Backmerge: #2341 - Save to Sequence and FASTA doesn't work for monomers loaded from HELM with inline SMILES #4604

Workflow file for this run

.github/workflows/indigo-ci.yaml at 58bba63

	name: Indigo CI

	env:
	OS_NAME_MAPPING_JSON: '{"ubuntu-latest": "linux", "windows-latest": "windows", "macos-13": "macos"}'

	on:
	push:
	branches:
	- master
	tags:
	- 'indigo-*'
	workflow_dispatch:
	pull_request:
	repository_dispatch:

	jobs:
	static_analysis:
	runs-on: ubuntu-latest
	container: epmlsop/indigo-tester:latest
	steps:
	- name: Checkout
	uses: actions/checkout@v3
	with:
	lfs: false
	fetch-depth: 500
	- name: Git fetch tags
	run: \|
	git config --global --add safe.directory '*'
	git fetch --tags -f
	- name: Check
	run: \|
	python3 -m pip install -r api/python/requirements_dev.txt
	.ci/static_analysis_check.sh

	build_indigo_libs_x86_64:
	strategy:
	fail-fast: false
	matrix:
	os: [ macos-13, ubuntu-latest, windows-latest ]
	runs-on: ${{ matrix.os }}
	needs: static_analysis
	steps:
	- name: Checkout
	uses: actions/checkout@v3
	with:
	lfs: false
	fetch-depth: 500
	- name: Git fetch tags
	run: \|
	git config --global --add safe.directory '*'
	git fetch --tags -f
	- name: Build Linux
	if: ${{ startsWith(matrix.os, 'ubuntu') }}
	uses: docker://epmlsop/buildpack-centos7:latest
	with:
	args: >
	/bin/sh -c "
	mkdir build &&
	cd build &&
	cmake .. -DBUILD_INDIGO=ON -DBUILD_INDIGO_WRAPPERS=OFF -DBUILD_INDIGO_UTILS=OFF -DBUILD_BINGO=OFF -DBUILD_BINGO_ELASTIC=OFF &&
	cmake --build . --config Release --target all -- -j $(nproc) &&
	ctest --verbose
	"
	- name: Build macOS
	if: ${{ startsWith(matrix.os, 'macos') }}
	run: \|
	mkdir build
	cd build
	cmake .. -DBUILD_INDIGO=ON -DBUILD_INDIGO_WRAPPERS=OFF -DBUILD_INDIGO_UTILS=OFF -DBUILD_BINGO=OFF -DBUILD_BINGO_ELASTIC=OFF
	cmake --build . --config Release --target all -- -j $(sysctl -n hw.logicalcpu)
	ctest --verbose
	- name: Build Windows
	if: ${{ startsWith(matrix.os, 'windows') }}
	run: \|
	mkdir build
	cd build
	cmake .. -DBUILD_INDIGO=ON -DBUILD_INDIGO_WRAPPERS=OFF -DBUILD_INDIGO_UTILS=OFF -DBUILD_BINGO=OFF -DBUILD_BINGO_ELASTIC=OFF
	cmake --build . --config Release --target ALL_BUILD
	ctest --verbose -C Release
	- name: Upload artifacts
	uses: actions/upload-artifact@v3
	with:
	name: indigo-libs-${{ fromJSON(env.OS_NAME_MAPPING_JSON)[matrix.os] }}-x86_64
	path: dist

	build_indigo_libs_i386:
	strategy:
	fail-fast: false
	matrix:
	os: [ windows-latest ]
	runs-on: ${{ matrix.os }}
	needs: static_analysis
	steps:
	- name: Checkout
	uses: actions/checkout@v3
	with:
	lfs: false
	fetch-depth: 500
	- name: Git fetch tags
	run: \|
	git config --global --add safe.directory '*'
	git fetch --tags -f
	- name: Build Windows
	if: ${{ startsWith(matrix.os, 'windows') }}
	run: \|
	mkdir build
	cd build
	cmake .. -G "Visual Studio 17 2022" -A Win32 -DBUILD_INDIGO=ON -DBUILD_INDIGO_WRAPPERS=OFF -DBUILD_INDIGO_UTILS=OFF -DBUILD_BINGO=OFF -DBUILD_BINGO_ELASTIC=OFF -DCMAKE_SYSTEM_PROCESSOR_LOWER=i386
	cmake --build . --config Release --target ALL_BUILD
	ctest --verbose -C Release
	- name: Upload artifacts
	uses: actions/upload-artifact@v3
	with:
	name: indigo-libs-${{ fromJSON(env.OS_NAME_MAPPING_JSON)[matrix.os] }}-i386
	path: dist

	build_indigo_libs_aarch64:
	strategy:
	fail-fast: false
	matrix:
	os: [ macos-13, ubuntu-latest ]
	runs-on: ${{ matrix.os }}
	needs: static_analysis
	steps:
	- name: Checkout
	uses: actions/checkout@v3
	with:
	lfs: false
	fetch-depth: 500
	- name: Git fetch tags
	run: \|
	git config --global --add safe.directory '*'
	git fetch --tags -f
	- name: Build Linux
	if: ${{ startsWith(matrix.os, 'ubuntu') }}
	uses: docker://epmlsop/buildpack-arm64:latest
	with:
	args: >
	/bin/sh -c "
	mkdir build &&
	cd build &&
	cmake .. -DBUILD_INDIGO=ON -DBUILD_INDIGO_WRAPPERS=OFF -DBUILD_INDIGO_UTILS=OFF -DBUILD_BINGO=OFF -DBUILD_BINGO_ELASTIC=OFF -DCMAKE_SYSTEM_PROCESSOR_LOWER=aarch64 &&
	cmake --build . --config Release --target all -- -j $(nproc) &&
	ctest --verbose -R dlopen
	"
	- name: Build macOS
	if: ${{ startsWith(matrix.os, 'macos') }}
	run: \|
	mkdir build
	cd build
	cmake .. -DBUILD_INDIGO=ON -DBUILD_INDIGO_WRAPPERS=OFF -DBUILD_INDIGO_UTILS=OFF -DBUILD_BINGO=OFF -DBUILD_BINGO_ELASTIC=OFF -DCMAKE_SYSTEM_PROCESSOR_LOWER=aarch64 -DCMAKE_OSX_ARCHITECTURES=arm64
	cmake --build . --config Release --target all -- -j $(sysctl -n hw.logicalcpu)
	# ctest --verbose # NOTE: We can't run tests until we have native ARM64 node
	- name: Upload artifacts
	uses: actions/upload-artifact@v3
	with:
	name: indigo-libs-${{ fromJSON(env.OS_NAME_MAPPING_JSON)[matrix.os] }}-aarch64
	path: dist

