fix and work for fully contained and partial first -> integrate #5

Workflow file for this run

.github/workflows/everything.yml at 80cee71

	#######################################
	# Ideally this would be done in seperate workflows but placing them all
	# in one is currently necessary to enforce job dependencies
	#######################################

	#######################################
	# Note the use of multiple checkout actions in most jobs. This has been
	# implemented to allow the use of CI scripts at a different ref or sha than
	# the source code they're evaluating. For push events (when a pull_request is
	# merged) there is no difference. However, for pull_request events this allows
	# us test code at the head of a pull_request using the CI scripts from the
	# prospectively merged pull_request, which will include any CI updates that
	# may have made it to the target branch after the pull_request was started.
	#######################################

	#######################################
	# Note regarding restore/save of cache for use by ccache:
	#
	# We only save cache on main branch runs. PR workflows only consume the
	# cache to avoid exceeding the 10 GB limit, which can cause cache thrashing.
	# Also, we only save the cache if there was not an exact match when cache
	# was restored. This avoids attempting to write to an existing cache key,
	# which results in failure to save the cache. While failure to save doesn't
	# cause job failures, it seems a waste and is easily avoidable.
	#######################################

	name: GitHub Actions

	on:
	push:
	branches:
	- master
	- release*
	pull_request:
	branches:
	- master
	- release*

	concurrency:
	group: ${{ github.head_ref \|\| github.run_id }}
	cancel-in-progress: true

	jobs:

	#######################################
	# Git checks
	#######################################

	git_checks:
	runs-on: ubuntu-latest
	outputs:
	num_code_changes: ${{ steps.get_code_changes.outputs.num_code_changes }}
	steps:
	- uses: actions/checkout@v4
	with:
	fetch-depth: 0
	- name: Check for appropriately named topic branch
	run: \|
	scripts/ci/gh-actions/check-branch-name.sh
	- name: Check for code changes
	id: get_code_changes
	run: \|
	scripts/ci/gh-actions/get-changed-files.sh
	echo "::group::Test script output files"
	ls -la *-changed-files.txt
	NUM_CHANGES=$(wc -l < filtered-changed-files.txt)
	echo "Number of files changed (filtered): ${NUM_CHANGES}"
	echo "::set-output name=num_code_changes::${NUM_CHANGES}"

	#######################################
	# Formatting jobs
	#######################################

	format:
	needs: git_checks
	if: needs.git_checks.outputs.num_code_changes > 0

	runs-on: ubuntu-latest
	container:
	image: ghcr.io/ornladios/adios2:ci-formatting

	steps:
	- uses: actions/checkout@v4
	with:
	path: gha
	- uses: actions/checkout@v4
	with:
	ref: ${{ github.event.pull_request.head.sha }}
	path: source
	- name: CXX
	working-directory: source
	run: ../gha/scripts/ci/scripts/run-clang-format.sh
	- name: Python
	working-directory: source
	run: ../gha/scripts/ci/scripts/run-flake8.sh
	- name: Shell
	working-directory: source
	run: ../gha/scripts/ci/scripts/run-shellcheck.sh


	#######################################
	# Build and test jobs
	#######################################

	linux_ubuntu:
	needs: [format, git_checks]
	if: needs.git_checks.outputs.num_code_changes > 0

	runs-on: ubuntu-20.04
	container:
	image: ghcr.io/ornladios/adios2:ci-spack-ubuntu20.04-${{ matrix.compiler }}
	options: --shm-size=1g
	env:
	GH_YML_JOBNAME: ${{ matrix.os }}-${{ matrix.compiler }}${{ matrix.shared == 'static' && '-static' \|\| ''}}-${{ matrix.parallel }}
	GH_YML_BASE_OS: Linux
	GH_YML_MATRIX_OS: ${{ matrix.os }}
	GH_YML_MATRIX_COMPILER: ${{ matrix.compiler }}
	GH_YML_MATRIX_PARALLEL: ${{ matrix.parallel }}
	CCACHE_BASEDIR: "${GITHUB_WORKSPACE}"
	CCACHE_DIR: "${GITHUB_WORKSPACE}/.ccache"
	CCACHE_COMPRESS: true
	CCACHE_COMPRESSLEVEL: 6

