[med-svn] [Git][med-team/bppphyview][master] 3 commits: New upstream version 0.6.0
Julien Y. Dutheil
gitlab at salsa.debian.org
Wed Apr 18 20:10:13 BST 2018
Julien Y. Dutheil pushed to branch master at Debian Med / bppphyview
Commits:
67019a0f by Julien Y. Dutheil at 2018-04-18T20:58:18+02:00
New upstream version 0.6.0
- - - - -
cce4b1a4 by Julien Y. Dutheil at 2018-04-18T20:58:19+02:00
Update upstream source from tag 'upstream/0.6.0'
Update to upstream version '0.6.0'
with Debian dir 0d2e62df9408d63bbb20e09c0e56cc513e47a7c3
- - - - -
4856cb37 by Julien Y. Dutheil at 2018-04-18T21:09:32+02:00
Drafted version 0.6.0.
- - - - -
11 changed files:
- CMakeLists.txt
- ChangeLog
- bppPhyView/CMakeLists.txt
- bppPhyView/PhyView.cpp
- bppPhyView/PhyView.h
- bppPhyView/TreeCommands.h
- bppphyview.spec
- debian/changelog
- debian/control
- debian/copyright
- debian/rules
Changes:
=====================================
CMakeLists.txt
=====================================
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -60,7 +60,8 @@ else ()
# Generate command line args (always add -c to output compressed file to stdout)
if (${COMPRESS_PROGRAM} STREQUAL "gzip")
# -n for no timestamp in files (reproducible builds)
- set (COMPRESS_ARGS -c -n)
+ # -9 for maximal compression (lintian warning)
+ set (COMPRESS_ARGS -c -9 -n)
else ()
set (COMPRESS_ARGS -c)
endif ()
@@ -73,13 +74,15 @@ if (CMAKE_INSTALL_PREFIX)
endif (CMAKE_INSTALL_PREFIX)
include (GNUInstallDirs)
-find_package (bpp-qt 1.0.1 REQUIRED)
+find_package (bpp-qt 2.0.0 REQUIRED)
# Find the Qt installation
-set (QT_USE_IMPORTED_TARGETS TRUE)
-find_package (Qt4 4.4.0 COMPONENTS QtCore QtGui REQUIRED)
-include (${QT_USE_FILE})
-set (qt-libs ${QT_QTCORE_LIBRARY} ${QT_QTGUI_LIBRARY})
+set(CMAKE_AUTOMOC ON)
+find_package (Qt5Widgets)
+find_package (Qt5Core)
+find_package (Qt5Gui)
+find_package (Qt5PrintSupport)
+set (qt-libs Qt5::Core Qt5::Gui Qt5::Widgets Qt5::PrintSupport)
# Subdirectories
add_subdirectory (bppPhyView)
@@ -90,10 +93,10 @@ ENDIF(NO_DEP_CHECK)
# Packager
SET(CPACK_PACKAGE_NAME "bppphyview")
SET(CPACK_PACKAGE_VENDOR "Bio++ Development Team")
-SET(CPACK_PACKAGE_VERSION "0.5.1")
+SET(CPACK_PACKAGE_VERSION "0.6.0")
SET(CPACK_PACKAGE_VERSION_MAJOR "0")
-SET(CPACK_PACKAGE_VERSION_MINOR "5")
-SET(CPACK_PACKAGE_VERSION_PATCH "1")
+SET(CPACK_PACKAGE_VERSION_MINOR "6")
+SET(CPACK_PACKAGE_VERSION_PATCH "0")
SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "The Bio++ Phylogenetic Viewer")
SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING.txt")
SET(CPACK_RESOURCE_FILE_AUTHORS "${CMAKE_SOURCE_DIR}/AUTHORS.txt")
=====================================
ChangeLog
=====================================
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,11 @@
+25/02/18 -*- Version 0.6.0 -*-
+
+27/12/17 Julien Dutheil
+* Added "removeAllLengths" command.
+
+13/09/17 Julien Dutheil
+* Ported to Qt5.
+
10/05/17 -*- Version 0.5.0 -*-
* Compatibility update with Bio++ 2.3.0.
=====================================
bppPhyView/CMakeLists.txt
=====================================
--- a/bppPhyView/CMakeLists.txt
+++ b/bppPhyView/CMakeLists.txt
@@ -13,10 +13,9 @@ set (H_MOC_FILES
PhyView.h
TreeSubWindow.h
)
-qt4_wrap_cpp (CPP_MOC_FILES ${H_MOC_FILES})
# Phyview
-add_executable (phyview ${CPP_FILES} ${CPP_MOC_FILES})
+add_executable (phyview ${CPP_FILES} ${CPP_FILES})
if (BUILD_STATIC)
target_link_libraries (phyview ${BPP_LIBS_STATIC} ${qt-libs})
else (BUILD_STATIC)
=====================================
bppPhyView/PhyView.cpp
=====================================
--- a/bppPhyView/PhyView.cpp
+++ b/bppPhyView/PhyView.cpp
@@ -43,6 +43,18 @@ knowledge of the CeCILL license and that you accept its terms.
