From 70a2849170a1b5793ed4c26f7b06cc6ae7d41ff0 Mon Sep 17 00:00:00 2001 From: Lance Parsons Date: Tue, 20 Jun 2017 17:28:21 -0400 Subject: [PATCH] Add maven_core as submodule This change makes maven the super project and moves the GUI build files into this repository Code was moved to teh src directory, split into maven (gui) and maven_core (libraries as a submodule). The follows the layout specified in https://wiki.qt.io/SUBDIRS_-_handling_dependencies. Also fixed dependencies for updated travis images Removed obsolete macdeployqtfix (qt 5.10 is patched as is homebrew qt 5.9) --- .gitmodules | 3 + .travis.yml | 42 ++++++ appveyor.yml | 40 ++++++ build.pro | 15 ++ ci/travis/before_install_linux.sh | 21 +++ ci/travis/before_install_osx.sh | 14 ++ make_dist_linux.sh | 76 ++++++++++ make_dist_osx.sh | 73 ++++++++++ make_dist_win32.sh | 64 +++++++++ maven.pro | 159 --------------------- .../maven/alignmentdialog.cpp | 0 alignmentdialog.h => src/maven/alignmentdialog.h | 0 .../maven/background_peaks_update.cpp | 0 .../maven/background_peaks_update.h | 0 barplot.cpp => src/maven/barplot.cpp | 0 barplot.h => src/maven/barplot.h | 0 boxplot.cpp => src/maven/boxplot.cpp | 0 boxplot.h => src/maven/boxplot.h | 0 .../maven/calibratedialog.cpp | 0 calibratedialog.h => src/maven/calibratedialog.h | 0 classifier.cpp => src/maven/classifier.cpp | 0 classifier.h => src/maven/classifier.h | 0 .../maven/classifierNeuralNet.cpp | 0 .../maven/classifierNeuralNet.h | 0 clusterdialog.cpp => src/maven/clusterdialog.cpp | 0 clusterdialog.h => src/maven/clusterdialog.h | 0 .../maven/comparesamplesdialog.cpp | 0 .../maven/comparesamplesdialog.h | 0 csvreports.cpp => src/maven/csvreports.cpp | 0 csvreports.h => src/maven/csvreports.h | 0 database.cpp => src/maven/database.cpp | 0 database.h => src/maven/database.h | 0 eicwidget.cpp => src/maven/eicwidget.cpp | 0 eicwidget.h => src/maven/eicwidget.h | 0 {forms => src/maven/forms}/adductwidget.ui | 0 {forms => src/maven/forms}/alignmentdialog.ui | 0 {forms => src/maven/forms}/calibrateform.ui | 0 {forms => src/maven/forms}/clusterdialog.ui | 0 {forms => src/maven/forms}/comparesamplesdialog.ui | 0 {forms => src/maven/forms}/covariantswidget.ui | 0 {forms => src/maven/forms}/isotopeswidget.ui | 0 {forms => src/maven/forms}/librarydialog.ui | 0 {forms => src/maven/forms}/masscalcwidget.ui | 0 {forms => src/maven/forms}/noteswidget.ui | 0 {forms => src/maven/forms}/peakdetectiondialog.ui | 0 {forms => src/maven/forms}/rconsolewidget.ui | 0 {forms => src/maven/forms}/settingsform.ui | 0 {forms => src/maven/forms}/spectramatching.ui | 0 {forms => src/maven/forms}/trainingdialog.ui | 0 gallerywidget.cpp => src/maven/gallerywidget.cpp | 0 gallerywidget.h => src/maven/gallerywidget.h | 0 src/maven/get_version.bat | 3 + src/maven/get_version.sh | 2 + globals.h => src/maven/globals.h | 0 heatmap.cpp => src/maven/heatmap.cpp | 0 heatmap.h => src/maven/heatmap.h | 0 highlighter.cpp => src/maven/highlighter.cpp | 0 highlighter.h => src/maven/highlighter.h | 0 history.cpp => src/maven/history.cpp | 0 history.h => src/maven/history.h | 0 {images => src/maven/images}/PDF.png | Bin {images => src/maven/images}/R.png | Bin {images => src/maven/images}/autofocus.png | Bin {images => src/maven/images}/autofocus.svg | 0 {images => src/maven/images}/averageSpectra.png | Bin {images => src/maven/images}/bad.png | Bin {images => src/maven/images}/bookmark.png | Bin {images => src/maven/images}/bug.png | Bin {images => src/maven/images}/cluster.png | Bin {images => src/maven/images}/colorfill.png | Bin {images => src/maven/images}/compound.png | Bin {images => src/maven/images}/contrast.png | Bin {images => src/maven/images}/copyCSV.png | Bin {images => src/maven/images}/copyPNG.png | Bin {images => src/maven/images}/covariants.png | Bin {images => src/maven/images}/dbsearch.png | Bin {images => src/maven/images}/delete.png | Bin {images => src/maven/images}/export.png | Bin {images => src/maven/images}/exportcsv.png | Bin {images => src/maven/images}/exportpdf.png | Bin {images => src/maven/images}/exportpng.png | Bin {images => src/maven/images}/exportxml.png | Bin {images => src/maven/images}/featuredetect.png | Bin {images => src/maven/images}/filenew.png | Bin {images => src/maven/images}/fileopen.png | Bin {images => src/maven/images}/fileprint.png | Bin {images => src/maven/images}/filesave.png | Bin {images => src/maven/images}/filter.png | Bin {images => src/maven/images}/findcompound.png | Bin {images => src/maven/images}/flip.png | Bin {images => src/maven/images}/flowerplot.png | Bin {images => src/maven/images}/gallery.png | Bin {images => src/maven/images}/good.png | Bin {images => src/maven/images}/heatmap.png | Bin {images => src/maven/images}/hide.png | Bin {images => src/maven/images}/icon.icns | Bin {images => src/maven/images}/icon.png | Bin {images => src/maven/images}/icons.svg | 0 {images => src/maven/images}/integrateArea.png | Bin {images => src/maven/images}/isotope.png | Bin {images => src/maven/images}/last.png | Bin {images => src/maven/images}/librarymanager.png | Bin {images => src/maven/images}/link.png | Bin {images => src/maven/images}/logo1.svg | 0 {images => src/maven/images}/markbad.png | Bin {images => src/maven/images}/markgood.png | Bin {images => src/maven/images}/molecule.png | Bin {images => src/maven/images}/negative_ion.png | Bin {images => src/maven/images}/newicons.svg | 0 {images => src/maven/images}/next.png | Bin {images => src/maven/images}/note.png | Bin {images => src/maven/images}/pathway.png | Bin {images => src/maven/images}/peakgroup.png | Bin {images => src/maven/images}/positive_ion.png | Bin {images => src/maven/images}/qqq.png | Bin {images => src/maven/images}/refresh.png | Bin {images => src/maven/images}/resetzoom.png | Bin {images => src/maven/images}/resetzoom2.png | Bin {images => src/maven/images}/samples.png | Bin {images => src/maven/images}/scatterplot.png | Bin {images => src/maven/images}/settings.png | Bin {images => src/maven/images}/showbookmarks.png | Bin {images => src/maven/images}/spectra.png | Bin {images => src/maven/images}/spectra_search.png | Bin {images => src/maven/images}/splash.png | Bin {images => src/maven/images}/spreadsheet.png | Bin {images => src/maven/images}/textcenter.png | Bin {images => src/maven/images}/tic.png | Bin {images => src/maven/images}/train.png | Bin {images => src/maven/images}/unknown_ion.png | Bin {images => src/maven/images}/zoomInEdge.png | Bin {images => src/maven/images}/zoomInNode.png | Bin {images => src/maven/images}/zoomInText.png | Bin {images => src/maven/images}/zoomOutEdge.png | Bin {images => src/maven/images}/zoomOutNode.png | Bin {images => src/maven/images}/zoomOutText.png | Bin {images => src/maven/images}/zoomin.png | Bin {images => src/maven/images}/zoomout.png | Bin isotopeplot.cpp => src/maven/isotopeplot.cpp | 0 isotopeplot.h => src/maven/isotopeplot.h | 0 isotopeswidget.cpp => src/maven/isotopeswidget.cpp | 0 isotopeswidget.h => src/maven/isotopeswidget.h | 0 librarydialog.cpp => src/maven/librarydialog.cpp | 0 librarydialog.h => src/maven/librarydialog.h | 0 ligandwidget.cpp => src/maven/ligandwidget.cpp | 0 ligandwidget.h => src/maven/ligandwidget.h | 0 line.cpp => src/maven/line.cpp | 0 line.h => src/maven/line.h | 0 main.cpp => src/maven/main.cpp | 0 mainwindow.cpp => src/maven/mainwindow.cpp | 0 mainwindow.h => src/maven/mainwindow.h | 0 masscalcgui.cpp => src/maven/masscalcgui.cpp | 0 masscalcgui.h => src/maven/masscalcgui.h | 0 mzroll.desktop => src/maven/maven.desktop | 0 src/maven/maven.pro | 159 +++++++++++++++++++++ mzfileio.cpp => src/maven/mzfileio.cpp | 0 mzfileio.h => src/maven/mzfileio.h | 0 mzroll.ico => src/maven/mzroll.ico | Bin mzroll.qrc => src/maven/mzroll.qrc | 0 mzroll.rc => src/maven/mzroll.rc | 0 note.cpp => src/maven/note.cpp | 0 note.h => src/maven/note.h | 0 .../maven/numeric_treewidgetitem.h | 0 .../maven/peakdetectiondialog.cpp | 0 .../maven/peakdetectiondialog.h | 0 plot_axes.cpp => src/maven/plot_axes.cpp | 0 plot_axes.h => src/maven/plot_axes.h | 0 plotdock.cpp => src/maven/plotdock.cpp | 0 plotdock.h => src/maven/plotdock.h | 0 point.cpp => src/maven/point.cpp | 0 point.h => src/maven/point.h | 0 projectDB.cpp => src/maven/projectDB.cpp | 0 projectDB.h => src/maven/projectDB.h | 0 .../maven/projectdockwidget.cpp | 0 .../maven/projectdockwidget.h | 0 rconsolewidget.cpp => src/maven/rconsolewidget.cpp | 0 rconsolewidget.h => src/maven/rconsolewidget.h | 0 scatterplot.cpp => src/maven/scatterplot.cpp | 0 scatterplot.h => src/maven/scatterplot.h | 0 settingsform.cpp => src/maven/settingsform.cpp | 0 settingsform.h => src/maven/settingsform.h | 0 spectralhit.h => src/maven/spectralhit.h | 0 .../maven/spectramatching.cpp | 0 spectramatching.h => src/maven/spectramatching.h | 0 spectrawidget.cpp => src/maven/spectrawidget.cpp | 0 spectrawidget.h => src/maven/spectrawidget.h | 0 stable.h => src/maven/stable.h | 0 suggest.cpp => src/maven/suggest.cpp | 0 suggest.h => src/maven/suggest.h | 0 .../maven/tabledockwidget.cpp | 0 tabledockwidget.h => src/maven/tabledockwidget.h | 0 test.cpp => src/maven/test.cpp | 0 tinyplot.cpp => src/maven/tinyplot.cpp | 0 tinyplot.h => src/maven/tinyplot.h | 0 traindialog.cpp => src/maven/traindialog.cpp | 0 traindialog.h => src/maven/traindialog.h | 0 treedockwidget.cpp => src/maven/treedockwidget.cpp | 0 treedockwidget.h => src/maven/treedockwidget.h | 0 src/maven_core | 1 + 199 files changed, 513 insertions(+), 159 deletions(-) create mode 100644 .gitmodules create mode 100644 .travis.yml create mode 100644 appveyor.yml create mode 100644 build.pro create mode 100755 ci/travis/before_install_linux.sh create mode 100755 ci/travis/before_install_osx.sh create mode 100755 make_dist_linux.sh create mode 100755 make_dist_osx.sh create mode 100755 make_dist_win32.sh delete mode 100644 maven.pro rename alignmentdialog.cpp => src/maven/alignmentdialog.cpp (100%) rename alignmentdialog.h => src/maven/alignmentdialog.h (100%) rename background_peaks_update.cpp => src/maven/background_peaks_update.cpp (100%) rename background_peaks_update.h => src/maven/background_peaks_update.h (100%) rename barplot.cpp => src/maven/barplot.cpp (100%) rename barplot.h => src/maven/barplot.h (100%) rename boxplot.cpp => src/maven/boxplot.cpp (100%) rename boxplot.h => src/maven/boxplot.h (100%) rename calibratedialog.cpp => src/maven/calibratedialog.cpp (100%) rename calibratedialog.h => src/maven/calibratedialog.h (100%) rename classifier.cpp => src/maven/classifier.cpp (100%) rename classifier.h => src/maven/classifier.h (100%) rename classifierNeuralNet.cpp => src/maven/classifierNeuralNet.cpp (100%) rename classifierNeuralNet.h => src/maven/classifierNeuralNet.h (100%) rename clusterdialog.cpp => src/maven/clusterdialog.cpp (100%) rename clusterdialog.h => src/maven/clusterdialog.h (100%) rename comparesamplesdialog.cpp => src/maven/comparesamplesdialog.cpp (100%) rename comparesamplesdialog.h => src/maven/comparesamplesdialog.h (100%) rename csvreports.cpp => src/maven/csvreports.cpp (100%) rename csvreports.h => src/maven/csvreports.h (100%) rename database.cpp => src/maven/database.cpp (100%) rename database.h => src/maven/database.h (100%) rename eicwidget.cpp => src/maven/eicwidget.cpp (100%) rename eicwidget.h => src/maven/eicwidget.h (100%) rename {forms => src/maven/forms}/adductwidget.ui (100%) rename {forms => src/maven/forms}/alignmentdialog.ui (100%) rename {forms => src/maven/forms}/calibrateform.ui (100%) rename {forms => src/maven/forms}/clusterdialog.ui (100%) rename {forms => src/maven/forms}/comparesamplesdialog.ui (100%) rename {forms => src/maven/forms}/covariantswidget.ui (100%) rename {forms => src/maven/forms}/isotopeswidget.ui (100%) rename {forms => src/maven/forms}/librarydialog.ui (100%) rename {forms => src/maven/forms}/masscalcwidget.ui (100%) rename {forms => src/maven/forms}/noteswidget.ui (100%) rename {forms => src/maven/forms}/peakdetectiondialog.ui (100%) rename {forms => src/maven/forms}/rconsolewidget.ui (100%) rename {forms => src/maven/forms}/settingsform.ui (100%) rename {forms => src/maven/forms}/spectramatching.ui (100%) rename {forms => src/maven/forms}/trainingdialog.ui (100%) rename gallerywidget.cpp => src/maven/gallerywidget.cpp (100%) rename gallerywidget.h => src/maven/gallerywidget.h (100%) create mode 100644 src/maven/get_version.bat create mode 100755 src/maven/get_version.sh rename globals.h => src/maven/globals.h (100%) rename heatmap.cpp => src/maven/heatmap.cpp (100%) rename heatmap.h => src/maven/heatmap.h (100%) rename highlighter.cpp => src/maven/highlighter.cpp (100%) rename highlighter.h => src/maven/highlighter.h (100%) rename history.cpp => src/maven/history.cpp (100%) rename history.h => src/maven/history.h (100%) rename {images => src/maven/images}/PDF.png (100%) rename {images => src/maven/images}/R.png (100%) rename {images => src/maven/images}/autofocus.png (100%) rename {images => src/maven/images}/autofocus.svg (100%) rename {images => src/maven/images}/averageSpectra.png (100%) rename {images => src/maven/images}/bad.png (100%) rename {images => src/maven/images}/bookmark.png (100%) rename {images => src/maven/images}/bug.png (100%) rename {images => src/maven/images}/cluster.png (100%) rename {images => src/maven/images}/colorfill.png (100%) rename {images => src/maven/images}/compound.png (100%) rename {images => src/maven/images}/contrast.png (100%) rename {images => src/maven/images}/copyCSV.png (100%) rename {images => src/maven/images}/copyPNG.png (100%) rename {images => src/maven/images}/covariants.png (100%) rename {images => src/maven/images}/dbsearch.png (100%) rename {images => src/maven/images}/delete.png (100%) rename {images => src/maven/images}/export.png (100%) rename {images => src/maven/images}/exportcsv.png (100%) rename {images => src/maven/images}/exportpdf.png (100%) rename {images => src/maven/images}/exportpng.png (100%) rename {images => src/maven/images}/exportxml.png (100%) rename {images => src/maven/images}/featuredetect.png (100%) rename {images => src/maven/images}/filenew.png (100%) rename {images => src/maven/images}/fileopen.png (100%) rename {images => src/maven/images}/fileprint.png (100%) rename {images => src/maven/images}/filesave.png (100%) rename {images => src/maven/images}/filter.png (100%) rename {images => src/maven/images}/findcompound.png (100%) rename {images => src/maven/images}/flip.png (100%) rename {images => src/maven/images}/flowerplot.png (100%) rename {images => src/maven/images}/gallery.png (100%) rename {images => src/maven/images}/good.png (100%) rename {images => src/maven/images}/heatmap.png (100%) rename {images => src/maven/images}/hide.png (100%) rename {images => src/maven/images}/icon.icns (100%) rename {images => src/maven/images}/icon.png (100%) rename {images => src/maven/images}/icons.svg (100%) rename {images => src/maven/images}/integrateArea.png (100%) rename {images => src/maven/images}/isotope.png (100%) rename {images => src/maven/images}/last.png (100%) rename {images => src/maven/images}/librarymanager.png (100%) rename {images => src/maven/images}/link.png (100%) rename {images => src/maven/images}/logo1.svg (100%) rename {images => src/maven/images}/markbad.png (100%) rename {images => src/maven/images}/markgood.png (100%) rename {images => src/maven/images}/molecule.png (100%) rename {images => src/maven/images}/negative_ion.png (100%) rename {images => src/maven/images}/newicons.svg (100%) rename {images => src/maven/images}/next.png (100%) rename {images => src/maven/images}/note.png (100%) rename {images => src/maven/images}/pathway.png (100%) rename {images => src/maven/images}/peakgroup.png (100%) rename {images => src/maven/images}/positive_ion.png (100%) rename {images => src/maven/images}/qqq.png (100%) rename {images => src/maven/images}/refresh.png (100%) rename {images => src/maven/images}/resetzoom.png (100%) rename {images => src/maven/images}/resetzoom2.png (100%) rename {images => src/maven/images}/samples.png (100%) rename {images => src/maven/images}/scatterplot.png (100%) rename {images => src/maven/images}/settings.png (100%) rename {images => src/maven/images}/showbookmarks.png (100%) rename {images => src/maven/images}/spectra.png (100%) rename {images => src/maven/images}/spectra_search.png (100%) rename {images => src/maven/images}/splash.png (100%) rename {images => src/maven/images}/spreadsheet.png (100%) rename {images => src/maven/images}/textcenter.png (100%) rename {images => src/maven/images}/tic.png (100%) rename {images => src/maven/images}/train.png (100%) rename {images => src/maven/images}/unknown_ion.png (100%) rename {images => src/maven/images}/zoomInEdge.png (100%) rename {images => src/maven/images}/zoomInNode.png (100%) rename {images => src/maven/images}/zoomInText.png (100%) rename {images => src/maven/images}/zoomOutEdge.png (100%) rename {images => src/maven/images}/zoomOutNode.png (100%) rename {images => src/maven/images}/zoomOutText.png (100%) rename {images => src/maven/images}/zoomin.png (100%) rename {images => src/maven/images}/zoomout.png (100%) rename isotopeplot.cpp => src/maven/isotopeplot.cpp (100%) rename isotopeplot.h => src/maven/isotopeplot.h (100%) rename isotopeswidget.cpp => src/maven/isotopeswidget.cpp (100%) rename isotopeswidget.h => src/maven/isotopeswidget.h (100%) rename librarydialog.cpp => src/maven/librarydialog.cpp (100%) rename librarydialog.h => src/maven/librarydialog.h (100%) rename ligandwidget.cpp => src/maven/ligandwidget.cpp (100%) rename ligandwidget.h => src/maven/ligandwidget.h (100%) rename line.cpp => src/maven/line.cpp (100%) rename line.h => src/maven/line.h (100%) rename main.cpp => src/maven/main.cpp (100%) rename mainwindow.cpp => src/maven/mainwindow.cpp (100%) rename mainwindow.h => src/maven/mainwindow.h (100%) rename masscalcgui.cpp => src/maven/masscalcgui.cpp (100%) rename masscalcgui.h => src/maven/masscalcgui.h (100%) rename mzroll.desktop => src/maven/maven.desktop (100%) create mode 100644 src/maven/maven.pro rename mzfileio.cpp => src/maven/mzfileio.cpp (100%) rename mzfileio.h => src/maven/mzfileio.h (100%) rename mzroll.ico => src/maven/mzroll.ico (100%) rename mzroll.qrc => src/maven/mzroll.qrc (100%) rename mzroll.rc => src/maven/mzroll.rc (100%) rename note.cpp => src/maven/note.cpp (100%) rename note.h => src/maven/note.h (100%) rename numeric_treewidgetitem.h => src/maven/numeric_treewidgetitem.h (100%) rename peakdetectiondialog.cpp => src/maven/peakdetectiondialog.cpp (100%) rename peakdetectiondialog.h => src/maven/peakdetectiondialog.h (100%) rename plot_axes.cpp => src/maven/plot_axes.cpp (100%) rename plot_axes.h => src/maven/plot_axes.h (100%) rename plotdock.cpp => src/maven/plotdock.cpp (100%) rename plotdock.h => src/maven/plotdock.h (100%) rename point.cpp => src/maven/point.cpp (100%) rename point.h => src/maven/point.h (100%) rename projectDB.cpp => src/maven/projectDB.cpp (100%) rename projectDB.h => src/maven/projectDB.h (100%) rename projectdockwidget.cpp => src/maven/projectdockwidget.cpp (100%) rename projectdockwidget.h => src/maven/projectdockwidget.h (100%) rename rconsolewidget.cpp => src/maven/rconsolewidget.cpp (100%) rename rconsolewidget.h => src/maven/rconsolewidget.h (100%) rename scatterplot.cpp => src/maven/scatterplot.cpp (100%) rename scatterplot.h => src/maven/scatterplot.h (100%) rename settingsform.cpp => src/maven/settingsform.cpp (100%) rename settingsform.h => src/maven/settingsform.h (100%) rename spectralhit.h => src/maven/spectralhit.h (100%) rename spectramatching.cpp => src/maven/spectramatching.cpp (100%) rename spectramatching.h => src/maven/spectramatching.h (100%) rename spectrawidget.cpp => src/maven/spectrawidget.cpp (100%) rename spectrawidget.h => src/maven/spectrawidget.h (100%) rename stable.h => src/maven/stable.h (100%) rename suggest.cpp => src/maven/suggest.cpp (100%) rename suggest.h => src/maven/suggest.h (100%) rename tabledockwidget.cpp => src/maven/tabledockwidget.cpp (100%) rename tabledockwidget.h => src/maven/tabledockwidget.h (100%) rename test.cpp => src/maven/test.cpp (100%) rename tinyplot.cpp => src/maven/tinyplot.cpp (100%) rename tinyplot.h => src/maven/tinyplot.h (100%) rename traindialog.cpp => src/maven/traindialog.cpp (100%) rename traindialog.h => src/maven/traindialog.h (100%) rename treedockwidget.cpp => src/maven/treedockwidget.cpp (100%) rename treedockwidget.h => src/maven/treedockwidget.h (100%) create mode 160000 src/maven_core diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 0000000..7a823ee --- /dev/null +++ b/.gitmodules @@ -0,0 +1,3 @@ +[submodule "src/maven_core"] + path = src/maven_core + url = https://github.com/eugenemel/maven_core.git diff --git a/.travis.yml b/.travis.yml new file mode 100644 index 0000000..d15b54a --- /dev/null +++ b/.travis.yml @@ -0,0 +1,42 @@ +matrix: + include: + - os: linux + dist: trusty + sudo: required + #group: deprecated-2017Q2 + group: edge + - os: osx + osx_image: xcode8.3 + +addons: + apt: + sources: + - sourceline: 'ppa:beineri/opt-qt58-trusty' + packages: + - qt58-meta-minimal + - mesa-common-dev + - libgl1-mesa-dev + - libsqlite3-dev + - libmysqlclient-dev + - libssl1.0.0 + - libssl-dev + +before_install: + - ./ci/travis/before_install_${TRAVIS_OS_NAME}.sh + #- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then ./ci/travis/brew_install_osx.sh; fi + #- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install qt5 ; fi + +script: + # Add installed Qt path to $PATH + - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then source /opt/qt*/bin/qt*-env.sh; fi + - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then source qt-5.env; fi + # Build and install + - qmake -r + - make -j2 + - make INSTALL_ROOT=appdir install + # Set VERSION env var + - export VERSION=$(src/maven/get_version.sh) + # Package deployment artifacts + - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then ./make_dist_linux.sh "src/maven/appdir/bin/maven_dev_${VERSION}"; fi + - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then ./make_dist_osx.sh "src/maven/appdir/bin/Maven.app"; fi + - ls -la dist/ diff --git a/appveyor.yml b/appveyor.yml new file mode 100644 index 0000000..149cf01 --- /dev/null +++ b/appveyor.yml @@ -0,0 +1,40 @@ +version: 1.0.{build} +environment: + matrix: + - COMPILER: msys2 + PLATFORM: x64 + MSYS2_ARCH: x86_64 + MSYS2_DIR: msys64 + MSYSTEM: MINGW64 + BIT: 64 + PATH: 'C:\%MSYS2_DIR%\%MSYSTEM%\bin;C:\%MSYS2_DIR%\usr\bin;%PATH%' + +build_script: + # Get submodules + - git submodule update --init --recursive + + # Not sure why, but seem to have to set path here + - SET "PATH=C:\%MSYS2_DIR%\%MSYSTEM%\bin;C:\%MSYS2_DIR%\usr\bin;%PATH%" + + # Install 64-bit QT + - bash -lc "pacman -S --needed --noconfirm mingw-w64-x86_64-qt-creator" + + # Install zlib + - bash -lc "pacman -S --needed --noconfirm zlib-devel" + + # Install sqlite3 + - bash -lc "pacman -S --needed --noconfirm mingw64/mingw-w64-x86_64-sqlite3" + + # Build MAVEN + - bash -lc "cd $APPVEYOR_BUILD_FOLDER; qmake -r" + - bash -lc "cd $APPVEYOR_BUILD_FOLDER; make -j2" + +after_build: + - SET "PATH=C:\%MSYS2_DIR%\%MSYSTEM%\bin;C:\%MSYS2_DIR%\usr\bin;%PATH%" + - src\maven\get_version.bat > version.txt + - SET /p VERSION= $ENVFILE +# export PATH=$PWD/Qt/5.8/gcc_64/bin:$PATH +# EOF + diff --git a/ci/travis/before_install_osx.sh b/ci/travis/before_install_osx.sh new file mode 100755 index 0000000..ee028b4 --- /dev/null +++ b/ci/travis/before_install_osx.sh @@ -0,0 +1,14 @@ +#!/bin/bash + +brew update +brew install qt5 +brew link qt5 --force + +ENVFILE=qt-5.env +echo Create $ENVFILE +cat << EOF > $ENVFILE +export PATH="/usr/local/opt/qt/bin:$PATH" +export LDFLAGS="-L/usr/local/opt/qt/lib" +export CPPFLAGS="-I/usr/local/opt/qt/include" +export PKG_CONFIG_PATH="/usr/local/opt/qt/lib/pkgconfig" +EOF diff --git a/make_dist_linux.sh b/make_dist_linux.sh new file mode 100755 index 0000000..cbc9962 --- /dev/null +++ b/make_dist_linux.sh @@ -0,0 +1,76 @@ +#!/bin/bash +set -e + +#Set Script Name variable +SCRIPT=`basename ${BASH_SOURCE[0]}` + +#Set fonts for Help. +NORM=`tput sgr0` +BOLD=`tput bold` +REV=`tput smso` + +#Help function +function HELP { + echo -e \\n"${REV}Basic usage:${NORM} ${BOLD}$SCRIPT file.exe${NORM}"\\n + echo -e "${REV}-h${NORM} --Displays this help message. No further functions are performed."\\n + echo -e "Example: ${BOLD}$SCRIPT \"bin/maven_dev_20170405\"${NORM}"\\n + exit 1 +} + +#Check the number of arguments. If none are passed, print help and exit. +NUMARGS=$# +if [ $NUMARGS -eq 0 ]; then + HELP +fi + +# A POSIX variable +OPTIND=1 # Reset in case getopts has been used previously in the shell. + +# Initialize our own variables: + +while getopts "h?f:" opt; do + case "$opt" in + h|\?) + show_help + exit 0 + ;; + esac +done + +shift $((OPTIND-1)) #This tells getopts to move on to the next argument. + +binpath=$1 +bindir=${binpath%/*} +binfn="${binpath##*/}" +distpath="dist" + +# TODO Resources must be copied to appdir prior to packaging +# See: RedTimer example at https://github.com/probonopd/linuxdeployqt/wiki +#echo "Copying resources to ${apppath}" +#mkdir -p "${apppath}/Contents/Resources/methods" +#cp src/maven_core/bin/methods/* "${apppath}/Contents/Resources/methods" +# TODO Should pathways be in the repo? +# mkdir "${apppath}/Contents/Resources/pathways" +# cp bin/pathways/* "${apppath}/Contents/Resources/pathways" +#mkdir -p "${apppath}/Contents/Resources/scripts" +#cp src/maven_core/bin/scripts/* "${apppath}/Contents/Resources/scripts" + +# Download linuxdeployqt +echo "Downloading linuxdeployqt" +wget -c "https://github.com/probonopd/linuxdeployqt/releases/download/continuous/linuxdeployqt-continuous-x86_64.AppImage" +chmod a+x linuxdeployqt*.AppImage +unset QTDIR; unset QT_PLUGIN_PATH; unset LD_LIBRARY_PATH + +echo "Running linuxdeployqt" +./linuxdeployqt*.AppImage "${binpath}" -bundle-non-qt-libs -verbose=2 +./linuxdeployqt*.AppImage "${binpath}" -appimage -verbose=2 +find "${bindir}" -executable -type f -exec ldd {} \; | grep " => /usr" | cut -d " " -f 2-3 | sort | uniq +#- curl --upload-file ./APPNAME*.AppImage https://transfer.sh/APPNAME-git.$(git rev-parse --short HEAD)-x86_64.AppImage +ls -la "${binpath}" + +echo "Copying AppImage to ${distpath}" +mkdir -p "${distpath}" +ls -la +cp -v "Maven-${VERSION}-x86_64.AppImage" "${distpath}/" +ls -la "${distpath}" + diff --git a/make_dist_osx.sh b/make_dist_osx.sh new file mode 100755 index 0000000..e53427b --- /dev/null +++ b/make_dist_osx.sh @@ -0,0 +1,73 @@ +#!