	strategy:
	fail-fast: false
	matrix:
	os: [ubuntu20.04]
	compiler: [gcc8, gcc9, gcc10, gcc11, clang6, clang10]
	shared: [shared]
	parallel: [mpich]
	include:
	- os: ubuntu20.04
	compiler: gcc8
	parallel: ompi
	- os: ubuntu20.04
	compiler: gcc8
	parallel: serial
	- os: ubuntu20.04
	compiler: clang6
	parallel: ompi
	- os: ubuntu20.04
	compiler: clang6
	parallel: serial
	- os: ubuntu20.04
	compiler: gcc8
	shared: static
	parallel: ompi
	constrains: build_only
	- os: ubuntu20.04
	compiler: clang6
	shared: static
	parallel: ompi
	constrains: build_only
	- os: ubuntu20.04
	compiler: gcc8
	shared: static
	parallel: serial
	steps:
	- uses: actions/checkout@v4
	with:
	path: gha
	- uses: actions/checkout@v4
	with:
	ref: ${{ github.event.pull_request.head.sha }}
	path: source
	- name: Restore cache
	uses: actions/cache/restore@v3
	id: restore-cache
	with:
	path: .ccache
	key: ccache-${{ matrix.os }}-${{ matrix.compiler }}-${{ matrix.parallel }}-${{ github.sha }}
	restore-keys: \|
	ccache-${{ matrix.os }}-${{ matrix.compiler }}-${{ matrix.parallel }}
	- name: Configure cache
	run: ccache -z
	- name: Setup
	run: gha/scripts/ci/gh-actions/linux-setup.sh
	- name: Update
	run: gha/scripts/ci/gh-actions/run.sh update
	- name: Configure
	run: gha/scripts/ci/gh-actions/run.sh configure
	- name: Build
	run: gha/scripts/ci/gh-actions/run.sh build
	- name: Print ccache statistics
	run: ccache -s
	- name: Save cache
	uses: actions/cache/save@v3
	if: ${{ github.ref_name == 'master' && steps.restore-cache.outputs.cache-hit != 'true' }}
	id: save-cache
	with:
	path: .ccache
	key: ccache-${{ matrix.os }}-${{ matrix.compiler }}-${{ matrix.parallel }}-${{ github.sha }}
	- name: Test
	if: ${{ matrix.constrains != 'build_only' }}
	run: gha/scripts/ci/gh-actions/run.sh test

	linux_el8:
	needs: [format, git_checks]
	if: needs.git_checks.outputs.num_code_changes > 0

	runs-on: ubuntu-latest
	container:
	image: ghcr.io/ornladios/adios2:ci-el8-${{ matrix.compiler }}
	options: --shm-size=1g
	env:
	GH_YML_JOBNAME: ${{ matrix.os }}-${{ matrix.compiler }}-${{ matrix.parallel }}
	GH_YML_BASE_OS: Linux
	GH_YML_MATRIX_OS: ${{ matrix.os }}
	GH_YML_MATRIX_COMPILER: ${{ matrix.compiler }}
	GH_YML_MATRIX_PARALLEL: ${{ matrix.parallel }}
	CCACHE_BASEDIR: "${GITHUB_WORKSPACE}"
	CCACHE_DIR: "${GITHUB_WORKSPACE}/.ccache"
	CCACHE_COMPRESS: true
	CCACHE_COMPRESSLEVEL: 6

	strategy:
	fail-fast: false
	matrix:
	os: [el8]
	compiler: [icc, oneapi]
	parallel: [mpich]

	steps:
	- uses: actions/checkout@v4
	with:
	path: gha
	- uses: actions/checkout@v4
	with:
	ref: ${{ github.event.pull_request.head.sha }}
	path: source
	- name: Restore cache
	uses: actions/cache/restore@v3
	id: restore-cache
	with:
	path: .ccache
	key: ccache-${{ matrix.os }}-${{ matrix.compiler }}-${{ matrix.parallel }}-${{ github.sha }}
	restore-keys: \|
	ccache-${{ matrix.os }}-${{ matrix.compiler }}-${{ matrix.parallel }}
	- name: Configure cache
	run: ccache -z
	- name: Setup
	run: gha/scripts/ci/gh-actions/linux-setup.sh
	- name: Update
	run: gha/scripts/ci/gh-actions/run.sh update
	- name: Configure
	run: gha/scripts/ci/gh-actions/run.sh configure
	- name: Build
	run: gha/scripts/ci/gh-actions/run.sh build
	- name: Print ccache statistics
	run: ccache -s
	- name: Save cache
	uses: actions/cache/save@v3
	if: ${{ github.ref_name == 'master' && steps.restore-cache.outputs.cache-hit != 'true' }}
	id: save-cache
	with:
	path: .ccache
	key: ccache-${{ matrix.os }}-${{ matrix.compiler }}-${{ matrix.parallel }}-${{ github.sha }}
	- name: Test
	run: gha/scripts/ci/gh-actions/run.sh test

