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openms_ci_matrix_full.yml
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# This does the whole cmake build of OpenMS on github's runners. It is intended to replace our current Jenkins based jobs.
# For Nightly and Release branches it builds the packages and submits them to our archive.
# NB: The actual upload is currently commented out so that this can get merged to develop. It will be re-added presently.
name: openms-ci-full
# Controls when the action will run. Triggers the workflow on push or pull request
# events or manually via workflow_dispatch
on:
workflow_dispatch:
inputs:
package:
type: boolean
description: Build and upload packages/installer?
default: false
knime:
type: boolean
description: Build and upload KNIME plugins and update site?
default: false
push:
branches:
- nightly
- release/*
pull_request:
branches:
- develop
# A workflow run is made up of one or more jobs that can run sequentially or in parallel
jobs:
build-and-test:
strategy:
fail-fast: false
matrix:
include:
- os: windows-2022
# cl.exe is currently the only supported. Needs a VS shell to be set up (especially if used without VS CMake Generator)
# clang.exe is also installed but untested (might crash with our VS specific compiler definitions)
# clang-cl.exe might be used instead.
compiler: cl.exe
compiler_ver: default
- os: macos-13
# Since the appleclang version is dependent on the XCode versions that are installed
# on the GH runners, use this as the choice for a specific version
# TODO currently unused but XCode/appleclang is the default
compiler: xcode
# TODO implement support for other versions
compiler_ver: 14.2
# Make sure the compilers are available in that version on the GH runners
# We are not installing anything.
- os: ubuntu-22.04
compiler: g++
compiler_ver: 11
- os: ubuntu-22.04
compiler: clang++
compiler_ver: 15
runs-on: ${{ matrix.os }}
steps:
- uses: actions/checkout@v3
with:
path: OpenMS
- name: Extract branch/PR infos
shell: bash
run: echo "RUN_NAME=${{ github.event.pull_request && github.event.number || github.ref_name }}" >> $GITHUB_OUTPUT
id: extract_branch
- id: set-vars
name: Set extra variables
run: |
DO_PACKAGE=$( [[ ( "${{ inputs.package }}" || "${{ steps.extract_branch.outputs.RUN_NAME }}" == "nightly" || "${{ steps.extract_branch.outputs.RUN_NAME }}" == "release*" ) && "${{ matrix.compiler }}" != "clang++" ]] && echo true || echo false)
echo $DO_PACKAGE
if [[ "${{ matrix.os }}" == ubuntu-* ]]; then
echo "tp_folder=Linux" >> $GITHUB_OUTPUT
echo "xvfb=xvfb-run" >> $GITHUB_OUTPUT
echo "static_boost=OFF" >> $GITHUB_OUTPUT
if [ "$DO_PACKAGE" = true ]; then
echo "pkg_type=deb" >> $GITHUB_OUTPUT
else
echo "pkg_type=none" >> $GITHUB_OUTPUT
fi
echo "cxx_compiler=${{ matrix.compiler }}-${{ matrix.compiler_ver }}" >> $GITHUB_OUTPUT
fi
if [[ "${{ matrix.os }}" == windows-* ]]; then
echo "tp_folder=Windows" >> $GITHUB_OUTPUT
echo "contrib_os=windows" >> $GITHUB_OUTPUT
echo "contrib_os_ver=" >> $GITHUB_OUTPUT
echo "contrib_compiler=msvc-14.2/" >> $GITHUB_OUTPUT
echo "xvfb=" >> $GITHUB_OUTPUT
echo "static_boost=ON" >> $GITHUB_OUTPUT
if [ "$DO_PACKAGE" = true ]; then
echo "pkg_type=nsis" >> $GITHUB_OUTPUT
else
echo "pkg_type=none" >> $GITHUB_OUTPUT
fi
echo "cxx_compiler=${{ matrix.compiler }}" >> $GITHUB_OUTPUT
