diff --git a/.bintray.yml b/.bintray.yml new file mode 100644 index 000000000..a57a2bd82 --- /dev/null +++ b/.bintray.yml @@ -0,0 +1,37 @@ +{ + "package": { + "name": "MIRTK", + "repo": "AppImages", + "subject": "schuhschuh", + "desc": "Medical Image Registration ToolKit", + "website_url": "https://mirtk.github.io", + "issue_tracker_url": "https://github.com/BioMedIA/MIRTK/issues", + "vcs_url": "https://github.com/BioMedIA/MIRTK.git", + "licenses": ["Apache-2.0"], + "labels": [ + "BioMedIA", + "MIRTK", + "medical imaging", + "image registration", + "cortical surface reconstruction", + "brain atlas construction" + ], + "public_download_numbers": false, + "public_stats": false + }, + "version": { + "name": "master", + "desc": "AppImage of MIRTK master HEAD deployed by Travis CI build", + "gpgSign": true + }, + "files": [ + { + "includePattern": "Deploy/(.*\\.AppImage)", + "uploadPattern": "$1", + "matrixParams": { + "override": 1 + } + } + ], + "publish": true +} \ No newline at end of file diff --git a/.travis.yml b/.travis.yml index 98f5181f2..02eed8895 100644 --- a/.travis.yml +++ b/.travis.yml @@ -7,6 +7,9 @@ compiler: - g++ - clang +git: + depth: 10 + os: - linux - osx @@ -47,15 +50,44 @@ cache: ccache: true timeout: 1000 directories: - - $HOME/VTK-$LINUX_VTK_VERSION - - $HOME/VTK-$MACOS_VTK_VERSION + - "$HOME/VTK-$LINUX_VTK_VERSION" + - "$HOME/VTK-$MACOS_VTK_VERSION" before_install: - . Scripts/install_depends.sh # sourcing should enable export of env variables - cd $TRAVIS_BUILD_DIR # working directory may have been changed +install: true + script: - Scripts/travis.sh +after_success: + - if [ "$AppImage_BUILD" = ON ] && [ "$(git rev-parse --abbrev-ref HEAD)" = "master" ] && [ "$TRAVIS_OS_NAME" = "linux" ] && [ "$WITH_VTK" = ON ]; then + Scripts/make_appimage.sh; + export AppImage_DEPLOY=ON; + else + export AppImage_DEPLOY=OFF; + fi + +deploy: + - provider: bintray + skip_cleanup: true + user: "schuhschuh" + key: + secure: "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" + file: ".bintray.yml" + on: + branch: master + condition: "$AppImage_DEPLOY = ON" + - provider: releases + skip_cleanup: true + api_key: + secure: "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" + file: "Deploy/*.AppImage" + file_glob: true + on: + tags: true + notifications: email: false diff --git a/Documentation/static/logo.svg b/Documentation/static/logo.svg new file mode 100644 index 000000000..e0121432e --- /dev/null +++ b/Documentation/static/logo.svg @@ -0,0 +1,9 @@ + + + + MIRTK Logo + + Layer 1 + MIRTK + + \ No newline at end of file diff --git a/README.md b/README.md index c8d646a30..eeeb7449f 100644 --- a/README.md +++ b/README.md @@ -1,12 +1,14 @@ Medical Image Registration ToolKit ================================== +[![Linux AppImage](https://api.bintray.com/packages/schuhschuh/AppImages/MIRTK/images/download.svg?version=master)](https://bintray.com/schuhschuh/AppImages/MIRTK/master#files) +  +[![Docker Image](https://images.microbadger.com/badges/image/biomedia/mirtk.svg)](https://microbadger.com/#/images/biomedia/mirtk) +  [![Travis CI status](https://travis-ci.org/BioMedIA/MIRTK.svg?branch=master)](https://travis-ci.org/BioMedIA/MIRTK)   [![AppVeyor status](https://ci.appveyor.com/api/projects/status/f4ef923d1h9lo9pm/branch/master?svg=true)](https://ci.appveyor.com/project/schuhschuh/mirtk/branch/master)   -[![Docker Image](https://images.microbadger.com/badges/image/biomedia/mirtk.svg)](https://microbadger.com/#/images/biomedia/mirtk) -  [![Join the chat at https://gitter.im/BioMedIA/MIRTK](https://badges.gitter.im/BioMedIA/MIRTK.svg)](https://gitter.im/BioMedIA/MIRTK?