Fix apptainer call in GaudiExec #1817

Workflow file for this run

.github/workflows/ci_push_testing.yml at 972720f

	name: CI Push Testing

	on:
	pull_request_target:
	branches: [ develop ]

	jobs:
	approve:
	name: Approval
	if: ${{github.event.pull_request.head.repo.full_name != 'ganga-devs/ganga'}}
	runs-on: ubuntu-latest
	environment:
	name: Integrate Pull Request
	steps:
	- name: Approve
	run: echo For security reasons, all pull requests need to be approved first before running any automated CI.

	lint:
	name: Linting
	runs-on: ubuntu-latest
	needs: [approve]
	if: always() && !failure() && !cancelled()
	continue-on-error: true
	outputs:
	files_to_lint: ${{ steps.flake8.outputs.files_to_lint }}
	steps:
	- uses: actions/checkout@v2
	with:
	ref: ${{ github.event.pull_request.head.sha }}
	fetch-depth: 0
	- name: Set up Python 3.11
	uses: actions/setup-python@v1
	with:
	python-version: 3.11

	- name: Get changed files
	id: changed-files
	uses: tj-actions/[email protected]
	with:
	base_sha: ${{ github.event.pull_request.head.sha }}

	- name: Install dependencies
	run: \|
	python3 -m pip install --upgrade pip setuptools wheel
	python3 -m pip install flake8
	- name: Setup flake8 annotations
	if: startsWith(github.head_ref, 'autopep8-patches')
	uses: rbialon/flake8-annotations@v1

	- name: Lint with flake8
	id: flake8
	run: \|
	files_to_lint=""
	count=0
	for file in ${{ steps.changed-files.outputs.all_changed_files }}; do
	if [[ $file == *.py ]]; then
	linting_output=`flake8 --count --exit-zero $file`
	count=`echo "$linting_output" \| tail -1`
	if [[ $count > 0 ]]; then
	files_to_lint="$files_to_lint $file"
	echo "$linting_output"
	fi
	fi
	done
	echo "files_to_lint=$files_to_lint" >> $GITHUB_OUTPUT
	- name: Fail on linting violations
	if: steps.flake8.outputs.files_to_lint != ''
	run: exit 1

	autofix_pr:
	name: Create autopep8 PR
	if: always() && !failure() && !cancelled() && startsWith(github.head_ref, 'autopep8-patches') == false && needs.lint.outputs.files_to_lint != ''
	runs-on: ubuntu-latest
	needs: lint
	steps:
	- uses: actions/checkout@v3
	with:
	ref: ${{ github.event.pull_request.head.sha }}

	- name: Run autopep8
	id: autopep8
	uses: peter-evans/[email protected]
	with:
	args: --exit-code --recursive --in-place --aggressive --aggressive ${{ needs.lint.outputs.files_to_lint }}

	- name: Set autopep8 branch name
	id: vars
	run: \|
	echo "branch-name=autopep8-patches/${{ github.head_ref }}" >> $GITHUB_OUTPUT
	PR_NUMBER=`echo ${{ github.event.pull_request.number }} \| cut -f 1 -d '/'`
	echo "pr-number=$PR_NUMBER" >> $GITHUB_OUTPUT
	- name: Create Pull Request
	if: steps.autopep8.outputs.exit-code == 2
	uses: peter-evans/[email protected]
	with:
	commit-message: autopep8 action fixes
	title: "PEP8 fixes for PR #${{ github.event.pull_request.number }} (${{ github.head_ref }}) by autopep8"
	body: This is an auto-generated PR with fixes by autopep8 for the ${{ github.head_ref }} branch.
	labels: autopep8, automated pr
	branch: "autopep8-patches/${{ github.head_ref }}"
	base: ${{ github.base_ref }}
	token: ${{ secrets.WORKFLOW }}