	build_indigo_wrappers:
	strategy:
	fail-fast: false
	matrix:
	wrapper: [ python, java, dotnet ]
	runs-on: ubuntu-latest
	needs: [ build_indigo_libs_x86_64, build_indigo_libs_aarch64, build_indigo_libs_i386 ]
	container: epmlsop/indigo-tester:latest
	steps:
	- name: Checkout
	uses: actions/checkout@v3
	with:
	lfs: false
	fetch-depth: 500
	- name: Git fetch tags
	run: \|
	git config --global --add safe.directory '*'
	git fetch --tags -f
	- name: Create folder for native libs
	run: mkdir dist
	- name: Download Linux native libs x86_64
	uses: actions/download-artifact@v3
	with:
	name: indigo-libs-linux-x86_64
	path: dist/
	- name: Download Linux native libs aarch64
	uses: actions/download-artifact@v3
	with:
	name: indigo-libs-linux-aarch64
	path: dist/
	- name: Download Windows native libs x86_64
	uses: actions/download-artifact@v3
	with:
	name: indigo-libs-windows-x86_64
	path: dist/
	- name: Download Windows native libs i386
	uses: actions/download-artifact@v3
	with:
	name: indigo-libs-windows-i386
	path: dist/
	- name: Download macOS native libs x86_64
	uses: actions/download-artifact@v3
	with:
	name: indigo-libs-macos-x86_64
	path: dist/
	- name: Download macOS native libs aarch64
	uses: actions/download-artifact@v3
	with:
	name: indigo-libs-macos-aarch64
	path: dist/
	- name: Install Python test dependencies
	run: python3 -m pip install -r api/python/requirements_dev.txt
	- name: Build wrappers
	run: \|
	mkdir build
	cd build
	cmake .. -DBUILD_INDIGO=OFF -DBUILD_INDIGO_UTILS=OFF -DBUILD_BINGO=OFF -DBUILD_BINGO_ELASTIC=OFF
	cmake --build . --config Release --target indigo-${{ matrix.wrapper }}
	- name: Upload native shared libs
	uses: actions/upload-artifact@v3
	with:
	name: indigo-native-shared-libs
	path: \|
	dist/lib
	- name: Upload Python wrappers
	if: ${{ matrix.wrapper == 'python' }}
	uses: actions/upload-artifact@v3
	with:
	name: indigo-python
	path: \|
	dist/*.whl
	- name: Upload Java wrappers
	if: ${{ matrix.wrapper == 'java' }}
	uses: actions/upload-artifact@v3
	with:
	name: indigo-java
	path: dist/*.jar
	- name: Upload .NET wrappers
	if: ${{ matrix.wrapper == 'dotnet' }}
	uses: actions/upload-artifact@v3
	with:
	name: indigo-dotnet
	path: dist/*.nupkg

	test_indigo_python_x86_64:
	timeout-minutes: 60
	strategy:
	fail-fast: false
	matrix:
	os: [ macos-13, ubuntu-latest, windows-latest ]
	runs-on: ${{ matrix.os }}
	needs: build_indigo_wrappers
	steps:
	- name: Checkout
	uses: actions/checkout@v3
	with:
	lfs: false
	fetch-depth: 500
	- name: Git fetch tags
	run: \|
	git config --global --add safe.directory '*'
	git fetch --tags -f
	- name: Create folder for native libs
	run: mkdir dist
	- name: Download wrappers
	uses: actions/download-artifact@v3
	with:
	name: indigo-python
	path: dist/
	- name: Install Pillow
	run: python3 -m pip install Pillow==9.5.0
	- name: Install wrappers Linux
	if: ${{ startsWith(matrix.os, 'ubuntu') }}
	run: python3 -m pip install dist/manylinux1_x86_64.whl
	- name: Install wrappers Windows
	if: ${{ startsWith(matrix.os, 'windows') }}
	run: Get-ChildItem dist -Filter win_amd64.whl -Recurse \| % { python3 -m pip install $_.FullName }
	- name: Install wrappers macOS
	if: ${{ startsWith(matrix.os, 'macos') }}
	run: python3 -m pip install dist/macosx_10_7_intel.whl
	- name: Test
	run: python3 -Wignore api/tests/integration/test.py -t 1 -j junit_report.xml
	- name: Publish Test Report
	if: always()
	uses: mikepenz/action-junit-report@v3
	with:
	report_paths: 'junit_report.xml'
	github_token: ${{ secrets.GITHUB_TOKEN }}
	check_name: "${{ matrix.os }}-x86_64-python_test_report"

	test_indigo_python_aarch64:
	timeout-minutes: 60
	strategy:
	fail-fast: false
	matrix:
	os: [ ubuntu-latest ]
	runs-on: ${{ matrix.os }}
	needs: build_indigo_wrappers
	steps:
	- name: Checkout
	uses: actions/checkout@v3
	with:
	lfs: false
	fetch-depth: 500
	- name: Git fetch tags
	run: \|
	git config --global --add safe.directory '*'
	git fetch --tags -f
	- name: Create folder for native libs
	run: mkdir dist
	- name: Download wrappers
	uses: actions/download-artifact@v3
	with:
	name: indigo-python
	path: dist/
	- name: Test Linux
	if: ${{ startsWith(matrix.os, 'ubuntu') }}
	uses: uraimo/run-on-arch-action@v2.0.5
	with:
	arch: aarch64
	distro: ubuntu20.04
	githubToken: ${{ github.token }}
	run: \|
	apt update
	apt install -y --no-install-recommends python3 python3-pip
	python3 -m pip install Pillow==9.5.0
	python3 -m pip install dist/manylinux2014_aarch64.whl
	python3 api/tests/integration/test.py -p basic/basic.py -t 1 -j junit_report.xml
	- name: Publish Test Report
	if: always()
	uses: mikepenz/action-junit-report@v3
	with:
	report_paths: 'junit_report.xml'
	github_token: ${{ secrets.GITHUB_TOKEN }}
	check_name: "${{ matrix.os }}-aarch64-python_test_report"

	test_indigo_python_i386:
	timeout-minutes: 60
	strategy:
	fail-fast: false
	matrix:
	os: [ windows-latest ]
	runs-on: ${{ matrix.os }}
	needs: build_indigo_wrappers
	steps:
	- name: Checkout
	uses: actions/checkout@v3
	with:
	lfs: false
	fetch-depth: 500
	- name: Git fetch tags
	run: \|
	git config --global --add safe.directory '*'
	git fetch --tags -f
	- name: Create folder for native libs
	run: mkdir dist
	- name: Download wrappers
	uses: actions/download-artifact@v3
	with:
	name: indigo-python
	path: dist/
	- name: Set up Python
	uses: actions/setup-python@v2
	with:
	python-version: 3.7
	architecture: x86
	- name: Install Pillow
	run: python -m pip install Pillow==9.5.0
	- name: Install wrappers Windows
	if: ${{ startsWith(matrix.os, 'windows') }}
	run: Get-ChildItem dist -Filter win32.whl -Recurse \| % { python -m pip install $_.FullName }
	- name: Test
	run: python api/tests/integration/test.py -t 1 -p basic/basic.py -j junit_report.xml
	- name: Publish Test Report
	if: always()
	uses: mikepenz/action-junit-report@v3
	with:
	report_paths: 'junit_report.xml'
	github_token: ${{ secrets.GITHUB_TOKEN }}
	check_name: "${{ matrix.os }}-i386-python_test_report"

