data plot with filters

.github/workflows/build-macos.yml

@@ -1,6 +1,6 @@
 name: Build macOS
 
-on: [push]
+on: [push, workflow_dispatch]
 
 jobs:
   build:

.gitignore

@@ -1,7 +1,5 @@
 # builds
-build/*
+build
-build_debug/*
-sandbox/*
 
 # Apple stuff
 *.xcodeproj
@@ -10,27 +8,12 @@ sandbox/*
 # VIM
 *.swp
 
-# autotools
+# Eigen headers and archives
-autom4te.cache/*
+/lib/LatAnalyze/Eigen
-*.in
+eigen-*.tar.bz2
-*.in~
-config.h*
-configure
-configure~
-.buildutils/*
-aclocal.m4
-
-# bison/flex generated sources
-lib/*Lexer.cpp
-lib/*Parser.cpp
-lib/*Parser.hpp
-
-# Eigen headers
-lib/Eigen/*
-lib/eigen_files.mk
 
 # CI builds
-ci-scripts/local/*
+/ci-scripts/local
 
 # VS Code Studio stuff
 .vscode

.travis.yml

@@ -1,63 +0,0 @@
-language: cpp
-  
-cache:
-  directories:
-    - ci-scripts/local
-    - ci-scripts/clang
-
-matrix:
-  include:
-    - os:        osx
-      osx_image: xcode10.1
-      compiler: clang
-    - os:        osx
-      osx_image: xcode10.1
-      compiler: gcc
-      env: VERSION=-7
-    - compiler: gcc
-      addons:
-        apt:
-          sources:
-            - ubuntu-toolchain-r-test
-          packages:
-            - g++-7
-            - flex
-            - bison
-      env: VERSION=-7
-    - compiler: clang
-      addons:
-        apt:
-          sources:
-            - ubuntu-toolchain-r-test
-          packages:
-            - g++-7
-            - flex
-            - bison
-      env: CLANG_LINK=http://releases.llvm.org/7.0.1/clang+llvm-7.0.1-x86_64-linux-gnu-ubuntu-14.04.tar.xz
-
-before_install:
-  - export LATDIR=`pwd`
-  - cd ci-scripts
-  - if [[ "$TRAVIS_OS_NAME" == "linux" ]] && [[ "$CC" == "clang" ]] && [ ! -e clang/bin ]; then wget $CLANG_LINK; tar -xf `basename $CLANG_LINK`; mkdir clang; mv clang+*/* clang/; fi
-  - if [[ "$TRAVIS_OS_NAME" == "linux" ]] && [[ "$CC" == "clang" ]]; then export PATH="${LATDIR}/ci-scripts/clang/bin:${PATH}"; fi
-  - if [[ "$TRAVIS_OS_NAME" == "linux" ]] && [[ "$CC" == "clang" ]]; then export LD_LIBRARY_PATH="${LATDIR}/ci-scripts/clang/lib:${LD_LIBRARY_PATH}"; fi
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew update; fi
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install bison flex cmake; export PATH="/usr/local/opt/flex/bin:/usr/local/opt/bison/bin:$PATH"; fi
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]] && [[ "$CC" == "gcc" ]]; then brew install gcc@${VERSION#-}; fi
-  
-install:
-  - export CC=$CC$VERSION
-  - export CXX=$CXX$VERSION
-  - echo $PATH
-  - which $CC
-  - $CC  --version
-  - which $CXX
-  - $CXX --version
-  - ./install-deps.sh `pwd`/local
-  - cd ..
-  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then export LD_LIBRARY_PATH=${LATDIR}/ci-scripts/local/lib:$LD_LIBRARY_PATH; fi
-  - if [[ "$CC" == "gcc-7" ]]; then export CXXFLAGS='-Wno-int-in-bool-context'; fi
-
-script:
-  - cd ci-scripts
-  - ./install-latan.sh `pwd`/local

CMakeLists.txt

@@ -0,0 +1,94 @@
+# package config
+cmake_minimum_required(VERSION 3.11.0)
+project(
+  LatAnalyze
+  VERSION 3.6
+  LANGUAGES C CXX)
+
+# includes
+include(CheckCXXCompilerFlag)
+include(CMakePackageConfigHelpers)
+include(FetchContent)
+include(FindPackageMessage)
+include(GNUInstallDirs)
+
+# C++ compile flags
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD_REQUIRED True)
+set(CMAKE_CXX_EXTENSIONS OFF)
+check_cxx_compiler_flag("-march=native" COMPILER_SUPPORTS_MARCH_NATIVE)
+if(COMPILER_SUPPORTS_MARCH_NATIVE)
+  set(MARCH_FLAG "-march=native")
+endif()
+check_cxx_compiler_flag("-mtune=native" COMPILER_SUPPORTS_MTUNE_NATIVE)
+if(COMPILER_SUPPORTS_MTUNE_NATIVE)
+  set(MTUNE_FLAG "-mtune=native")
+endif()
+set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG ${MARCH_FLAG} ${MTUNE_FLAG}")
+set(CMAKE_CXX_FLAGS_RELWITHDEBINFO
+    "-O3 -g -DNDEBUG ${MARCH_FLAG} ${MTUNE_FLAG}")
+set(gcc_like_cxx "$<COMPILE_LANG_AND_ID:CXX,ARMClang,AppleClang,Clang,GNU,LCC>")
+add_library(compiler_flags INTERFACE)
+target_compile_features(compiler_flags INTERFACE cxx_std_17)
+target_compile_options(
+  compiler_flags
+  INTERFACE "$<${gcc_like_cxx}:-Wall;-Wextra;-Wshadow;-Wformat=2;-Wunused>")
+
+# position idependent code
+set(CMAKE_POSITION_INDEPENDENT_CODE ON)
+
+# installation rpath setup
+set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR}")
+
+# fetch and create symbolic link to Eigen headers
+set(FETCHCONTENT_BASE_DIR ${CMAKE_BINARY_DIR}/deps)
+FetchContent_Declare(
+  Eigen3
+  GIT_REPOSITORY https://gitlab.com/libeigen/eigen.git
+  GIT_TAG 3.4.0)
+FetchContent_GetProperties(Eigen3)
+if(NOT eigen3_POPULATED)
+  FetchContent_Populate(Eigen3)
+  message(STATUS "Eigen3 fetched")
+endif()
+file(CREATE_LINK ${eigen3_SOURCE_DIR}/Eigen
+     ${CMAKE_SOURCE_DIR}/lib/LatAnalyze/Eigen SYMBOLIC)
+
+# dependencies
+find_package(Threads REQUIRED)
+find_package(GSL REQUIRED)
+find_package(HDF5 REQUIRED COMPONENTS C CXX)
+find_package(Minuit2 QUIET)
+if(Minuit2_FOUND)
+  set(Minuit2_MSG "yes")
+  find_package_message(
+    Minuit2
+    "Found Minuit2: ${Minuit2_DIR} (found version \"${Minuit2_VERSION}\")" " ")
+else()
+  set(Minuit2_MSG "no")
+  message(STATUS "Minuit2 not found")
+endif()
+find_package(NLopt QUIET)
+if(NLopt_FOUND)
+  set(NLopt_MSG "yes")
+  find_package_message(
+    NLopt "Found NLopt: ${NLopt_DIR} (found version \"${NLopt_VERSION}\")" " ")
+else()
+  set(NLopt_MSG "no")
+  message(STATUS "NLopt not found")
+endif()
+
+# subdirectories
+add_subdirectory(lib)
+add_subdirectory(examples)
+add_subdirectory(physics)
+add_subdirectory(utils)
+
+# summary
+message(STATUS "---------------------------")
+message(STATUS "LatAnalyze v${PROJECT_VERSION} configured")
+message(STATUS "---------------------------")
+message(STATUS "    install prefix: ${CMAKE_INSTALL_PREFIX}")
+message(STATUS "Minuit2 minimisers: ${Minuit2_MSG}")
+message(STATUS "  NLopt minimisers: ${NLopt_MSG}")
+message(STATUS "---------------------------")

Makefile.am

@@ -1,5 +0,0 @@
-SUBDIRS = lib utils physics examples
-
-bin_SCRIPTS=latan-config
-
-ACLOCAL_AMFLAGS = -I .buildutils/m4

Readme.md

@@ -3,19 +3,19 @@
 [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0) [![DOI](https://zenodo.org/badge/10201777.svg)](https://zenodo.org/badge/latestdoi/10201777) [![Build Ubuntu](https://github.com/aportelli/LatAnalyze/actions/workflows/build-ubuntu.yml/badge.svg)](https://github.com/aportelli/LatAnalyze/actions/workflows/build-ubuntu.yml) [![Build macOS](https://github.com/aportelli/LatAnalyze/actions/workflows/build-macos.yml/badge.svg)](https://github.com/aportelli/LatAnalyze/actions/workflows/build-macos.yml)
 
 ## Description
-LatAnalyze is a C++11 library for statistical data analysis based on bootstrap
+LatAnalyze is a C++14 library for statistical data analysis based on bootstrap
 resampling. It has been written with lattice QCD data analysis in mind (hence
 the name), but its features are not lattice specific and can be used more general statistical context.
 
-Sadly a proper documentation was never written, but some comprehensive examples covering most features can be found in the `examples` directory.
+Sadly a proper documentation was never written, but some comprehensive examples covering several key features can be found in the `examples` directory.
 
 The main features are the following:
 
 * Array and matrix types with fast arithmetic operations based on [Eigen](http://eigen.tuxfamily.org).
 * High-level types for bootstrap sample manipulation (including various statistical estimators and histogramming).
 * Mathematical expression parser for runtime defined functions.
-* Data I/O in ASCII and HDF5 (optional).
+* Data I/O in ASCII, XML, and HDF5.
-* High-level wrappers to minimisation routines from the [GSL](http://www.gnu.org/software/gsl/), [Minuit](http://seal.web.cern.ch/seal/snapshot/work-packages/mathlibs/minuit/) (optional) and [NLopt](http://ab-initio.mit.edu/wiki/index.php/NLopt).
+* High-level wrappers to minimisation routines from the [GSL](http://www.gnu.org/software/gsl/), [Minuit 2](https://github.com/root-project/root/tree/master/math/minuit2) (optional) and [NLopt](http://ab-initio.mit.edu/wiki/index.php/NLopt).
 * Non-linear regression with error on independent variables (through total least squares).
 * High-level wrappers to numerical integrator and non-linear solver from the [GSL](http://www.gnu.org/software/gsl/).
 * High-level functional types for function of model. General functions can be defined from C pointers, C++ objects, strings of mathematical expressions or tabulated data.
@@ -24,14 +24,14 @@ The main features are the following:
 ## Installation
 The head of the `master` branch always points to the latest stable release. The `develop` branch is the main unstable branch of LatAnalyze.
 
