_)
 
-#if(APPLE)
-#	set(CMAKE_MACOSX_RPATH 1)
-#endif()
-#set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
+#cmake_policy(SET CMP0077 NEW)
+#cmake_policy(SET CMP0068 NEW)
+
+# FIX Warning with rpath on macosx
+if(APPLE)
+set(CMAKE_MACOSX_RPATH 1)
+set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
+endif()
+
 #
 # ROOT MANDATORY
 #

doc/sonar/sonar-project.properties

@@ -14,6 +14,6 @@ sonar.cxx.cppcheck.reportPath=./cppcheck_output/
 #sonar.cxx.coverage.forceZeroCoverage=true
 # Encoding of the source code. Default is default system encoding
 #sonar.sourceEncoding=UTF-8
-sonar.host.url=https://sonar.ipnl.in2p3.fr
+sonar.host.url=https://sonar.ip2i.in2p3.fr
 sonar.scm.provider=git
 sonar.exclusions=**/*.xml,config/**,cmake/**,debug/**,demos/**,doc/**,doxyfiles/**,macros/**,ndb/**,scripts/**,**/*.in

src/adf/BasicAFP.cpp

@@ -27,6 +27,7 @@
 #include <iostream>
 #include <iomanip>
 #include <fstream>
+#include <algorithm>
 
 using namespace ADF; 
 
@@ -67,17 +68,24 @@ Bool_t BasicAFP::NewFile()
 		fCurrentFile = 0x0;
 		std::cout << "  -BasicAFP: the input file has just been closed " << fCurrentFileName << std::endl;
 	}
-	
-	// open the first file to be ready to be run
-	std::string tmp = fPath;
-	if ( tmp.size() > 0 && !(tmp.at(tmp.size()-1) == '/') ) 
-		tmp += '/';
-	
-	std::ostringstream filename;
-	filename << tmp << fBaseForName
-	<< std::setfill('0') << std::setw(4) << fCurrentFileNumber++ << std::setfill(' ')
-	<< ".adf";
-	fCurrentFileName = filename.str();
+
+    if(fListOfIndividualFiles.size()) {
+        if(fCurrentFileNumber<fListOfIndividualFiles.size()) fCurrentFileName = fListOfIndividualFiles.at(fCurrentFileNumber);
+        else fCurrentFileName.clear();
+        fCurrentFileNumber++;
+    }
+    else {
+        // open the first file to be ready to be run
+        std::string tmp = fPath;
+        if ( tmp.size() > 0 && !(tmp.at(tmp.size()-1) == '/') )
+        tmp += '/';
+
+        std::ostringstream filename;
+        filename << tmp << fBaseForName
+                 << std::setfill('0') << std::setw(4) << fCurrentFileNumber++ << std::setfill(' ')
+                 << ".adf";
+        fCurrentFileName = filename.str();
+    }
 	
 	fCurrentFile = ::fopen(fCurrentFileName.c_str(),"rb");
 	if ( fCurrentFile != 0x0 ) {
@@ -92,8 +100,8 @@ Bool_t BasicAFP::NewFile()
 		fCurrentName = fCurrentFileName.substr(lpt+1, len-lpt-1);
 		ok = true;
 	}
-	else {
-		Log << "Could not open input file " << fCurrentFileName << nline;
+    else {
+        if(fCurrentFileName.length()) Log << "Could not open input file " << fCurrentFileName << nline;
 		GetFrameIO().SetStatus(BaseFrameIO::kFinished); 
 		ok = false;
 	}
@@ -176,23 +184,40 @@ void BasicAFP::process_initialise (UInt_t *error_code)
 	*error_code = 0u;
 	Log.ClearMessage(); Log.SetProcessMethod("process_initialise");
 	
-	// read an input file to get the base filename and the path  
-	std::string conffile = GetConfPath() + "BasicAFP.conf";
-	
+    // read an input file to get the base filename and the path
+    std::string conffile = GetConfPath() + "BasicAFP.conf";
+
 	std::ifstream filein(conffile.data());
-	if ( filein.is_open() == true ) { 
-		
-		std::string pathforfiles, basename; 
-		UInt_t starting_number;
-		
-		filein >> pathforfiles >> basename >> starting_number;
-		if ( filein.good() ) {
-			fPath = pathforfiles;
-			fBaseForName = basename;
-			fCurrentFileNumber = starting_number;
-			std::cout << "BasicAFP::process_initialise " << pathforfiles << " " << basename << " " << starting_number << std::endl;
-		}
-	}
+    if ( filein.is_open() == true ) {
+
+        // check with the first line if the files are given one by one
+        std::string line;
+        std::getline(filein,line);
+        int nblank = std::count(line.begin(), line.end(),' ');
+        filein.seekg(0);
+        // case where a list of files is given
+        if(nblank==0) {
+            while(filein.good()) {
+                std::getline(filein,line);
+                if(line.length()) fListOfIndividualFiles.push_back(line);
+            }
+            fCurrentFileNumber = 0;
+            std::cout << "BasicAFP::process_initialise => list of files to process:" << std::endl;
+            for(auto &i: fListOfIndividualFiles) std::cout << "   -- " << i << std::endl;
+        }
+        else {
+            std::string pathforfiles, basename;
+            UInt_t starting_number;
+
+            filein >> pathforfiles >> basename >> starting_number;
+            if ( filein.good() ) {
+                fPath = pathforfiles;
+                fBaseForName = basename;
+                fCurrentFileNumber = starting_number;
+                std::cout << "BasicAFP::process_initialise " << pathforfiles << " " << basename << " " << starting_number << std::endl;
+            }
+        }
+    }
 	filein.close();
 	