	test_indigo_java_x86_64:
	timeout-minutes: 60
	strategy:
	fail-fast: false
	matrix:
	os: [ macos-13, ubuntu-latest, windows-latest ]
	runs-on: ${{ matrix.os }}
	needs: build_indigo_wrappers
	steps:
	- name: Checkout
	uses: actions/checkout@v3
	with:
	lfs: false
	fetch-depth: 500
	- name: Git fetch tags
	run: \|
	git config --global --add safe.directory '*'
	git fetch --tags -f
	- name: Create folder for native libs
	run: mkdir dist
	- name: Download wrappers
	uses: actions/download-artifact@v3
	with:
	name: indigo-java
	path: dist/
	- name: Install Jython
	run: \|
	curl -L https://repo1.maven.org/maven2/org/python/jython-standalone/2.7.2/jython-standalone-2.7.2.jar -o jython.jar
	- name: Test
	env:
	INDIGO_PATH: ${{ github.workspace }}/dist
	run: \|
	java -Xss4m -jar jython.jar api/tests/integration/test.py -t 1 -j junit_report.xml
	- name: Publish Test Report
	if: always()
	uses: mikepenz/action-junit-report@v3
	with:
	report_paths: 'junit_report.xml'
	github_token: ${{ secrets.GITHUB_TOKEN }}
	check_name: "${{ matrix.os }}-x86_64-java_test_report"

	test_indigo_java_aarch64:
	timeout-minutes: 60
	strategy:
	fail-fast: false
	matrix:
	os: [ ubuntu-latest ]
	runs-on: ${{ matrix.os }}
	needs: build_indigo_wrappers
	steps:
	- name: Checkout
	uses: actions/checkout@v3
	with:
	lfs: false
	fetch-depth: 500
	- name: Git fetch tags
	run: \|
	git config --global --add safe.directory '*'
	git fetch --tags -f
	- name: Create folder for native libs
	run: mkdir dist
	- name: Download wrappers
	uses: actions/download-artifact@v3
	with:
	name: indigo-java
	path: dist/
	- name: Test Linux
	if: ${{ startsWith(matrix.os, 'ubuntu') }}
	uses: uraimo/run-on-arch-action@v2.0.5
	with:
	arch: aarch64
	distro: ubuntu20.04
	githubToken: ${{ github.token }}
	run: \|
	apt update
	apt install -y curl default-jre
	curl -L https://repo1.maven.org/maven2/org/python/jython-standalone/2.7.2/jython-standalone-2.7.2.jar -o jython.jar
	export INDIGO_PATH=${{ github.workspace }}/dist
	java -Xss4m -jar jython.jar api/tests/integration/test.py -p basic/basic.py -t 1 -j junit_report.xml
	- name: Publish Test Report
	if: always()
	uses: mikepenz/action-junit-report@v3
	with:
	report_paths: 'junit_report.xml'
	github_token: ${{ secrets.GITHUB_TOKEN }}
	check_name: "${{ matrix.os }}-aarch64-java_test_report"

	test_indigo_java_i386:
	timeout-minutes: 60
	strategy:
	fail-fast: false
	matrix:
	os: [ windows-latest ]
	runs-on: ${{ matrix.os }}
	needs: build_indigo_wrappers
	steps:
	- name: Checkout
	uses: actions/checkout@v3
	with:
	lfs: false
	fetch-depth: 500
	- name: Git fetch tags
	run: \|
	git config --global --add safe.directory '*'
	git fetch --tags -f
	- name: Create folder for native libs
	run: mkdir dist
	- name: Download wrappers
	uses: actions/download-artifact@v3
	with:
	name: indigo-java
	path: dist/
	- uses: actions/setup-java@v2
	with:
	distribution: 'adopt-hotspot'
	java-version: '11'
	architecture: x86
	- name: Install Jython
	run: \|
	curl -L https://repo1.maven.org/maven2/org/python/jython-standalone/2.7.2/jython-standalone-2.7.2.jar -o jython.jar
	- name: Test
	env:
	INDIGO_PATH: ${{ github.workspace }}/dist
	run: \|
	java -Xss4m -jar jython.jar api/tests/integration/test.py -t 1 -p basic/basic.py -j junit_report.xml
	- name: Publish Test Report
	if: always()
	uses: mikepenz/action-junit-report@v3
	with:
	report_paths: 'junit_report.xml'
	github_token: ${{ secrets.GITHUB_TOKEN }}
	check_name: "${{ matrix.os }}-i386-java_test_report"

	test_indigo_dotnet_x86_64:
	timeout-minutes: 60
	strategy:
	fail-fast: false
	matrix:
	os: [ macos-13, ubuntu-latest, windows-latest ]
	runs-on: ${{ matrix.os }}
	needs: build_indigo_wrappers
	steps:
	- name: Checkout
	uses: actions/checkout@v3
	with:
	lfs: false
	fetch-depth: 500
	- name: Git fetch tags
	run: \|
	git config --global --add safe.directory '*'
	git fetch --tags -f
	- name: Create folder for native libs
	run: mkdir dist
	- name: Download wrappers
	uses: actions/download-artifact@v3
	with:
	name: indigo-dotnet
	path: dist/
	- name: Prepare Common
	run: \|
	mkdir IronPython
	mkdir tmp
	cd IronPython
	curl -OL https://github.com/IronLanguages/ironpython3/releases/download/v3.4.0/IronPython.3.4.0.zip
	- name: Install dotnet 6
	if: ${{ startsWith(matrix.os, 'macos') }}
	run: \|
	curl -Lo dotnet.tar.gz https://download.visualstudio.microsoft.com/download/pr/270b615f-5281-4c58-980f-d9f7a08db642/3e874492a9cb0d5b87195c596b46d609/dotnet-sdk-6.0.421-osx-x64.tar.gz
	mkdir -p ${{ github.workspace }}/tmp/dotnet && tar zxf dotnet.tar.gz -C ${{ github.workspace }}/tmp/dotnet
	- name: Prepare UNIX
	if: ${{ !startsWith(matrix.os, 'windows') }}
	run: \|
	cd IronPython
	unzip IronPython.3.4.0.zip
	cd ../tmp
	unzip ../dist/Indigo.Net.*.nupkg
	chmod -R a+rw .
	- name: Prepare Windows
	if: ${{ startsWith(matrix.os, 'windows') }}
	run: \|
	cd IronPython
	Expand-Archive IronPython.3.4.0.zip .
	cd ../tmp
	Expand-Archive ../dist/Indigo.Net.*.nupkg .
	- name: Test Linux
	if: ${{ startsWith(matrix.os, 'ubuntu') }}
	env:
	INDIGO_PATH: ${{ github.workspace }}/tmp/lib/netstandard2.0/Indigo.Net.dll
	LD_LIBRARY_PATH: ${{ github.workspace }}/tmp/runtimes/linux-x64/native
	run: \|
	dotnet IronPython/net6.0/ipy.dll api/tests/integration/test.py -t 1 -j junit_report.xml
	- name: Test macOS
	if: ${{ startsWith(matrix.os, 'macos') }}
	env:
	INDIGO_PATH: ${{ github.workspace }}/tmp/lib/netstandard2.0/Indigo.Net.dll
	DOTNET_ROOT: ${{ github.workspace }}/tmp/dotnet
	PATH: ${{ github.workspace }}/tmp/dotnet:$PATH
	run: \|
	export DYLD_LIBRARY_PATH=${PWD}/tmp/runtimes/osx-x64/native
	dotnet IronPython/net6.0/ipy.dll api/tests/integration/test.py -t 1 -j junit_report.xml
	- name: Test Windows
	if: ${{ startsWith(matrix.os, 'windows') }}
	env:
	INDIGO_PATH: ${{ github.workspace }}/tmp/lib/netstandard2.0/Indigo.Net.dll
	PATH: ${{ env.PATH }};${{ github.workspace }}/tmp/runtimes/win-x64/native
	run: ./IronPython/net462/ipy.exe api/tests/integration/test.py -t 1 -j junit_report.xml
	- name: Publish Test Report
	if: always()
	uses: mikepenz/action-junit-report@v3
	with:
	report_paths: 'junit_report.xml'
	github_token: ${{ secrets.GITHUB_TOKEN }}
	check_name: "${{ matrix.os }}-x86_64-dotnet_test_report"