-LatAnalyze is written in C++11 and requires a rather recent C++ compiler to be built. It has been successfully built on various Linux and OS X platforms using clang (from 3.7), GCC (from 4.9) and the Intel C++ compiler (2016).
+LatAnalyze is written in C++14. It has been successfully built on various Unix platform using reasonably recent versions of Clang or GCC.
-The only strict dependencies is the [GSL](http://www.gnu.org/software/gsl/).
+The only strict dependencies are the [GSL](http://www.gnu.org/software/gsl/) and [HDF5](https://www.hdfgroup.org/HDF5/) (built with C++ support).
-Additionally, autoconf, automake (from 1.11), libtool, bison (from 3.0) and flex are necessary to build the library. Unless you use a very exotic system, these tools are standard on any Unix platform and should be already present or easy to install through a package manager.
+Additionally, cmake (from 3.11), bison (from 3.0) and flex are necessary to build the library. Unless you use a very exotic system, these tools are standard on any Unix platform and should be already present or easy to install through a package manager.
-Optional dependencies are [HDF5](https://www.hdfgroup.org/HDF5/) (built with C++ support), [Minuit](http://seal.web.cern.ch/seal/snapshot/work-packages/mathlibs/minuit/) and [NLopt](http://ab-initio.mit.edu/wiki/index.php/NLopt).
+Optional dependencies are [Minuit 2](https://github.com/root-project/root/tree/master/math/minuit2) and [NLopt](http://ab-initio.mit.edu/wiki/index.php/NLopt).
 
-Below are instructions for a quick installation. For a more customised installation, one first needs to generate the build system by running `./bootstrap.sh` in the root directory. Then the library can be built and installed through the usual GNU mantra `./configure <options> && make && make install`. Use `./configure --help` to obtain a list of possible options for `./configure`. Because Eigen expressions rely a lot on inlining and compiler optimisations it is strongly recommended to set the `CXXFLAGS` variable to `-O3 -march=native -mtune=native`.
+LatAnalyze is built through CMake. Below are example instructions for compiling and installing LatAnalyze. 
 