#include <QApplication>
#include <QtGui>
+#include <QVBoxLayout>
+#include <QFormLayout>
+#include <QPushButton>
+#include <QMessageBox>
+#include <QButtonGroup>
+#include <QDockWidget>
+#include <QUndoView>
+#include <QLineEdit>
+#include <QAction>
+#include <QMenuBar>
+#include <QInputDialog>
+#include <QGraphicsTextItem>
#include <Bpp/Qt/QtGraphicDevice.h>
@@ -79,8 +91,9 @@ TranslateNameChooser::TranslateNameChooser(PhyView* phyview) :
fileFilters_ << "Coma separated columns (*.txt *.csv)"
<< "Tab separated columns (*.txt *.csv)";
fileDialog_->setNameFilters(fileFilters_);
+ fileDialog_->setOptions(QFileDialog::DontUseNativeDialog);
hasHeader_ = new QCheckBox(tr("File has header line"));
- QGridLayout *dlayout = dynamic_cast<QGridLayout*>(fileDialog_->layout());
+ QGridLayout *dlayout = dynamic_cast<QGridLayout*>(fileDialog_->layout()); //Check that here!!
dlayout->addWidget(hasHeader_, 4, 0);
QFormLayout* layout = new QFormLayout;
fromList_ = new QComboBox;
@@ -555,6 +568,11 @@ void PhyView::createBrlenPanel_()
brlenLayout->addWidget(brlenSetLengthsBox);
+ //Remove all branch lengths:
+ QPushButton* brlenRemoveAll = new QPushButton(tr("Remove all lengths"));
+ connect(brlenRemoveAll, SIGNAL(clicked(bool)), this, SLOT(deleteAllLengths()));
+ brlenLayout->addWidget(brlenRemoveAll);
+
//Grafen method:
QPushButton* brlenInitGrafen = new QPushButton(tr("Init"));
connect(brlenInitGrafen, SIGNAL(clicked(bool)), this, SLOT(initLengthsGrafen()));
@@ -1020,15 +1038,15 @@ void PhyView::exit()
void PhyView::aboutBpp()
{
QMessageBox msgBox;
- msgBox.setText("Bio++ 2.3.0.");
- msgBox.setInformativeText("bpp-core 2.3.0\nbpp-seq 2.3.0.\nbpp-phyl 2.3.0.\nbpp-qt 2.3.0");
+ msgBox.setText("Bio++ 2.4.0.");
+ msgBox.setInformativeText("bpp-core 2.4.0\nbpp-seq 2.4.0.\nbpp-phyl 2.4.0.\nbpp-qt 2.4.0");
msgBox.exec();
}
void PhyView::about()
{
QMessageBox msgBox;
- msgBox.setText("This is Bio++ Phylogenetic Viewer version 0.5.0.");
+ msgBox.setText("This is Bio++ Phylogenetic Viewer version 0.6.0.");
msgBox.setInformativeText("Julien Dutheil <dutheil at evolbio.mpg.de>.");
msgBox.exec();
}
@@ -1071,6 +1089,13 @@ void PhyView::midpointRooting()
}
}
+void PhyView::deleteAllLengths()
+{
+ if (hasActiveDocument())
+ submitCommand(new DeleteLengthCommand(getActiveDocument()));
+}
+
+
void PhyView::unresolveUncertainNodes()
{
if (hasActiveDocument()) {
@@ -1302,7 +1327,7 @@ int main(int argc, char *argv[])
//Parse command line arguments:
QStringList args = app.arguments();
string format = IOTreeFactory::NEWICK_FORMAT;
- QTextCodec* codec = QTextCodec::codecForLocale();
+ //QTextCodec* codec = QTextCodec::codecForLocale(); Not supported in Qt5...
for (int i = 1; i < args.size(); ++i) {
if (args[i] == "--nhx") {
format = IOTreeFactory::NHX_FORMAT;
@@ -1310,18 +1335,17 @@ int main(int argc, char *argv[])
format = IOTreeFactory::NEWICK_FORMAT;
} else if (args[i] == "--newick") {
format = IOTreeFactory::NEWICK_FORMAT;
- } else if (args[i] == "--enc") {
- if (i == args.size() - 1) {
- cerr << "You must specify a text encoding after --enc tag." << endl;
- exit(1);
- }
- ++i;
- codec = QTextCodec::codecForName(args[i].toStdString().c_str());
+ //} else if (args[i] == "--enc") {
+ // if (i == args.size() - 1) {
+ // cerr << "You must specify a text encoding after --enc tag." << endl;
+ // exit(1);
+ // }
+ // ++i;
+ // codec = QTextCodec::codecForName(args[i].toStdString().c_str());
} else {
phyview->readTree(args[i], format);
}
}
- QTextCodec::setCodecForCStrings(codec);
return app.exec();
}
=====================================
bppPhyView/PhyView.h
=====================================
--- a/bppPhyView/PhyView.h
+++ b/bppPhyView/PhyView.h
@@ -369,6 +369,7 @@ class PhyView :
void computeLengthsGrafen();
void convertToClockTree();
void midpointRooting();
+ void deleteAllLengths();
void unresolveUncertainNodes();
void translateNames();
=====================================
bppPhyView/TreeCommands.h
=====================================
--- a/bppPhyView/TreeCommands.h
+++ b/bppPhyView/TreeCommands.h
@@ -45,7 +45,7 @@ knowledge of the CeCILL license and that you accept its terms.