	test_indigo_dotnet_i386:
	timeout-minutes: 60
	strategy:
	fail-fast: false
	matrix:
	os: [ windows-latest ]
	runs-on: ${{ matrix.os }}
	needs: build_indigo_wrappers
	steps:
	- name: Checkout
	uses: actions/checkout@v3
	with:
	lfs: false
	fetch-depth: 500
	- name: Git fetch tags
	run: \|
	git config --global --add safe.directory '*'
	git fetch --tags -f
	- name: Create folder for native libs
	run: mkdir dist
	- name: Download wrappers
	uses: actions/download-artifact@v3
	with:
	name: indigo-dotnet
	path: dist/
	- name: Prepare Common
	run: \|
	mkdir IronPython
	mkdir tmp
	cd IronPython
	curl -OL https://github.com/IronLanguages/ironpython3/releases/download/v3.4.0/IronPython.3.4.0.zip
	- name: Prepare Windows
	if: ${{ startsWith(matrix.os, 'windows') }}
	run: \|
	cd IronPython
	Expand-Archive IronPython.3.4.0.zip .
	cd ../tmp
	Expand-Archive ../dist/Indigo.Net.*.nupkg .
	- name: Test Windows
	if: ${{ matrix.os == 'windows' }}
	env:
	INDIGO_PATH: ${{ github.workspace }}/tmp/lib/netstandard2.0/Indigo.Net.dll
	PATH: ${{ env.PATH }};${{ github.workspace }}/tmp/runtimes/win-x86/native
	run: ./IronPython/net462/ipy32.exe api/tests/integration/test.py -t 1 -p basic/basic.py -j junit_report.xml
	- name: Publish Test Report
	if: always()
	uses: mikepenz/action-junit-report@v3
	with:
	report_paths: 'junit_report.xml'
	github_token: ${{ secrets.GITHUB_TOKEN }}
	check_name: "${{ matrix.os }}_i386_dotnet_test_report"

	test_bingo_elastic_python_linux_x86_64:
	runs-on: ubuntu-latest
	strategy:
	fail-fast: false
	matrix:
	python-version: [ '3.7', '3.10' ]
	needs: build_indigo_wrappers
	steps:
	- uses: actions/checkout@v3
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v2
	with:
	python-version: ${{ matrix.python-version }}
	lfs: false
	fetch-depth: 500
	- name: Create folder for native libs
	run: mkdir dist
	- name: Download wrappers
	uses: actions/download-artifact@v3
	with:
	name: indigo-python
	path: dist/
	- name: Install latest indigo version
	run: pip install ${GITHUB_WORKSPACE}/dist/epam.indigo-*manylinux1_x86_64.whl
	working-directory: bingo/bingo-elastic/python
	- name: Install dev dependencies
	run: pip install ".[dev]"
	working-directory: bingo/bingo-elastic/python
	- name: Setup elasticsearch
	run: docker run -d -p 9200:9200 -p 9300:9300 -e "discovery.type=single-node" -e "indices.query.bool.max_clause_count=4096" docker.elastic.co/elasticsearch/elasticsearch:7.16.2
	- name: Wait elastic is ready
	run: sleep 30s
	- name: Build wheel
	working-directory: bingo/bingo-elastic/python
	run: \|
	pip install ".[async]"
	python setup.py bdist_wheel
	cp dist/*.whl ${GITHUB_WORKSPACE}/dist/
	- name: Run pylint
	run: pylint --max-args 10 bingo_elastic
	working-directory: bingo/bingo-elastic/python
	- name: Run tests
	run: pytest tests
	working-directory: bingo/bingo-elastic/python
	- name: Upload artifacts
	uses: actions/upload-artifact@v3
	with:
	name: bingo-elastic-python
	path: dist

	test_bingo_elastic_java_linux_x86_64:
	strategy:
	fail-fast: false
	matrix:
	java-version: [ 1.8, 1.11 ]
	runs-on: ubuntu-latest
	needs: build_indigo_wrappers
	steps:
	- name: Checkout
	uses: actions/checkout@v3
	with:
	lfs: false
	fetch-depth: 500
	- name: Set up JDK 1.8
	uses: actions/setup-java@v1
	with:
	java-version: ${{ matrix.java-version }}
	- name: Cache Maven packages
	uses: actions/cache@v2
	with:
	path: ~/.m2
	key: ${{ runner.os }}-m2-${{ hashFiles('**/pom.xml') }}
	restore-keys: ${{ runner.os }}-m2
	- name: Download wrappers
	uses: actions/download-artifact@v3
	with:
	name: indigo-java
	path: dist/
	- name: Install Indigo jars
	run: find dist -name ".jar" -not -name "javadoc" -not -name "sources*" -exec mvn org.apache.maven.plugins:maven-install-plugin:2.5.2:install-file -Dfile={} \;
	- name: Build bingo-elastic
	run: mvn -B --file pom.xml -Dmaven.repo.local=/home/runner/.m2/repository clean test
	working-directory: bingo/bingo-elastic/java

	build_indigo_windows_mingw_x86_64:
	timeout-minutes: 60
	runs-on: windows-latest
	needs: static_analysis
	defaults:
	run:
	shell: msys2 {0}
	steps:
	- name: Checkout
	uses: actions/checkout@v3
	with:
	lfs: false
	fetch-depth: 500
	- uses: msys2/setup-msys2@v2
	with:
	msystem: mingw64
	install: mingw-w64-x86_64-gcc mingw-w64-x86_64-make mingw-w64-x86_64-cmake git mingw-w64-x86_64-python mingw-w64-x86_64-python-pip mingw-w64-x86_64-python-wheel mingw-w64-x86_64-python-pillow
	- name: Git fetch tags
	run: \|
	git config --global --add safe.directory '*'
	git fetch --tags -f
	- name: Build native libs
	run: \|
	mkdir build
	cd build
	cmake .. -G "MinGW Makefiles" -DBUILD_INDIGO_WRAPPERS=OFF -DBUILD_BINGO=OFF -DBUILD_BINGO_ELASTIC=OFF -DPython3_ROOT_DIR=/mingw64
	cmake --build . --config Release --target all -- -j $(nproc) --output-sync
	- name: Test native libs
	run: \|
	cd build
	ctest --verbose
	# - name: Install Python test dependencies
	# run: python3 -m pip install -r api/python/requirements_dev.txt
	# - name: Prepare integration tests
	# run: \|
	# cd build
	# cmake .. -G "MinGW Makefiles" -DBUILD_INDIGO_WRAPPERS=ON -DBUILD_BINGO=OFF -DBUILD_BINGO_ELASTIC=OFF -DPython3_ROOT_DIR=/mingw64
	# cmake --build . --config Release --target indigo-python -- -j $(nproc) --output-sync
	# - name: Run integration tests
	# run: \|
	# python api/tests/integration/test.py -t 1 -j junit_report.xml -platform mingw
	# - name: Publish Test Report
	# if: always()
	# uses: mikepenz/action-junit-report@v3
	# with:
	# report_paths: 'junit_report.xml'
	# github_token: ${{ secrets.GITHUB_TOKEN }}
	# check_name: "windows-mingw_python_test_report"
	- name: Upload artifacts
	uses: actions/upload-artifact@v3
	with:
	name: indigo-libs-windows-mingw-x86_64
	path: dist

