[med-svn] [Git][med-team/beads][master] 10 commits: Merge after git pull salsa upstream --allow-unrelated-histories
Filippo Rusconi (@lopippo)
gitlab at salsa.debian.org
Wed Dec 14 16:29:59 GMT 2022
Filippo Rusconi pushed to branch master at Debian Med / beads
Commits:
0e133abd by Filippo Rusconi (Uploading Debian Developer) at 2020-05-06T17:56:34+02:00
Merge after git pull salsa upstream --allow-unrelated-histories
- - - - -
5caacd6f by Rusconi Filippo at 2022-12-14T13:28:01+01:00
New upstream version 1.1.21
- - - - -
5654dc4d by Rusconi Filippo at 2022-12-14T13:29:26+01:00
Update upstream source from tag 'upstream/1.1.21'
Update to upstream version '1.1.21'
with Debian dir 0051bf2cd3cb65d1f68eea2068633c1bddbfb7ba
- - - - -
91183d26 by Rusconi Filippo at 2022-12-14T13:30:20+01:00
Preparing version 1.1.21.
- - - - -
a6d03442 by Rusconi Filippo at 2022-12-14T14:21:56+01:00
Last minute modifs by Olivier Langella.
- - - - -
4f102d70 by Rusconi Filippo at 2022-12-14T14:27:27+01:00
New upstream version 1.1.21
- - - - -
f7a72cd7 by Rusconi Filippo at 2022-12-14T14:28:51+01:00
Update upstream source from tag 'upstream/1.1.21'
Update to upstream version '1.1.21'
with Debian dir dd64a01a703eeb6365d3e886e0d00f1350d4a24d
- - - - -
89698151 by Rusconi Filippo at 2022-12-14T16:15:39+01:00
Last updates to the packaging.
- - - - -
a80ffa77 by Rusconi Filippo at 2022-12-14T16:17:05+01:00
New upstream version 1.1.21
- - - - -
1a05ea24 by Rusconi Filippo at 2022-12-14T16:18:31+01:00
Update upstream source from tag 'upstream/1.1.21'
Update to upstream version '1.1.21'
with Debian dir 955226c82bcae577fb12c9f56de82606a0bbc9ff
- - - - -
8 changed files:
- CMakeLists.txt
- debian/changelog
- debian/control
- src/CMakeLists.txt
- src/qtbeads/CMakeLists.txt
- src/qtbeads/main_window.cpp
- src/qtbeads/properties.cpp
- src/qtbeads/q_gel_image.cpp
Changes:
=====================================
CMakeLists.txt
=====================================
@@ -5,7 +5,7 @@
# cmake .
# make
# make install
-cmake_minimum_required(VERSION 2.6)
+cmake_minimum_required(VERSION 2.18.4)
# The name of our project is "beads". CMakeLists files in this project can
@@ -77,8 +77,8 @@ set(CMAKE_CXX_FLAGS_DEBUG "-g -s")
set(CMAKE_CXX_FLAGS_MINSIZEREL "-Os -DNDEBUG")
set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-O2 -g")
-set(BEADS_VERSION "1.1.20")
-set(VERSION 1.1.20)
+set(BEADS_VERSION "1.1.21")
+set(VERSION 1.1.21)
set(CPACK_CMAKE_GENERATOR "Unix Makefiles")
set(CPACK_GENERATOR "STGZ;TGZ;TZ")
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+beads (1.1.21-1) unstable; urgency=low
+
+ * Port to Qt6.
+ * Update version of libodsstream-dev build-dep package.
+ * Fixes in the CMake-based system.
+ * Standards-Version: 4.6.1 (routine update).