	core-unit:
	name: GangaCore Unit
	needs: lint
	if: always() && !failure() && !cancelled()
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v2
	with:
	ref: ${{ github.event.pull_request.head.sha }}
	fetch-depth: 0
	- name: Set up Python 3.11
	uses: actions/setup-python@v1
	with:
	python-version: 3.11
	- name: Install dependencies
	run: \|
	python -m venv ~/venv
	. ~/venv/bin/activate
	python -m pip install --upgrade pip setuptools wheel
	python -m pip install -e .[dev]
	- name: Test with pytest
	run: \|
	. ~/venv/bin/activate
	python -m pytest --cov-report term-missing --cov ganga/GangaCore/Core --cov ganga/GangaCore/GPI --cov ganga/GangaCore/GPIDev --cov ganga/GangaCore/Lib --cov ganga/GangaCore/Runtime --cov ganga/GangaCore/PACKAGE.py --cov ganga/GangaCore/Utility --cov ganga/GangaCore/__init__.py ganga/GangaCore/test/Unit

	core-integration:
	name: GangaCore Integration
	needs: core-unit
	if: always() && !failure() && !cancelled()
	runs-on: ubuntu-latest

	steps:
	- uses: actions/checkout@v2
	with:
	ref: ${{ github.event.pull_request.head.sha }}
	fetch-depth: 0
	- name: Set up Python 3.11
	uses: actions/setup-python@v1
	with:
	python-version: 3.11
	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip setuptools wheel
	python -m pip install -e .[dev]
	- name: Test with pytest
	run: python -m pytest --cov-report term-missing --cov ganga/GangaCore/Core --cov ganga/GangaCore/GPI --cov ganga/GangaCore/GPIDev --cov ganga/GangaCore/Lib --cov ganga/GangaCore/Runtime --cov ganga/GangaCore/PACKAGE.py --cov ganga/GangaCore/Utility --cov ganga/GangaCore/__init__.py ganga/GangaCore/test/GPI

	condor:
	name: Condor
	needs: lint
	if: always() && !failure() && !cancelled()
	runs-on: ubuntu-latest
	container: htcondor/mini
	steps:
	- uses: actions/checkout@v2
	with:
	ref: ${{ github.event.pull_request.head.sha }}
	- name: Set up Python 3
	run: \|
	dnf install -y python3.11 python3.11-pip
	/usr/bin/python3.11 -m venv venv
	source venv/bin/activate
	python -m pip install --upgrade pip setuptools wheel pytest
	- name: Install source
	run: \|
	source venv/bin/activate
	python -m pip install -e .[dev]
	- name: Start Condor
	run: \|
	/start.sh > start.stdout &
	sleep 30
	condor_status
	- name: Test with pytest
	run: \|
	source venv/bin/activate
	pwd
	find . -exec chown submituser:submituser {} \;
	su submituser -s $(pwd)/venv/bin/python -- -m pytest --cov-report term-missing --cov ganga/GangaCore/Lib/Condor ganga/GangaCore/test/Condor
	condor_status
	condor_q

	dirac-unit:
	name: GangaDirac Unit
	needs: lint
	if: always() && !failure() && !cancelled()
	runs-on: ubuntu-latest
	container: almalinux:9
	steps:
	- uses: actions/checkout@v2
	with:
	ref: ${{ github.event.pull_request.head.sha }}
	- name: Set up
	run: \|
	dnf install -y gcc which
	- name: Install Robot certificate
	env: # Or as an environment variable
	ROBOT_CERT: ${{ secrets.GangaRobot_UserCert }}
	ROBOT_KEY: ${{ secrets.GangaRobot_UserKey }}
	run: \|
	mkdir ~/.globus
	echo "$ROBOT_CERT" > ~/.globus/usercert.pem
	echo "$ROBOT_KEY" > ~/.globus/userkey.pem
	chmod 644 ~/.globus/usercert.pem
	chmod 400 ~/.globus/userkey.pem
	- name: Install DIRAC UI
	run: \|
	curl -LO https://github.com/DIRACGrid/DIRACOS2/releases/latest/download/DIRACOS-Linux-$(uname -m).sh
	bash DIRACOS-Linux-$(uname -m).sh
	source diracos/diracosrc
	python -m pip install DIRAC
	mkdir ~/.proxy
	DIRAC_PROXY_INIT=`which dirac-proxy-init`
	export PATH=~/.proxy:"$PATH"
	printf '#!/bin/sh\necho abcd \| '"$DIRAC_PROXY_INIT"' -p $@ \n' > ~/.proxy/dirac-proxy-init
	chmod +x ~/.proxy/dirac-proxy-init
	dirac-proxy-init -x
	dirac-configure -F -S GridPP -C dips://dirac01.grid.hep.ph.ic.ac.uk:9135/Configuration/Server -I
	dirac-proxy-init -g gridpp_user -M
	- name: Install dependencies
	run: \|
	source diracos/diracosrc
	python -m pip install --upgrade pip setuptools wheel
	python -m pip install -e .[dev,Dirac]
	- name: Test with pytest
	run: \|
	source diracos/diracosrc
	export PATH=~/.proxy:"$PATH"
	python -m pytest --cov-report term-missing --cov ganga/GangaDirac ganga/GangaDirac/test/Unit