 	// open the first file

src/adf/BasicAFP.h

@@ -48,6 +48,8 @@ private:
 	std::string fPath;
 	//! base for all the files produced
 	std::string fBaseForName;
+    //! in case files are given one by one
+    std::vector<std::string> fListOfIndividualFiles;
 	//! current file 
 	FILE *fCurrentFile;
 	//! current file number

src/root/gui/cubix/CMakeLists.txt

@@ -41,7 +41,7 @@ LINK_DIRECTORIES( ${ROOT_LIBRARY_DIR} )
 SET(EXTRA_EXTERNAL_LIBRARIES ${EXTRA_EXTERNAL_LIBRARIES} Matrix Rint)
 
 # gw
-set(EXTRA_INTERNAL_LIBRARIES GWPHYSICS )
+set(EXTRA_INTERNAL_LIBRARIES GWPHYSICS GWTOOLS)
 
 ####################
 ### define files ###
@@ -72,7 +72,7 @@ ROOT_GENERATE_DICTIONARY(G__${Lib_NAME} ${headers} MODULE ${Lib_NAME} LINKDEF ${
 #####################
 
 #---Create a shared library with geneated dictionary
-add_library(${Lib_NAME} SHARED ${sources} G__${Lib_NAME}.cxx)
+add_library(${Lib_NAME} SHARED ${sources} ${headers} G__${Lib_NAME}.cxx)
 target_link_libraries(${Lib_NAME} ${EXTRA_EXTERNAL_LIBRARIES} ${EXTRA_INTERNAL_LIBRARIES})
 
 #####################

src/root/gui/cubix/DataBase/LevelScheme/README

 How to create/update the database
 
-1) dowload, in the DataBase/LevelScheme/Downloads folder (create it if not existing), the zip files (3 files) from: https://www.nndc.bnl.gov/ensarchivals/
+1) download, in the DataBase/LevelScheme/Downloads folder (create it if not existing), the zip files (3 files) from: https://www.nndc.bnl.gov/ensarchivals/
 
-ex: for the data from 01/11/2018
+ex: for the data from 04/10/2019
 
-wget https://www.nndc.bnl.gov/ensarchivals/distributions/dist18/ensdf_181101_099.zip -P Downloads/
-wget https://www.nndc.bnl.gov/ensarchivals/distributions/dist18/ensdf_181101_199.zip -P Downloads/
-wget https://www.nndc.bnl.gov/ensarchivals/distributions/dist18/ensdf_181101_299.zip -P Downloads/
+mkdir -p $GWSYS/DataBase/LevelScheme/Downloads
+cd $GWSYS/DataBase/LevelScheme/
+
+wget https://www.nndc.bnl.gov/ensarchivals/distributions/dist19/ensdf_191004_099.zip -P Downloads/
+wget https://www.nndc.bnl.gov/ensarchivals/distributions/dist19/ensdf_191004_199.zip -P Downloads/
+wget https://www.nndc.bnl.gov/ensarchivals/distributions/dist19/ensdf_191004_300.zip -P Downloads/
 
 2) execute the ExtractFiles script, giving the files to process in argument:
 
-chmod u+w src/compile.sh
-src/compile.sh
+chmod u+x src/compile.sh
+./src/compile.sh
 ./ExtractFiles Downloads/ensdf_181101_*.zip

src/root/gui/cubix/DataBase/LevelScheme/src/compile.sh

@@ -2,4 +2,4 @@
 NAME=ExtractFiles
 NAME2=src/ExtractFiles.cpp
 
-g++ $NAME2 -o $NAME -O6 -g `root-config --cflags` `root-config --cflags --libs` -lProof
+g++ $NAME2 -o $NAME -O3 -g `root-config --cflags` `root-config --cflags --libs` -lProof

src/root/gui/cubix/DataBase/Sources/133Ba.source

+ 53.156
+ 79.623
+ 80.999
+160.609
+223.116
+276.404
+302.858
+356.014
+383.859

src/root/gui/cubix/DataBase/Sources/134Cs.source

+ 475.36
+ 563.27
+ 569.30
+ 604.68
+ 795.78
+ 801.86
+1038.53
+1167.89
+1365.17

src/root/gui/cubix/DataBase/Sources/137Cs.source

+661.661

src/root/gui/cubix/DataBase/Sources/152Eu.source

+ 121.7793
+ 244.6927
+ 344.2724
+ 411.111
+ 443.979
+ 778.890
+ 964.014
+1085.793
+#1089.700
+1112.070
+1407.993

src/root/gui/cubix/DataBase/Sources/208Pb.source

+2614.5

src/root/gui/cubix/DataBase/Sources/226Ra.source

+ 186.211
+ 241.981
+ 295.213
+ 351.921
+ 609.312
+ 768.356
+ 934.061
+1120.287
+1238.110
+1377.669
+1509.228
+1729.595
+1764.494
+1847.420
+2118.551
+2204.215
+2447.810

src/root/gui/cubix/DataBase/Sources/22Na.source

+ 511.006
+1274.545