-### General quick installation
+### Portable quick installation
 For a quick installation with all possible extensions execute: 
 ```
 ./install-latan.sh <prefix>
@@ -43,19 +43,53 @@ All the dependencies of LatAnalyze can be installed through the [Homebrew](https
 ```
 brew install automake autoconf libtool bison flex gsl minuit2 nlopt hdf5
 ```
-Then generate the build system in LatAnalyze main directory by running the `./bootstrap.sh` script. Finally, build the library
+Then build the library with `cmake`
 ```
 mkdir build
 cd build
-../configure --prefix=<prefix> --with-minuit=/usr/local --with-nlopt=/usr/local \
+cmake -DCMAKE_INSTALL_PREFIX=<prefix> -DCMAKE_BUILD_TYPE=Release ..
-             --with-hdf5=/usr/local --with-gsl=/usr/local                       \
-             CXXFLAGS='-g -O3 -march=native -mtune=native'
 make -j <n>
 make install
 ```
-where `<prefix>` should be replaced by the desired prefix for LatAnalyze installation, and `<n>` is the number of parallel build processes (typically twice your number of cores).
+where `<prefix>` should be replaced by the desired prefix for LatAnalyze installation, and `<n>` is the number of parallel build processes.
+
+### Dependencies through Homebrew/Linuxbrew
+If you use Homebrew/Linuxbrew to manage packages, the following command can install all the dependencies of LatAnalyze (including optional ones)
+
+## Using LatAnalyze in CMake projects
+When LatAnalyze is installed, the necessary CMake module configuration files to link against the library are available in the installation prefix.
+
+To link against LatAnalyze in a downstream CMake project, simply use
+```cmake
+find_package(LatAnalyze)
+target_link_libraries(<my_app> LatAnalyze::LatAnalyze)
+```
+where `<my_app>` is a CMake target. If LatAnalyze was installed in a non-standard prefix, you might have to set `CMAKE_PREFIX_PATH` accordingly for `find_package` to be successful.
+
+You can additionally modify the `find_package` to ensure specific components are supported
+```cmake
+find_package(LatAnalyze REQUIRED COMPONENTS <...>)
+```
+where `<...>` is a space separated list of components. Currently available components are
+- `MINUIT2`: Minuit 2 minimisers
+- `NLOPT`: NLopt minimisers
 
 ## History
+#### v3.6
+Build system:
+* automake build discontinued, now using CMake
+* CI through GitHub Actions
+
+Additions:
+* Discrete wavelet transform
+* Thread pools
+* Correlation dynamic range (CDR) calculation
+* Data filtering and CDR optimisation
+
+Changes:
+* Significant optimisation of covariance matrix calculation
+* Covariance matrix available for any `StatArray` (not only resampled arrays)
+
 #### v3.5.1
 Various fixes and cleaning of outdated code.
 

acinclude.m4

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-#   The optional macro argument should be either 'serial' or 'parallel'. The
-#   former only looks for serial HDF5 installations via h5cc. The latter
-#   only looks for parallel HDF5 installations via h5pcc. If the optional
-#   argument is omitted, serial installations will be preferred over
-#   parallel ones.
-#
-#   The macro adds a --with-hdf5 option accepting one of three values:
-#
-#     no   - do not check for the HDF5 library.
-#     yes  - do check for HDF5 library in standard locations.
-#     path - complete path to the HDF5 helper script h5cc or h5pcc.
-#
-#   If HDF5 is successfully found, this macro calls
-#
-#     AC_SUBST(HDF5_VERSION)
-#     AC_SUBST(HDF5_CC)
-#     AC_SUBST(HDF5_CFLAGS)
-#     AC_SUBST(HDF5_CPPFLAGS)
-#     AC_SUBST(HDF5_LDFLAGS)
-#     AC_SUBST(HDF5_LIBS)
-#     AC_SUBST(HDF5_FC)
-#     AC_SUBST(HDF5_FFLAGS)
-#     AC_SUBST(HDF5_FLIBS)
-#     AC_DEFINE(HAVE_HDF5)
-#
-#   and sets with_hdf5="yes".  Additionally, the macro sets
-#   with_hdf5_fortran="yes" if a matching Fortran wrapper script is found.
-#   Note that Autconf's Fortran support is not used to perform this check.
-#   H5CC and H5FC will contain the appropriate serial or parallel HDF5
-#   wrapper script locations.
-#
-#   If HDF5 is disabled or not found, this macros sets with_hdf5="no" and
-#   with_hdf5_fortran="no".
-#
-#   Your configuration script can test $with_hdf to take any further
-#   actions. HDF5_{C,CPP,LD}FLAGS may be used when building with C or C++.
-#   HDF5_F{FLAGS,LIBS} should be used when building Fortran applications.
-#
-#   To use the macro, one would code one of the following in "configure.ac"
-#   before AC_OUTPUT:
-#
-#     1) dnl Check for HDF5 support
-#        AX_LIB_HDF5()
-#
-#     2) dnl Check for serial HDF5 support
-#        AX_LIB_HDF5([serial])
-#
-#     3) dnl Check for parallel HDF5 support
-#        AX_LIB_HDF5([parallel])
-#
-#   One could test $with_hdf5 for the outcome or display it as follows
-#
-#     echo "HDF5 support:  $with_hdf5"
-#
-#   You could also for example, override the default CC in "configure.ac" to
-#   enforce compilation with the compiler that HDF5 uses:
-#
-#     AX_LIB_HDF5([parallel])
-#     if test "$with_hdf5" = "yes"; then
-#             CC="$HDF5_CC"
-#     else
-#             AC_MSG_ERROR([Unable to find HDF5, we need parallel HDF5.])
-#     fi
-#
-# LICENSE
-#
-#   Copyright (c) 2009 Timothy Brown <tbrown@freeshell.org>
-#   Copyright (c) 2010 Rhys Ulerich <rhys.ulerich@gmail.com>
-#
-#   Copying and distribution of this file, with or without modification, are
-#   permitted in any medium without royalty provided the copyright notice
-#   and this notice are preserved. This file is offered as-is, without any
-#   warranty.
-
-AC_DEFUN([AX_LIB_HDF5], [
-
-AC_REQUIRE([AC_PROG_SED])
-AC_REQUIRE([AC_PROG_AWK])
-AC_REQUIRE([AC_PROG_GREP])
-
-dnl Check first argument is one of the recognized values.
-dnl Fail eagerly if is incorrect as this simplifies case statements below.
-if   test "m4_normalize(m4_default([$1],[]))" = ""        ; then
-    : # Recognized value
-elif test "m4_normalize(m4_default([$1],[]))" = "serial"  ; then
-    : # Recognized value
-elif test "m4_normalize(m4_default([$1],[]))" = "parallel"; then
-    : # Recognized value
-else
-    AC_MSG_ERROR([
-Unrecognized value for AX[]_LIB_HDF5 within configure.ac.
-If supplied, argument 1 must be either 'serial' or 'parallel'.
-])
-fi
-
-dnl Add a default --with-hdf5 configuration option.
-AC_ARG_WITH([hdf5],
-  AS_HELP_STRING(
-    [--with-hdf5=[yes/no/PATH]],
-    m4_case(m4_normalize([$1]),
-            [serial],   [location of h5cc for serial HDF5 configuration],
-            [parallel], [location of h5pcc for parallel HDF5 configuration],
-            [location of h5cc or h5pcc for HDF5 configuration])
-  ),
-  [if test "$withval" = "no"; then
-     with_hdf5="no"
-   elif test "$withval" = "yes"; then
-     with_hdf5="yes"
-   else
-     with_hdf5="yes"
-     H5CC="$withval"
-   fi],
-   [with_hdf5="yes"]
-)
-
-dnl Set defaults to blank
-HDF5_CC=""
-HDF5_VERSION=""
-HDF5_CFLAGS=""
-HDF5_CPPFLAGS=""
-HDF5_LDFLAGS=""
-HDF5_LIBS=""
-HDF5_FC=""
-HDF5_FFLAGS=""
-HDF5_FLIBS=""
-
-dnl Try and find hdf5 compiler tools and options.
-if test "$with_hdf5" = "yes"; then
-    if test -z "$H5CC"; then
-        dnl Check to see if H5CC is in the path.
-        AC_PATH_PROGS(
-            [H5CC],
-            m4_case(m4_normalize([$1]),
-                [serial],   [h5cc],
-                [parallel], [h5pcc],
-                [h5cc h5pcc]),
-            [])
-    else
-        AC_MSG_CHECKING([Using provided HDF5 C wrapper])
-        AC_MSG_RESULT([$H5CC])
-    fi
-    AC_MSG_CHECKING([for HDF5 libraries])
-    if test ! -f "$H5CC" || test ! -x "$H5CC"; then
-        AC_MSG_RESULT([no])
-        AC_MSG_WARN(m4_case(m4_normalize([$1]),
-            [serial],  [
-Unable to locate serial HDF5 compilation helper script 'h5cc'.
-Please specify --with-hdf5=<LOCATION> as the full path to h5cc.
-HDF5 support is being disabled (equivalent to --with-hdf5=no).
-],            [parallel],[
-Unable to locate parallel HDF5 compilation helper script 'h5pcc'.
-Please specify --with-hdf5=<LOCATION> as the full path to h5pcc.
-HDF5 support is being disabled (equivalent to --with-hdf5=no).
-],            [
-Unable to locate HDF5 compilation helper scripts 'h5cc' or 'h5pcc'.
-Please specify --with-hdf5=<LOCATION> as the full path to h5cc or h5pcc.
-HDF5 support is being disabled (equivalent to --with-hdf5=no).
-]))
-        with_hdf5="no"
-        with_hdf5_fortran="no"
-    else
-        dnl Get the h5cc output
-        HDF5_SHOW=$(eval $H5CC -show)
-
-        dnl Get the actual compiler used
-        HDF5_CC=$(eval $H5CC -show | $AWK '{print $[]1}')
-        if test "$HDF5_CC" = "ccache"; then
-            HDF5_CC=$(eval $H5CC -show | $AWK '{print $[]2}')
-        fi
-
-        dnl h5cc provides both AM_ and non-AM_ options
-        dnl depending on how it was compiled either one of
-        dnl these are empty. Lets roll them both into one.
-
-        dnl Look for "HDF5 Version: X.Y.Z"
-        HDF5_VERSION=$(eval $H5CC -showconfig | $GREP 'HDF5 Version:' \
-            | $AWK '{print $[]3}')
-
-        dnl A ideal situation would be where everything we needed was
-        dnl in the AM_* variables. However most systems are not like this
-        dnl and seem to have the values in the non-AM variables.
-        dnl
-        dnl We try the following to find the flags:
-        dnl (1) Look for "NAME:" tags
-        dnl (2) Look for "H5_NAME:" tags
-        dnl (3) Look for "AM_NAME:" tags
-        dnl
-        HDF5_tmp_flags=$(eval $H5CC -showconfig \
-            | $GREP 'FLAGS\|Extra libraries:' \
-            | $AWK -F: '{printf("%s "), $[]2}' )
-
-        dnl Find the installation directory and append include/
-        HDF5_tmp_inst=$(eval $H5CC -showconfig \
-            | $GREP 'Installation point:' \
-            | $AWK '{print $[]NF}' )
-
-        dnl Add this to the CPPFLAGS
-        HDF5_CPPFLAGS="-I${HDF5_tmp_inst}/include"
-
-        dnl Now sort the flags out based upon their prefixes