fi
if [[ "${{ matrix.os }}" == macos-* ]]; then
echo "tp_folder=MacOS" >> $GITHUB_OUTPUT
echo "contrib_os=macOS" >> $GITHUB_OUTPUT
echo "contrib_os_ver=10.15.5/" >> $GITHUB_OUTPUT
echo "contrib_compiler=appleclang-11.0.0/" >> $GITHUB_OUTPUT
echo "xvfb=" >> $GITHUB_OUTPUT
echo "static_boost=ON" >> $GITHUB_OUTPUT
if [ "$DO_PACKAGE" = true ]; then
echo "pkg_type=pkg" >> $GITHUB_OUTPUT
else
echo "pkg_type=none" >> $GITHUB_OUTPUT
fi
if [[ "${{ matrix.compiler }}" == "xcode" ]]; then
sudo xcode-select -s '/Applications/Xcode_${{ matrix.compiler_ver }}.app/Contents/Developer'
echo "cxx_compiler=clang++" >> $GITHUB_OUTPUT
elif [[ "${{ matrix.compiler }}" == "clang++" ]]; then
echo "cxx_compiler=$(brew --prefix llvm@${{ matrix.compiler_ver }})/bin/clang++" >> $GITHUB_OUTPUT
else
echo "Unsupported compiler"
exit 1
fi
fi
shell: bash
- if: startsWith(matrix.os, 'windows')
name: Emulate a Visual Studio shell (Windows)
uses: egor-tensin/vs-shell@v2
with:
# NOTE: x64 is hardcoded. No support for 32bit
arch: x64
- if: startsWith(matrix.os, 'macos') || startsWith(matrix.os, 'windows')
name: Install Qt (Windows and macOS)
uses: jurplel/install-qt-action@v3
with:
version: '5.15.2' # 5.12.7 is broken https://bugreports.qt.io/browse/QTBUG-81715, > 5.15.2 is not available on official archives (https://github.com/miurahr/aqtinstall/issues/636)
cache: 'false'
aqtversion: '==3.1.*'
archives: 'qtsvg qtimageformats qtbase'
- name: Setup build tools (and system contrib on Linux)
id: tools-prefix
shell: bash
run: |
if [[ "${{ matrix.os }}" == ubuntu-* ]]; then
sudo add-apt-repository universe
sudo apt update
sudo apt-get -qq install -y build-essential cmake autoconf patch libtool git automake ninja-build xvfb ccache
sudo apt-get -qq install -y qtbase5-dev libqt5svg5-dev libqt5opengl5-dev
sudo apt-get -qq install -y libeigen3-dev libboost-random-dev libboost-regex-dev libboost-iostreams-dev \
libboost-date-time-dev libboost-math-dev libxerces-c-dev zlib1g-dev libsvm-dev libbz2-dev coinor-libcoinmp-dev libhdf5-dev
echo "cmake_prefix=" >> $GITHUB_OUTPUT
if [[ "${{ steps.set-vars.outputs.pkg_type }}" != "none" ]]; then
sudo apt-get -qq install -y doxygen ghostscript graphviz
fi
fi
if [[ "${{ matrix.os }}" == windows-* ]]; then
# Qt5_DIR set by Install Qt5 step
echo "cmake_prefix=$Qt5_DIR/lib/cmake;$Qt5_DIR" >> $GITHUB_OUTPUT
choco install ccache ninja cmake -y --no-progress
## GH CLI "SHOULD BE" installed. Sometimes I had to manually install nonetheless. Super weird.
# https://github.com/actions/runner-images/blob/main/images/win/scripts/Installers/Install-GitHub-CLI.ps1
echo "C:\Program Files (x86)\GitHub CLI" >> $GITHUB_PATH
if [[ "${{ steps.set-vars.outputs.pkg_type }}" != "none" ]]; then
choco install doxygen.portable ghostscript graphviz -y --no-progress
# TODO save this zip somewhere on our infrastructure or github since the project is deprecated
curl --no-progress-meter -L -o UltraModernUI_2.0b6.zip https://github.com/SuperPat45/UltraModernUI/releases/download/2.0b6/UltraModernUI_2.0b6.zip
7z -y x UltraModernUI_2.0b6.zip -o"C:/Program Files (x86)/NSIS/"
fi
fi
if [[ "${{ matrix.os }}" == macos-* ]]; then
# Qt5_DIR set by Install Qt5 step
echo "cmake_prefix=$Qt5_DIR/lib/cmake;$Qt5_DIR" >> $GITHUB_OUTPUT