+
+ -- Filippo Rusconi <lopippo at debian.org> Wed, 14 Dec 2022 12:45:41 +0100
+
beads (1.1.20-4) UNRELEASED; urgency=low
[ Filippo Rusconi ]
=====================================
debian/control
=====================================
@@ -5,11 +5,11 @@ Uploaders: Andreas Tille <tille at debian.org>,
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
- cmake,
- qtbase5-dev,
- cimg-dev,
- libodsstream-dev
-Standards-Version: 4.6.0
+ cmake,
+ qtbase5-dev,
+ cimg-dev,
+ libodsstream-dev (>= 0.9.1),
+Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/med-team/beads
Vcs-Git: https://salsa.debian.org/med-team/beads.git
Homepage: http://pappso.inrae.fr/bioinfo/beads
@@ -18,8 +18,8 @@ Rules-Requires-Root: no
Package: beads
Architecture: any
Depends: ${shlibs:Depends},
- ${misc:Depends},
- imagemagick
+ ${misc:Depends},
+ imagemagick,
Description: 2-DE electrophoresis gel image spot detection
Beads is a program for spot detection on 2-D gel images. It is based on
an analogy with beads flowing uphill on the surface of the gel image and
=====================================
src/CMakeLists.txt
=====================================
@@ -1,4 +1,5 @@
-find_package( Qt5 COMPONENTS Core Gui Xml REQUIRED )
+find_package( Qt6 COMPONENTS Core Gui Xml REQUIRED )
+find_package(QuaZip-Qt6 REQUIRED)
list( APPEND CMAKE_MODULE_PATH
${PROJECT_SOURCE_DIR}/cmake_modules
@@ -39,29 +40,29 @@ endif(MINGW32)
set( BEADS_FOR_QT_CPP
- ConfigFile/ConfigFile
- parameters
- encode/base64
+ ConfigFile/ConfigFile.cpp
+ parameters.cpp
+ encode/base64.cpp
images/imageIntensity.cpp
images/imageDirect.cpp
- images/imageCode
- images/imageCoule
- images/imagePaths
- images/imageConfluent
- images/imageProb
- images/parameterProb
- parameterDetection
- images/parameterConfluent
- detection
- images/imageDetection
- images/imageNumber
- images/parameterNumber
- images/imageContours
- spotPROTICdbDocument
- spot
- spotDocument
- spotSvgDocument
- images/imageDeNovo
+ images/imageCode.h
+ images/imageCoule.cpp
+ images/imagePaths.cpp
+ images/imageConfluent.cpp
+ images/imageProb.cpp
+ images/parameterProb.cpp
+ parameterDetection.cpp
+ images/parameterConfluent.cpp
+ detection.cpp
+ images/imageDetection.cpp
+ images/imageNumber.cpp
+ images/parameterNumber.cpp
+ images/imageContours.cpp
+ spotPROTICdbDocument.cpp
+ spot.cpp
+ spotDocument.cpp
+ spotSvgDocument.cpp
+ images/imageDeNovo.cpp
)
if(WIN32)
@@ -91,24 +92,24 @@ set_target_properties(beads
CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${CImg_CFLAGS}"
)
-target_link_libraries(beads cppbeads
+target_link_libraries(beads cppbeads
${CImg_SYSTEM_LIBS}
${CImg_CFLAGS}
- Qt5::Core
- Qt5::Gui
- Qt5::Xml
+ Qt6::Core
+ Qt6::Gui
+ Qt6::Xml
OdsStream::Core
)
-add_library( cppbeads STATIC
+add_library(cppbeads STATIC
${BEADS_FOR_QT_CPP}
)
target_include_directories(cppbeads PUBLIC ${OdsStream_INCLUDE_DIRS}
${CImg_INCLUDE_DIRS} ${CImg_SYSTEM_LIBS_DIR})
set_target_properties(cppbeads
- PROPERTIES OUTPUT_NAME cppbeads-qt5
+ PROPERTIES OUTPUT_NAME cppbeads-qt6
CLEAN_DIRECT_OUTPUT 1
CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${CImg_CFLAGS}"
)
@@ -116,9 +117,9 @@ set_target_properties(cppbeads
target_link_libraries(cppbeads
${CImg_SYSTEM_LIBS}
${CImg_CFLAGS}
- Qt5::Core
- Qt5::Gui
- Qt5::Xml
+ Qt6::Core
+ Qt6::Gui
+ Qt6::Xml
OdsStream::Core