#include <Bpp/Text/TextTools.h>
#include <Bpp/Numeric/DataTable.h>
-//From PhylLib:
+//From bpp-phyl:
#include <Bpp/Phyl/TreeTools.h>
//From Qt:
@@ -105,6 +105,17 @@ class SetLengthCommand: public AbstractCommand
}
};
+class DeleteLengthCommand: public AbstractCommand
+{
+ public:
+ DeleteLengthCommand(TreeDocument* doc):
+ AbstractCommand(QtTools::toQt("Delete all branch length."), doc)
+ {
+ new_ = new TreeTemplate<Node>(*old_);
+ TreeTemplateTools::deleteBranchLengths(*new_->getRootNode());
+ }
+};
+
class InitGrafenCommand: public AbstractCommand
{
public:
=====================================
bppphyview.spec
=====================================
--- a/bppphyview.spec
+++ b/bppphyview.spec
@@ -1,62 +1,83 @@
-%define _basename bppphyview
-%define _version 0.5.1
-%define _release 1
%define _prefix /usr
-URL: http://biopp.univ-montp2.fr/forge/bppphyview
+URL: https://github.com/BioPP/bppphyview
-Name: %{_basename}
-Version: %{_version}
-Release: %{_release}
+Name: bppphyview
+Version: 0.6.0
+Release: 1%{?dist}
License: CECILL-2.0
Vendor: The Bio++ Project
-Source: http://biopp.univ-montp2.fr/repos/sources/%{_basename}-%{_version}.tar.gz
+Source: %{name}-%{version}.tar.gz
Summary: Bio++ Phylogenetic Viewer
Group: Productivity/Scientific/Other
-Requires: libbpp-phyl11 = 2.3.1
-Requires: libbpp-core3 = 2.3.1
-Requires: libbpp-qt1 = 2.3.1
-%if 0%{?fedora} || 0%{?rhel_version} || 0%{?centos_version}
-Requires: qt >= 4.6.0
+Requires: libbpp-phyl12 = 2.4.0
+Requires: libbpp-core4 = 2.4.0
+Requires: libbpp-qt2 = 2.4.0
+
+%if 0%{?fedora} || 0%{?rhel_version} || 0%{?centos_version} || 0%{?scientificlinux_version}
+Requires: libqt5core5 >= 5.0.0
+Requires: libqt5gui5 >= 5.0.0
+Requires: libqt5widgets5 >= 5.0.0
%endif
%if 0%{?suse_version}
-Requires: libqt4 >= 4.6.0
+Requires: libQt5Core5 >= 5.0.0
+Requires: libQt5Gui5 >= 5.0.0
+Requires: libQt5Widgets5 >= 5.0.0
%endif
-%if 0%{?mdkversion}
+%if 0%{?mageia} || 0%{?mdkversion}
%ifarch x86_64
-Requires: lib64qtgui4 >= 4.6.0
+Requires: lib64proxy-webkit >= 0.4.14
+Requires: lib64qt5core5 >= 5.0.0
+Requires: lib64qt5gui5 >= 5.0.0
+Requires: lib64qt5widgets5 >= 5.0.0
+Requires: qt5-qtdeclarative >= 5.0.0
+Requires: qt5-qtbase >= 5.0.0
%else
-Requires: libqtgui4 >= 4.6.0
+Requires: libproxy-webkit >= 0.4.14
+Requires: libqt5core5 >= 5.0.0
+Requires: libqt5gui5 >= 5.0.0
+Requires: libqt5widgets5 >= 5.0.0
+Requires: qt5-qtdeclarative >= 5.0.0
+Requires: qt5-qtbase >= 5.0.0
%endif
%endif
-BuildRoot: %{_builddir}/%{_basename}-root
+BuildRoot: %{_builddir}/%{name}-root
BuildRequires: cmake >= 2.8.11
BuildRequires: gcc-c++ >= 4.7.0
BuildRequires: groff
-BuildRequires: libbpp-core3 = 2.3.1
-BuildRequires: libbpp-core-devel = 2.3.1
-BuildRequires: libbpp-phyl11 = 2.3.1
-BuildRequires: libbpp-phyl-devel = 2.3.1
-BuildRequires: libbpp-qt1 = 2.3.1
-BuildRequires: libbpp-qt-devel = 2.3.1
-
-%if 0%{?fedora} || 0%{?rhel_version} || 0%{?centos_version}
-BuildRequires: qt >= 4.6.0
-BuildRequires: qt-devel >= 4.6.0
+BuildRequires: libbpp-core4 = 2.4.0
+BuildRequires: libbpp-core-devel = 2.4.0
+BuildRequires: libbpp-phyl12 = 2.4.0
+BuildRequires: libbpp-phyl-devel = 2.4.0
+BuildRequires: libbpp-qt2 = 2.4.0
+BuildRequires: libbpp-qt-devel = 2.4.0
+
+%if 0%{?fedora} || 0%{?rhel_version} || 0%{?centos_version} || 0%{?scientificlinux_version}
+BuildRequires: qt >= 5.0.0
+BuildRequires: qt-devel >= 5.0.0
%endif
%if 0%{?suse_version}
-BuildRequires: libqt4 >= 4.6.0
-BuildRequires: libqt4-devel >= 4.6.0
+BuildRequires: libQt5Core5 >= 5.0.0
+BuildRequires: libQt5Gui5 >= 5.0.0
+BuildRequires: libQt5Widgets5 >= 5.0.0
+BuildRequires: libqt5-qtdeclarative-devel >= 5.0.0
+BuildRequires: libqt5-qtbase-devel >= 5.0.0
%endif
-%if 0%{?mdkversion}
+%if 0%{?mageia} || 0%{?mdkversion}