brew install --quiet ccache autoconf automake libtool ninja && brew link --overwrite ccache
if [[ "${{ steps.set-vars.outputs.pkg_type }}" != "none" ]]; then
brew install --quiet doxygen ghostscript graphviz
fi
fi
- if: startsWith(matrix.os, 'macos') || startsWith(matrix.os, 'windows')
name: Cache contrib (Windows and macOS)
id: cache-contrib
uses: actions/cache@v3
with:
path: ${{ github.workspace }}/OpenMS/contrib
key: ${{ runner.os }}-contrib3
- if: (startsWith(matrix.os, 'macos') || startsWith(matrix.os, 'windows')) && steps.cache-contrib.outputs.cache-hit != 'true'
name: Download contrib build from archive (Windows and macOS)
shell: bash
run: |
cd OpenMS/contrib
curl --no-progress-meter -L -o contribbld.tar.gz https://abibuilder.cs.uni-tuebingen.de/archive/openms/contrib/${{ steps.set-vars.outputs.contrib_os }}/${{ steps.set-vars.outputs.contrib_os_ver }}x64/${{ steps.set-vars.outputs.contrib_compiler }}contrib_build.tar.gz
7z x -so contribbld.tar.gz | 7z x -si -ttar
rm contribbld.tar.gz
ls -la
- if: startsWith(matrix.os, 'macos')
name: Fix contrib install names (macOS)
shell: bash
run: |
shopt -s nullglob # ensure that for loop is only executed if there is at least one .dylib file
for lib in $GITHUB_WORKSPACE/OpenMS/contrib/lib/*.dylib
do
install_name_tool -id $lib $lib
done
# create symlinks like brew https://github.com/Homebrew/homebrew-core/blob/master/Formula/qt.rb#L61
# Warning: Qt5_DIR will change meaning in the new jurplel/install-qt-action. Use QT_ROOT_DIR instead
# https://github.com/jurplel/install-qt-action/blob/master/README_upgrade_guide.md
pushd $Qt5_DIR/include
for f in $Qt5_DIR/lib/*.framework/Headers
do
lnknm=$(basename "${f%/*}" ".framework")
ln -s $f $lnknm
done
for f in $Qt5_DIR/lib/*.framework/Versions/5/Qt*
do
install_name_tool -id $f $f
done
popd
- name: Setup ccache cache
uses: actions/cache@v3
with:
path: .ccache
key: ${{ runner.os }}-ccache-${{ steps.extract_branch.outputs.RUN_NAME }}-${{ github.run_number }}
# Restoring: From current branch/PR, otherwise from nightly, otherwise from any branch.
restore-keys: |
${{ runner.os }}-ccache-${{ steps.extract_branch.outputs.RUN_NAME }}
${{ runner.os }}-ccache-nightly
${{ runner.os }}-ccache-
- name: Add THIRDPARTY
shell: bash
run: |
# initialize THIRDPARTY
cd OpenMS
git submodule update --init THIRDPARTY
cd ..
# add third-party binaries to PATH
# use flat THIRDPARTY structure
mkdir -p _thirdparty
cp -R OpenMS/THIRDPARTY/${{ steps.set-vars.outputs.tp_folder }}/64bit/* _thirdparty/
cp -R OpenMS/THIRDPARTY/All/* _thirdparty/
# add third-party binaries to PATH
for thirdpartytool in '${{ github.workspace }}/_thirdparty'/*
do
if [[ "${{ matrix.os }}" == windows-* ]]; then
# substitute slashes
echo ${thirdpartytool//\//\\} >> $GITHUB_PATH
else
echo $thirdpartytool >> $GITHUB_PATH
fi
done
- name: Build
shell: bash
run: |
# do not fail immediately
set +e
mkdir $GITHUB_WORKSPACE/OpenMS/bld/
${{ steps.set-vars.outputs.xvfb }} ctest --output-on-failure -V -S ../OpenMS/OpenMS/tools/ci/cibuild.cmake
retVal=$?
if [ $retVal -ne 0 ]; then
echo -e "\033[0;31m Errors in build:"
# TODO upload logs as artifact?
find $GITHUB_WORKSPACE/OpenMS/bld/ -name "LastBuild*" -type f -exec cat {} \;
# remove for next steps
find $GITHUB_WORKSPACE/OpenMS/bld/ -name "LastBuild*" -type f -exec rm {} \;
fi
exit $retVal
env:
# TODO allow actual choice of compiler instead of using default.
# Problem: not all compilers are always in the PATH.
CMAKE_CXX_COMPILER: ${{ steps.set-vars.outputs.cxx_compiler }}
CMAKE_PREFIX_PATH: ${{ steps.tools-prefix.outputs.cmake_prefix }}
OPENMS_CONTRIB_LIBS: "${{ github.workspace }}/OpenMS/contrib"
CI_PROVIDER: "GitHub-Actions"
CMAKE_GENERATOR: "Ninja"
SOURCE_DIRECTORY: "${{ github.workspace }}/OpenMS"
BUILD_NAME: "${{ steps.extract_branch.outputs.RUN_NAME }}-${{ steps.set-vars.outputs.tp_folder }}-${{ matrix.compiler }}-class-topp-${{ github.run_number }}"
ENABLE_STYLE_TESTING: "OFF"
ENABLE_TOPP_TESTING: "ON"
ENABLE_CLASS_TESTING: "ON"
ENABLE_TUTORIALS: "OFF"
ENABLE_GCC_WERROR: "OFF" # TODO think about that
SEARCH_ENGINES_DIRECTORY: ${{ github.workspace }}/_thirdparty
WITH_GUI: "ON"
ADDRESS_SANITIZER: "Off"
BUILD_TYPE: "Release"
OPENMP: "ON"
BOOST_USE_STATIC: ${{ steps.set-vars.outputs.static_boost }}
# BUILD_FLAGS: "-p:CL_MPCount=2" # For VS Generator and MSBuild
BUILD_FLAGS: "-j2" # Ninja will otherwise use all cores (doesn't go well in GHA). TODO make dependent on runner
CMAKE_CCACHE_EXE: "ccache"
CCACHE_BASEDIR: ${{ github.workspace }}
CCACHE_DIR: ${{ github.workspace }}/.ccache
CCACHE_COMPRESS: true
CCACHE_COMPRESSLEVEL: 12
CCACHE_MAXSIZE: 400M
# TODO evaluate those options (we had them only on Linux before)
CCACHE_SLOPPINESS: time_macros,include_file_ctime,include_file_mtime
CCACHE_COMPILERCHECK: content
WITH_THERMORAWFILEPARSER_TEST: "OFF"
- name: Test
shell: bash
run: |
${{ steps.set-vars.outputs.xvfb }} ctest --output-on-failure -V -S $GITHUB_WORKSPACE/OpenMS/tools/ci/citest.cmake
env:
SOURCE_DIRECTORY: "${{ github.workspace }}/OpenMS"
CI_PROVIDER: "GitHub-Actions"
BUILD_NAME: "${{ steps.extract_branch.outputs.RUN_NAME }}-${{ steps.set-vars.outputs.tp_folder }}-${{ matrix.compiler }}-class-topp-${{ github.run_number }}"
# The rest of the vars should be saved in the CMakeCache
- if: steps.set-vars.outputs.pkg_type != 'none'
name: Package
shell: bash
run: |
# do not fail immediately
set +e
${{ steps.set-vars.outputs.xvfb }} ctest --output-on-failure -V -S $GITHUB_WORKSPACE/OpenMS/tools/ci/cipackage.cmake
retVal=$?
if [ $retVal -ne 0 ]; then
echo -e "\033[0;31m Errors in packaging:"
# TODO upload logs as artifact?
find $GITHUB_WORKSPACE/OpenMS/bld/ -name "LastBuild*" -type f -exec cat {} \;
# remove for next steps
find $GITHUB_WORKSPACE/OpenMS/bld/ -name "LastBuild*" -type f -exec rm {} \;
# only on win
cat OpenMS/bld/_CPack_Packages/win64/NSIS/NSISOutput.log || true
fi
exit $retVal
env:
SOURCE_DIRECTORY: "${{ github.workspace }}/OpenMS"
PACKAGE_TYPE: ${{ steps.set-vars.outputs.pkg_type }}
SEARCH_ENGINES_DIRECTORY: "${{ github.workspace }}/_thirdparty"
CI_PROVIDER: "GitHub-Actions"
BUILD_NAME: "${{ steps.extract_branch.outputs.RUN_NAME }}-${{ steps.set-vars.outputs.tp_folder }}-${{ matrix.compiler }}-class-topp-${{ github.run_number }}"