)
=====================================
src/qtbeads/CMakeLists.txt
=====================================
@@ -1,5 +1,5 @@
-find_package( Qt5 COMPONENTS Core Gui Xml Widgets PrintSupport REQUIRED )
+find_package( Qt6 COMPONENTS Core Gui Xml Widgets PrintSupport REQUIRED )
# add some useful macros and variables
# (QT_USE_FILE is a variable defined by FIND_PACKAGE( Qt4 ) that contains a path to CMake script)
@@ -48,13 +48,13 @@ set( QTBEADS_MOC_HDRS
# this command will generate rules that will run rcc on all files from SAMPLE_RCS
# in result SAMPLE_RC_SRCS variable will contain paths to files produced by rcc
-qt5_add_resources( QTBEADS_SRCS ${SAMPLE_RCS} )
+qt6_add_resources( QTBEADS_SRCS ${SAMPLE_RCS} )
# this will run uic on .ui files:
#QT4_WRAP_UI( SAMPLE_UI_HDRS ${SAMPLE_UIS} )
# and finally this will run moc:
-qt5_wrap_cpp( QTBEADS_MOC_SRCS ${QTBEADS_MOC_HDRS} )
+qt6_wrap_cpp( QTBEADS_MOC_SRCS ${QTBEADS_MOC_HDRS} )
# we need this to be able to include headers produced by uic in our code
# (CMAKE_BINARY_DIR holds a path to the build directory, while INCLUDE_DIRECTORIES() works just like INCLUDEPATH from qmake)
@@ -85,6 +85,6 @@ else(WIN32)
)
endif(WIN32)
-target_link_libraries(qtbeads cppbeads OdsStream::Core ${CImg_SYSTEM_LIBS} Qt5::Core Qt5::Gui Qt5::Xml Qt5::Widgets Qt5::PrintSupport)
+target_link_libraries(qtbeads cppbeads OdsStream::Core ${CImg_SYSTEM_LIBS} Qt6::Core Qt6::Gui Qt6::Xml Qt6::Widgets Qt6::PrintSupport)
=====================================
src/qtbeads/main_window.cpp
=====================================
@@ -22,10 +22,8 @@
#include "../images/imageCoule.h"
#include "../images/imageProb.h"
#include "../images/imagePaths.h"
-#include "../images/imageDetection.h"
#include "../images/imageConfluent.h"
#include "../images/imageContours.h"
-#include "../images/imageDeNovo.h"
#include "../parameters.h"
bool copy_file(QString inputfile, QString outputfile) {
@@ -149,7 +147,7 @@ void MainWindow::moveGelImage(QMouseEvent * event) {
_before_x = event->x();
_before_y = event->y();
- qDebug() << event->x() << " " << event->y() << endl;
+ qDebug() << event->x() << " " << event->y() << Qt::endl;
//scrollArea->widget()->move(event->x(), event->y());
scrollArea->horizontalScrollBar()->setSliderPosition(
scrollArea->horizontalScrollBar()->value() - dx);
@@ -245,16 +243,28 @@ void MainWindow::saveStepsDirectory() {
}
void MainWindow::print() {
- Q_ASSERT(scrollArea->getGelImage()->pixmap());
+#if QT_VERSION < 0x060000
+ Q_ASSERT(!scrollArea->getGelImage()->pixmap(Qt::ReturnByValue).isNull());
+#else
+ Q_ASSERT(!scrollArea->getGelImage()->pixmap().isNull());
+#endif
QPrintDialog dialog(&printer, this);
if (dialog.exec()) {
QPainter painter(&printer);
QRect rect = painter.viewport();
- QSize size = scrollArea->getGelImage()->pixmap()->size();
+#if QT_VERSION < 0x060000
+ QSize size = scrollArea->getGelImage()->pixmap(Qt::ReturnByValue).size();
size.scale(rect.size(), Qt::KeepAspectRatio);
painter.setViewport(rect.x(), rect.y(), size.width(), size.height());
- painter.setWindow(scrollArea->getGelImage()->pixmap()->rect());
- painter.drawPixmap(0, 0, *scrollArea->getGelImage()->pixmap());
+ painter.setWindow(scrollArea->getGelImage()->pixmap(Qt::ReturnByValue).rect());
+ painter.drawPixmap(0, 0, scrollArea->getGelImage()->pixmap(Qt::ReturnByValue));