	dirac-integration:
	name: GangaDirac Integration
	needs: dirac-unit
	if: always() && !failure() && !cancelled()
	runs-on: ubuntu-latest
	container: almalinux:9
	steps:
	- uses: actions/checkout@v2
	with:
	ref: ${{ github.event.pull_request.head.sha }}
	- name: Set up
	run: \|
	dnf install -y gcc which
	- name: Install Robot certificate
	env: # Or as an environment variable
	ROBOT_CERT: ${{ secrets.GangaRobot_UserCert }}
	ROBOT_KEY: ${{ secrets.GangaRobot_UserKey }}
	run: \|
	mkdir ~/.globus
	echo "$ROBOT_CERT" > ~/.globus/usercert.pem
	echo "$ROBOT_KEY" > ~/.globus/userkey.pem
	chmod 644 ~/.globus/usercert.pem
	chmod 400 ~/.globus/userkey.pem
	- name: Install DIRAC UI
	run: \|
	curl -LO https://github.com/DIRACGrid/DIRACOS2/releases/latest/download/DIRACOS-Linux-$(uname -m).sh
	bash DIRACOS-Linux-$(uname -m).sh
	source diracos/diracosrc
	python -m pip install DIRAC
	mkdir ~/.proxy
	DIRAC_PROXY_INIT=`which dirac-proxy-init`
	export PATH=~/.proxy:"$PATH"
	printf '#!/bin/sh\necho abcd \| '"$DIRAC_PROXY_INIT"' -p $@ \n' > ~/.proxy/dirac-proxy-init
	chmod +x ~/.proxy/dirac-proxy-init
	dirac-proxy-init -x
	dirac-configure -F -S GridPP -C dips://dirac01.grid.hep.ph.ic.ac.uk:9135/Configuration/Server -I
	dirac-proxy-init -g gridpp_user -M
	- name: Install gangarc file
	run: \|
	echo -e "[DIRAC]\nDiracEnvSource = ~/diracos/diracosrc" > ~/.gangarc
	echo -e "[Configuration]\nRUNTIME_PATH=GangaDirac" >> ~/.gangarc
	echo -e "[defaults_DiracProxy]\ngroup=gridpp_user\nencodeDefaultProxyFileName=False" >> ~/.gangarc
	- name: Install dependencies
	run: \|
	source diracos/diracosrc
	python -m pip install --upgrade pip setuptools wheel
	python -m pip install -e .[dev,Dirac]
	- name: Test with pytest
	env:
	GANGA_CONFIG_FILE: ~/.gangarc
	GANGA_CONFIG_PATH: GangaDirac/Dirac.ini
	DIRAC_DEPRECATED_FAIL: True
	run: \|
	source diracos/diracosrc
	export PATH=~/.proxy:"$PATH"
	python -m pytest --cov-report term-missing --cov ganga/GangaDirac ganga/GangaDirac/test/GPI