-        for arg in $HDF5_SHOW $HDF5_tmp_flags ; do
-          case "$arg" in
-            -I*) echo $HDF5_CPPFLAGS | $GREP -e "$arg" 2>&1 >/dev/null \
-                  || HDF5_CPPFLAGS="$arg $HDF5_CPPFLAGS"
-              ;;
-            -L*) echo $HDF5_LDFLAGS | $GREP -e "$arg" 2>&1 >/dev/null \
-                  || HDF5_LDFLAGS="$arg $HDF5_LDFLAGS"
-              ;;
-            -l*) echo $HDF5_LIBS | $GREP -e "$arg" 2>&1 >/dev/null \
-                  || HDF5_LIBS="$arg $HDF5_LIBS"
-              ;;
-          esac
-        done
-
-        HDF5_LIBS="$HDF5_LIBS -lhdf5"
-        AC_MSG_RESULT([yes (version $[HDF5_VERSION])])
-
-        dnl See if we can compile
-        ax_lib_hdf5_save_CC=$CC
-        ax_lib_hdf5_save_CPPFLAGS=$CPPFLAGS
-        ax_lib_hdf5_save_LIBS=$LIBS
-        ax_lib_hdf5_save_LDFLAGS=$LDFLAGS
-        CC=$HDF5_CC
-        CPPFLAGS=$HDF5_CPPFLAGS
-        LIBS=$HDF5_LIBS
-        LDFLAGS=$HDF5_LDFLAGS
-        AC_CHECK_HEADER([hdf5.h], [ac_cv_hadf5_h=yes], [ac_cv_hadf5_h=no])
-        AC_CHECK_LIB([hdf5], [H5Fcreate], [ac_cv_libhdf5=yes],
-                     [ac_cv_libhdf5=no])
-        if test "$ac_cv_hadf5_h" = "no" && test "$ac_cv_libhdf5" = "no" ; then
-          AC_MSG_WARN([Unable to compile HDF5 test program])
-        fi
-        dnl Look for HDF5's high level library
-        AC_HAVE_LIBRARY([hdf5_hl], [HDF5_LIBS="$HDF5_LIBS -lhdf5_hl"], [], [])
-
-        CC=$ax_lib_hdf5_save_CC
-        CPPFLAGS=$ax_lib_hdf5_save_CPPFLAGS
-        LIBS=$ax_lib_hdf5_save_LIBS
-        LDFLAGS=$ax_lib_hdf5_save_LDFLAGS
-
-        AC_MSG_CHECKING([for matching HDF5 Fortran wrapper])
-        dnl Presume HDF5 Fortran wrapper is just a name variant from H5CC
-        H5FC=$(eval echo -n $H5CC | $SED -n 's/cc$/fc/p')
-        if test -x "$H5FC"; then
-            AC_MSG_RESULT([$H5FC])
-            with_hdf5_fortran="yes"
-            AC_SUBST([H5FC])
-
-            dnl Again, pry any remaining -Idir/-Ldir from compiler wrapper
-            for arg in `$H5FC -show`
-            do
-              case "$arg" in #(
-                -I*) echo $HDF5_FFLAGS | $GREP -e "$arg" >/dev/null \
-                      || HDF5_FFLAGS="$arg $HDF5_FFLAGS"
-                  ;;#(
-                -L*) echo $HDF5_FFLAGS | $GREP -e "$arg" >/dev/null \
-                      || HDF5_FFLAGS="$arg $HDF5_FFLAGS"
-                     dnl HDF5 installs .mod files in with libraries,
-                     dnl but some compilers need to find them with -I
-                     echo $HDF5_FFLAGS | $GREP -e "-I${arg#-L}" >/dev/null \
-                      || HDF5_FFLAGS="-I${arg#-L} $HDF5_FFLAGS"
-                  ;;
-              esac
-            done
-
-            dnl Make Fortran link line by inserting Fortran libraries
-            for arg in $HDF5_LIBS
-            do
-              case "$arg" in #(
-                -lhdf5_hl) HDF5_FLIBS="$HDF5_FLIBS -lhdf5hl_fortran $arg"
-                  ;; #(
-                -lhdf5)    HDF5_FLIBS="$HDF5_FLIBS -lhdf5_fortran $arg"
-                  ;; #(
-                *) HDF5_FLIBS="$HDF5_FLIBS $arg"
-                  ;;
-              esac
-            done
-        else
-            AC_MSG_RESULT([no])
-            with_hdf5_fortran="no"
-        fi
-
-	AC_SUBST([HDF5_VERSION])
-	AC_SUBST([HDF5_CC])
-	AC_SUBST([HDF5_CFLAGS])
-	AC_SUBST([HDF5_CPPFLAGS])
-	AC_SUBST([HDF5_LDFLAGS])
-	AC_SUBST([HDF5_LIBS])
-	AC_SUBST([HDF5_FC])
-	AC_SUBST([HDF5_FFLAGS])
-	AC_SUBST([HDF5_FLIBS])
-	AC_DEFINE([HAVE_HDF5], [1], [Defined if you have HDF5 support])
-    fi
-fi
-])
-

bootstrap.sh

@@ -1,6 +0,0 @@
-#!/usr/bin/env bash
-
-rm -rf .buildutils
-mkdir -p .buildutils/m4
-./update_eigen.sh eigen-3.3.8.tar.bz2
-autoreconf -fvi

build.sh

@@ -1,24 +0,0 @@
-#!/bin/bash
-
-set -e
-
-PREFIX=`cat Makefile | grep '^prefix =' | awk '{print $3}'`
-case $1 in
-    '')
-        echo '-- building...'
-        make -j8
-        echo '-- installing...'
-        make uninstall 1>/dev/null
-        make install 1>/dev/null;;
-#        if [[ `basename \`pwd\`` == "lib" ]]
-#        then
-#            echo '-- creating debug symbols...'
-#            dsymutil .libs/libLatAnalyze.0.dylib -o ${PREFIX}/lib/libLatAnalyze.0.dylib.dSYM
-#        fi;;
-    'clean')
-        echo '-- cleaning...'
-        make -j8 clean;;
-    *)
-        echo 'error: unknown action' 1>&2
-        exit 1;;
-esac

ci-scripts/install-deps.sh

@@ -1,16 +1,16 @@
 #!/usr/bin/env bash
 
-if (( $# != 2 )); then
+if (($# != 2)); then
-  echo "usage: `basename $0` <prefix> <ntasks>" 1>&2
+  echo "usage: $(basename "$0") <prefix> <ntasks>" 1>&2
   exit 1
 fi
-PREFIX=$1
+prefix=$1
-NTASKS=$2
+ntasks=$2
 
 set -ex
 mkdir -p local/build
 for d in gsl nlopt minuit hdf5; do
   if [ ! -e local/.built.${d} ]; then
-    ./install-${d}.sh ${PREFIX} ${NTASKS}
+    ./install-${d}.sh "${prefix}" "${ntasks}"
   fi
 done

ci-scripts/install-gsl.sh

@@ -1,27 +1,27 @@
 #!/usr/bin/env bash
 
-NAME='gsl-2.6'
+name='gsl-2.6'
 
-if (( $# != 2 )); then
+if (($# != 2)); then
-  echo "usage: `basename $0` <prefix> <ntasks>" 1>&2
+  echo "usage: $(basename "$0") <prefix> <ntasks>" 1>&2
   exit 1
 fi
-PREFIX=$1
+prefix=$1
-NTASKS=$2
+ntasks=$2
 
 set -ex
-INITDIR=$(pwd -P)
+init_dir=$(pwd -P)
-mkdir -p ${PREFIX}
+mkdir -p "${prefix}"
-cd ${PREFIX}
+cd "${prefix}"
-PREFIX=$(pwd -P)
+prefix=$(pwd -P)
-cd ${INITDIR}/local/build
+cd "${init_dir}/local/build"
-wget http://ftpmirror.gnu.org/gsl/${NAME}.tar.gz
+wget http://ftpmirror.gnu.org/gsl/${name}.tar.gz
-tar -xzvf ${NAME}.tar.gz
+tar -xzvf ${name}.tar.gz
-mkdir -p ${NAME}/build
+mkdir -p ${name}/build
-cd ${NAME}/build
+cd ${name}/build
-../configure --prefix=${PREFIX}
+../configure --prefix="${prefix}"
-make -j${NTASKS}
+make -j"${ntasks}"
 make install
-cd ${INITDIR}/local
+cd "${init_dir}/local"
 touch .built.gsl
-cd ${INITDIR}
+cd "${init_dir}"

ci-scripts/install-hdf5.sh

@@ -1,27 +1,27 @@
 #!/usr/bin/env bash
 
-NAME='hdf5-1.10.8'
+name='hdf5-1.14.3'
 
-if (( $# != 2 )); then
+if (($# != 2)); then
-  echo "usage: `basename $0` <prefix> <ntasks>" 1>&2
+  echo "usage: $(basename "$0") <prefix> <ntasks>" 1>&2
   exit 1
 fi
-PREFIX=$1
+prefix=$1
-NTASKS=$2
+ntasks=$2
 
 set -ex
-INITDIR=$(pwd -P)
+init_dir=$(pwd -P)
-mkdir -p ${PREFIX}
+mkdir -p "${prefix}"
-cd ${PREFIX}
+cd "${prefix}"
-PREFIX=$(pwd -P)
+prefix=$(pwd -P)
-cd ${INITDIR}/local/build
+cd "${init_dir}/local/build"
-wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/${NAME}/src/${NAME}.tar.gz
+wget "https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.14/${name}/src/${name}.tar.gz"
-tar -xzvf ${NAME}.tar.gz
+tar -xzvf ${name}.tar.gz
-mkdir ${NAME}/build
+mkdir ${name}/build
-cd ${NAME}/build
+cd ${name}/build
-../configure --prefix=${PREFIX} --enable-cxx
+../configure --prefix="${prefix}" --enable-cxx
-make -j${NTASKS}
+make -j "${ntasks}"
 make install
-cd ${INITDIR}/local
+cd "${init_dir}/local"
 touch .built.hdf5
-cd ${INITDIR}
+cd "${init_dir}"

ci-scripts/install-latan.sh

@@ -1,23 +1,22 @@
 #!/usr/bin/env bash
 
-if (( $# != 2 )); then
+if (($# != 2)); then
-  echo "usage: `basename $0` <prefix> <ntasks>" 1>&2
+  echo "usage: $(basename "$0") <prefix> <ntasks>" 1>&2
   exit 1
 fi
-PREFIX=$1
+prefix=$1
-NTASKS=$2
+ntasks=$2
 
 set -ex
-INITDIR=$(pwd -P)
+init_dir=$(pwd -P)
-mkdir -p ${PREFIX}
+mkdir -p "${prefix}"
-cd ${PREFIX}
+cd "${prefix}"
-PREFIX=$(pwd -P)
+prefix=$(pwd -P)
-cd ${INITDIR}
+cd "${init_dir}"
-./install-deps.sh ${PREFIX} ${NTASKS}
+./install-deps.sh "${prefix}" "${ntasks}"
-cd ..
+mkdir -p "${init_dir}/local/build/latan"
-./bootstrap.sh
+cd "${init_dir}/local/build/latan"
-mkdir -p build
+cmake -DCMAKE_INSTALL_PREFIX="${prefix}" -DCMAKE_PREFIX_PATH="${prefix}" \
-cd build
+  -DCMAKE_BUILD_TYPE="RelWithDebInfo" "${init_dir}/.."
-../configure --prefix=${PREFIX} --with-minuit=${PREFIX} --with-nlopt=${PREFIX} --with-hdf5=${PREFIX} --with-gsl=${PREFIX} CXXFLAGS="${CXXFLAGS} -O3 -march=native -mtune=native"
+make -j "${ntasks}"
-make -j${NTASKS}
 make install

ci-scripts/install-minuit.sh

@@ -1,26 +1,26 @@
 #!/usr/bin/env bash
 
-
+if (($# != 2)); then
-if (( $# != 2 )); then
+  echo "usage: $(basename "$0") <prefix> <ntasks>" 1>&2
-  echo "usage: `basename $0` <prefix> <ntasks>" 1>&2
   exit 1
 fi
-PREFIX=$1
+prefix=$1
-NTASKS=$2
+ntasks=$2
 
 set -ex
-INITDIR=$(pwd -P)
+init_dir=$(pwd -P)
-mkdir -p ${PREFIX}
+mkdir -p "${prefix}"
-cd ${PREFIX}
+cd "${prefix}"
-PREFIX=$(pwd -P)
+prefix=$(pwd -P)
-cd ${INITDIR}/local/build
+cd "${init_dir}/local/build"
 rm -rf root
 git clone https://github.com/root-project/root.git
 cd root/math/minuit2/
-mkdir build; cd build
+mkdir build
-cmake .. -Dminuit2_standalone=ON -DCMAKE_INSTALL_PREFIX=${PREFIX}
+cd build
-make -j${NTASKS}
+cmake .. -Dminuit2_standalone=ON -DCMAKE_INSTALL_PREFIX="${prefix}"
+make -j "${ntasks}"
 make install
-cd ${INITDIR}/local
+cd "${init_dir}/local"
 touch .built.minuit
-cd ${INITDIR}
+cd "${init_dir}"

ci-scripts/install-nlopt.sh

@@ -1,28 +1,30 @@
 #!/usr/bin/env bash
 
-NAME='2.6.1'
+name='2.6.1'
 
-if (( $# != 2 )); then
+if (($# != 2)); then
-  echo "usage: `basename $0` <prefix> <ntasks>" 1>&2
+  echo "usage: $(basename "$0") <prefix> <ntasks>" 1>&2
   exit 1
 fi
-PREFIX=$1
+prefix=$1
-NTASKS=$2
+ntasks=$2
 
 set -ex
-INITDIR=$(pwd -P)
+init_dir=$(pwd -P)
-mkdir -p ${PREFIX}
+mkdir -p "${prefix}"
-cd ${PREFIX}
+cd "${prefix}"
-PREFIX=$(pwd -P)
+prefix=$(pwd -P)
-cd ${INITDIR}/local/build
+cd "${init_dir}/local/build"
-wget https://github.com/stevengj/nlopt/archive/v${NAME}.tar.gz
+wget "https://github.com/stevengj/nlopt/archive/v${name}.tar.gz"
-tar -xzvf v${NAME}.tar.gz
+tar -xzvf v${name}.tar.gz
-NAME=nlopt-${NAME}
+name=nlopt-${name}
-mkdir -p ${NAME}/build
+mkdir -p ${name}/build
-cd ${NAME}/build
+cd ${name}/build
-cmake -DCMAKE_INSTALL_PREFIX=${PREFIX} -DCMAKE_BUILD_WITH_INSTALL_NAME_DIR=TRUE -DCMAKE_INSTALL_NAME_DIR="${PREFIX}/lib" ..