+#else
+ QSize size = scrollArea->getGelImage()->pixmap().size();
+ size.scale(rect.size(), Qt::KeepAspectRatio);
+ painter.setViewport(rect.x(), rect.y(), size.width(), size.height());
+ painter.setWindow(scrollArea->getGelImage()->pixmap().rect());
+ painter.drawPixmap(0, 0, scrollArea->getGelImage()->pixmap());
+#endif
}
}
@@ -403,7 +413,11 @@ void MainWindow::updateActions() {
}
void MainWindow::scaleImage(double factor) {
- Q_ASSERT(scrollArea->getGelImage()->pixmap());
+#if QT_VERSION < 0x060000
+ Q_ASSERT(!scrollArea->getGelImage()->pixmap(Qt::ReturnByValue).isNull());
+#else
+ Q_ASSERT(!scrollArea->getGelImage()->pixmap().isNull());
+#endif
scrollArea->scaleImage(factor);
adjustScrollBar(scrollArea->horizontalScrollBar(), factor);
@@ -467,7 +481,7 @@ void MainWindow::runDetection(QString directory_to_save_all_steps) {
qDebug() << "MainWindow::runDetection _properties.isInverse() "
<< _properties.isInverse();
- qDebug() << "Computing bead directions " << endl;
+ qDebug() << "Computing bead directions " << Qt::endl;
imageDirect directions;
const parameterDirect & parameter_direct =
beads_params.get_parameter_direction();
@@ -477,7 +491,7 @@ void MainWindow::runDetection(QString directory_to_save_all_steps) {
directions.save(directory_to_save_all_steps + "/DIRECTIONS.png");
}
- qDebug() << "Beads are rolling" << endl;
+ qDebug() << "Beads are rolling" << Qt::endl;
imageCoule rolling;
rolling.compute_from_direct(directions);
if (!directory_to_save_all_steps.isEmpty()) {
@@ -485,7 +499,7 @@ void MainWindow::runDetection(QString directory_to_save_all_steps) {
}
//using confluent method :
- qDebug() << "Computing bead paths" << endl;
+ qDebug() << "Computing bead paths" << Qt::endl;
imagePaths path;
path.compute_from_direct_and_coule(directions, rolling);
@@ -493,13 +507,13 @@ void MainWindow::runDetection(QString directory_to_save_all_steps) {
path.save(directory_to_save_all_steps + "/PATHS.png");
}
- qDebug() << "Detecting merging paths and arrival positions" << endl;
+ qDebug() << "Detecting merging paths and arrival positions" << Qt::endl;
const parameterConfluent & parameter_confl =
beads_params.get_parameter_confluent();
- qDebug() << " minflux : " << parameter_confl.get_minflux() << endl;
- qDebug() << " minpath : " << parameter_confl.get_minpath() << endl;
- qDebug() << " winconfl : " << parameter_confl.get_winconfl() << endl;
- qDebug() << " minbeads : " << parameter_confl.get_minbeads() << endl;
+ qDebug() << " minflux : " << parameter_confl.get_minflux() << Qt::endl;
+ qDebug() << " minpath : " << parameter_confl.get_minpath() << Qt::endl;
+ qDebug() << " winconfl : " << parameter_confl.get_winconfl() << Qt::endl;
+ qDebug() << " minbeads : " << parameter_confl.get_minbeads() << Qt::endl;
imageConfluent confluent;
confluent.compute_from_direct_and_paths(directions, path, *p_gel_image,
@@ -508,12 +522,12 @@ void MainWindow::runDetection(QString directory_to_save_all_steps) {
confluent.save(directory_to_save_all_steps + "/SELECT.png");
}
- qDebug() << "Computing probabilites of spot positions" << endl;
+ qDebug() << "Computing probabilites of spot positions" << Qt::endl;
const parameterProb & parameter_prob =
beads_params.get_parameter_prob();
- qDebug() << " threshold : " << parameter_prob.get_threshold() << endl;
- qDebug() << " sx : " << parameter_prob.get_sx() << endl;