	build_indigo_ketcher:
	runs-on: ubuntu-latest
	needs: static_analysis
	container: emscripten/emsdk:3.1.60
	steps:
	- name: Checkout
	uses: actions/checkout@v3
	with:
	lfs: false
	fetch-depth: 500
	- name: Git fetch tags
	run: \|
	git config --global --add safe.directory '*'
	git fetch --tags -f
	- name: Update version
	run: \|
	cd api/wasm/indigo-ketcher
	ver=$(git describe --abbrev=0 --tags --match "indigo-")-$(git rev-list $(git describe --abbrev=0 --tags --match "indigo-").. --count)
	ver=$(echo $ver \| sed 's/indigo-//g' \| sed 's/-0//g')
	npm version --allow-same-version ${ver}
	- name: Build, Test, Pack
	run: \|
	mkdir build
	cd build
	emcmake cmake .. -DCMAKE_BUILD_TYPE=Release
	cmake --build . --config Release --target indigo-ketcher-package -- -j $(nproc)
	- name: Upload artifacts
	uses: actions/upload-artifact@v3
	with:
	name: indigo-ketcher
	path: dist/indigo-ketcher*.tgz

	build_indigo_ketcher_cjk:
	runs-on: ubuntu-latest
	needs: static_analysis
	container: emscripten/emsdk:3.1.60
	steps:
	- name: Checkout
	uses: actions/checkout@v3
	with:
	lfs: false
	fetch-depth: 500
	- name: Git fetch tags
	run: \|
	git config --global --add safe.directory '*'
	git fetch --tags -f
	- name: Update version
	run: \|
	cd api/wasm/indigo-ketcher
	ver=$(git describe --abbrev=0 --tags --match "indigo-")-$(git rev-list $(git describe --abbrev=0 --tags --match "indigo-").. --count)
	ver=$(echo $ver \| sed 's/indigo-//g' \| sed 's/-0//g')
	npm version --allow-same-version ${ver}
	- name: Build, Test, Pack
	run: \|
	mkdir build
	cd build
	emcmake cmake .. -DCMAKE_BUILD_TYPE=Release -DRENDER_ENABLE_CJK=ON
	cmake --build . --config Release --target indigo-ketcher-package -- -j $(nproc)
	- name: Upload artifacts
	uses: actions/upload-artifact@v3
	with:
	name: indigo-ketcher-cjk
	path: dist/indigo-ketcher*.tgz

	build_indigo_utils_x86_64:
	strategy:
	fail-fast: false
	matrix:
	os: [ macos-13, ubuntu-latest, windows-latest ]
	runs-on: ${{ matrix.os }}
	needs: static_analysis
	steps:
	- name: Checkout
	uses: actions/checkout@v3
	with:
	lfs: false
	fetch-depth: 500
	- name: Git fetch tags
	run: \|
	git config --global --add safe.directory '*'
	git fetch --tags -f
	- name: Build utils Linux
	if: ${{ startsWith(matrix.os, 'ubuntu') }}
	uses: docker://epmlsop/buildpack-centos7:latest
	with:
	args: >
	/bin/sh -c "
	mkdir build &&
	cd build &&
	cmake .. -DBUILD_INDIGO=OFF -DBUILD_INDIGO_WRAPPERS=OFF -DBUILD_BINGO=OFF -DBUILD_BINGO_ELASTIC=OFF -DBUILD_INDIGO_UTILS=ON &&
	cmake --build . --config Release --target all -- -j $(nproc) &&
	ctest --verbose
	"
	- name: Build utils macOS
	if: ${{ startsWith(matrix.os, 'macos') }}
	run: \|
	mkdir build
	cd build
	cmake .. -DBUILD_INDIGO=OFF -DBUILD_INDIGO_WRAPPERS=OFF -DBUILD_BINGO=OFF -DBUILD_BINGO_ELASTIC=OFF -DBUILD_INDIGO_UTILS=ON
	cmake --build . --config Release --target all -- -j $(sysctl -n hw.logicalcpu)
	ctest --verbose
	- name: Build utils Windows
	if: ${{ startsWith(matrix.os, 'windows') }}
	run: \|
	mkdir build
	cd build
	cmake .. -DBUILD_INDIGO=OFF -DBUILD_INDIGO_WRAPPERS=OFF -DBUILD_BINGO=OFF -DBUILD_BINGO_ELASTIC=OFF -DBUILD_INDIGO_UTILS=ON
	cmake --build . --config Release --target ALL_BUILD
	ctest --verbose -C Release
	- name: Upload artifacts
	uses: actions/upload-artifact@v3
	with:
	name: indigo-utils-${{ fromJSON(env.OS_NAME_MAPPING_JSON)[matrix.os] }}-x86_64
	path: dist/utils

	build_bingo_oracle_linux_x86_64:
	runs-on: ubuntu-latest
	needs: static_analysis
	steps:
	- name: Checkout
	uses: actions/checkout@v3
	with:
	lfs: false
	fetch-depth: 500
	- name: Git fetch tags
	run: \|
	git config --global --add safe.directory '*'
	git fetch --tags -f
	- name: Build bingo-oracle
	uses: docker://epmlsop/buildpack-centos7:latest
	with:
	args: >
	/bin/sh -c "
	set -eux &&
	mkdir build &&
	cd build &&
	cmake .. -DBUILD_BINGO_ORACLE=ON -DBUILD_BINGO_SQLSERVER=OFF -DBUILD_BINGO_POSTGRES=OFF -DBUILD_INDIGO=OFF -DBUILD_INDIGO_WRAPPERS=OFF -DBUILD_INDIGO_UTILS=OFF -DBUILD_BINGO_ELASTIC=OFF &&
	cmake --build . --config Release --target package-bingo-oracle -- -j $(nproc)
	"
	- name: Upload artifacts
	uses: actions/upload-artifact@v3
	with:
	name: bingo-oracle-linux-x86_64
	path: dist/bingo-oracle*.tgz