%ifarch x86_64
-BuildRequires: lib64qtgui4 >= 4.6.0
-BuildRequires: lib64qt4-devel >= 4.6.0
+BuildRequires: lib64proxy-webkit >= 0.4.14
+BuildRequires: lib64qt5core5 >= 5.0.0
+BuildRequires: lib64qt5gui5 >= 5.0.0
+BuildRequires: lib64qt5widgets5 >= 5.0.0
+BuildRequires: lib64qt5base5-devel >= 5.0.0
%else
-BuildRequires: libqtgui4 >= 4.6.0
-BuildRequires: libqt4-devel >= 4.6.0
+BuildRequires: libproxy-webkit >= 0.4.14
+BuildRequires: libqt5core5 >= 5.0.0
+BuildRequires: libqt5gui5 >= 5.0.0
+BuildRequires: libqt5widgets5 >= 5.0.0
+BuildRequires: libqt5base5-devel >= 5.0.0
%endif
%endif
@@ -72,7 +93,7 @@ BuildRequires: lzma
%define compress_program lzma
%endif
%else
-%if 0%{?distribution:1} && "%{distribution}" == "Mageia"
+%if 0%{?mageia}
BuildRequires: xz
%define compress_program xz
%else
@@ -111,6 +132,9 @@ rm -rf $RPM_BUILD_ROOT
%{_prefix}/share/man/man1/phyview.1*
%changelog
+* Mon Mar 12 2018 Julien Dutheil <julien.dutheil at univ-montp2.fr> 0.6.0-1
+- Compatibility update with Bio++ 2.4.0.
+- More options in branch lengths panel.
* Thu Jun 8 2017 Julien Dutheil <julien.dutheil at univ-montp2.fr> 0.5.1-1
- Compatibility update with Bio++ 2.3.1.
* Wed May 10 2017 Julien Dutheil <julien.dutheil at univ-montp2.fr> 0.5.0-1
=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,14 @@
+bppphyview (0.6.0-1) UNRELEASED; urgency=medium
+
+ * New upstream version
+ * Added full text of CeCILL license.
+ * Compiles with -DCMAKE_BUILD_TYPE=RelWithDebInfo to generate debug info
+ * Point Vcs-fields to salsa.debian.org
+ * Standards-Version: 4.1.4
+ * debhelper 11
+
+ -- Julien Dutheil <julien.dutheil at univ-montp2.fr> Wed, 18 Apr 2018 21:03:35 +0200
+
bppphyview (0.5.1-1) unstable; urgency=medium
* New upstream version
=====================================
debian/control
=====================================
--- a/debian/control
+++ b/debian/control
@@ -4,14 +4,14 @@ Uploaders: Julien Dutheil <julien.dutheil at univ-montp2.fr>,
Andreas Tille <tille at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 10),
+Build-Depends: debhelper (>= 11~),
cmake,
- qt4-qmake,
- libqt4-dev,
- libbpp-qt-dev (>= 2.3.1)
-Standards-Version: 4.1.0
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/bppphyview.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/bppphyview.git
+ qt5-qmake,
+ qtdeclarative5-dev,
+ libbpp-qt-dev (>= 2.4.0)
+Standards-Version: 4.1.4
+Vcs-Browser: https://salsa.debian.org/med-team/bppphyview.git
+Vcs-Git: https://salsa.debian.org/med-team/bppphyview.git
Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
Package: bppphyview
=====================================
debian/copyright
=====================================
--- a/debian/copyright
+++ b/debian/copyright
@@ -4,39 +4,9 @@ Upstream-Contact: Julien Yann Dutheil <julien.dutheil at univ-montp2.fr>
Source: https://github.com/BioPP/bppphyview
Files: *
-Copyright: 2010-2017 Julien Yann Dutheil <julien.dutheil at univ-montp2.fr>
- Bio++ Development Team
+Copyright: 2010-2018 Julien Yann Dutheil <julien.dutheil at univ-montp2.fr>
+ Bio++ Development Team
License: CeCILL
- The provided software is distributed under the CeCILL license:
- .
- This software is governed by the CeCILL license under French law and
- abiding by the rules of distribution of free software. You can use,
- modify and/ or redistribute the software under the terms of the CeCILL
- license as circulated by CEA, CNRS and INRIA at the following URL
- "http://www.cecill.info".
- .
- As a counterpart to the access to the source code and rights to copy,
- modify and redistribute granted by the license, users are provided only
- with a limited warranty and the software's author, the holder of the
- economic rights, and the successive licensors have only limited
- liability.
- .