+cmake -DCMAKE_INSTALL_PREFIX="${prefix}" -DCMAKE_BUILD_WITH_INSTALL_NAME_DIR=TRUE \
-make -j${NTASKS}
+  -DCMAKE_INSTALL_NAME_DIR="${prefix}/lib" -DNLOPT_PYTHON=OFF -DNLOPT_OCTAVE=OFF \
+  -DNLOPT_MATLAB=OFF -DNLOPT_GUILE=OFF -DNLOPT_SWIG=OFF ..
+make -j "${ntasks}"
 make install
-cd ${INITDIR}/local
+cd "${init_dir}/local"
 touch .built.nlopt
-cd ${INITDIR}
+cd "${init_dir}"

configure.ac

@@ -1,167 +0,0 @@
-# Process this file with autoconf to produce a configure script.
-
-# Initialization
-AC_PREREQ([2.63])
-AC_INIT([LatAnalyze],[3.5.1-dev],[antonin.portelli@me.com],[LatAnalyze])
-AC_CONFIG_AUX_DIR([.buildutils])
-AC_CONFIG_SRCDIR([lib/Global.cpp])
-AC_CONFIG_SRCDIR([utils/sample_read.cpp])
-AC_CONFIG_SRCDIR([examples/exMathInterpreter.cpp])
-AC_CONFIG_MACRO_DIR([.buildutils/m4])
-AM_INIT_AUTOMAKE([1.11 -Wall -Werror foreign subdir-objects])
-AM_SILENT_RULES([yes])
-AC_CONFIG_HEADERS([config.h])
-AM_CONDITIONAL([HAVE_AM_MINOR_LE_11],
-               [test `automake --version | grep automake | awk -F '.' '{print $2}'` -le 11])
-# Checks for programs
-AC_PROG_CXX
-AC_PROG_AWK
-AC_PROG_CC
-AC_PROG_CPP
-AC_PROG_INSTALL
-AC_PROG_LN_S
-AC_PROG_MAKE_SET
-AC_PROG_LEX
-AC_PROG_YACC
-m4_ifdef([AM_PROG_AR],[AM_PROG_AR])
-
-LT_INIT
-
-# Options
-AC_ARG_WITH([gsl],
-    [AS_HELP_STRING([--with-gsl=prefix],
-		[try this for a non-standard install prefix of the GSL library])],
-	[AM_CXXFLAGS="$AM_CXXFLAGS -I$with_gsl/include"]
-	[AM_LDFLAGS="$AM_LDFLAGS -L$with_gsl/lib"])
-AC_ARG_WITH([minuit],
-    [AS_HELP_STRING([--with-minuit=prefix],
-		[try this for a non-standard install prefix of the Minuit2 library])],
-    [AM_CXXFLAGS="$AM_CXXFLAGS -I$with_minuit/include -I$with_minuit/include/Minuit2 -I$with_minuit/include/Fit"]
-	[AM_LDFLAGS="$AM_LDFLAGS -L$with_minuit/lib"])
-AC_ARG_WITH([nlopt],
-    [AS_HELP_STRING([--with-nlopt=prefix],
-        [try this for a non-standard install prefix of the NLopt library])],
-    [AM_CXXFLAGS="$AM_CXXFLAGS -I$with_nlopt/include"]
-    [AM_LDFLAGS="$AM_LDFLAGS -L$with_nlopt/lib"])
-AC_ARG_WITH([hdf5],
-    [AS_HELP_STRING([--with-hdf5=prefix],
-    [try this for a non-standard install prefix of the HDF5 library])],
-    [AM_CXXFLAGS="$AM_CXXFLAGS -I$with_hdf5/include"]
-    [AM_LDFLAGS="$AM_LDFLAGS -L$with_hdf5/lib"])
-
-# Get compilers informations
-AX_COMPILER_VENDOR
-AC_DEFINE_UNQUOTED([C_COMP_VENDOR],["$ax_cv_c_compiler_vendor"],
-			[vendor of C compiler that will compile the code])
-AM_CONDITIONAL([CC_GNU],[test $ax_cv_c_compiler_vendor = "gnu"])
-AM_CONDITIONAL([CC_INTEL],[test $ax_cv_c_compiler_vendor = "intel"])
-AC_LANG([C++])
-AX_CXX_COMPILE_STDCXX_11([noext],[mandatory])
-AX_COMPILER_VENDOR
-AC_DEFINE_UNQUOTED([CXX_COMP_VENDOR],["$ax_cv_cxx_compiler_vendor"],
-			[vendor of C++ compiler that will compile the code])
-AM_CONDITIONAL([CXX_GNU],[test $ax_cv_cxx_compiler_vendor = "gnu"])
-AM_CONDITIONAL([CXX_INTEL],[test $ax_cv_cxx_compiler_vendor = "intel"])
-AX_GCC_VERSION
-AC_DEFINE_UNQUOTED([GCC_VERSION],["$GCC_VERSION"],
-			[version of gcc that will compile the code])
-AX_GXX_VERSION
-AC_DEFINE_UNQUOTED([GXX_VERSION],["$GXX_VERSION"],
-			[version of g++ that will compile the code])
-
-# Checks for libraries.
-CXXFLAGS_CPY=$CXXFLAGS
-LDFLAGS_CPY=$LDFLAGS
-CXXFLAGS="$AM_CXXFLAGS $CXXFLAGS"
-LDFLAGS="$AM_LDFLAGS $LDFLAGS"
-AC_CHECK_LIB([pthread],[pthread_create],[],[AC_MSG_ERROR([pthread library not found])])
-AC_CHECK_LIB([m],[cos],[],[AC_MSG_ERROR([libm library not found])])
-AC_CHECK_LIB([gslcblas],[cblas_dgemm],[],
-             [AC_MSG_ERROR([GSL CBLAS library not found])])
-AC_CHECK_LIB([gsl],[gsl_blas_dgemm],[],[AC_MSG_ERROR([GSL library not found])])
-AC_CHECK_LIB([nlopt],[nlopt_create],
-    [AC_DEFINE([HAVE_NLOPT],
-    [1],
-    [Define to 1 if you have the `NLopt' library (-lnlopt).])]
-    [have_nlopt=true]
-    [LIBS="$LIBS -lnlopt"],[])
-AM_CONDITIONAL([HAVE_NLOPT], [test x$have_nlopt = xtrue])
-AC_CHECK_LIB([hdf5_cpp],[H5Fopen],
-    [LIBS="$LIBS -lhdf5_cpp -lhdf5"],
-    [AC_MSG_ERROR([HDF5 library not found])], [-lhdf5])
-SAVED_LDFLAGS=$LDFLAGS
-LDFLAGS="$LDFLAGS -lMinuit2"
-AC_MSG_CHECKING([for ROOT::Minuit2::VariableMetricMinimizer in -lMinuit2]);
-AC_LINK_IFELSE(
-	[AC_LANG_PROGRAM([#include <Minuit2/VariableMetricMinimizer.h>],
-	[ROOT::Minuit2::VariableMetricMinimizer dummy()])],
-	[LIBS="$LIBS -lMinuit2"]
-	[AC_DEFINE([HAVE_MINUIT2],
-				[1],
-				[Define to 1 if you have the `Minuit2' library (-lMinuit2).])]
-    [have_minuit=true]
-	[AC_MSG_RESULT([yes])],
-	[have_minuit=false]
-    [AC_MSG_RESULT([no])])
-AM_CONDITIONAL([HAVE_MINUIT], [test x$have_minuit = xtrue])
-LDFLAGS="$LDFLAGS -lMinuit2Math"
-AC_MSG_CHECKING([for ROOT::Math::MinimizerOptions in -lMinuit2Math]);
-AC_LINK_IFELSE(
-	[AC_LANG_PROGRAM([#include <Minuit2/Math/MinimizerOptions.h>],
-	[ROOT::Math::MinimizerOptions dummy()])],
-	[LIBS="$LIBS -lMinuit2Math"]
-	[AC_DEFINE([HAVE_MINUIT2MATH],
-				[1],
-				[Define to 1 if you have the `Minuit2Math' library (-lMinuit2Math).])]
-    [have_minuitmath=true]
-	[AC_MSG_RESULT([yes])],
-	[have_minuitmath=false]
-    [AC_MSG_RESULT([no])])
-AM_CONDITIONAL([HAVE_MINUITMATH], [test x$have_minuit = xtrue])
-LDFLAGS=$SAVED_LDFLAGS
-CXXFLAGS=$CXXFLAGS_CPY
-LDFLAGS=$LDFLAGS_CPY
-
-# Checks for header files.
-AC_HEADER_STDC
-
-cwd=`pwd -P`; cd ${srcdir}; abs_srcdir=`pwd -P`; cd ${cwd}
-LATAN_CXXFLAGS="$AM_CXXFLAGS $CXXFLAGS"
-LATAN_LDFLAGS="$AM_LDFLAGS $LDFLAGS"
-LATAN_LIBS=$LIBS
-LATAN_SHORT_SHA=`git rev-parse --short HEAD`
-LATAN_SHA=`git rev-parse HEAD`
-LATAN_BRANCH=`git rev-parse --abbrev-ref HEAD`
-AM_CXXFLAGS="-I${abs_srcdir}/lib $AM_CXXFLAGS"
-AM_CFLAGS="-I${abs_srcdir}/lib $AM_CFLAGS"
-CXXFLAGS="$AM_CXXFLAGS $CXXFLAGS"
-LDFLAGS="$AM_LDFLAGS $LDFLAGS"
-AC_SUBST([LIBS])
-AC_SUBST([AM_CXXFLAGS])
-AC_SUBST([AM_LDFLAGS])
-AC_SUBST([LATAN_CXXFLAGS])
-AC_SUBST([LATAN_LDFLAGS])
-AC_SUBST([LATAN_LIBS])
-AC_SUBST([LATAN_SHA])
-AC_SUBST([LATAN_BRANCH])
-
-AC_CONFIG_FILES([latan-config], [chmod +x latan-config])
-AC_CONFIG_FILES([Makefile])
-AC_CONFIG_FILES([lib/Makefile])
-AC_CONFIG_FILES([utils/Makefile])
-AC_CONFIG_FILES([physics/Makefile])
-AC_CONFIG_FILES([examples/Makefile])
-AC_OUTPUT
-
-echo "*********************************************"
-echo "* ${PACKAGE_NAME} v${VERSION}" build options
-echo "*********************************************"
-echo "* C++ compiler     : $CXX"
-echo "* Minuit minimizers: `test x$HAVE_MINUIT_TRUE = 'x' && echo yes \
-                                                          || echo no`"
-echo "* NLopt minimizers : `test x$HAVE_NLOPT_TRUE = 'x'  && echo yes \
-                                                          || echo no`"
-echo "*********************************************"
-
-
-

examples/CMakeLists.txt

@@ -0,0 +1,21 @@
+set(EXAMPLES_STEM
+    exCompiledDoubleFunction
+    exDerivative
+    exDWT
+    exFit
+    exFitSample
+    exIntegrator
+    exInterp
+    exMat
+    exMathInterpreter
+    exMin
+    exPlot
+    exPValue
+    exRand
+    exRootFinder
+    exThreadPool)
+
+foreach(_stem ${EXAMPLES_STEM})
+  add_executable(${_stem} ${_stem}.cpp)
+  target_link_libraries(${_stem} LatAnalyze compiler_flags)
+endforeach()

examples/LatAnalyze

@@ -1 +0,0 @@
-../lib

examples/Makefile.am

@@ -1,86 +0,0 @@
-if CXX_GNU
-    COM_CXXFLAGS = -Wall -W -pedantic -Wno-deprecated-declarations
-else
-if CXX_INTEL
-    COM_CXXFLAGS = -wd1682 -Wall
-endif
-endif
-
-noinst_PROGRAMS =           \
-    exCompiledDoubleFunction\
-    exDerivative            \
-    exDWT                   \
-    exFit                   \
-    exFitSample             \
-    exIntegrator            \
-    exInterp                \
-    exMat                   \
-    exMathInterpreter       \
-    exMin                   \
-    exPlot                  \
-    exPValue                \
-    exRand                  \
-    exRootFinder            \
-    exThreadPool
-
-exCompiledDoubleFunction_SOURCES  = exCompiledDoubleFunction.cpp
-exCompiledDoubleFunction_CXXFLAGS = $(COM_CXXFLAGS)
-exCompiledDoubleFunction_LDFLAGS  = -L../lib/.libs -lLatAnalyze
-
-exDerivative_SOURCES              = exDerivative.cpp
-exDerivative_CXXFLAGS             = $(COM_CXXFLAGS)
-exDerivative_LDFLAGS              = -L../lib/.libs -lLatAnalyze
-
-exDWT_SOURCES                     = exDWT.cpp
-exDWT_CXXFLAGS                    = $(COM_CXXFLAGS)
-exDWT_LDFLAGS                     = -L../lib/.libs -lLatAnalyze
-
-exFit_SOURCES                     = exFit.cpp
-exFit_CXXFLAGS                    = $(COM_CXXFLAGS)
-exFit_LDFLAGS                     = -L../lib/.libs -lLatAnalyze
-
-exFitSample_SOURCES               = exFitSample.cpp
-exFitSample_CXXFLAGS              = $(COM_CXXFLAGS)
-exFitSample_LDFLAGS               = -L../lib/.libs -lLatAnalyze
-
-exInterp_SOURCES                  = exInterp.cpp
-exInterp_CXXFLAGS                 = $(COM_CXXFLAGS)
-exInterp_LDFLAGS                  = -L../lib/.libs -lLatAnalyze
-
-exIntegrator_SOURCES              = exIntegrator.cpp
-exIntegrator_CXXFLAGS             = $(COM_CXXFLAGS)
-exIntegrator_LDFLAGS              = -L../lib/.libs -lLatAnalyze
-
-exMat_SOURCES                     = exMat.cpp
-exMat_CXXFLAGS                    = $(COM_CXXFLAGS)
-exMat_LDFLAGS                     = -L../lib/.libs -lLatAnalyze
-
-exMin_SOURCES                     = exMin.cpp
-exMin_CXXFLAGS                    = $(COM_CXXFLAGS)
-exMin_LDFLAGS                     = -L../lib/.libs -lLatAnalyze
-
-exMathInterpreter_SOURCES         = exMathInterpreter.cpp
-exMathInterpreter_CXXFLAGS        = $(COM_CXXFLAGS)
-exMathInterpreter_LDFLAGS         = -L../lib/.libs -lLatAnalyze
-
-exPlot_SOURCES                    = exPlot.cpp
-exPlot_CXXFLAGS                   = $(COM_CXXFLAGS)
-exPlot_LDFLAGS                    = -L../lib/.libs -lLatAnalyze
-
-exPValue_SOURCES                  = exPValue.cpp
-exPValue_CXXFLAGS                 = $(COM_CXXFLAGS)