	build_bingo_oracle_windows_mingw_x86_64:
	runs-on: windows-latest
	needs: static_analysis
	defaults:
	run:
	shell: msys2 {0}
	steps:
	- name: Checkout
	uses: actions/checkout@v3
	with:
	lfs: false
	fetch-depth: 500
	- uses: msys2/setup-msys2@v2
	with:
	msystem: mingw64
	install: mingw-w64-x86_64-gcc mingw-w64-x86_64-make mingw-w64-x86_64-cmake git
	- name: Git fetch tags
	run: \|
	git config --global --add safe.directory '*'
	git fetch --tags -f
	- name: Build bingo-oracle
	run: \|
	mkdir build
	cd build
	cmake .. -G "MinGW Makefiles" -DBUILD_BINGO_ORACLE=ON -DBUILD_BINGO_SQLSERVER=OFF -DBUILD_BINGO_POSTGRES=OFF -DBUILD_INDIGO=OFF -DBUILD_INDIGO_WRAPPERS=OFF -DBUILD_INDIGO_UTILS=OFF -DBUILD_BINGO_ELASTIC=OFF
	cmake --build . --config Release --target package-bingo-oracle -- -j $(nproc)
	- name: Upload artifacts
	uses: actions/upload-artifact@v3
	with:
	name: bingo-oracle-windows-mingw-x86_64
	path: dist/bingo-oracle*.zip

	build_bingo_oracle_windows_msvc_x86_64:
	runs-on: windows-latest
	needs: static_analysis
	steps:
	- name: Checkout
	uses: actions/checkout@v3
	with:
	lfs: false
	fetch-depth: 500
	- name: Git fetch tags
	run: \|
	git config --global --add safe.directory '*'
	git fetch --tags -f
	- name: Build bingo-oracle
	run: \|
	mkdir build
	cd build
	cmake .. -DBUILD_BINGO_ORACLE=ON -DBUILD_BINGO_SQLSERVER=OFF -DBUILD_BINGO_POSTGRES=OFF -DBUILD_INDIGO=OFF -DBUILD_INDIGO_WRAPPERS=OFF -DBUILD_INDIGO_UTILS=OFF -DBUILD_BINGO_ELASTIC=OFF
	cmake --build . --config Release --target package-bingo-oracle
	- name: Upload artifacts
	uses: actions/upload-artifact@v3
	with:
	name: bingo-oracle-windows-msvc-x86_64
	path: dist/bingo-oracle*.zip

	build_bingo_postgres_linux_x86_64:
	strategy:
	fail-fast: false
	matrix:
	postgres_major_version: [ 12, 13, 14, 15 ]
	runs-on: ubuntu-latest
	needs: static_analysis
	steps:
	- name: Checkout
	uses: actions/checkout@v3
	with:
	lfs: false
	fetch-depth: 500
	- name: Set up Python
	uses: actions/setup-python@v2
	with:
	python-version: 3.7
	- name: Git fetch tags
	run: \|
	git config --global --add safe.directory '*'
	git fetch --tags -f
	- name: Install postgres server headers and build bingo-postgres
	uses: docker://epmlsop/buildpack-centos7:latest
	with:
	args: >
	/bin/sh -c "
	set -eux &&
	yum install -y --disablerepo base --disablerepo centos-sclo-rh --disablerepo centos-sclo-sclo --disablerepo extras --disablerepo updates https://download.postgresql.org/pub/repos/yum/reporpms/EL-7-x86_64/pgdg-redhat-repo-latest.noarch.rpm yum-utils &&
	curl -OL https://download.postgresql.org/pub/repos/yum/keys/PGDG-RPM-GPG-KEY-RHEL &&
	rpm --import PGDG-RPM-GPG-KEY-RHEL &&
	yumdownloader -y --disablerepo base --disablerepo centos-sclo-rh --disablerepo centos-sclo-sclo --disablerepo extras --disablerepo updates postgresql${{ matrix.postgres_major_version }}-devel &&
	rpm -i --nodeps postgresql${{ matrix.postgres_major_version }}*.rpm &&
	ls -alh /usr &&
	mkdir build &&
	cd build &&
	cmake .. -DBUILD_BINGO_POSTGRES=ON -DBUILD_BINGO_SQLSERVER=OFF -DBUILD_BINGO_ORACLE=OFF -DBUILD_INDIGO=OFF -DBUILD_INDIGO_WRAPPERS=OFF -DBUILD_INDIGO_UTILS=OFF -DBUILD_BINGO_ELASTIC=OFF -DCMAKE_PREFIX_PATH=/usr/pgsql-${{ matrix.postgres_major_version }} &&
	cmake --build . --config Release --target package-bingo-postgres -- -j $(nproc)
	"
	- name: Upload artifacts
	uses: actions/upload-artifact@v3
	with:
	name: bingo-postgres-${{ matrix.postgres_major_version }}-linux-x86_64
	path: dist/bingo-postgres*.tgz
	- name: Build Docker image
	run: \|
	docker build --tag epmlsop/bingo-postgres:${{ matrix.postgres_major_version }}-latest -f bingo/postgres/Dockerfile --build-arg BINGO_PG_VERSION=${{ matrix.postgres_major_version }} .
	- name: Start Docker container
	run: \|
	docker run --rm -d -p 5432:5432 -e "POSTGRES_PASSWORD=password" -v /home:/home epmlsop/bingo-postgres:${{ matrix.postgres_major_version }}-latest
	- name: Install dev dependencies
	run: \|
	pip install -r bingo/tests/requirements.txt
	- name: Run Bingo tests
	run: \|
	export PYTHONPATH=${{ github.workspace }}/bingo/bingo-elastic/python
	pytest --tb=no --db postgres --junit-xml=junit_report.xml
	working-directory: bingo/tests
	- name: Login to DockerHub
	if: startsWith(github.ref, 'refs/tags/indigo-')
	uses: docker/login-action@v1
	with:
	username: ${{ secrets.DOCKERHUB_USERNAME }}
	password: ${{ secrets.DOCKERHUB_TOKEN }}
	- name: Publish Docker images
	if: startsWith(github.ref, 'refs/tags/indigo-')
	run: docker push epmlsop/bingo-postgres:${{ matrix.postgres_major_version }}-latest
	- name: Publish Test Report
	if: always()
	uses: mikepenz/action-junit-report@v3
	with:
	report_paths: 'bingo/tests/junit_report.xml'
	github_token: ${{ secrets.GITHUB_TOKEN }}
	check_name: "bingo_postgres_${{ matrix.postgres_major_version }}_test_report"

	build_bingo_postgres_windows_msvc_x86_64:
	strategy:
	fail-fast: false
	matrix:
	postgres_major_version: [ "12", "13", "14", "15" ]
	runs-on: windows-latest
	needs: static_analysis
	steps:
	- name: Checkout
	uses: actions/checkout@v3
	with:
	lfs: false
	fetch-depth: 500
	- name: Git fetch tags
	run: \|
	git config --global --add safe.directory '*'
	git fetch --tags -f
	- name: Setup Postgres
	run: \|
	$pg_version = switch(${{ matrix.postgres_major_version }}) { "15" { "15.1" } "14" { "14.6" } "13" { "13.9" } "12" { "12.13" } }
	curl -O https://get.enterprisedb.com/postgresql/postgresql-${pg_version}-1-windows-x64-binaries.zip
	Expand-Archive postgresql-${pg_version}-1-windows-x64-binaries.zip
	mv postgresql-${pg_version}-1-windows-x64-binaries/pgsql pgsql
	cp bingo/postgres/patches/generic-msvc.h pgsql/include/server/port/atomics/generic-msvc.h
	- name: Build bingo-postgres
	run: \|
	mkdir build
	cd build
	cmake .. -DBUILD_BINGO_POSTGRES=ON -DBUILD_BINGO_SQLSERVER=OFF -DBUILD_BINGO_ORACLE=OFF -DBUILD_INDIGO=OFF -DBUILD_INDIGO_WRAPPERS=OFF -DBUILD_INDIGO_UTILS=OFF -DBUILD_BINGO_ELASTIC=OFF -DPostgreSQL_ROOT="$(resolve-path $pwd/../pgsql)"
	cmake --build . --config Release --target package-bingo-postgres
	- name: Upload artifacts
	uses: actions/upload-artifact@v3
	with:
	name: bingo-postgres-${{ matrix.postgres_major_version }}-windows-x86_64
	path: dist/bingo-postgres*.zip