- In this respect, the user's attention is drawn to the risks associated
- with loading, using, modifying and/or developing or reproducing the
- software by the user in light of its specific status of free software,
- that may mean that it is complicated to manipulate, and that also
- therefore means that it is reserved for developers and experienced
- professionals having in-depth computer knowledge. Users are therefore
- encouraged to load and test the software's suitability as regards their
- requirements in conditions enabling the security of their systems and/or
- data to be ensured and, more generally, to use and operate it in the
- same conditions as regards security.
- .
- The fact that you are presently reading this means that you have had
- knowledge of the CeCILL license and that you accept its terms.
- .
- The complete text of the license may be found here:
- http://www.cecill.info/licences/Licence_CeCILL_V2-en.html
Files: debian/*
Copyright: 2014 Julien Yann Dutheil <julien.dutheil at univ-montp2.fr>
@@ -44,6 +14,511 @@ Copyright: 2014 Julien Yann Dutheil <julien.dutheil at univ-montp2.fr>
2017 Andreas Tille <tille at debian.org>
License: GPL-2+
+License: CeCILL
+ CeCILL FREE SOFTWARE LICENSE AGREEMENT
+ .
+ Notice
+ .
+ This Agreement is a Free Software license agreement that is the result
+ of discussions between its authors in order to ensure compliance with
+ the two main principles guiding its drafting:
+ .
+ * firstly, compliance with the principles governing the distribution
+ of Free Software: access to source code, broad rights granted to
+ users,
+ * secondly, the election of a governing law, French law, with which
+ it is conformant, both as regards the law of torts and
+ intellectual property law, and the protection that it offers to
+ both authors and holders of the economic rights over software.
+ .
+ The authors of the CeCILL (for Ce[a] C[nrs] I[nria] L[logiciel] L[ibre])
+ license are:
+ .
+ Commissariat à l'Energie Atomique - CEA, a public scientific, technical
+ and industrial establishment, having its principal place of business at
+ 31-33 rue de la Fédération, 75752 Paris cedex 15, France.
+ .
+ Centre National de la Recherche Scientifique - CNRS, a public scientific
+ and technological establishment, having its principal place of business
+ at 3 rue Michel-Ange 75794 Paris cedex 16, France.
+ .
+ Institut National de Recherche en Informatique et en Automatique -
+ INRIA, a public scientific and technological establishment, having its
+ principal place of business at Domaine de Voluceau, Rocquencourt, BP
+ 105, 78153 Le Chesnay cedex, France.
+ .
+ .
+ Preamble
+ .
+ The purpose of this Free Software license agreement is to grant users
+ the right to modify and redistribute the software governed by this
+ license within the framework of an open source distribution model.
+ .
+ The exercising of these rights is conditional upon certain obligations
+ for users so as to preserve this status for all subsequent redistributions.
+ .
+ In consideration of access to the source code and the rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors only have limited liability.
+ .
+ In this respect, the risks associated with loading, using, modifying
+ and/or developing or reproducing the software by the user are brought to
+ the user's attention, given its Free Software status, which may make it
+ complicated to use, with the result that its use is reserved for
+ developers and experienced professionals having in-depth computer
+ knowledge. Users are therefore encouraged to load and test the
+ Software's suitability as regards their requirements in conditions
+ enabling the security of their systems and/or data to be ensured and,
+ more generally, to use and operate it in the same conditions of
+ security. This Agreement may be freely reproduced and published,
+ provided it is not altered, and that no provisions are either added or
+ removed herefrom.
+ .
+ This Agreement may apply to any or all software for which the holder of
+ the economic rights decides to submit the use thereof to its provisions.
+ .
+ .
+ Article 1 - DEFINITIONS
+ .
+ For the purpose of this Agreement, when the following expressions
+ commence with a capital letter, they shall have the following meaning:
+ .
+ Agreement: means this license agreement, and its possible subsequent
+ versions and annexes.
+ .
+ Software: means the software in its Object Code and/or Source Code form
+ and, where applicable, its documentation, "as is" when the Licensee
+ accepts the Agreement.
+ .
+ Initial Software: means the Software in its Source Code and possibly its
+ Object Code form and, where applicable, its documentation, "as is" when
+ it is first distributed under the terms and conditions of the Agreement.
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+ that they both execute in the same address space.
+ .
+ GNU GPL: means the GNU General Public License version 2 or any
+ subsequent version, as published by the Free Software Foundation Inc.
+ .
+ Parties: mean both the Licensee and the Licensor.
+ .
+ These expressions may be used both in singular and plural form.
+ .
+ .
+ Article 2 - PURPOSE
+ .
+ The purpose of the Agreement is the grant by the Licensor to the
+ Licensee of a non-exclusive, transferable and worldwide license for the
+ Software as set forth in Article 5 hereinafter for the whole term of the
+ protection granted by the rights over said Software.
+ .
+ .
+ Article 3 - ACCEPTANCE
+ .
+ 3.1 The Licensee shall be deemed as having accepted the terms and
+ conditions of this Agreement upon the occurrence of the first of the
+ following events:
+ .
+ * (i) loading the Software by any or all means, notably, by
+ downloading from a remote server, or by loading from a physical
+ medium;
+ * (ii) the first time the Licensee exercises any of the rights
+ granted hereunder.
+ .
+ 3.2 One copy of the Agreement, containing a notice relating to the
+ characteristics of the Software, to the limited warranty, and to the
+ fact that its use is restricted to experienced users has been provided
+ to the Licensee prior to its acceptance as set forth in Article 3.1
+ hereinabove, and the Licensee hereby acknowledges that it has read and
+ understood it.