# WARNING: Here you have to make sure that only one matrix configuration per OS produces packages. See set-vars steps.
- if: steps.set-vars.outputs.pkg_type != 'none'
name: Upload packages as artifacts
uses: actions/upload-artifact@v3
with:
name: installer-${{ steps.set-vars.outputs.tp_folder }}
path: |
${{ github.workspace }}/OpenMS/bld/*.exe
${{ github.workspace }}/OpenMS/bld/*.deb
${{ github.workspace }}/OpenMS/bld/*.pkg
- if: steps.set-vars.outputs.pkg_type != 'none' || inputs.knime
name: Generate KNIME descriptors and payloads
shell: bash
run: |
cd $GITHUB_WORKSPACE/OpenMS/bld/
# TODO use CTest or script to upload to CDash?
cmake -DSEARCH_ENGINES_DIRECTORY="$GITHUB_WORKSPACE/_thirdparty" -DENABLE_PREPARE_KNIME_PACKAGE=ON .
cmake --build . --target prepare_knime_package
- if: steps.set-vars.outputs.pkg_type != 'none' || inputs.knime
name: Upload KNIME payload and descriptors as artifacts
uses: actions/upload-artifact@v3
with:
name: knime-${{ steps.set-vars.outputs.tp_folder }}
path: ${{ github.workspace }}/OpenMS/bld/knime/**/*
deploy-installer:
if: github.ref == 'refs/heads/nightly' || contains(github.ref, 'release/') || inputs.package
runs-on: ubuntu-latest
needs: build-and-test
steps:
- name: Extract branch/PR infos
shell: bash
run: echo "RUN_NAME=${{ github.event.pull_request && github.event.number || github.ref_name }}" >> $GITHUB_ENV
# WOW, you cannot download with wildcard. INCREDIBLY ANNOYING https://github.com/actions/download-artifact/issues/6
# Maybe in the next 3 years......
- name: Download macos installer artifacts
uses: actions/download-artifact@v3
with:
name: installer-MacOS
- name: Download win installer artifacts
uses: actions/download-artifact@v3
with:
name: installer-Windows
- name: Download lnx installer artifacts
uses: actions/download-artifact@v3
with:
name: installer-Linux
- name: Upload installer
shell: bash
env:
PASS: ${{ secrets.ARCHIVE_RRSYNC_SSH }}
USER: ${{ secrets.ARCHIVE_RRSYNC_USER }}
HOST: ${{ secrets.ARCHIVE_RRSYNC_HOST }}
run: |
echo "Upload"
if [[ "${{ env.RUN_NAME }}" == "nightly" ]]; then
folder=nightly
elif [[ "${{ env.RUN_NAME }}" == "release/*" ]]; then
tmpfolder=${{ env.RUN_NAME }}
folder=${tmpfolder/release/RC}
else
folder=experimental/${{ env.RUN_NAME }}
fi
echo $folder
mkdir -p ~/.ssh/
echo "$PASS" > ~/.ssh/private.key
sudo chmod 600 ~/.ssh/private.key
rsync --progress -avz -e "ssh -i ~/.ssh/private.key -o StrictHostKeyChecking=no" $GITHUB_WORKSPACE/* "$USER@$HOST:/OpenMSInstaller/${folder}"
# TODO create softlinks to latest nightly
# TODO create and upload file hashes, at least for release candidate
build-deploy-knime-updatesite:
env:
KNIME: 5.1
JAVA_VER: 17
PLUGIN_BUILD: ${{ github.workspace }}/plugin-build
PLUGIN_SOURCE: ${{ github.workspace }}/plugin-source
if: github.ref == 'refs/heads/nightly' || contains(github.ref, 'release/') || inputs.knime
runs-on: ubuntu-latest
needs: build-and-test
steps:
- name: Extract branch/PR infos
shell: bash
run: echo "RUN_NAME=${{ github.event.pull_request && github.event.number || github.ref_name }}" >> $GITHUB_ENV
# WOW, you cannot download with wildcard. INCREDIBLY ANNOYING https://github.com/actions/download-artifact/issues/6
# Maybe in the next 3 years......
- name: Download macos installer artifacts
uses: actions/download-artifact@v3
with:
name: knime-MacOS
path: ${{ env.PLUGIN_SOURCE }}
- name: Download win installer artifacts
uses: actions/download-artifact@v3
with:
name: knime-Windows
path: ${{ env.PLUGIN_SOURCE }}
- name: Download lnx installer artifacts
uses: actions/download-artifact@v3
with:
name: knime-Linux
path: ${{ env.PLUGIN_SOURCE }}
# Should be the default.
- name: Set up JDK
uses: actions/setup-java@v3
with:
java-version: ${{ env.JAVA_VER }}
distribution: 'temurin'
- name: Generate KNIME plugin sources
shell: bash
run: |
## Setup functions
function replace_qualifier {
find $1 -name MANIFEST.MF -exec sed -i -e "s/qualifier/$2/g" {} \;
}
## replace only first occurence of SNAPSHOT (second is the version of the parent pom).
function replace_snapshot {
find $1 -name pom.xml -exec sed -i -e "1 h;1! H;\$! d;$ {g;s/-SNAPSHOT/\.$2/;}" {} \;
}
## Setup variables
## GKN git clone (see SCM subfolder settings above)
GKN_PLUGIN_PATH=${GITHUB_WORKSPACE}/GenericKnimeNodes
git clone -q https://github.com/genericworkflownodes/GenericKnimeNodes/ --branch develop --single-branch $GKN_PLUGIN_PATH
## Create folders
mkdir ${PLUGIN_BUILD}
PLUGIN_SOURCE_CONTRIB_PLUGINS=${PLUGIN_SOURCE}/de.openms.feature/contributing-plugins
mkdir -p ${PLUGIN_SOURCE_CONTRIB_PLUGINS}
PLUGIN_SOURCE_THIRDPARTY_CONTRIB_PLUGINS=${PLUGIN_SOURCE}/de.openms.thirdparty.feature/contributing-plugins
mkdir -p ${PLUGIN_SOURCE_THIRDPARTY_CONTRIB_PLUGINS}
## We check exemplarily in de.openms.lib. It should never happen that one platform produced one plugin but not the other.
pushd ${PLUGIN_SOURCE}/de.openms.feature/de.openms.lib/
amount=$(ls -1 payload | wc -l)
if [ $amount -le 2 ]; then
echo "Not enough payloads for each platform. Aborting..."
exit 1
fi
popd
## Clone the contributing plugins into the plugin source folder and update their "last modified" date to
## the last git commit
pushd ${PLUGIN_SOURCE_CONTRIB_PLUGINS}
git clone -q https://github.com/OpenMS/de.openms.knime --branch develop --single-branch .
CONTRIBUTING_DATE=$(git log -1 --format="%cd" --date="format:%Y%m%d%H%M")
echo "Setting qualifier/SNAPSHOT for de.openms.knime contrib plugins to ${CONTRIBUTING_DATE}!"
git log -1 --format="%cd" --date=iso
# TODO just iterate over all folders?
replace_qualifier de.openms.knime.startupCheck ${CONTRIBUTING_DATE}
replace_qualifier de.openms.knime.mzTab ${CONTRIBUTING_DATE}
replace_qualifier de.openms.knime.textexporter_reader ${CONTRIBUTING_DATE}
replace_qualifier de.openms.knime.importers ${CONTRIBUTING_DATE}
replace_qualifier de.openms.knime.qchandling ${CONTRIBUTING_DATE}
replace_qualifier de.openms.thirdparty.knime.startupCheck ${CONTRIBUTING_DATE}
replace_snapshot de.openms.knime.startupCheck ${CONTRIBUTING_DATE}
replace_snapshot de.openms.knime.mzTab ${CONTRIBUTING_DATE}
replace_snapshot de.openms.knime.textexporter_reader ${CONTRIBUTING_DATE}
replace_snapshot de.openms.knime.importers ${CONTRIBUTING_DATE}
replace_snapshot de.openms.knime.qchandling ${CONTRIBUTING_DATE}
replace_snapshot de.openms.thirdparty.knime.startupCheck ${CONTRIBUTING_DATE}
# move to thirdparty feature so they get installed together
mv de.openms.thirdparty.knime.startupCheck ${PLUGIN_SOURCE_THIRDPARTY_CONTRIB_PLUGINS}/de.openms.thirdparty.knime.startupCheck
rm -r .git
rm -r de.openms.knime.startupCheck.test
popd
## New contrib plugin: de.openms.knime.dynamicJSViewers
git clone -q https://github.com/genericworkflownodes/de.openms.knime.dynamicJSViewers --branch master --single-branch
pushd de.openms.knime.dynamicJSViewers
CONTRIBUTING_DATE=$(git log -1 --format="%cd" --date="format:%Y%m%d%H%M")