-exPValue_LDFLAGS                  = -L../lib/.libs -lLatAnalyze
-
-exRand_SOURCES                    = exRand.cpp
-exRand_CXXFLAGS                   = $(COM_CXXFLAGS)
-exRand_LDFLAGS                    = -L../lib/.libs -lLatAnalyze
-
-exRootFinder_SOURCES              = exRootFinder.cpp
-exRootFinder_CXXFLAGS             = $(COM_CXXFLAGS)
-exRootFinder_LDFLAGS              = -L../lib/.libs -lLatAnalyze
-
-exThreadPool_SOURCES              = exThreadPool.cpp
-exThreadPool_CXXFLAGS             = $(COM_CXXFLAGS)
-exThreadPool_LDFLAGS              = -L../lib/.libs -lLatAnalyze
-
-ACLOCAL_AMFLAGS = -I .buildutils/m4

examples/exRand.cpp

@@ -7,7 +7,7 @@
 using namespace std;
 using namespace Latan;
 
-constexpr Index  size          = 8;
+constexpr Index  n             = 8;
 constexpr Index  nDraw         = 20000;
 constexpr Index  nSample       = 2000;
 const     string stateFileName = "exRand.seed";
@@ -40,14 +40,14 @@ int main(void)
     p << PlotFunction(compile("return exp(-x_0^2/2)/sqrt(2*pi);", 1), -5., 5.);
     p.display();
 
-    DMat       var(size, size);
+    DMat       var(n, n);
-    DVec       mean(size);
+    DVec       mean(n);
-    DMatSample sample(nSample, size, 1);
+    DMatSample sample(nSample, n, 1);
 
     cout << "-- generating " << nSample << " Gaussian random vectors..." << endl;
-    var   = DMat::Random(size, size);
+    var   = DMat::Random(n, n);
     var  *= var.adjoint();
-    mean  = DVec::Random(size); 
+    mean  = DVec::Random(n); 
     RandomNormal mgauss(mean, var, rd());
     sample[central] = mgauss();
     FOR_STAT_ARRAY(sample, s)

latan-config.in

@@ -1,79 +0,0 @@
-#! /bin/sh
-
-prefix=@prefix@
-exec_prefix=@exec_prefix@
-includedir=@includedir@
-
-usage()
-{
-  cat <<EOF
-Usage: latan-config [OPTION]
-
-Known values for OPTION are:
-
-  --prefix     show LatAnalyze installation prefix
-  --cxxflags   print pre-processor and compiler flags
-  --ldflags    print library linking flags
-  --libs       print library linking information
-  --help       display this help and exit
-  --version    output version information
-  --git        print git revision
-
-EOF
-  
-  exit $1
-}
-
-if test $# -eq 0; then
-  usage 1
-fi
-
-cflags=false
-libs=false
-
-while test $# -gt 0; do
-  case "$1" in
-    -*=*) optarg=`echo "$1" | sed 's/[-_a-zA-Z0-9]*=//'` ;;
-    *) optarg= ;;
-  esac
-  
-  case "$1" in
-    --prefix)
-      echo $prefix
-    ;;
-    
-    --version)
-      echo @VERSION@
-      exit 0
-    ;;
-    
-    --git)
-      echo "@LATAN_BRANCH@ @LATAN_SHA@"
-      exit 0
-    ;;
-    
-    --help)
-      usage 0
-    ;;
-    
-    --cxxflags)
-      echo @LATAN_CXXFLAGS@
-    ;;
-    
-    --ldflags)
-      echo @LATAN_LDFLAGS@
-    ;;
-    
-    --libs)
-      echo @LIBS@
-    ;;
-    
-    *)
-      usage
-      exit 1
-    ;;
-  esac
-  shift
-done
-
-exit 0

lib/CMakeLists.txt

@@ -0,0 +1,101 @@
+# config.h header for package version and name
+execute_process(
+  COMMAND git rev-parse --short HEAD
+  OUTPUT_VARIABLE LATAN_SHORT_SHA
+  OUTPUT_STRIP_TRAILING_WHITESPACE)
+execute_process(
+  COMMAND git rev-parse HEAD
+  OUTPUT_VARIABLE LATAN_SHA
+  OUTPUT_STRIP_TRAILING_WHITESPACE)
+execute_process(
+  COMMAND git rev-parse --abbrev-ref HEAD
+  OUTPUT_VARIABLE LATAN_BRANCH
+  OUTPUT_STRIP_TRAILING_WHITESPACE)
+configure_file(config.h.in ${CMAKE_CURRENT_BINARY_DIR}/config.h @ONLY)
+
+# find bison & flex
+find_package(BISON REQUIRED)
+find_package(FLEX REQUIRED)
+
+# ASCII parser
+bison_target(
+  AsciiParser LatAnalyze/Io/AsciiParser.ypp
+  ${CMAKE_CURRENT_BINARY_DIR}/AsciiParser.cpp COMPILE_FLAGS "-Wno-deprecated")
+flex_target(AsciiLexer LatAnalyze/Io/AsciiLexer.lpp
+            ${CMAKE_CURRENT_BINARY_DIR}/AsciiLexer.cpp)
+add_flex_bison_dependency(AsciiLexer AsciiParser)
+
+# math parser
+bison_target(
+  MathParser LatAnalyze/Core/MathParser.ypp
+  ${CMAKE_CURRENT_BINARY_DIR}/MathParser.cpp COMPILE_FLAGS "-Wno-deprecated")
+flex_target(MathLexer LatAnalyze/Core/MathLexer.lpp
+            ${CMAKE_CURRENT_BINARY_DIR}/MathLexer.cpp)
+add_flex_bison_dependency(MathLexer MathParser)
+
+# intermediate libraries
+add_library(parsers STATIC)
+target_include_directories(parsers PRIVATE ${CMAKE_CURRENT_SOURCE_DIR})
+target_sources(
+  parsers PRIVATE ${BISON_AsciiParser_OUTPUTS} ${FLEX_AsciiLexer_OUTPUTS}
+                  ${BISON_MathParser_OUTPUTS} ${FLEX_MathLexer_OUTPUTS})
+
+add_library(tinyxml2 STATIC)
+target_include_directories(parsers PRIVATE ${CMAKE_CURRENT_SOURCE_DIR})
+target_sources(tinyxml2 PRIVATE LatAnalyze/Io/Xml/tinyxml2.hpp
+                                LatAnalyze/Io/Xml/tinyxml2.cpp)
+
+# library target
+add_library(LatAnalyze SHARED)
+file(GLOB_RECURSE EIGEN_HEADERS LatAnalyze/Eigen/*)
+target_include_directories(LatAnalyze PRIVATE ${CMAKE_CURRENT_BINARY_DIR})
+include(source-list.cmake)
+target_sources(
+  LatAnalyze
+  PRIVATE ${CMAKE_CURRENT_BINARY_DIR}/config.h ${LATAN_SOURCES}
+  PUBLIC FILE_SET
+         public_headers
+         TYPE
+         HEADERS
+         FILES
+         ${EIGEN_HEADERS}
+         ${LATAN_HEADERS})
+target_link_libraries(LatAnalyze PRIVATE compiler_flags parsers tinyxml2)
+target_link_libraries(LatAnalyze PUBLIC GSL::gsl hdf5::hdf5 hdf5::hdf5_cpp
+                                        ${CMAKE_THREAD_LIBS_INIT})
+if(Minuit2_FOUND)
+  target_link_libraries(LatAnalyze PUBLIC Minuit2::Minuit2)
+endif()
+if(NLopt_FOUND)
+  target_link_libraries(LatAnalyze PUBLIC NLopt::nlopt)
+endif()
+set_target_properties(LatAnalyze PROPERTIES VERSION ${PROJECT_VERSION})
+target_include_directories(
+  LatAnalyze PUBLIC $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>
+                    $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>)
+
+# installation
+install(
+  TARGETS LatAnalyze
+  EXPORT LatAnalyzeTargets
+  LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
+  ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
+  RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
+          FILE_SET public_headers
+          DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
+install(
+  EXPORT LatAnalyzeTargets
+  FILE LatAnalyzeTargets.cmake
+  NAMESPACE LatAnalyze::
+  DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/LatAnalyze)
+configure_package_config_file(
+  ${CMAKE_CURRENT_SOURCE_DIR}/Config.cmake.in
+  "${CMAKE_CURRENT_BINARY_DIR}/LatAnalyzeConfig.cmake"
+  INSTALL_DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/LatAnalyze)
+write_basic_package_version_file(
+  "${CMAKE_CURRENT_BINARY_DIR}/LatAnalyzeConfigVersion.cmake"
+  VERSION "${PROJECT_VERSION}"
+  COMPATIBILITY AnyNewerVersion)
+install(FILES "${CMAKE_CURRENT_BINARY_DIR}/LatAnalyzeConfig.cmake"
+              "${CMAKE_CURRENT_BINARY_DIR}/LatAnalyzeConfigVersion.cmake"
+        DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/LatAnalyze)

lib/Config.cmake.in

@@ -0,0 +1,28 @@
+@PACKAGE_INIT@
+
+include(CMakeFindDependencyMacro)
+
+find_dependency(GSL REQUIRED)
+find_dependency(HDF5 REQUIRED COMPONENTS C CXX)
+set(HAVE_Minuit2 @Minuit2_FOUND@)
+set(HAVE_NLopt @NLopt_FOUND@)
+if(HAVE_Minuit2)
+  find_dependency(Minuit2 REQUIRED)
+  list(APPEND _LatAnalyze_supported_components MINUIT2)
+  set(LatAnalyze_MINUIT2_FOUND True)
+endif()
+if(HAVE_NLopt)
+  find_dependency(NLopt REQUIRED)
+  list(APPEND _LatAnalyze_supported_components NLOPT)
+  set(LatAnalyze_NLOPT_FOUND True)
+endif()
+foreach(_comp ${LatAnalyze_FIND_COMPONENTS})
+  if (NOT ";${_LatAnalyze_supported_components};" MATCHES ";${_comp};")
+    set(LatAnalyze_FOUND False)
+    set(LatAnalyze_NOT_FOUND_MESSAGE "Unsupported LatAnalyze component: ${_comp}")
+  endif()
+endforeach()
+
+include("${CMAKE_CURRENT_LIST_DIR}/LatAnalyzeTargets.cmake")
+
+check_required_components(LatAnalyze)

lib/LatAnalyze

@@ -1 +0,0 @@
-.

lib/LatAnalyze/Core/Math.cpp

@@ -18,6 +18,7 @@
  */
 
 #include <LatAnalyze/Core/Math.hpp>
+#include <LatAnalyze/Numerical/GslFFT.hpp>
 #include <LatAnalyze/includes.hpp>
 #include <gsl/gsl_cdf.h>
 
@@ -48,16 +49,42 @@ DMat MATH_NAMESPACE::corrToVar(const DMat &corr, const DVec &varDiag)
     return res;
 }
 
-double MATH_NAMESPACE::svdDynamicRange(const DMat &mat)
+double MATH_NAMESPACE::conditionNumber(const DMat &mat)
 {
     DVec s = mat.singularValues();
 
     return s.maxCoeff()/s.minCoeff();
 }
 
-double MATH_NAMESPACE::svdDynamicRangeDb(const DMat &mat)
+double MATH_NAMESPACE::cdr(const DMat &mat)
 {
-    return 10.*log10(svdDynamicRange(mat));
+    return 10.*log10(conditionNumber(mat));
+}
+
+template <typename FFT>
+double nsdr(const DMat &m)
+{
+    Index  n = m.rows();
+    FFT    fft(n);
+    CMat   buf(n, 1);
+
+    FOR_VEC(buf, i)
+    {
+        buf(i) = 0.;
+        for (Index j = 0; j < n; ++j)
+        {
+            buf(i) += m(j, (i+j) % n);
+        }
+        buf(i) /= n;
+    }
+    fft(buf, FFT::Forward);
+
+    return 10.*log10(buf.real().maxCoeff()/buf.real().minCoeff());
+}
+
+double MATH_NAMESPACE::nsdr(const DMat &mat)
+{
+    return ::nsdr<GslFFT>(mat);
 }
 
 /******************************************************************************

lib/LatAnalyze/Core/Math.hpp

@@ -73,8 +73,9 @@ namespace MATH_NAMESPACE
     DMat corrToVar(const DMat &corr, const DVec &varDiag);
 
     // matrix SVD dynamic range
-    double svdDynamicRange(const DMat &mat);
+    double conditionNumber(const DMat &mat);
-    double svdDynamicRangeDb(const DMat &mat);
+    double cdr(const DMat &mat);
+    double nsdr(const DMat &mat);
     
     // Constants
     constexpr double pi  = 3.1415926535897932384626433832795028841970;

lib/LatAnalyze/Core/MathInterpreter.cpp

@@ -36,7 +36,7 @@ unsigned int RunContext::addFunction(const string &name, DoubleFunction *init)
         
         return getFunctionAddress(name);
     }
-    catch (Exceptions::Definition)
+    catch (Exceptions::Definition &)
     {
         unsigned int address = fTable_.size();
         