+ .
+ .
+ Article 4 - EFFECTIVE DATE AND TERM
+ .
+ .
+ 4.1 EFFECTIVE DATE
+ .
+ The Agreement shall become effective on the date when it is accepted by
+ the Licensee as set forth in Article 3.1.
+ .
+ .
+ 4.2 TERM
+ .
+ The Agreement shall remain in force for the entire legal term of
+ protection of the economic rights over the Software.
+ .
+ .
+ Article 5 - SCOPE OF RIGHTS GRANTED
+ .
+ The Licensor hereby grants to the Licensee, who accepts, the following
+ rights over the Software for any or all use, and for the term of the
+ Agreement, on the basis of the terms and conditions set forth hereinafter.
+ .
+ Besides, if the Licensor owns or comes to own one or more patents
+ protecting all or part of the functions of the Software or of its
+ components, the Licensor undertakes not to enforce the rights granted by
+ these patents against successive Licensees using, exploiting or
+ modifying the Software. If these patents are transferred, the Licensor
+ undertakes to have the transferees subscribe to the obligations set
+ forth in this paragraph.
+ .
+ .
+ 5.1 RIGHT OF USE
+ .
+ The Licensee is authorized to use the Software, without any limitation
+ as to its fields of application, with it being hereinafter specified
+ that this comprises:
+ .
+ 1. permanent or temporary reproduction of all or part of the Software
+ by any or all means and in any or all form.
+ .
+ 2. loading, displaying, running, or storing the Software on any or
+ all medium.
+ .
+ 3. entitlement to observe, study or test its operation so as to
+ determine the ideas and principles behind any or all constituent
+ elements of said Software. This shall apply when the Licensee
+ carries out any or all loading, displaying, running, transmission
+ or storage operation as regards the Software, that it is entitled
+ to carry out hereunder.
+ .
+ .
+ 5.2 ENTITLEMENT TO MAKE CONTRIBUTIONS
+ .
+ The right to make Contributions includes the right to translate, adapt,
+ arrange, or make any or all modifications to the Software, and the right
+ to reproduce the resulting Software.
+ .
+ The Licensee is authorized to make any or all Contributions to the
+ Software provided that it includes an explicit notice that it is the
+ author of said Contribution and indicates the date of the creation thereof.
+ .
+ .
+ 5.3 RIGHT OF DISTRIBUTION
+ .
+ In particular, the right of distribution includes the right to publish,
+ transmit and communicate the Software to the general public on any or
+ all medium, and by any or all means, and the right to market, either in
+ consideration of a fee, or free of charge, one or more copies of the
+ Software by any means.
+ .
+ The Licensee is further authorized to distribute copies of the modified
+ or unmodified Software to third parties according to the terms and
+ conditions set forth hereinafter.
+ .
+ .
+ 5.3.1 DISTRIBUTION OF SOFTWARE WITHOUT MODIFICATION
+ .
+ The Licensee is authorized to distribute true copies of the Software in
+ Source Code or Object Code form, provided that said distribution
+ complies with all the provisions of the Agreement and is accompanied by:
+ .
+ 1. a copy of the Agreement,
+ .
+ 2. a notice relating to the limitation of both the Licensor's
+ warranty and liability as set forth in Articles 8 and 9,
+ .
+ and that, in the event that only the Object Code of the Software is
+ redistributed, the Licensee allows future Licensees unhindered access to
+ the full Source Code of the Software by indicating how to access it, it
+ being understood that the additional cost of acquiring the Source Code
+ shall not exceed the cost of transferring the data.
+ .
+ .
+ 5.3.2 DISTRIBUTION OF MODIFIED SOFTWARE
+ .
+ When the Licensee makes a Contribution to the Software, the terms and
+ conditions for the distribution of the Modified Software become subject
+ to all the provisions of this Agreement.
+ .
+ The Licensee is authorized to distribute the Modified Software, in
+ Source Code or Object Code form, provided that said distribution
+ complies with all the provisions of the Agreement and is accompanied by:
+ .
+ 1. a copy of the Agreement,
+ .
+ 2. a notice relating to the limitation of both the Licensor's
+ warranty and liability as set forth in Articles 8 and 9,
+ .
+ and that, in the event that only the Object Code of the Modified
+ Software is redistributed, the Licensee allows future Licensees
+ unhindered access to the full Source Code of the Modified Software by
+ indicating how to access it, it being understood that the additional
+ cost of acquiring the Source Code shall not exceed the cost of
+ transferring the data.
+ .
+ .
+ 5.3.3 DISTRIBUTION OF EXTERNAL MODULES
+ .
+ When the Licensee has developed an External Module, the terms and
+ conditions of this Agreement do not apply to said External Module, that
+ may be distributed under a separate license agreement.
+ .
+ .
+ 5.3.4 COMPATIBILITY WITH THE GNU GPL
+ .
+ The Licensee can include a code that is subject to the provisions of one
+ of the versions of the GNU GPL in the Modified or unmodified Software,
+ and distribute that entire code under the terms of the same version of
+ the GNU GPL.
+ .