popd
mv de.openms.knime.dynamicJSViewers/de.openms.knime.dynamicJSViewers.feature ${PLUGIN_SOURCE}/
mkdir ${PLUGIN_SOURCE}/de.openms.knime.dynamicJSViewers.feature/contributing-plugins
rm -rf ${PLUGIN_SOURCE}/de.openms.knime.dynamicJSViewers.feature/.settings
mv de.openms.knime.dynamicJSViewers/de.openms.knime.dynamicJSViewers ${PLUGIN_SOURCE}/de.openms.knime.dynamicJSViewers.feature/contributing-plugins/
pushd ${PLUGIN_SOURCE}/de.openms.knime.dynamicJSViewers.feature/contributing-plugins/
echo "Setting qualifier/SNAPSHOT for de.openms.knime.dynamicJSViewers to ${CONTRIBUTING_DATE}"
replace_qualifier de.openms.knime.dynamicJSViewers ${CONTRIBUTING_DATE}
replace_snapshot de.openms.knime.dynamicJSViewers ${CONTRIBUTING_DATE}
popd
rm -rf de.openms.knime.dynamicJSViewers
# build the plugin source code
cd ${GKN_PLUGIN_PATH}
ant -Dplugin.dir=${PLUGIN_SOURCE} -Dgenerate.extra.arguments="-r -u" -Dcustom.plugin.generator.target=${PLUGIN_BUILD}
- name: Build KNIME update site
shell: bash
env:
KNIME: 5.1
run: |
# fix folder structure
mv ${PLUGIN_BUILD}/.mvn ./
mv ${PLUGIN_BUILD}/* ./
git clone --depth 1 --branch master https://github.com/genericworkflownodes/buildresources
# a special class that maps node names from old openms to openms thirdparty (we should be able to remove it future releases)
cp buildresources/de.openms.thirdparty/src/de/openms/thirdparty/knime/OpenMSNodeFactoryClassMapper.java de.openms.thirdparty/src/de/openms/thirdparty/knime/
# insert contents of the snippet before </plugin> in the plugin.xml. The snippet registers the class mapper.
cat buildresources/de.openms.thirdparty/plugin.xml.snippet
f1="$(cat buildresources/de.openms.thirdparty/plugin.xml.snippet)"
awk -vf1="$f1" '/<\/plugin>/{print f1;print;next}1' de.openms.thirdparty/plugin.xml > buildresources/my.tmp && mv buildresources/my.tmp de.openms.thirdparty/plugin.xml
rm -r buildresources
rm -r plugin-build
# remove maven pom.xmls since we will do a full pomless build. poms are only necessary if you want to develop on a single plugin, e.g., in eclipse.
find . -mindepth 2 -name "pom.xml*" -exec rm {} \;
# Build update site. Downloads necessary plugins from the dependency update sites from KNIME and GKN (for the correct KNIME version)
mvn --no-transfer-progress "-Dknime.version=${KNIME}" "-Djava.majorversion=${JAVA_VER}" "-Dgkn.update.site=https://abibuilder.cs.uni-tuebingen.de/archive/gkn/updateSite/${KNIME}/" clean verify
- name: Upload KNIME update site
shell: bash
env:
PASS: ${{ secrets.ARCHIVE_RRSYNC_SSH }}
USER: ${{ secrets.ARCHIVE_RRSYNC_USER }}
HOST: ${{ secrets.ARCHIVE_RRSYNC_HOST }}
run: |
echo "Upload"
if [[ "${{ env.RUN_NAME }}" == "nightly" ]]; then
folder=nightly
elif [[ "${{ env.RUN_NAME }}" == "release/*" ]]; then
tmpfolder=${{ env.RUN_NAME }}
folder=${tmpfolder/release/RC}
else
folder=experimental/${{ env.RUN_NAME }}
fi
echo $folder
# correct permissions of files to upload
chmod -R o+r $GITHUB_WORKSPACE/*
chmod o+x features
chmod o+x plugins
#Load private key into file
mkdir -p ~/.ssh/
echo "$PASS" > ~/.ssh/private.key
sudo chmod 600 ~/.ssh/private.key
rsync --progress -avz -e "ssh -i ~/.ssh/private.key -o StrictHostKeyChecking=no" $GITHUB_WORKSPACE/* "$USER@$HOST:/knime-plugin/updateSite/$folder"