	macos:
	needs: [format, git_checks]
	if: needs.git_checks.outputs.num_code_changes > 0

	runs-on: ${{ matrix.image }}
	env:
	GH_YML_JOBNAME: ${{ matrix.os }}-${{ matrix.compiler }}-${{ matrix.parallel }}
	GH_YML_BASE_OS: macOS
	GH_YML_MATRIX_OS: ${{ matrix.os }}
	GH_YML_MATRIX_COMPILER: ${{ matrix.compiler }}
	GH_YML_MATRIX_PARALLEL: ${{ matrix.parallel }}
	CCACHE_BASEDIR: "${GITHUB_WORKSPACE}"
	CCACHE_DIR: "${GITHUB_WORKSPACE}/.ccache"
	CCACHE_COMPRESS: true
	CCACHE_COMPRESSLEVEL: 6

	strategy:
	fail-fast: false
	matrix:
	os: [macos11, macos12]
	parallel: [serial]
	include:
	- os: macos11
	image: macos-11
	compiler: xcode13_0
	- os: macos12
	image: macos-12
	compiler: xcode13_4_1

	steps:
	- uses: actions/checkout@v4
	with:
	path: gha
	- uses: actions/checkout@v4
	with:
	ref: ${{ github.event.pull_request.head.sha }}
	path: source
	- name: Setup
	run: gha/scripts/ci/gh-actions/macos-setup.sh
	- name: Restore cache
	uses: actions/cache/restore@v3
	id: restore-cache
	with:
	path: .ccache
	key: ccache-${{ matrix.os }}-${{ matrix.compiler }}-${{ matrix.parallel }}-${{ github.sha }}
	restore-keys: \|
	ccache-${{ matrix.os }}-${{ matrix.compiler }}-${{ matrix.parallel }}
	- name: Configure cache
	run: ccache -z
	- name: Update
	run: gha/scripts/ci/gh-actions/run.sh update
	- name: Configure
	run: gha/scripts/ci/gh-actions/run.sh configure
	- name: Build
	run: gha/scripts/ci/gh-actions/run.sh build
	- name: Print ccache statistics
	run: ccache -s
	- name: Save cache
	uses: actions/cache/save@v3
	if: ${{ github.ref_name == 'master' && steps.restore-cache.outputs.cache-hit != 'true' }}
	id: save-cache
	with:
	path: .ccache
	key: ccache-${{ matrix.os }}-${{ matrix.compiler }}-${{ matrix.parallel }}-${{ github.sha }}
	- name: Test
	run: gha/scripts/ci/gh-actions/run.sh test

	windows:
	needs: [format, git_checks]
	if: needs.git_checks.outputs.num_code_changes > 0

	runs-on: ${{ matrix.image }}
	env:
	GH_YML_JOBNAME: ${{ matrix.os }}-${{ matrix.compiler }}-${{ matrix.parallel }}
	GH_YML_BASE_OS: Windows
	GH_YML_MATRIX_OS: ${{ matrix.os }}
	GH_YML_MATRIX_COMPILER: ${{ matrix.compiler }}
	GH_YML_MATRIX_PARALLEL: ${{ matrix.parallel }}

	strategy:
	fail-fast: false
	matrix:
	os: [win2019, win2022]
	parallel: [serial, ompi]
	include:
	- os: win2019
	image: windows-2019
	compiler: vs2019
	- os: win2022
	image: windows-2022
	compiler: vs2022

	defaults:
	run:
	shell: bash

	steps:
	- uses: actions/checkout@v4
	with:
	path: gha
	- uses: actions/checkout@v4
	with:
	ref: ${{ github.event.pull_request.head.sha }}
	path: source
	- name: Setup
	shell: pwsh
	run: gha/scripts/ci/gh-actions/windows-setup.ps1
	- name: Update
	run: gha/scripts/ci/gh-actions/run.sh update
	- name: Configure
	run: gha/scripts/ci/gh-actions/run.sh configure
	- name: Build
	run: gha/scripts/ci/gh-actions/run.sh build
	- name: Test
	run: gha/scripts/ci/gh-actions/run.sh test