@@ -55,7 +55,7 @@ unsigned int RunContext::addVariable(const string &name, double init)
         
         return getVariableAddress(name);
     }
-    catch (Exceptions::Definition)
+    catch (Exceptions::Definition &)
     {
         unsigned int address = vTable_.size();
         
@@ -92,7 +92,7 @@ unsigned int RunContext::getFunctionAddress(const string &name) const
     {
         return fTable_.at(name);
     }
-    catch (out_of_range)
+    catch (out_of_range &)
     {
         LATAN_ERROR(Definition, "undefined function '" + name + "'");
     }
@@ -139,7 +139,7 @@ unsigned int RunContext::getVariableAddress(const string &name) const
     {
         return vTable_.at(name);
     }
-    catch (out_of_range)
+    catch (out_of_range &)
     {
         LATAN_ERROR(Definition, "undefined variable '" + name + "'");
     }
@@ -449,7 +449,7 @@ try\
 {\
     address = (table).at(name);\
 }\
-catch (out_of_range)\
+catch (out_of_range &)\
 {\
     address         = (table).size();\
     (table)[(name)] = address;\

lib/LatAnalyze/Core/Plot.cpp

@@ -72,7 +72,7 @@ string PlotObject::dumpToTmpFile(const DMat &m)
     for (Index j = 0; j < m.cols(); ++j)
     {
     }
-    sprintf(tmpFileName, "%s/latan_plot_tmp.XXXXXX.dat", P_tmpdir);
+    snprintf(tmpFileName, sizeof(tmpFileName), "%s/latan_plot_tmp.XXXXXX.dat", P_tmpdir);
     fd = mkstemps(tmpFileName, 4);
     if (fd == -1)
     {
@@ -206,6 +206,42 @@ PlotData::PlotData(const XYStatData &data, const Index i, const Index j, const b
     setCommand("'" + tmpFileName + "' " + usingCmd);
 }
 
+PlotData::PlotData(const XYStatData & data, XYStatData::CoordFilter f, Index i, const Index j, const bool abs)
+{
+    string usingCmd, tmpFileName;
+    
+    if (!abs)
+    {
+        usingCmd = (data.isXExact(i)) ? "u 1:3:4 w yerr" : "u 1:3:2:4 w xyerr";
+    }
+    else
+    {
+        usingCmd = (data.isXExact(i)) ? "u 1:(abs($3)):4 w yerr" : "u 1:(abs($3)):2:4 w xyerr";
+    }
+   
+    tmpFileName = dumpToTmpFile(data.getTable(i, j, f));
+    pushTmpFile(tmpFileName);
+    setCommand("'" + tmpFileName + "' " + usingCmd);
+}
+
+PlotData::PlotData(const XYStatData & data, XYStatData::PointFilter f, Index i, const Index j, const bool abs)
+{
+    string usingCmd, tmpFileName;
+    
+    if (!abs)
+    {
+        usingCmd = (data.isXExact(i)) ? "u 1:3:4 w yerr" : "u 1:3:2:4 w xyerr";
+    }
+    else
+    {
+        usingCmd = (data.isXExact(i)) ? "u 1:(abs($3)):4 w yerr" : "u 1:(abs($3)):2:4 w xyerr";
+    }
+   
+    tmpFileName = dumpToTmpFile(data.getTable(i, j, f));
+    pushTmpFile(tmpFileName);
+    setCommand("'" + tmpFileName + "' " + usingCmd);
+}
+
 // PlotPoint constructor ///////////////////////////////////////////////////////
 PlotPoint::PlotPoint(const double x, const double y)
 {
@@ -515,14 +551,16 @@ void Dash::operator()(PlotOptions &option) const
 }
 
 // LogScale constructor ////////////////////////////////////////////////////////
-LogScale::LogScale(const Axis axis)
+LogScale::LogScale(const Axis axis, const double basis)
 : axis_(axis)
+, basis_(basis)
 {}
 
 // Logscale modifier ///////////////////////////////////////////////////////////
 void LogScale::operator()(PlotOptions &option) const
 {
-    option.scaleMode[static_cast<int>(axis_)] |= Plot::Scale::log;
+    option.scaleMode[static_cast<int>(axis_)]     |= Plot::Scale::log;
+    option.logScaleBasis[static_cast<int>(axis_)]  = basis_;
 }
 
 // PlotRange constructors //////////////////////////////////////////////////////
@@ -697,7 +735,7 @@ Plot & Plot::operator<<(PlotModifier &&modifier)
 
 // find gnuplot ////////////////////////////////////////////////////////////////
 #define SEARCH_DIR(dir) \
-sprintf(buf, "%s/%s", dir, gnuplotBin_.c_str());\
+snprintf(buf, sizeof(buf), "%s/%s", dir, gnuplotBin_.c_str());\
 if (access(buf, X_OK) == 0)\
 {\
     return dir;\
@@ -773,7 +811,7 @@ void Plot::display(void)
         ostringstream scriptBuf;
 
         getProgramPath();
-        command     = gnuplotPath_ + "/" + gnuplotBin_ + " 2>/dev/null";
+        command     = gnuplotPath_ + "/" + gnuplotBin_;
         gnuplotPipe = popen(command.c_str(), "w");
         if (!gnuplotPipe)
         {
@@ -915,11 +953,11 @@ ostream & Latan::operator<<(ostream &out, const Plot &plot)
     out << "unset log" << endl;
     if (plot.options_.scaleMode[x] & Plot::Scale::log)
     {
-        out << "set log x" << endl;
+        out << "set log x " << plot.options_.logScaleBasis[x] << endl;;
     }
     if (plot.options_.scaleMode[y] & Plot::Scale::log)
     {
-        out << "set log y" << endl;
+        out << "set log y " << plot.options_.logScaleBasis[y] << endl;
     }
     if (!plot.options_.label[x].empty())
     {

lib/LatAnalyze/Core/Plot.hpp

@@ -94,6 +94,10 @@ public:
     PlotData(const DMatSample &x, const DVec       &y, const bool abs = false);
     PlotData(const XYStatData &data, const Index i = 0, const Index j = 0, 
              const bool abs = false);
+    PlotData(const XYStatData &data, XYStatData::CoordFilter f, Index i = 0, 
+             const Index j = 0, const bool abs = false);
+    PlotData(const XYStatData &data, XYStatData::PointFilter f, Index i = 0, 
+             const Index j = 0, const bool abs = false);
     // destructor
     virtual ~PlotData(void) = default;
 };
@@ -227,6 +231,7 @@ struct PlotOptions
     std::string              caption;
     std::string              title;
     unsigned int             scaleMode[2];
+    double                   logScaleBasis[2];
     Range                    scale[2];
     std::string              label[2];
     std::string              lineColor;
@@ -314,13 +319,14 @@ class LogScale: public PlotModifier
 {
 public:
     // constructor
-    explicit LogScale(const Axis axis);
+    explicit LogScale(const Axis axis, const double basis = 10);
     // destructor
     virtual ~LogScale(void) = default;
     // modifier
     virtual void operator()(PlotOptions &option) const;
 private:
     const Axis axis_;
+    const double basis_;
 };
 
 class PlotRange: public PlotModifier

lib/LatAnalyze/Core/Utilities.hpp

@@ -108,23 +108,6 @@ inline std::string strFrom(const T x)
 }
 
 // specialization for vectors
-template<>
-inline std::vector<Index> strTo<std::vector<Index>>(const std::string &str)
-{
-    std::vector<Index>  res;
-    std::vector<double> vbuf;
-    double              buf;
-    std::istringstream  stream(str);
-    
-    while (!stream.eof())
-    {
-        stream >> buf;
-        res.push_back(buf);
-    }
-    
-    return res;
-}
-
 template<>
 inline DVec strTo<DVec>(const std::string &str)
 {

lib/LatAnalyze/Global.cpp

@@ -25,11 +25,13 @@ using namespace Latan;
 
 PlaceHolder Latan::_;
 
-const string Env::fullName  = PACKAGE_STRING;
+const string Env::fullName  = strFrom(PROJECT_NAME) + " " + strFrom(LATAN_SHORT_SHA) + " (v" + strFrom(PROJECT_VERSION) + ")";
-const string Env::name      = PACKAGE_NAME;
+const string Env::name      = PROJECT_NAME;
-const string Env::version   = PACKAGE_VERSION;
+const string Env::version   = PROJECT_VERSION;
-const string Env::msgPrefix = "[" + strFrom(PACKAGE_NAME) + " v"
+const string Env::gitShortSha = LATAN_SHORT_SHA;
-                              + strFrom(PACKAGE_VERSION) + "] ";
+const string Env::gitSha = LATAN_SHA;
+const string Env::gitBranch = LATAN_BRANCH;
+const string Env::msgPrefix = "[" + Env::fullName + "] ";
 
 void Env::function(void)
 {}

lib/LatAnalyze/Global.hpp

@@ -54,6 +54,9 @@ namespace Env
     extern const std::string fullName;
     extern const std::string name;
     extern const std::string version;
+    extern const std::string gitShortSha;
+    extern const std::string gitSha;
+    extern const std::string gitBranch;
     extern const std::string msgPrefix;
     // empty function for library test
     void function(void);

lib/LatAnalyze/Io/File.hpp

@@ -105,12 +105,12 @@ const IoT& File::getData(const std::string &name) const
     {
         return dynamic_cast<const IoT &>(*(data_.at(name)));
     }
-    catch(std::out_of_range)
+    catch (std::out_of_range &)
     {
         LATAN_ERROR(Definition, "no data with name '" + name + "' in file "
                     + name_);
     }
-    catch(std::bad_cast)
+    catch (std::bad_cast &)
     {
         LATAN_ERROR(Definition, "data with name '" + name + "' in file "
                     + name_ + " does not have type '" + typeid(IoT).name()

lib/LatAnalyze/Makefile.am

@@ -58,6 +58,7 @@ libLatAnalyze_la_SOURCES =           \
     Numerical/RootFinder.cpp         \
     Numerical/Solver.cpp             \
     Physics/CorrelatorFitter.cpp     \
+    Physics/DataFilter.cpp           \
     Physics/EffectiveMass.cpp        \
     Statistics/FitInterface.cpp      \
     Statistics/Histogram.cpp         \
@@ -106,6 +107,7 @@ HPPFILES =                           \
     Numerical/RootFinder.hpp         \
     Numerical/Solver.hpp             \
     Physics/CorrelatorFitter.hpp     \
+    Physics/DataFilter.hpp           \
     Physics/EffectiveMass.hpp        \
     Statistics/Dataset.hpp           \
     Statistics/FitInterface.hpp      \

lib/LatAnalyze/Numerical/CompositeMinimizer.cpp

@@ -0,0 +1,71 @@
+/*
+ * CompositeMinimizer.cpp, part of LatAnalyze 3
+ *
+ * Copyright (C) 2013 - 2024 Antonin Portelli
+ *
+ * LatAnalyze 3 is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * LatAnalyze 3 is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with LatAnalyze 3.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#include <LatAnalyze/Numerical/CompositeMinimizer.hpp>
+#include <LatAnalyze/includes.hpp>
+#include "CompositeMinimizer.hpp"
+
+using namespace std;
+using namespace Latan;
+
+/******************************************************************************
+ *                   CompositeMinimizer implementation                        *
+ ******************************************************************************/