+ The Licensee can include the Modified or unmodified Software in a code
+ that is subject to the provisions of one of the versions of the GNU GPL,
+ and distribute that entire code under the terms of the same version of
+ the GNU GPL.
+ .
+ .
+ Article 6 - INTELLECTUAL PROPERTY
+ .
+ .
+ 6.1 OVER THE INITIAL SOFTWARE
+ .
+ The Holder owns the economic rights over the Initial Software. Any or
+ all use of the Initial Software is subject to compliance with the terms
+ and conditions under which the Holder has elected to distribute its work
+ and no one shall be entitled to modify the terms and conditions for the
+ distribution of said Initial Software.
+ .
+ The Holder undertakes that the Initial Software will remain ruled at
+ least by the current license, for the duration set forth in article 4.2.
+ .
+ .
+ 6.2 OVER THE CONTRIBUTIONS
+ .
+ A Licensee who develops a Contribution is the owner of the intellectual
+ property rights over this Contribution as defined by applicable law.
+ .
+ .
+ 6.3 OVER THE EXTERNAL MODULES
+ .
+ A Licensee who develops an External Module is the owner of the
+ intellectual property rights over this External Module as defined by
+ applicable law and is free to choose the type of agreement that shall
+ govern its distribution.
+ .
+ .
+ 6.4 JOINT PROVISIONS
+ .
+ The Licensee expressly undertakes:
+ .
+ 1. not to remove, or modify, in any manner, the intellectual property
+ notices attached to the Software;
+ .
+ 2. to reproduce said notices, in an identical manner, in the copies
+ of the Software modified or not.
+ .
+ The Licensee undertakes not to directly or indirectly infringe the
+ intellectual property rights of the Holder and/or Contributors on the
+ Software and to take, where applicable, vis-à-vis its staff, any and all
+ measures required to ensure respect of said intellectual property rights
+ of the Holder and/or Contributors.
+ .
+ .
+ Article 7 - RELATED SERVICES
+ .
+ 7.1 Under no circumstances shall the Agreement oblige the Licensor to
+ provide technical assistance or maintenance services for the Software.
+ .
+ However, the Licensor is entitled to offer this type of services. The
+ terms and conditions of such technical assistance, and/or such
+ maintenance, shall be set forth in a separate instrument. Only the
+ Licensor offering said maintenance and/or technical assistance services
+ shall incur liability therefor.
+ .
+ 7.2 Similarly, any Licensor is entitled to offer to its licensees, under
+ its sole responsibility, a warranty, that shall only be binding upon
+ itself, for the redistribution of the Software and/or the Modified
+ Software, under terms and conditions that it is free to decide. Said
+ warranty, and the financial terms and conditions of its application,
+ shall be subject of a separate instrument executed between the Licensor
+ and the Licensee.
+ .
+ .
+ Article 8 - LIABILITY
+ .
+ 8.1 Subject to the provisions of Article 8.2, the Licensee shall be
+ entitled to claim compensation for any direct loss it may have suffered
+ from the Software as a result of a fault on the part of the relevant
+ Licensor, subject to providing evidence thereof.
+ .
+ 8.2 The Licensor's liability is limited to the commitments made under
+ this Agreement and shall not be incurred as a result of in particular:
+ (i) loss due the Licensee's total or partial failure to fulfill its
+ obligations, (ii) direct or consequential loss that is suffered by the
+ Licensee due to the use or performance of the Software, and (iii) more
+ generally, any consequential loss. In particular the Parties expressly
+ agree that any or all pecuniary or business loss (i.e. loss of data,
+ loss of profits, operating loss, loss of customers or orders,
+ opportunity cost, any disturbance to business activities) or any or all
+ legal proceedings instituted against the Licensee by a third party,
+ shall constitute consequential loss and shall not provide entitlement to
+ any or all compensation from the Licensor.
+ .
+ .
+ Article 9 - WARRANTY
+ .
+ 9.1 The Licensee acknowledges that the scientific and technical
+ state-of-the-art when the Software was distributed did not enable all
+ possible uses to be tested and verified, nor for the presence of
+ possible defects to be detected. In this respect, the Licensee's
+ attention has been drawn to the risks associated with loading, using,
+ modifying and/or developing and reproducing the Software which are
+ reserved for experienced users.
+ .
+ The Licensee shall be responsible for verifying, by any or all means,
+ the product's suitability for its requirements, its good working order,
+ and for ensuring that it shall not cause damage to either persons or
+ properties.
+ .
+ 9.2 The Licensor hereby represents, in good faith, that it is entitled
+ to grant all the rights over the Software (including in particular the
+ rights set forth in Article 5).
+ .
+ 9.3 The Licensee acknowledges that the Software is supplied "as is" by
+ the Licensor without any other express or tacit warranty, other than
+ that provided for in Article 9.2 and, in particular, without any warranty
+ as to its commercial value, its secured, safe, innovative or relevant
+ nature.
+ .
+ Specifically, the Licensor does not warrant that the Software is free
+ from any error, that it will operate without interruption, that it will
+ be compatible with the Licensee's own equipment and software
+ configuration, nor that it will meet the Licensee's requirements.
+ .