/bin/bash +set -e + +#Set Script Name variable +SCRIPT=`basename ${BASH_SOURCE[0]}` + +#Set fonts for Help. +NORM=`tput sgr0` +BOLD=`tput bold` +REV=`tput smso` + +#Help function +function HELP { + echo -e \\n"${REV}Basic usage:${NORM} ${BOLD}$SCRIPT Maven.app${NORM}"\\n + echo -e "${REV}-h${NORM} --Displays this help message. No further functions are performed."\\n + echo -e "Example: ${BOLD}$SCRIPT \"${apppath}\"${NORM}"\\n + exit 1 +} + +#Check the number of arguments. If none are passed, print help and exit. +NUMARGS=$# +if [ $NUMARGS -eq 0 ]; then + HELP +fi + +# A POSIX variable +OPTIND=1 # Reset in case getopts has been used previously in the shell. + +# Initialize our own variables: + +while getopts "h?f:" opt; do + case "$opt" in + h|\?) + show_help + exit 0 + ;; + esac +done + +shift $((OPTIND-1)) #This tells getopts to move on to the next argument. + +apppath=$1 +basepath="${apppath%.app}" +appfn="${apppath##*/}" +distpath="dist" +basefn="${appfn%.app}" +# Get version +VERSION=$("src/maven/get_version.sh") +dmgfn="${basefn}_${VERSION}.dmg" + +rm -rf "${distpath}" +mkdir -p "${distpath}" + +echo "Copying resources to ${apppath}" +mkdir -p "${apppath}/Contents/Resources/methods" +cp src/maven_core/bin/methods/* "${apppath}/Contents/Resources/methods" +mkdir -p "${apppath}/Contents/Resources/scripts" +cp src/maven_core/bin/scripts/* "${apppath}/Contents/Resources/scripts" +# TODO Should pathways be in the repo? +# mkdir "${apppath}/Contents/Resources/pathways" +# cp bin/pathways/* "${apppath}/Contents/Resources/pathways" +# TODO Should these be in the repo? +# cp bin/*.csv "${apppath}/Contents/Resources" +# cp bin/*.model "${apppath}/Contents/Resources" + +echo "Running macdeployqt" +macdeployqt "${apppath}" +# TODO This doesn't appear to get built, is that correct or are we missing something? +# macdeployqt "bin/peakdetector.app" -dmg + +echo "Making DMG" +hdiutil create "${distpath}/${dmgfn}" -srcfolder "${apppath}" -ov + diff --git a/make_dist_win32.sh b/make_dist_win32.sh new file mode 100755 index 0000000..0b31b16 --- /dev/null +++ b/make_dist_win32.sh @@ -0,0 +1,64 @@ +#!/bin/bash +set -e + +#Set Script Name variable +SCRIPT=`basename ${BASH_SOURCE[0]}` + +#Set fonts for Help. +NORM=`tput sgr0` +BOLD=`tput bold` +REV=`tput smso` + +#Help function +function HELP { + echo -e \\n"${REV}Basic usage:${NORM} ${BOLD}$SCRIPT file.exe${NORM}"\\n + echo -e "${REV}-h${NORM} --Displays this help message. No further functions are performed."\\n + echo -e "Example: ${BOLD}$SCRIPT \"bin/maven_dev_20170405.exe\"${NORM}"\\n + exit 1 +} + +#Check the number of arguments. If none are passed, print help and exit. +NUMARGS=$# +if [ $NUMARGS -eq 0 ]; then + HELP +fi + +# A POSIX variable +OPTIND=1 # Reset in case getopts has been used previously in the shell. + +# Initialize our own variables: + +while getopts "h?f:" opt; do + case "$opt" in + h|\?) + show_help + exit 0 + ;; + esac +done + +shift $((OPTIND-1)) #This tells getopts to move on to the next argument. + +exepath=$1 +exefn="${exepath##*/}" +distpath="dist/${exefn%.exe}" +zipfn="${exefn%.exe}.zip" + +rm -rf "${distpath}" +mkdir -p "${distpath}" +windeployqt.exe "${exepath}" --dir "${distpath}/${b}" + +for f in $(ldd "${exepath}" | awk '{print $3}' | grep 'mingw64'); do + b=${f##*/} + cp -v "${f}" "${distpath}/${b}" +done +mkdir -p "${distpath}/methods" +cp -v src/maven_core/bin/methods/* "${distpath}/methods" +# mkdir -p "${distpath}/pathways" +# cp -v bin/pathways/* "${distpath}/pathways" +mkdir -p "${distpath}/scripts" +cp -v src/maven_core/bin/scripts/* "${distpath}/scripts" +cp -v "${exepath}" "${distpath}/" + +rm -rf "dist/${zipfn}" +(cd "${distpath}" && 7z a -tzip "../${zipfn}" *) diff --git a/maven.pro b/maven.pro deleted file mode 100644 index b84591e..0000000 --- a/maven.pro +++ /dev/null @@ -1,159 +0,0 @@ -include(../libmaven.pri) -#TEMPLATE = app -CONFIG += qt thread sql svg console std++14 -QMAKE_STRIP=echo -#PRECOMPILED_HEADER = stable.h - -#add version information during compilation -win32 { - VERSION = $$system("..\get_version.bat") -} else { - VERSION = $$system("../get_version.sh") -} -DEFINES += "MAVEN_VERSION=$$VERSION" -DEFINES += "PLATFORM=\"$$QMAKE_HOST.os\"" - -TARGET = maven_dev_$$VERSION -macx:TARGET=Maven - -RC_FILE = mzroll.rc -RESOURCES += mzroll.qrc -ICON = images/icon.icns - -DESTDIR = ../bin - -QT += sql xml printsupport opengl -QT += network - -#DEFINES += QT_CORE_LIB QT_DLL QT_NETWORK_LIB QT_SQL_LIB QT_THREAD_LIB -#INCLUDEPATH += /usr/include/qt4/QtXml/ /usr/include/qt/QtSql - -INCLUDEPATH += ../libmaven ../maven ../pugixml/src ../libneural ../MSToolkit/include -LIBS += -L. -L../lib -L../build/lib -L../MSToolkit -lmaven -lpugixml -lneural -lmstoolkitlite -lz -message($$LIBS) - -FORMS = forms/settingsform.ui \ - forms/masscalcwidget.ui \ - forms/isotopeswidget.ui \ - forms/peakdetectiondialog.ui \ - forms/comparesamplesdialog.ui \ - forms/trainingdialog.ui \ - forms/alignmentdialog.ui \ - forms/rconsolewidget.ui \ - forms/clusterdialog.ui \ - forms/spectramatching.ui \ - forms/calibrateform.ui \ - forms/librarydialog.ui \ - - -HEADERS += stable.h \ - globals.h \ - mainwindow.h \ - tinyplot.h \ - plotdock.h \ - settingsform.h \ - database.h \ - classifier.h \ - classifierNeuralNet.h \ - csvreports.h \ - background_peaks_update.h \ - isotopeplot.h\ - barplot.h \ - boxplot.h \ - line.h \ - point.h \ - history.h \ - plot_axes.h \ - spectrawidget.h\ - masscalcgui.h \ - isotopeswidget.h \ - ligandwidget.h \ - eicwidget.h \ - peakdetectiondialog.h \ - comparesamplesdialog.h \ - traindialog.h \ - tabledockwidget.h \ - treedockwidget.h \ - heatmap.h \ - note.h \ - suggest.h \ - alignmentdialog.h \ - scatterplot.h \ - gallerywidget.h \ - rconsolewidget.h \ - highlighter.h \ - projectdockwidget.h \ - spectramatching.h \ - mzfileio.h \ - spectralhit.h \ - clusterdialog.h \ - projectDB.h \ - librarydialog.h \ - calibratedialog.h - - -SOURCES += mainwindow.cpp \ -classifier.cpp \ -classifierNeuralNet.cpp \ -database.cpp \ -csvreports.cpp \ - plotdock.cpp \ - treedockwidget.cpp \ - tinyplot.cpp \ - settingsform.cpp \ - background_peaks_update.cpp \ - isotopeplot.cpp \ - barplot.cpp \ - boxplot.cpp \ - point.cpp \ - history.cpp \ - spectrawidget.cpp \ - masscalcgui.cpp \ - isotopeswidget.cpp \ - ligandwidget.cpp \ - main.cpp \ - eicwidget.cpp \ - plot_axes.cpp \ - tabledockwidget.cpp \ - peakdetectiondialog.cpp \ - comparesamplesdialog.cpp \ - traindialog.cpp \ - line.cpp \ - heatmap.cpp \ - note.cpp \ - suggest.cpp \ - alignmentdialog.cpp\ - scatterplot.cpp \ - gallerywidget.cpp \ - highlighter.cpp \ - rconsolewidget.cpp \ - clusterdialog.cpp \ - projectdockwidget.cpp \ - spectramatching.cpp \ - mzfileio.cpp \ - projectDB.cpp \ - librarydialog.cpp \ - calibratedialog.cpp - - -sources.files = $$HEADERS \ - $$RESOURCES \ - $$SOURCES \ - *.doc \ - *.html \ - *.pro \ - images -sources.path = ./src -target.path = $${INSTALL_PREFIX}/bin -desktop.path = $${INSTALL_PREFIX}/share/applications -desktop.files = mzroll.desktop - -INSTALLS += target desktop - -build_all { - !build_pass { - CONFIG -= build_all - } -} - - diff --git a/alignmentdialog.cpp b/src/maven/alignmentdialog.cpp similarity index 100% rename from alignmentdialog.cpp rename to src/maven/alignmentdialog.cpp diff --git a/alignmentdialog.h b/src/maven/alignmentdialog.h similarity index 100% rename from alignmentdialog.h rename to src/maven/alignmentdialog.h diff --git a/background_peaks_update.cpp b/src/maven/background_peaks_update.cpp similarity index 100% rename from background_peaks_update.cpp rename to src/maven/background_peaks_update.cpp diff --git a/background_peaks_update.h b/src/maven/background_peaks_update.h similarity index 100% rename from background_peaks_update.h rename to src/maven/background_peaks_update.h diff --git a/barplot.cpp b/src/maven/barplot.cpp similarity index 100% rename from barplot.cpp rename to src/maven/barplot.cpp diff --git a/barplot.h b/src/maven/barplot.h similarity index 100% rename from barplot.h rename to src/maven/barplot.h diff --git a/boxplot.cpp b/src/maven/boxplot.cpp similarity index 100% rename from boxplot.cpp rename to src/maven/boxplot.cpp diff --git a/boxplot.h b/src/maven/boxplot.h similarity index 100% rename from boxplot.h rename to src/maven/boxplot.h diff --git a/calibratedialog.cpp b/src/maven/calibratedialog.cpp similarity index 100% rename from calibratedialog.cpp rename to src/maven/calibratedialog.cpp diff --git a/calibratedialog.h b/src/maven/calibratedialog.h similarity index 100% rename from calibratedialog.h rename to src/maven/calibratedialog.h diff --git a/classifier.cpp b/src/maven/classifier.cpp similarity index 100% rename from classifier.cpp rename to src/maven/classifier.cpp diff --git a/classifier.h b/src/maven/classifier.h similarity index 100% rename from classifier.h rename to src/maven/classifier.h diff --git a/classifierNeuralNet.cpp b/src/maven/classifierNeuralNet.cpp similarity index 100% rename from classifierNeuralNet.cpp rename to src/maven/classifierNeuralNet.cpp diff --git a/classifierNeuralNet.h b/src/maven/classifierNeuralNet.h similarity index 100% rename from classifierNeuralNet.h rename to src/maven/classifierNeuralNet.h diff --git a/clusterdialog.cpp b/src/maven/clusterdialog.cpp similarity index 100% rename from clusterdialog.cpp rename to src/maven/clusterdialog.cpp diff --git a/clusterdialog.h b/src/maven/clusterdialog.h similarity index 100% rename from clusterdialog.h rename to src/maven/clusterdialog.h diff --git a/comparesamplesdialog.cpp b/src/maven/comparesamplesdialog.cpp similarity index 100% rename from comparesamplesdialog.cpp rename to src/maven/comparesamplesdialog.cpp diff --git a/comparesamplesdialog.h b/src/maven/comparesamplesdialog.h similarity index 100% rename from comparesamplesdialog.h rename to src/maven/comparesamplesdialog.h diff --git a/csvreports.cpp b/src/maven/csvreports.cpp similarity index 100% rename from csvreports.cpp rename to src/maven/csvreports.cpp diff --git a/csvreports.h b/src/maven/csvreports.h similarity index 100% rename from csvreports.h rename to src/maven/csvreports.h diff --git a/database.cpp b/src/maven/database.cpp similarity index 100% rename from database.cpp rename to src/maven/database.cpp diff --git a/database.h b/src/maven/database.h similarity index 100% rename from database.h rename to src/maven/database.h diff --git a/eicwidget.cpp b/src/maven/eicwidget.cpp similarity index 100% rename from eicwidget.cpp rename to src/maven/eicwidget.cpp diff --git a/eicwidget.h b/src/maven/eicwidget.h similarity index 100% rename from eicwidget.h rename to src/maven/eicwidget.h diff --git a/forms/adductwidget.ui b/src/maven/forms/adductwidget.ui similarity index 100% rename from forms/adductwidget.ui rename to src/maven/forms/adductwidget.ui diff --git a/forms/alignmentdialog.ui b/src/maven/forms/alignmentdialog.ui similarity index 100% rename from forms/alignmentdialog.ui rename to src/maven/forms/alignmentdialog.ui diff --git a/forms/calibrateform.ui b/src/maven/forms/calibrateform.ui similarity index 100% rename from forms/calibrateform.ui rename to src/maven/forms/calibrateform.ui diff --git a/forms/clusterdialog.ui b/src/maven/forms/clusterdialog.ui similarity index 100% rename from forms/clusterdialog.ui rename to src/maven/forms/clusterdialog.ui diff --git a/forms/comparesamplesdialog.ui b/src/maven/forms/comparesamplesdialog.ui similarity index 100% rename from forms/comparesamplesdialog.ui rename to src/maven/forms/comparesamplesdialog.ui diff --git a/forms/covariantswidget.ui b/src/maven/forms/covariantswidget.ui similarity index 100% rename from forms/covariantswidget.ui rename to src/maven/forms/covariantswidget.ui diff --git a/forms/isotopeswidget.ui b/src/maven/forms/isotopeswidget.ui similarity index 100% rename from forms/isotopeswidget.ui rename to src/maven/forms/isotopeswidget.ui diff --git a/forms/librarydialog.ui b/src/maven/forms/librarydialog.ui similarity index 100% rename from forms/librarydialog.ui rename to src/maven/forms/librarydialog.ui diff --git a/forms/masscalcwidget.ui b/src/maven/forms/masscalcwidget.ui similarity index 100% rename from forms/masscalcwidget.ui rename to src/maven/forms/masscalcwidget.ui diff --git a/forms/noteswidget.ui b/src/maven/forms/noteswidget.ui similarity index 100% rename from forms/noteswidget.ui rename to src/maven/forms/noteswidget.ui diff --git a/forms/peakdetectiondialog.ui b/src/maven/forms/peakdetectiondialog.ui similarity index 100% rename from forms/peakdetectiondialog.ui rename to src/maven/forms/peakdetectiondialog.ui diff --git a/forms/rconsolewidget.ui b/src/maven/forms/rconsolewidget.ui similarity index 100% rename from forms/rconsolewidget.ui rename to src/maven/forms/rconsolewidget.ui diff --git a/forms/settingsform.ui b/src/maven/forms/settingsform.ui similarity index 100% rename from forms/settingsform.ui rename to src/maven/forms/settingsform.ui diff --git a/forms/spectramatching.ui b/src/maven/forms/spectramatching.ui similarity index 100% rename from forms/spectramatching.ui rename to src/maven/forms/spectramatching.ui diff --git a/forms/trainingdialog.ui b/src/maven/forms/trainingdialog.ui similarity index 100% rename from forms/trainingdialog.ui rename to src/maven/forms/trainingdialog.ui diff --git a/gallerywidget.cpp b/src/maven/gallerywidget.cpp similarity index 100% rename from gallerywidget.cpp rename to src/maven/gallerywidget.cpp diff --git a/gallerywidget.h b/src/maven/gallerywidget.h similarity index 100% rename from gallerywidget.h rename to src/maven/gallerywidget.h diff --git a/src/maven/get_version.bat b/src/maven/get_version.bat new file mode 100644 index 0000000..99f0de3 --- /dev/null +++ b/src/maven/get_version.bat @@ -0,0 +1,3 @@ +@echo off +SET CURRENT_DATE=%date:~10,4%%date:~4,2%%date:~7,2% +echo %CURRENT_DATE% \ No newline at end of file diff --git a/src/maven/get_version.sh b/src/maven/get_version.sh new file mode 100755 index 0000000..b4da069 --- /dev/null +++ b/src/maven/get_version.sh @@ -0,0 +1,2 @@ +#!