- qDebug() << " sy : " << parameter_prob.get_sy() << endl;
+ qDebug() << " threshold : " << parameter_prob.get_threshold() << Qt::endl;
+ qDebug() << " sx : " << parameter_prob.get_sx() << Qt::endl;
+ qDebug() << " sy : " << parameter_prob.get_sy() << Qt::endl;
imageProb dest_image_prob;
@@ -523,11 +537,11 @@ void MainWindow::runDetection(QString directory_to_save_all_steps) {
+ "/PROBABILITIES.png");
}
- qDebug() << "Detecting spots" << endl;
+ qDebug() << "Detecting spots" << Qt::endl;
const parameterDetection & parameter_detection =
beads_params.get_parameter_detection();
qDebug() << " minproba : " << parameter_detection.get_minproba()
- << endl;
+ << Qt::endl;
detection * p_the_detection_from_prob = new detection();
p_the_detection_from_prob->detect_from_prob(dest_image_prob,
@@ -535,7 +549,7 @@ void MainWindow::runDetection(QString directory_to_save_all_steps) {
//imageDetection img_detect(*p_the_detection_from_prob);
- qDebug() << "Quantification" << endl;
+ qDebug() << "Quantification" << Qt::endl;
const parameterNumber & parameter_number =
beads_params.get_parameter_number();
=====================================
src/qtbeads/properties.cpp
=====================================
@@ -20,53 +20,53 @@ void create_default_parameter_file(const QFileInfo & filename) {
}
QTextStream param_stream(¶m_file);
- param_stream << "#" << filename.absoluteFilePath() << endl;
- param_stream << "# beads configuration file" << endl;
+ param_stream << "#" << filename.absoluteFilePath() << Qt::endl;
+ param_stream << "# beads configuration file" << Qt::endl;
param_stream << "# default parameters, optimized for silver staining"
- << endl;
- param_stream << endl;
- param_stream << "################################" << endl;
- param_stream << "# parameters for DIRECTIONS #" << endl;
- param_stream << "################################" << endl;
- param_stream << endl;
- param_stream << "burned_pixel_threshold = 63000" << endl;
- param_stream << endl;
- param_stream << "################################" << endl;
- param_stream << "# parameters for SELECT #" << endl;
- param_stream << "################################" << endl;
- param_stream << endl;
- param_stream << "minflux = 100" << endl;
- param_stream << "minpath = 2" << endl;
- param_stream << "winconfl = 300" << endl;
- param_stream << "minbeads = 200" << endl;
- param_stream << "confluent_intmax = 60000" << endl;
- param_stream << "confluent_minpct = 1" << endl;
- param_stream << endl;
- param_stream << "################################" << endl;
- param_stream << "# parameters for PROBABILITIES #" << endl;
- param_stream << "################################" << endl;
- param_stream << endl;
- param_stream << "prob_threshold = 10" << endl;
- param_stream << "sx = 3" << endl;
- param_stream << "sy = 3" << endl;
- param_stream << "sx_bottom = 5" << endl;
- param_stream << "sy_bottom = 5" << endl;
- param_stream << endl;
-
- param_stream << "################################" << endl;
- param_stream << "# parameters for detections #" << endl;
- param_stream << "################################" << endl;
- param_stream << endl;
- param_stream << "minproba = 400" << endl;
- param_stream << endl;
-
- param_stream << "################################" << endl;