+// constructor ////////////////////////////////////////////////////////////////
+CompositeMinimizer::CompositeMinimizer(const std::vector<Minimizer *> &minimizer)
+: minVec_(minimizer)
+{
+    if (minVec_.size() == 0)
+    {
+        LATAN_ERROR(Size, "minimizer vector has size 0");
+    }
+}
+
+// access /////////////////////////////////////////////////////////////////////
+bool CompositeMinimizer::supportLimits(void) const
+{
+    return false;
+}
+
+// minimization ///////////////////////////////////////////////////////////////
+const DVec &CompositeMinimizer::operator()(const DoubleFunction &f)
+{
+    DVec &x = getState();
+    DVec tmp;
+    unsigned int i = 1, nMin = minVec_.size();
+
+    // resize minimizer state to match function number of arguments
+    if (f.getNArg() != x.size())
+    {
+        resize(f.getNArg());
+    }
+
+    for (auto &m: minVec_)
+    {
+        if (getVerbosity() >= Verbosity::Normal)
+        {
+            cout << "********** Composite minimizer step " << i << "/" << nMin << endl;
+        }
+        m->setInit(x);
+        x = (*m)(f);
+        i++;
+    }
+
+    return x;
+}

lib/LatAnalyze/Numerical/CompositeMinimizer.hpp

@@ -0,0 +1,68 @@
+/*
+ * CompositeMinimizer.hpp, part of LatAnalyze 3
+ *
+ * Copyright (C) 2013 - 2024 Antonin Portelli
+ *
+ * LatAnalyze 3 is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * LatAnalyze 3 is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with LatAnalyze 3.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#ifndef Latan_CompositeMinimizer_hpp_
+#define Latan_CompositeMinimizer_hpp_
+
+#include <LatAnalyze/Global.hpp>
+#include <LatAnalyze/Functional/Function.hpp>
+#include <LatAnalyze/Numerical/Minimizer.hpp>
+
+BEGIN_LATAN_NAMESPACE
+
+/******************************************************************************
+ *                       Class for chaining minimizers                        *
+ ******************************************************************************/
+class CompositeMinimizer: public Minimizer
+{
+public:
+    // constructors
+    explicit CompositeMinimizer(const std::vector<Minimizer *> &minimizer);
+    template <typename... Ts>
+    CompositeMinimizer(Minimizer &min, Ts & ... minimisers);
+    // destructor
+    virtual ~CompositeMinimizer(void) = default;
+    // access
+    virtual bool supportLimits(void) const;
+    // minimization
+    virtual const DVec & operator()(const DoubleFunction &f);
+private:
+    std::vector<Minimizer *> minVec_;
+};
+
+/******************************************************************************
+ *              CompositeMinimizer template implementation                    *
+ ******************************************************************************/
+template <typename... Ts>
+CompositeMinimizer::CompositeMinimizer(Minimizer &min, Ts & ... minimisers)
+{
+    static_assert(static_or<std::is_assignable<Minimizer &, Ts>::value...>::value,
+                  "model arguments are not compatible with Minimizer");
+
+
+    minVec_ = {&min, &minimisers...};
+    if (minVec_.size() == 0)
+    {
+        LATAN_ERROR(Size, "minimizer vector has size 0");
+    }
+}
+
+END_LATAN_NAMESPACE
+
+#endif // Latan_CompositeMinimizer_hpp_

lib/LatAnalyze/Numerical/DWT.cpp

@@ -32,46 +32,91 @@ DWT::DWT(const DWTFilter &filter)
 {}
 
 // convolution primitive ///////////////////////////////////////////////////////
-void DWT::filterConvolution(DVec &out, const DVec &data, 
+template <typename MatType>
-                            const std::vector<double> &filter, const Index offset)
+void filterConvolution(MatType &out, const MatType &data, 
+                       const std::vector<double> &filter, const Index offset)
 {
-    Index n = data.size(), nf = n*filter.size();
+    Index n = data.rows(), nf = n*filter.size();
 
-    out.resize(n);
+    out.resizeLike(data);
     out.fill(0.);
     for (unsigned int i = 0; i < filter.size(); ++i)
     {
-        FOR_VEC(out, j)
+        FOR_MAT(out, j, k)
         {
-            out(j) += filter[i]*data((j + i + nf - offset) % n);
+            out(j, k) += filter[i]*data((j + i + nf - offset) % n, k);
         }
     }
 }
 
+void DWT::filterConvolution(DVec &out, const DVec &data, 
+                            const std::vector<double> &filter, const Index offset)
+{
+    ::filterConvolution(out, data, filter, offset);
+}
+
+void DWT::filterConvolution(DMat &out, const DMat &data, 
+                            const std::vector<double> &filter, const Index offset)
+{
+    ::filterConvolution(out, data, filter, offset);
+}
+
 // downsampling/upsampling primitives //////////////////////////////////////////
+template <typename MatType>
+void downsample(MatType &out, const MatType &in)
+{
+    if (out.rows() < in.rows()/2)
+    {
+        LATAN_ERROR(Size, "output rows smaller than half the input vector rows");
+    }
+    if (out.cols() != in.cols())
+    {
+        LATAN_ERROR(Size, "output and input number of columns mismatch");
+    }
+    for (Index j = 0; j < in.cols(); j++)
+    for (Index i = 0; i < in.rows(); i += 2)
+    {
+        out(i/2, j) = in(i, j);
+    }
+}
+
 void DWT::downsample(DVec &out, const DVec &in)
 {
-    if (out.size() < in.size()/2)
+    ::downsample(out, in);
+}
+
+void DWT::downsample(DMat &out, const DMat &in)
+{
+    ::downsample(out, in);
+}
+
+template <typename MatType>
+void upsample(MatType &out, const MatType &in)
+{
+    if (out.size() < 2*in.size())
     {
-        LATAN_ERROR(Size, "output vector smaller than half the input vector size");
+        LATAN_ERROR(Size, "output rows smaller than twice the input rows");
     }
-    for (Index i = 0; i < in.size(); i += 2)
+    if (out.cols() != in.cols())
     {
-        out(i/2) = in(i);
+        LATAN_ERROR(Size, "output and input number of columns mismatch");
+    }
+    out.block(0, 0, 2*in.size(), out.cols()).fill(0.);
+    for (Index j = 0; j < in.cols(); j++)
+    for (Index i = 0; i < in.size(); i ++)
+    {
+        out(2*i, j) = in(i, j);
     }
 }
 
 void DWT::upsample(DVec &out, const DVec &in)
 {
-    if (out.size() < 2*in.size())
+    ::upsample(out, in);
-    {
+}
-        LATAN_ERROR(Size, "output vector smaller than twice the input vector size");
+
-    }
+void DWT::upsample(DMat &out, const DMat &in)
-    out.segment(0, 2*in.size()).fill(0.);
+{
-    for (Index i = 0; i < in.size(); i ++)
+    ::upsample(out, in);
-    {
-        out(2*i) = in(i);
-    }
 }
 
 // DWT /////////////////////////////////////////////////////////////////////////
@@ -135,3 +180,26 @@ DVec DWT::backward(const std::vector<DWTLevel>& dwt) const
 
     return res;
 }
+
+// concatenate levels //////////////////////////////////////////////////////////
+DVec DWT::concat(const std::vector<DWTLevel> &dwt, const int maxLevel, const bool dropLow)
+{
+    unsigned int level = ((maxLevel >= 0) ? (maxLevel + 1) : dwt.size());
+    Index nlast = dwt[level - 1].first.size();
+    Index n = 2*dwt.front().first.size() - ((dropLow) ? nlast : 0);
+    Index pt = n, nl;
+    DVec  res(n);
+
+    for (unsigned int l = 0; l < level; ++l)
+    {
+        nl  = dwt[l].second.size();
+        pt -= nl;
+        res.segment(pt, nl) = dwt[l].second;
+    }
+    if (!dropLow)
+    {
+        res.segment(0, nl) = dwt[level-1].first;
+    }
+
+    return res;
+}

lib/LatAnalyze/Numerical/DWT.hpp

@@ -22,6 +22,7 @@
 
 #include <LatAnalyze/Global.hpp>
 #include <LatAnalyze/Numerical/DWTFilters.hpp>
+#include <LatAnalyze/Core/Mat.hpp>
 
 BEGIN_LATAN_NAMESPACE
 
@@ -40,12 +41,18 @@ public:
     // convolution primitive
     static void filterConvolution(DVec &out, const DVec &data, 
                                   const std::vector<double> &filter, const Index offset);
+    static void filterConvolution(DMat &out, const DMat &data, 
+                                  const std::vector<double> &filter, const Index offset);
     // downsampling/upsampling primitives
     static void downsample(DVec &out, const DVec &in);
+    static void downsample(DMat &out, const DMat &in);
     static void upsample(DVec &out, const DVec &in);
+    static void upsample(DMat &out, const DMat &in);
     // DWT
     std::vector<DWTLevel> forward(const DVec &data, const unsigned int level) const;
     DVec                  backward(const std::vector<DWTLevel>& dwt) const;
+    // concatenate levels
+    static DVec concat(const std::vector<DWTLevel>& dwt, const int maxLevel = -1, const bool dropLow = false);
 private:
     DWTFilter filter_;
 };

lib/LatAnalyze/Numerical/MinuitMinimizer.cpp

@@ -30,8 +30,12 @@ namespace ROOT
 };
 
 // macros necessary in the ROOT-based version of Minuit2
+#ifndef ROOT_Math_VecTypes
 #define ROOT_Math_VecTypes
+#endif
+#ifndef MATHCORE_STANDALONE
 #define MATHCORE_STANDALONE
+#endif
 
 #include <Minuit2/Minuit2Minimizer.h>
 #include <Math/Functor.h>
@@ -160,8 +164,7 @@ const DVec & MinuitMinimizer::operator()(const DoubleFunction &f)
     {
         if (getVerbosity() >= Verbosity::Normal)
         {
-            cout << "========== Minuit minimization, pass #" << n + 1;
+            cout << "========== Minuit minimization, pass #" << n + 1 << endl;
-            cout << " =========" << endl;
         }
         min.Minimize();
         status = min.Status();

lib/LatAnalyze/Numerical/NloptMinimizer.cpp

@@ -94,8 +94,7 @@ const DVec & NloptMinimizer::operator()(const DoubleFunction &f)
     {
         if (getVerbosity() >= Verbosity::Normal)
         {
-            cout << "========== NLopt minimization, pass #" << n + 1;
+            cout << "========== NLopt minimization, pass #" << n + 1 << endl;
-            cout << " ==========" << endl;
             cout << "Algorithm: " << min.get_algorithm_name() << endl;
             cout << "Max eval.= " << min.get_maxeval();
             cout << " -- Precision= " << min.get_xtol_rel() << endl;