/bin/sh +date +%Y%m%d \ No newline at end of file diff --git a/globals.h b/src/maven/globals.h similarity index 100% rename from globals.h rename to src/maven/globals.h diff --git a/heatmap.cpp b/src/maven/heatmap.cpp similarity index 100% rename from heatmap.cpp rename to src/maven/heatmap.cpp diff --git a/heatmap.h b/src/maven/heatmap.h similarity index 100% rename from heatmap.h rename to src/maven/heatmap.h diff --git a/highlighter.cpp b/src/maven/highlighter.cpp 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src/maven/isotopeplot.cpp diff --git a/isotopeplot.h b/src/maven/isotopeplot.h similarity index 100% rename from isotopeplot.h rename to src/maven/isotopeplot.h diff --git a/isotopeswidget.cpp b/src/maven/isotopeswidget.cpp similarity index 100% rename from isotopeswidget.cpp rename to src/maven/isotopeswidget.cpp diff --git a/isotopeswidget.h b/src/maven/isotopeswidget.h similarity index 100% rename from isotopeswidget.h rename to src/maven/isotopeswidget.h diff --git a/librarydialog.cpp b/src/maven/librarydialog.cpp similarity index 100% rename from librarydialog.cpp rename to src/maven/librarydialog.cpp diff --git a/librarydialog.h b/src/maven/librarydialog.h similarity index 100% rename from librarydialog.h rename to src/maven/librarydialog.h diff --git a/ligandwidget.cpp b/src/maven/ligandwidget.cpp similarity index 100% rename from ligandwidget.cpp rename to src/maven/ligandwidget.cpp diff --git a/ligandwidget.h b/src/maven/ligandwidget.h similarity index 100% rename from ligandwidget.h rename to src/maven/ligandwidget.h diff --git a/line.cpp b/src/maven/line.cpp similarity index 100% rename from line.cpp rename to src/maven/line.cpp diff --git a/line.h b/src/maven/line.h similarity index 100% rename from line.h rename to src/maven/line.h diff --git a/main.cpp b/src/maven/main.cpp similarity index 100% rename from main.cpp rename to src/maven/main.cpp diff --git a/mainwindow.cpp b/src/maven/mainwindow.cpp similarity index 100% rename from mainwindow.cpp rename to src/maven/mainwindow.cpp diff --git a/mainwindow.h b/src/maven/mainwindow.h similarity index 100% rename from mainwindow.h rename to src/maven/mainwindow.h diff --git a/masscalcgui.cpp b/src/maven/masscalcgui.cpp similarity index 100% rename from masscalcgui.cpp rename to src/maven/masscalcgui.cpp diff --git a/masscalcgui.h b/src/maven/masscalcgui.h similarity index 100% rename from masscalcgui.h rename to src/maven/masscalcgui.h diff --git a/mzroll.desktop b/src/maven/maven.desktop similarity index 100% rename from mzroll.desktop rename to src/maven/maven.desktop diff --git a/src/maven/maven.pro b/src/maven/maven.pro new file mode 100644 index 0000000..eeb797b --- /dev/null +++ b/src/maven/maven.pro @@ -0,0 +1,159 @@ +include(../maven_core/libmaven.pri) +TEMPLATE = app +CONFIG += qt thread sql svg console std++14 +QMAKE_STRIP=echo +#PRECOMPILED_HEADER = stable.h + +#add version information during compilation +win32 { + VERSION = $$system(".\get_version.bat") +} else { + VERSION = $$system("./get_version.sh") +} +DEFINES += "MAVEN_VERSION=$$VERSION" +DEFINES += "PLATFORM=\"$$QMAKE_HOST.os\"" + +TARGET = maven_dev_$$VERSION +macx:TARGET=Maven + +RC_FILE = mzroll.rc +RESOURCES += mzroll.qrc +ICON = images/icon.icns + +DESTDIR = bin + +QT += sql xml printsupport opengl +QT += network + +#DEFINES += QT_CORE_LIB QT_DLL QT_NETWORK_LIB QT_SQL_LIB QT_THREAD_LIB +#INCLUDEPATH += /usr/include/qt4/QtXml/ /usr/include/qt/QtSql + +INCLUDEPATH += ../maven_core/libmaven src ../maven_core/pugixml/src ../maven_core/libneural ../maven_core/MSToolkit/include +LIBS += -L. -L../maven_core/lib -L../maven_core/build/lib -L../maven_core/MSToolkit -lmaven -lpugixml -lneural -lmstoolkitlite -lz +message($$LIBS) + +FORMS = forms/settingsform.ui \ + forms/masscalcwidget.ui \ + forms/isotopeswidget.ui \ + forms/peakdetectiondialog.ui \ + forms/comparesamplesdialog.ui \ + forms/trainingdialog.ui \ + forms/alignmentdialog.ui \ + forms/rconsolewidget.ui \ + forms/clusterdialog.ui \ + forms/spectramatching.ui \ + forms/calibrateform.ui \ + forms/librarydialog.ui \ + + +HEADERS += stable.h \ + globals.h \ + mainwindow.h \ + tinyplot.h \ + plotdock.h \ + settingsform.h \ + database.h \ + classifier.h \ + classifierNeuralNet.h \ + csvreports.h \ + background_peaks_update.h \ + isotopeplot.h\ + barplot.h \ + boxplot.h \ + line.h \ + point.h \ + history.h \ + plot_axes.h \ + spectrawidget.h\ + masscalcgui.h \ + isotopeswidget.h \ + ligandwidget.h \ + eicwidget.h \ + peakdetectiondialog.h \ + comparesamplesdialog.h \ + traindialog.h \ + tabledockwidget.h \ + treedockwidget.h \ + heatmap.h \ + note.h \ + suggest.h \ + alignmentdialog.h \ + scatterplot.h \ + gallerywidget.h \ + rconsolewidget.h \ + highlighter.h \ + projectdockwidget.h \ + spectramatching.h \ + mzfileio.h \ + spectralhit.h \ + clusterdialog.h \ + projectDB.h \ + librarydialog.h \ + calibratedialog.h + + +SOURCES += mainwindow.cpp \ + classifier.cpp \ + classifierNeuralNet.cpp \ + database.cpp \ + csvreports.cpp \ + plotdock.cpp \ + treedockwidget.cpp \ + tinyplot.cpp \ + settingsform.cpp \ + background_peaks_update.cpp \ + isotopeplot.cpp \ + barplot.cpp \ + boxplot.cpp \ + point.cpp \ + history.cpp \ + spectrawidget.cpp \ + masscalcgui.cpp \ + isotopeswidget.cpp \ + ligandwidget.cpp \ + main.cpp \ + eicwidget.cpp \ + plot_axes.cpp \ + tabledockwidget.cpp \ + peakdetectiondialog.cpp \ + comparesamplesdialog.cpp \ + traindialog.cpp \ + line.cpp \ + heatmap.cpp \ + note.cpp \ + suggest.cpp \ + alignmentdialog.cpp\ + scatterplot.cpp \ + gallerywidget.cpp \ + highlighter.cpp \ + rconsolewidget.cpp \ + clusterdialog.cpp \ + projectdockwidget.cpp \ + spectramatching.cpp \ + mzfileio.cpp \ + projectDB.cpp \ + librarydialog.cpp \ + calibratedialog.cpp + + +sources.files = $$HEADERS \ + $$RESOURCES \ + $$SOURCES \ + *.doc \ + *.html \ + *.pro \ + images +sources.path = ./src +target.path = $${INSTALL_PREFIX}/bin +desktop.path = $${INSTALL_PREFIX}/share/applications +desktop.files = maven.desktop + +INSTALLS += target desktop + +build_all { + !build_pass { + CONFIG -= build_all + } +} + + diff --git a/mzfileio.cpp b/src/maven/mzfileio.cpp similarity index 100% rename from mzfileio.cpp rename to src/maven/mzfileio.cpp diff --git a/mzfileio.h b/src/maven/mzfileio.h similarity index 100% rename from mzfileio.h rename to src/maven/mzfileio.h diff --git a/mzroll.ico b/src/maven/mzroll.ico similarity index 100% rename from mzroll.ico rename to src/maven/mzroll.ico diff --git a/mzroll.qrc b/src/maven/mzroll.qrc similarity index 100% rename from mzroll.qrc rename to src/maven/mzroll.qrc diff --git a/mzroll.rc b/src/maven/mzroll.rc similarity index 100% rename from mzroll.rc rename to src/maven/mzroll.rc diff --git a/note.cpp b/src/maven/note.cpp similarity index 100% rename from note.cpp rename to src/maven/note.cpp diff --git a/note.h b/src/maven/note.h similarity index 100% rename from note.h rename to src/maven/note.h diff --git a/numeric_treewidgetitem.h b/src/maven/numeric_treewidgetitem.h similarity index 100% rename from numeric_treewidgetitem.h rename to src/maven/numeric_treewidgetitem.h diff --git a/peakdetectiondialog.cpp b/src/maven/peakdetectiondialog.cpp similarity index 100% rename from peakdetectiondialog.cpp rename to src/maven/peakdetectiondialog.cpp diff --git a/peakdetectiondialog.h b/src/maven/peakdetectiondialog.h similarity index 100% rename from peakdetectiondialog.h rename to src/maven/peakdetectiondialog.h diff --git a/plot_axes.cpp b/src/maven/plot_axes.cpp similarity index 100% rename from plot_axes.cpp rename to src/maven/plot_axes.cpp diff --git a/plot_axes.h b/src/maven/plot_axes.h similarity index 100% rename from plot_axes.h rename to src/maven/plot_axes.h diff --git a/plotdock.cpp b/src/maven/plotdock.cpp similarity index 100% rename from plotdock.cpp rename to src/maven/plotdock.cpp diff --git a/plotdock.h b/src/maven/plotdock.h similarity index 100% rename from plotdock.h rename to src/maven/plotdock.h diff --git a/point.cpp b/src/maven/point.cpp similarity index 100% rename from point.cpp rename to src/maven/point.cpp diff --git a/point.h b/src/maven/point.h similarity index 100% rename from point.h rename to src/maven/point.h diff --git a/projectDB.cpp b/src/maven/projectDB.cpp similarity index 100% rename from projectDB.cpp rename to src/maven/projectDB.cpp diff --git a/projectDB.h b/src/maven/projectDB.h similarity index 100% rename from projectDB.h rename to src/maven/projectDB.h diff --git a/projectdockwidget.cpp b/src/maven/projectdockwidget.cpp similarity index 100% rename from projectdockwidget.cpp rename to src/maven/projectdockwidget.cpp diff --git a/projectdockwidget.h b/src/maven/projectdockwidget.h similarity index 100% rename from projectdockwidget.h rename to src/maven/projectdockwidget.h diff --git a/rconsolewidget.cpp b/src/maven/rconsolewidget.cpp similarity index 100% rename from rconsolewidget.cpp rename to src/maven/rconsolewidget.cpp diff --git a/rconsolewidget.h b/src/maven/rconsolewidget.h similarity index 100% rename from rconsolewidget.h rename to src/maven/rconsolewidget.h diff --git a/scatterplot.cpp b/src/maven/scatterplot.cpp similarity index 100% rename from scatterplot.cpp rename to src/maven/scatterplot.cpp diff --git a/scatterplot.h b/src/maven/scatterplot.h similarity index 100% rename from scatterplot.h rename to src/maven/scatterplot.h diff --git a/settingsform.cpp b/src/maven/settingsform.cpp similarity index 100% rename from settingsform.cpp rename to src/maven/settingsform.cpp diff --git a/settingsform.h b/src/maven/settingsform.h similarity index 100% rename from settingsform.h rename to src/maven/settingsform.h diff --git a/spectralhit.h b/src/maven/spectralhit.h similarity index 100% rename from spectralhit.h rename to src/maven/spectralhit.h diff --git a/spectramatching.cpp b/src/maven/spectramatching.cpp similarity index 100% rename from spectramatching.cpp rename to src/maven/spectramatching.cpp diff --git a/spectramatching.h b/src/maven/spectramatching.h similarity index 100% rename from spectramatching.h rename to src/maven/spectramatching.h diff --git a/spectrawidget.cpp b/src/maven/spectrawidget.cpp similarity index 100% rename from spectrawidget.cpp rename to src/maven/spectrawidget.cpp diff --git a/spectrawidget.h b/src/maven/spectrawidget.h similarity index 100% rename from spectrawidget.h rename to src/maven/spectrawidget.h diff --git a/stable.h b/src/maven/stable.h similarity index 100% rename from stable.h rename to src/maven/stable.h diff --git a/suggest.cpp b/src/maven/suggest.cpp similarity index 100% rename from suggest.cpp rename to src/maven/suggest.cpp diff --git a/suggest.h b/src/maven/suggest.h similarity index 100% rename from suggest.h rename to src/maven/suggest.h diff --git a/tabledockwidget.cpp b/src/maven/tabledockwidget.cpp similarity index 100% rename from tabledockwidget.cpp rename to src/maven/tabledockwidget.cpp diff --git a/tabledockwidget.h b/src/maven/tabledockwidget.h similarity index 100% rename from tabledockwidget.h rename to src/maven/tabledockwidget.h diff --git a/test.cpp b/src/maven/test.cpp similarity index 100% rename from test.cpp rename to src/maven/test.cpp diff --git a/tinyplot.cpp b/src/maven/tinyplot.cpp similarity index 100% rename from tinyplot.cpp rename to src/maven/tinyplot.cpp diff --git a/tinyplot.h b/src/maven/tinyplot.h similarity index 100% rename from tinyplot.h rename to src/maven/tinyplot.h diff --git a/traindialog.cpp b/src/maven/traindialog.cpp similarity index 100% rename from traindialog.cpp rename to src/maven/traindialog.cpp diff --git a/traindialog.h b/src/maven/traindialog.h similarity index 100% rename from traindialog.h rename to src/maven/traindialog.h diff --git a/treedockwidget.cpp b/src/maven/treedockwidget.cpp similarity index 100% rename from treedockwidget.cpp rename to src/maven/treedockwidget.cpp diff --git a/treedockwidget.h b/src/maven/treedockwidget.h similarity index 100% rename from treedockwidget.h rename to src/maven/treedockwidget.h diff --git a/src/maven_core b/src/maven_core new file mode 160000 index 0000000..d0ff60a --- /dev/null +++ b/src/maven_core @@ -0,0 +1 @@ +Subproject commit d0ff60a52c91b6b82349a2fe4e3a6b5fe22519ca