- param_stream << "# parameters for quantification #" << endl;
- param_stream << "################################" << endl;
- param_stream << endl;
- param_stream << "quantification_enlarge_fusion = 3" << endl;
- param_stream << "npass = 10" << endl;
- param_stream << endl;
+ << Qt::endl;
+ param_stream << Qt::endl;
+ param_stream << "################################" << Qt::endl;
+ param_stream << "# parameters for DIRECTIONS #" << Qt::endl;
+ param_stream << "################################" << Qt::endl;
+ param_stream << Qt::endl;
+ param_stream << "burned_pixel_threshold = 63000" << Qt::endl;
+ param_stream << Qt::endl;
+ param_stream << "################################" << Qt::endl;
+ param_stream << "# parameters for SELECT #" << Qt::endl;
+ param_stream << "################################" << Qt::endl;
+ param_stream << Qt::endl;
+ param_stream << "minflux = 100" << Qt::endl;
+ param_stream << "minpath = 2" << Qt::endl;
+ param_stream << "winconfl = 300" << Qt::endl;
+ param_stream << "minbeads = 200" << Qt::endl;
+ param_stream << "confluent_intmax = 60000" << Qt::endl;
+ param_stream << "confluent_minpct = 1" << Qt::endl;
+ param_stream << Qt::endl;
+ param_stream << "################################" << Qt::endl;
+ param_stream << "# parameters for PROBABILITIES #" << Qt::endl;
+ param_stream << "################################" << Qt::endl;
+ param_stream << Qt::endl;
+ param_stream << "prob_threshold = 10" << Qt::endl;
+ param_stream << "sx = 3" << Qt::endl;
+ param_stream << "sy = 3" << Qt::endl;
+ param_stream << "sx_bottom = 5" << Qt::endl;
+ param_stream << "sy_bottom = 5" << Qt::endl;
+ param_stream << Qt::endl;
+
+ param_stream << "################################" << Qt::endl;
+ param_stream << "# parameters for detections #" << Qt::endl;
+ param_stream << "################################" << Qt::endl;
+ param_stream << Qt::endl;
+ param_stream << "minproba = 400" << Qt::endl;
+ param_stream << Qt::endl;
+
+ param_stream << "################################" << Qt::endl;
+ param_stream << "# parameters for quantification #" << Qt::endl;
+ param_stream << "################################" << Qt::endl;
+ param_stream << Qt::endl;
+ param_stream << "quantification_enlarge_fusion = 3" << Qt::endl;
+ param_stream << "npass = 10" << Qt::endl;
+ param_stream << Qt::endl;
param_stream.flush();
param_file.close();
}
=====================================
src/qtbeads/q_gel_image.cpp
=====================================
@@ -55,7 +55,11 @@ void QGelImage::setScaleFactor(double scale_factor) {
void QGelImage::scaleImage(double factor) {
_scaleFactor *= factor;
- this->resize(_scaleFactor * this->pixmap()->size());
+#if QT_VERSION < 0x060000
+ this->resize(_scaleFactor * this->pixmap(Qt::ReturnByValue).size());
+#else
+ this->resize(_scaleFactor * this->pixmap().size());
+#endif
}
int QGelImage::getX(int real_x) const {
View it on GitLab: https://salsa.debian.org/med-team/beads/-/compare/f42ceebbb9ca97b8a65f501db1764cca4462e1a8...1a05ea24066d45fb17935e1931944a95f273368d
--
View it on GitLab: https://salsa.debian.org/med-team/beads/-/compare/f42ceebbb9ca97b8a65f501db1764cca4462e1a8...1a05ea24066d45fb17935e1931944a95f273368d
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20221214/b35f6e54/attachment-0001.htm>
More information about the debian-med-commit
mailing list