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) The Medical Image Registration ToolKit (MIRTK) is a research-focused image processing toolkit, @@ -42,4 +44,5 @@ Citation and acknowledgements ----------------------------- In the event you found the MIRTK useful, please consider giving appropriate credit to the software. -See the [publications list](https://mirtk.github.io/publications.html). + +See the [publications list](https://mirtk.github.io/publications.html) for suitable citations. diff --git a/Scripts/install_depends.sh b/Scripts/install_depends.sh index 5dc324c1a..c4df1cf79 100755 --- a/Scripts/install_depends.sh +++ b/Scripts/install_depends.sh @@ -59,9 +59,9 @@ if [ $os = linux ] || [ $os = Linux ]; then libpng12-dev \ ) - [ $TESTING = OFF ] || deps=(${deps[@]} libgtest-dev) - [ $WITH_TBB = OFF ] || deps=(${deps[@]} libtbb-dev) - [ $WITH_FLANN = OFF ] || deps=(${deps[@]} libflann-dev) + [ $TESTING = OFF ] || deps=(${deps[@]} libgtest-dev) + [ $WITH_TBB = OFF ] || deps=(${deps[@]} libtbb-dev) + [ $WITH_FLANN = OFF ] || deps=(${deps[@]} libflann-dev) [ $WITH_ARPACK = OFF ] || deps=(${deps[@]} libarpack2-dev) if [ $WITH_UMFPACK = ON ]; then diff --git a/Scripts/make_appimage.sh b/Scripts/make_appimage.sh new file mode 100755 index 000000000..65fd5b306 --- /dev/null +++ b/Scripts/make_appimage.sh @@ -0,0 +1,217 @@ +#!/bin/bash +set -e + +######################################################################## +# Package the binaries built on Travis CI as an AppImage +# +# For more information, see http://appimage.org/ +######################################################################## + +# Output something before any command can fail (cf. 'set -e') +# If this is the only output in build log, use 'set -ex' above +echo "Creating AppImage" +echo + +norm_option_value() +{ + if [ "$1" = on ] || [ "$1" = ON ] || [ "$1" = yes ] || [ "$1" = YES ] || [ "$1" = y ] || [ "$1" = Y ] || [ "$1" = 1 ] || [ "$1" = true ] || [ "$1" = TRUE ]; then + echo ON + elif [ "$1" = off ] || [ "$1" = OFF ] || [ "$1" = no ] || [ "$1" = NO ] || [ "$1" = n ] || [ "$1" = N ] || [ "$1" = 0 ] || [ "$1" = false ] || [ "$1" = FALSE ]; then + echo OFF + elif [ -n "$2" ]; then + echo "$2" + else + echo OFF + fi +} + +TRAVIS=`norm_option_value "$TRAVIS" OFF` +WITH_VTK=`norm_option_value "$WITH_VTK" OFF` +TRANSFER=`norm_option_value "$TRANSFER_AppImage" OFF` +AppImage_LATEST=`norm_option_value "$AppImage_LATEST" OFF` +PYTHON="/usr/bin/env python" # target system Python interpreter + +if [ $TRAVIS = ON ]; then + sudo apt-get install -y tree + cd "$TRAVIS_BUILD_DIR/Build" + OUTDIR="$TRAVIS_BUILD_DIR/Deploy" +else + OUTDIR="$(cd "$(dirname "$BASH_SOURCE")/.." && pwd)/Deploy" +fi + +APP='MIRTK' +LOWERAPP=${APP,,} +VERSION=$(git describe --tags --exact-match --abbrev=0 HEAD 2> /dev/null || true) +if [ -n "$VERSION" ]; then + RELEASE="$VERSION" +else + VERSION=$(git rev-parse --short HEAD) + if [ $AppImage_LATEST = ON ]; then + RELEASE="latest" # overwrite previous "latest" BinTray AppImage + else + RELEASE="$VERSION" + fi +fi +APPDIR="/tmp/$APP/$APP.AppDir" +export ARCH=$(arch) + +echo "Name: $APP" +echo "Version: $VERSION" +echo "Release: $RELEASE" +echo "Arch: $ARCH" +echo +echo "Populating AppDir..." +make install DESTDIR="$APPDIR" + +cd "$APPDIR/.." +wget -q https://github.com/probonopd/AppImages/raw/master/functions.sh -O ./functions.sh +. ./functions.sh +cd "$APPDIR" + +######################################################################## +# Copy in dependencies that may not be available on all target systems +######################################################################## + +if [ $WITH_VTK = ON ] && [ -n "$VTK_VERSION" ]; then + export LD_LIBRARY_PATH="${VTK_PREFIX:-$HOME/VTK-$VTK_VERSION}/lib:$LD_LIBRARY_PATH" +fi +copy_deps +move_lib + +######################################################################## +# Delete stuff that should not go into the AppImage +######################################################################## + +# Delete dangerous libraries +# See https://github.com/probonopd/AppImages/blob/master/excludelist +delete_blacklisted + +if [ -d usr/lib/$ARCH-linux-gnu ]; then + mv usr/lib/$ARCH-linux-gnu/* usr/lib/ + rmdir usr/lib/$ARCH-linux-gnu +fi + +if [ -d usr/lib/mirtk ]; then + mv usr/lib/mirtk/* usr/lib/ + rmdir usr/lib/mirtk + sed -i s:lib/mirtk:lib:g usr/bin/mirtk +fi + +rm -f usr/bin/uninstall-mirtk || true +rm -rf usr/include || true +rm -rf usr/lib/cmake || true +rm -rf usr/doc || true +rm -rf usr/share || true +rmdir usr/lib64 || true + +find . -name *.so -or -name *.so.* -exec strip {} \; +for f in $(find . -type f -executable -exec file -- {} \; | grep ELF | cut -d: -f1); do + strip "$f" +done + +######################################################################## +# Fix she-bang interpreter specifications +######################################################################## + +for f in $(grep -rl '^#!.*python' usr); do + echo -n "$f: replace '$(head -n1 "$f")'" + sed -i'' "s:#!.*python:#!$PYTHON:" "$f" + echo " by '$(head -n1 "$f")'" +done + +######################################################################## +# Write custom AppRun script +######################################################################## + +cp "$TRAVIS_BUILD_DIR/Documentation/static/logo.svg" "$APP.svg" + +cat -- > "$APP.desktop" < "AppRun" < /dev/null || true +./appimagetool-${ARCH}.AppImage -n -v "$APPDIR" "$OUTDIR/$APPIMAGE" + +echo "Generating AppImage... done" + +######################################################################## +# Clean up +######################################################################## + +if [ $TRAVIS = OFF ]; then + rm -rf "$APPDIR" "/tmp/$APP" || true +fi + +######################################################################## +# Upload AppImage +######################################################################## + +if [ $TRANSFER = ON ]; then + echo + echo "Transferring AppImage ..." + transfer "$OUTDIR/$APPIMAGE" + echo + echo "Transferring AppImage... done" +fi + +cat -- < docker run --rm -it --privileged=true --cap-add MKNOD --cap-add SYS_ADMIN --device /dev/fuse ubuntu + +Inside the Docker container run: +> URL="Copy and paste MIRTK AppImage transfer.sh, bintray.com, or github.com URL here" +> apt-get update && apt-get install -y sshfs wget python +> wget -O mirtk "\$URL" && chmod a+x mirtk +> ./mirtk -h + +# Extracting the AppImage and calling squashfs-root/AppRun + +Pull and run Docker container: +> docker run --rm -it ubuntu + +Inside the Docker container run: +> URL="Copy and paste MIRTK AppImage transfer.sh, bintray.com, or github.com URL here" +> apt-get update && apt-get install -y wget python +> wget -O MIRTK.AppImage "\$URL" && chmod a+x MIRTK.AppImage +> ./MIRTK.AppImage --appimage-extract +> ./squashfs-root/AppRun -h +EOF diff --git a/Scripts/travis.sh b/Scripts/travis.sh index f979455c1..e0370f213 100755 --- a/Scripts/travis.sh +++ b/Scripts/travis.sh @@ -60,7 +60,8 @@ for module in ${modules[@]}; do done mkdir Build && cd Build -run cmake -D CMAKE_INSTALL_PREFIX=$HOME/local \ +run cmake \ + -D CMAKE_INSTALL_PREFIX=/usr \ -D CMAKE_BUILD_TYPE=Release \ -D BUILD_SHARED_LIBS=ON \ -D BUILD_APPLICATIONS=ON \