	build_bingo_postgres_macos_x86_64:
	strategy:
	fail-fast: false
	matrix:
	postgres_major_version: [ 12, 13, 14, 15 ]
	runs-on: macos-13
	needs: static_analysis
	steps:
	- name: Checkout
	uses: actions/checkout@v3
	with:
	lfs: false
	fetch-depth: 500
	- name: Git fetch tags
	run: \|
	git config --global --add safe.directory '*'
	git fetch --tags -f
	- name: Setup Postgres
	run: \|
	case ${{ matrix.postgres_major_version }} in 15) pg_version=15.1;; 14) pg_version=14.6;; 13) pg_version=13.9;; 12) pg_version=12.13;; esac;
	curl -O https://get.enterprisedb.com/postgresql/postgresql-${pg_version}-1-osx-binaries.zip
	unzip postgresql-${pg_version}-1-osx-binaries.zip
	mv pgsql/include/zlib.h pgsql/include/zlib.h.bck
	- name: Build bingo-postgres
	run: \|
	mkdir build
	cd build
	cmake .. -DBUILD_BINGO_POSTGRES=ON -DBUILD_BINGO_SQLSERVER=OFF -DBUILD_BINGO_ORACLE=OFF -DBUILD_INDIGO=OFF -DBUILD_INDIGO_WRAPPERS=OFF -DBUILD_INDIGO_UTILS=OFF -DBUILD_BINGO_ELASTIC=OFF -DPostgreSQL_ROOT="$(dirname $PWD)/pgsql" -DPostgreSQL_ADDITIONAL_VERSIONS=${{ matrix.postgres_major_version }}
	cmake --build . --config Release --target package-bingo-postgres
	- name: Upload artifacts
	uses: actions/upload-artifact@v3
	with:
	name: bingo-postgres-${{ matrix.postgres_major_version }}-macos-x86_64
	path: dist/bingo-postgres*.tgz

	build_bingo_sqlserver_windows_msvc_x86_64:
	strategy:
	fail-fast: false
	matrix:
	os: [ windows-latest ]
	runs-on: ${{ matrix.os }}
	needs: static_analysis
	steps:
	- name: Checkout
	uses: actions/checkout@v3
	with:
	lfs: false
	fetch-depth: 500
	- name: Git fetch tags
	run: \|
	git config --global --add safe.directory '*'
	git fetch --tags -f
	- name: Build
	run: \|
	mkdir build
	cd build
	cmake .. -DBUILD_BINGO_SQLSERVER=ON -DBUILD_BINGO_POSTGRES=OFF -DBUILD_BINGO_ORACLE=OFF -DBUILD_INDIGO=OFF -DBUILD_INDIGO_WRAPPERS=OFF -DBUILD_INDIGO_UTILS=OFF -DBUILD_BINGO_ELASTIC=OFF
	cmake --build . --config Release --target package-bingo-sqlserver
	- name: Upload artifacts
	uses: actions/upload-artifact@v3
	with:
	name: bingo-sqlserver-${{ matrix.os }}-x86_64
	path: dist/bingo-sqlserver*.zip

	publish_indigo_to_pypi:
	if: startsWith(github.ref, 'refs/tags/indigo-')
	runs-on: ubuntu-latest
	needs: [test_indigo_python_x86_64, test_indigo_java_x86_64, test_indigo_dotnet_x86_64, test_indigo_python_i386, test_indigo_java_i386, test_indigo_dotnet_i386, test_indigo_python_aarch64, test_indigo_java_aarch64, test_bingo_elastic_python_linux_x86_64, test_bingo_elastic_java_linux_x86_64, build_indigo_ketcher]
	container: epmlsop/indigo-tester:latest
	steps:
	- name: Checkout
	uses: actions/checkout@v3
	with:
	lfs: false
	fetch-depth: 500
	- name: Git fetch tags
	run: \|
	git config --global --add safe.directory '*'
	git fetch --tags -f
	- name: Create folder for native libs
	run: mkdir -p dist/lib
	- name: Download native shared libraries
	uses: actions/download-artifact@v3
	with:
	name: indigo-native-shared-libs
	path: dist/lib
	- name: Download Python wheels
	uses: actions/download-artifact@v3
	with:
	name: indigo-python
	path: dist/
	- name: Download bingo-elastic-python
	uses: actions/download-artifact@v3
	with:
	name: bingo-elastic-python
	path: dist/
	- name: Publish Python wheels to PyPI
	env:
	PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }}
	run: \|
	twine upload -u __token__ -p ${PYPI_TOKEN} --skip-existing dist/*.whl

	publish_indigo_to_nuget:
	if: startsWith(github.ref, 'refs/tags/indigo-')
	runs-on: ubuntu-latest
	needs: [test_indigo_python_x86_64, test_indigo_java_x86_64, test_indigo_dotnet_x86_64, test_indigo_python_i386, test_indigo_java_i386, test_indigo_dotnet_i386, test_indigo_python_aarch64, test_indigo_java_aarch64, test_bingo_elastic_python_linux_x86_64, test_bingo_elastic_java_linux_x86_64, build_indigo_ketcher]
	container: epmlsop/indigo-tester:latest
	steps:
	- name: Checkout
	uses: actions/checkout@v3
	with:
	lfs: false
	fetch-depth: 500
	- name: Git fetch tags
	run: \|
	git config --global --add safe.directory '*'
	git fetch --tags -f
	- name: Create folder for native libs
	run: mkdir -p dist/lib
	- name: Download native shared libraries
	uses: actions/download-artifact@v3
	with:
	name: indigo-native-shared-libs
	path: dist/lib
	- name: Download .NET nupkg
	uses: actions/download-artifact@v3
	with:
	name: indigo-dotnet
	path: dist/
	- name: Publish .NET nupkg to Nuget
	env:
	NUGET_API_KEY: ${{ secrets.NUGET_API_KEY }}
	run: dotnet nuget push dist/*.nupkg --api-key ${NUGET_API_KEY} --source https://api.nuget.org/v3/index.json --skip-duplicate