	lhcb-unit:
	name: GangaLHCb Unit
	needs: lint
	if: always() && !failure() && !cancelled()
	runs-on: ubuntu-latest
	container:
	image: centos:7
	options: --privileged
	steps:
	- name: Install CVM-FS
	run: \|
	yum install -y https://ecsft.cern.ch/dist/cvmfs/cvmfs-release/cvmfs-release-latest.noarch.rpm
	yum install -y cvmfs cvmfs-config-default
	cvmfs_config setup
	echo "CVMFS_REPOSITORIES=lhcb.cern.ch,sft.cern.ch" > /etc/cvmfs/default.local
	echo "CVMFS_HTTP_PROXY=DIRECT" >> /etc/cvmfs/default.local
	mkdir -p /cvmfs/lhcb.cern.ch
	mkdir -p /cvmfs/sft.cern.ch
	mount -t cvmfs lhcb.cern.ch /cvmfs/lhcb.cern.ch
	mount -t cvmfs sft.cern.ch /cvmfs/sft.cern.ch
	- uses: actions/checkout@v2
	with:
	ref: ${{ github.event.pull_request.head.sha }}
	- name: Install virtualenv and dependencies
	run: \|
	/cvmfs/sft.cern.ch/lcg/releases/LCG_100/Python/3.8.6/x86_64-centos7-gcc9-opt/bin/python3 -m venv ~/venv
	. ~/venv/bin/activate
	yum install -y glibc-devel
	export CC=/cvmfs/sft.cern.ch/lcg/releases/gcc/7.3.0/x86_64-centos7/bin/gcc
	python3 -m pip install --upgrade pip setuptools wheel
	python3 -m pip install -e .[dev,LHCb,Dirac]
	- name: Test with pytest
	run: \|
	. ~/venv/bin/activate
	python3 -m pytest --cov-report term-missing --cov ganga/GangaLHCb ganga/GangaLHCb/test/Unit

	lhcb-integration:
	name: GangaLHCb Integration
	needs: lhcb-unit
	if: always() && !failure() && !cancelled()
	runs-on: ubuntu-latest
	container:
	image: centos:7
	options: --privileged
	steps:
	- name: Install git
	run: yum install -y git
	- name: Install CVM-FS
	run: \|
	yum install -y https://ecsft.cern.ch/dist/cvmfs/cvmfs-release/cvmfs-release-latest.noarch.rpm
	yum install -y cvmfs cvmfs-config-default
	cvmfs_config setup
	echo "CVMFS_REPOSITORIES=lhcb.cern.ch,sft.cern.ch" > /etc/cvmfs/default.local
	echo "CVMFS_HTTP_PROXY=DIRECT" >> /etc/cvmfs/default.local
	mkdir -p /cvmfs/lhcb.cern.ch
	mkdir -p /cvmfs/sft.cern.ch
	mount -t cvmfs lhcb.cern.ch /cvmfs/lhcb.cern.ch
	mount -t cvmfs sft.cern.ch /cvmfs/sft.cern.ch
	- name: Install Robot certificate
	env: # Or as an environment variable
	ROBOT_CERT: ${{ secrets.GangaRobot_UserCert }}
	ROBOT_KEY: ${{ secrets.GangaRobot_UserKey }}
	run: \|
	mkdir ~/.globus
	echo "$ROBOT_CERT" > ~/.globus/usercert.pem
	echo "$ROBOT_KEY" > ~/.globus/userkey.pem
	chmod 644 ~/.globus/usercert.pem
	chmod 400 ~/.globus/userkey.pem
	- uses: actions/checkout@v2
	with:
	ref: ${{ github.event.pull_request.head.sha }}
	- name: Install virtualenv and dependencies
	run: \|
	/cvmfs/sft.cern.ch/lcg/releases/LCG_100/Python/3.8.6/x86_64-centos7-gcc9-opt/bin/python3 -m venv ~/venv
	. ~/venv/bin/activate
	yum install -y glibc-devel
	export CC=/cvmfs/sft.cern.ch/lcg/releases/gcc/7.3.0/x86_64-centos7/bin/gcc
	python3 -m pip install --upgrade pip setuptools wheel
	python3 -m pip install -e .[dev,LHCb,Dirac]
	- name: Install gangarc file
	run: \|
	echo -e "[Configuration]\nRUNTIME_PATH=GangaDirac:GangaGaudi:GangaLHCb" > ~/.gangarc
	- name: Test with pytest
	env:
	GANGA_CONFIG_PATH: GangaLHCb/LHCb.ini
	GANGA_CONFIG_FILE: ~/.gangarc
	run: \|
	source /cvmfs/lhcb.cern.ch/lib/LbEnv 2>&1
	echo abcd \| lhcb-proxy-init -p
	. ~/venv/bin/activate
	python3 -m pytest --cov-report term-missing --cov ganga/GangaLHCb ganga/GangaLHCb/test/GPI

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Fix apptainer call in GaudiExec #1817

Workflow file

Fix apptainer call in GaudiExec #1817

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Workflow file for this run