+ 9.4 The Licensor does not either expressly or tacitly warrant that the
+ Software does not infringe any third party intellectual property right
+ relating to a patent, software or any other property right. Therefore,
+ the Licensor disclaims any and all liability towards the Licensee
+ arising out of any or all proceedings for infringement that may be
+ instituted in respect of the use, modification and redistribution of the
+ Software. Nevertheless, should such proceedings be instituted against
+ the Licensee, the Licensor shall provide it with technical and legal
+ assistance for its defense. Such technical and legal assistance shall be
+ decided on a case-by-case basis between the relevant Licensor and the
+ Licensee pursuant to a memorandum of understanding. The Licensor
+ disclaims any and all liability as regards the Licensee's use of the
+ name of the Software. No warranty is given as regards the existence of
+ prior rights over the name of the Software or as regards the existence
+ of a trademark.
+ .
+ .
+ Article 10 - TERMINATION
+ .
+ 10.1 In the event of a breach by the Licensee of its obligations
+ hereunder, the Licensor may automatically terminate this Agreement
+ thirty (30) days after notice has been sent to the Licensee and has
+ remained ineffective.
+ .
+ 10.2 A Licensee whose Agreement is terminated shall no longer be
+ authorized to use, modify or distribute the Software. However, any
+ licenses that it may have granted prior to termination of the Agreement
+ shall remain valid subject to their having been granted in compliance
+ with the terms and conditions hereof.
+ .
+ .
+ Article 11 - MISCELLANEOUS
+ .
+ .
+ 11.1 EXCUSABLE EVENTS
+ .
+ Neither Party shall be liable for any or all delay, or failure to
+ perform the Agreement, that may be attributable to an event of force
+ majeure, an act of God or an outside cause, such as defective
+ functioning or interruptions of the electricity or telecommunications
+ networks, network paralysis following a virus attack, intervention by
+ government authorities, natural disasters, water damage, earthquakes,
+ fire, explosions, strikes and labor unrest, war, etc.
+ .
+ 11.2 Any Failure by either Party, on one or more occasions, to invoke
+ one or more of the provisions hereof, shall under no circumstances be
+ interpreted as being a waiver by the interested Party of its right to
+ invoke said provision(s) subsequently.
+ .
+ 11.3 The Agreement cancels and replaces any or all previous agreements,
+ whether written or oral, between the Parties and having the same
+ purpose, and constitutes the entirety of the agreement between said
+ Parties concerning said purpose. No supplement or modification to the
+ terms and conditions hereof shall be effective as between the Parties
+ unless it is made in writing and signed by their duly authorized
+ representatives.
+ .
+ 11.4 In the event that one or more of the provisions hereof were to
+ conflict with a current or future applicable act or legislative text,
+ said act or legislative text shall prevail, and the Parties shall make
+ the necessary amendments so as to comply with said act or legislative
+ text. All other provisions shall remain effective. Similarly, invalidity
+ of a provision of the Agreement, for any reason whatsoever, shall not
+ cause the Agreement as a whole to be invalid.
+ .
+ .
+ 11.5 LANGUAGE
+ .
+ The Agreement is drafted in both French and English and both versions
+ are deemed authentic.
+ .
+ .
+ Article 12 - NEW VERSIONS OF THE AGREEMENT
+ .
+ 12.1 Any person is authorized to duplicate and distribute copies of this
+ Agreement.
+ .
+ 12.2 So as to ensure coherence, the wording of this Agreement is
+ protected and may only be modified by the authors of the License, who
+ reserve the right to periodically publish updates or new versions of the
+ Agreement, each with a separate number. These subsequent versions may
+ address new issues encountered by Free Software.
+ .
+ 12.3 Any Software distributed under a given version of the Agreement may
+ only be subsequently distributed under the same version of the Agreement
+ or a subsequent version, subject to the provisions of Article 5.3.4.
+ .
+ .
+ Article 13 - GOVERNING LAW AND JURISDICTION
+ .
+ 13.1 The Agreement is governed by French law. The Parties agree to
+ endeavor to seek an amicable solution to any disagreements or disputes
+ that may arise during the performance of the Agreement.
+ .
+ 13.2 Failing an amicable solution within two (2) months as from their
+ occurrence, and unless emergency proceedings are necessary, the
+ disagreements or disputes shall be referred to the Paris Courts having
+ jurisdiction, by the more diligent Party.
+ .
+ .
+ Version 2.0 dated 2005-05-21.
+
License: GPL-2+
This package is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
@@ -61,4 +536,3 @@ License: GPL-2+
.
On Debian systems, the complete text of the GNU General
Public License can be found in `/usr/share/common-licenses/GPL'.
-
=====================================
debian/rules
=====================================
--- a/debian/rules
+++ b/debian/rules
@@ -6,3 +6,7 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all
%:
dh $@
+
+override_dh_auto_configure:
+ dh_auto_configure -- -DCMAKE_BUILD_TYPE=RelWithDebInfo
+
View it on GitLab: https://salsa.debian.org/med-team/bppphyview/compare/7cc189c93e2cb39346df800c28e684a011efc799...4856cb370578b9f15c03592bc40d693c7fcc40da
---
View it on GitLab: https://salsa.debian.org/med-team/bppphyview/compare/7cc189c93e2cb39346df800c28e684a011efc799...4856cb370578b9f15c03592bc40d693c7fcc40da
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