	publish_indigo_to_npm:
	if: startsWith(github.ref, 'refs/tags/indigo-')
	runs-on: ubuntu-latest
	needs: [test_indigo_python_x86_64, test_indigo_java_x86_64, test_indigo_dotnet_x86_64, test_indigo_python_i386, test_indigo_java_i386, test_indigo_dotnet_i386, test_indigo_python_aarch64, test_indigo_java_aarch64, test_bingo_elastic_python_linux_x86_64, test_bingo_elastic_java_linux_x86_64, build_indigo_ketcher]
	container: epmlsop/indigo-tester:latest
	steps:
	- name: Checkout
	uses: actions/checkout@v3
	with:
	lfs: false
	fetch-depth: 500
	- name: Git fetch tags
	run: \|
	git config --global --add safe.directory '*'
	git fetch --tags -f
	- name: Create folder for native libs
	run: mkdir -p dist/lib
	- name: Download native shared libraries
	uses: actions/download-artifact@v3
	with:
	name: indigo-native-shared-libs
	path: dist/lib
	- name: Download indigo-ketcher NPM package
	uses: actions/download-artifact@v3
	with:
	name: indigo-ketcher
	path: dist/
	- name: Publish indigo-ketcher to NPM
	env:
	NPM_TOKEN: ${{ secrets.NPM_TOKEN }}
	NPM_EMAIL: ${{ secrets.NPM_EMAIL }}
	run: \|
	echo //registry.npmjs.org/:_authToken=${NPM_TOKEN} >> ~/.npmrc
	echo email=${NPM_EMAIL} >> ~/.npmrc
	echo always-auth=true >> ~/.npmrc
	bash .ci/publish_npm.sh

	publish_indigo_to_maven:
	if: startsWith(github.ref, 'refs/tags/indigo-')
	runs-on: ubuntu-latest
	needs: [test_indigo_python_x86_64, test_indigo_java_x86_64, test_indigo_dotnet_x86_64, test_indigo_python_i386, test_indigo_java_i386, test_indigo_dotnet_i386, test_indigo_python_aarch64, test_indigo_java_aarch64, test_bingo_elastic_python_linux_x86_64, test_bingo_elastic_java_linux_x86_64, build_indigo_ketcher]
	container: epmlsop/indigo-tester:latest
	steps:
	- name: Checkout
	uses: actions/checkout@v3
	with:
	lfs: false
	fetch-depth: 500
	- name: Git fetch tags
	run: \|
	git config --global --add safe.directory '*'
	git fetch --tags -f
	- name: Create folder for native libs
	run: mkdir -p dist/lib
	- name: Download native shared libraries
	uses: actions/download-artifact@v3
	with:
	name: indigo-native-shared-libs
	path: dist/lib
	- name: Publish Java jars to Maven Central
	env:
	MAVEN_SETTINGS: ${{ secrets.MAVEN_SETTINGS }}
	MAVEN_USER: ${{ secrets.MAVEN_USER }}
	MAVEN_PASSWORD: ${{ secrets.MAVEN_PASSWORD }}
	GPG_PRIVATE_KEY: ${{ secrets.MK_GPG_PRIVATE_KEY }}
	GPG_PASSPHRASE: ${{ secrets.MK_GPG_PASSPHRASE }}
	run: \|
	pwd
	set -eux
	apt install -y gnupg
	mkdir /root/.m2
	echo ${MAVEN_SETTINGS} > /root/.m2/settings.xml
	echo ${GPG_PRIVATE_KEY} > gpg.key
	gpg --batch --import gpg.key
	rm gpg.key
	cd api/java
	./mvnw -q deploy -P sign-artifacts -Dossrh.user=${MAVEN_USER} -Dossrh.password=${MAVEN_PASSWORD} -Dgpg.passphrase=${GPG_PASSPHRASE}
	cd ${GITHUB_WORKSPACE}/bingo/bingo-elastic/java/
	${GITHUB_WORKSPACE}/api/java/mvnw -DskipTests -Dmaven.test.skip=true -q deploy -P sign-artifacts -Dossrh.user=${MAVEN_USER} -Dossrh.password=${MAVEN_PASSWORD} -Dgpg.passphrase=${GPG_PASSPHRASE}

	build_test_publish_indigo_service_old:
	timeout-minutes: 60
	runs-on: ubuntu-latest
	needs: build_indigo_wrappers
	steps:
	- name: Checkout
	uses: actions/checkout@v3
	with:
	lfs: false
	fetch-depth: 500
	- name: Git fetch tags
	run: \|
	git config --global --add safe.directory '*'
	git fetch --tags -f
	- name: Download wrappers
	uses: actions/download-artifact@v3
	with:
	name: indigo-python
	path: utils/indigo-service/backend/lib/
	- name: Build
	run: docker build -f ./utils/indigo-service/backend/Dockerfile -t epmlsop/indigo-service:latest ./utils/indigo-service/backend
	- name: Test Imago & Indigo
	run: \|
	docker run --rm=true -d -p 8080:80 --name=indigo_service epmlsop/indigo-service:latest
	sleep 10
	docker logs indigo_service
	docker ps
	export INDIGO_SERVICE_URL=http://localhost:8080/v2
	python3 utils/indigo-service/backend/service/tests/api/imago_test.py
	python3 utils/indigo-service/backend/service/tests/api/indigo_test.py
	docker logs indigo_service
	docker stop indigo_service
	# TODO: add indigo tests
	# - name: Test
	# run: \|
	# container_id=$(docker run --detach -it --rm -p 12345:80 epmlsop/indigo-service:latest)
	# echo ${container_id}
	# docker logs ${container_id}
	# docker ps
	# curl http://localhost:12345/v2/indigo/info
	# docker logs ${container_id}
	# docker stop ${container_id}
	- name: Login to DockerHub
	if: startsWith(github.ref, 'refs/tags/indigo-')
	uses: docker/login-action@v1
	with:
	username: ${{ secrets.DOCKERHUB_USERNAME }}
	password: ${{ secrets.DOCKERHUB_TOKEN }}
	- name: Publish release
	if: startsWith(github.ref, 'refs/tags/indigo-')
	run: \|
	export tag=${{ github.ref }}
	export clean_tag=${tag/refs\/tags\/indigo-/}
	docker tag epmlsop/indigo-service:latest epmlsop/indigo-service:${clean_tag}
	docker push epmlsop/indigo-service:${clean_tag}
	docker push epmlsop/indigo-service:latest

	build_test_publish_indigo_service_new:
	timeout-minutes: 60
	runs-on: ubuntu-latest
	needs: build_indigo_wrappers
	steps:
	- name: Checkout
	uses: actions/checkout@v3
	with:
	lfs: false
	fetch-depth: 500
	- name: Git fetch tags
	run: \|
	git config --global --add safe.directory '*'
	git fetch --tags -f
	- name: Download wrappers
	uses: actions/download-artifact@v3
	with:
	name: indigo-python
	path: api/http/
	- name: Build
	run: docker build -f ./api/http/Dockerfile -t epmlsop/indigo-service:enhanced-latest ./api/http
	- name: Login to DockerHub
	if: startsWith(github.ref, 'refs/tags/indigo-')
	uses: docker/login-action@v1
	with:
	username: ${{ secrets.DOCKERHUB_USERNAME }}
	password: ${{ secrets.DOCKERHUB_TOKEN }}
	- name: Publish release
	if: startsWith(github.ref, 'refs/tags/indigo-')
	run: \|
	export tag=${{ github.ref }}
	export clean_tag=${tag/refs\/tags\/indigo-/}
	docker tag epmlsop/indigo-service:enhanced-latest epmlsop/indigo-service:enhanced-${clean_tag}
	docker push epmlsop/indigo-service:enhanced-${clean_tag}
	docker push epmlsop/indigo-service:enhanced-latest

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