	#######################################
	# Docker container jobs
	#######################################

	docker:
	needs: [format, git_checks]
	if: needs.git_checks.outputs.num_code_changes > 0

	runs-on: ubuntu-latest
	strategy:
	fail-fast: false
	matrix:
	baseos: [ubuntu-bionic]

	steps:
	- uses: actions/checkout@v4
	with:
	ref: ${{ github.event.pull_request.head.sha }}
	path: ci-source
	- name: Re-configure docker daemon
	run: \|
	sudo systemctl stop docker
	echo $'{\n "experimental": true\n}' \| \
	sudo tee /etc/docker/daemon.json
	sudo systemctl start docker
	- name: Build image
	run: \|
	docker build \
	--rm --squash \
	-t ornladios/adios2:ci-tmp \
	--build-arg baseos=${{ matrix.baseos }} \
	--build-arg ci_source_dir=ci-source \
	-f ci-source/scripts/ci/images/spack/Dockerfile \
	.
	- name: Save image as a tar file
	run: \|
	docker save -o ci-docker.tar ornladios/adios2:ci-tmp
	ls -lah ci-docker.tar
	- name: Upload
	uses: actions/upload-artifact@v2
	with:
	retention-days: 1
	name: ci-docker ${{ matrix.baseos }} ${{ github.sha }}
	path: ci-docker.tar
	- name: Push image to Docker Hub
	if: github.event_name == 'push'
	env:
	DOCKERHUB_USERNAME: ${{ secrets.DOCKERHUB_USERNAME }}
	DOCKERHUB_PASSWORD: ${{ secrets.DOCKERHUB_PASSWORD }}
	run: \|
	target_tag="${GITHUB_REF##refs/heads/}-${{ matrix.baseos }}"
	docker tag \
	ornladios/adios2:ci-tmp \
	ornladios/adios2:${target_tag}
	docker login \
	--username="${DOCKERHUB_USERNAME}" \
	--password="${DOCKERHUB_PASSWORD}"
	docker push \
	ornladios/adios2:${target_tag}

	#######################################
	# Contract testing jobs
	#######################################

	# These contract testing jobs use the container built in the previous
	# docker job and runs it in a way similar to how a typical GitHub
	# Actions container job does. Using the "messy" default shell for
	# run steps lets the steps be written as though they too were using a
	# standard container job.
	contract:
	needs: [format, git_checks, docker]
	if: needs.git_checks.outputs.num_code_changes > 0

	runs-on: ubuntu-latest
	strategy:
	fail-fast: false
	matrix:
	code: [examples, lammps, tau]
	include:
	- code: examples
	- code: lammps
	repo: pnorbert/lammps
	ref: fix-deprecated-adios-init
	- code: tau
	defaults:
	run:
	shell: bash -c "docker exec adios2-ci bash --login -e $(echo {0} \| sed 's\|/home/runner/work\|/__w\|g')"

	steps:
	- uses: actions/checkout@v4
	if: ${{ matrix.repo != '' }}
	with:
	repository: ${{ matrix.repo }}
	ref: ${{ matrix.ref }}
	path: source
	- name: Download CI docker image
	uses: actions/download-artifact@v2
	with:
	name: ci-docker ubuntu-bionic ${{ github.sha }}
	- name: Initialize containers
	shell: bash -e {0}
	run: \|
	sudo chown 1000:1000 .
	docker load -i ci-docker.tar
	docker create \
	--name adios2-ci --workdir /__w/ADIOS2/ADIOS2 \
	-v "/home/runner/work":"/__w" \
	--entrypoint "tail" ornladios/adios2:ci-tmp \
	"-f" "/dev/null"
	docker start adios2-ci
	- name: Dependencies
	run: /opt/adios2/source/testing/contract/${{ matrix.code }}/depends.sh
	- name: Configure
	run: /opt/adios2/source/testing/contract/${{ matrix.code }}/config.sh
	- name: Build
	run: /opt/adios2/source/testing/contract/${{ matrix.code }}/build.sh
	- name: Install
	run: /opt/adios2/source/testing/contract/${{ matrix.code }}/install.sh
	- name: Test
	run: /opt/adios2/source/testing/contract/${{ matrix.code }}/test.sh

	#######################################
	# Code analysis builds
	#######################################

	analyze:
	needs: [format, git_checks]
	name: CodeQL
	runs-on: ubuntu-latest
	container:
	image: 'ghcr.io/ornladios/adios2:ci-spack-ubuntu20.04-gcc8'
	env:
	GH_YML_JOBNAME: ubuntu20.04-gcc8-serial-codeql
	GH_YML_BASE_OS: Linux
	GH_YML_MATRIX_OS: ubuntu20.04
	GH_YML_MATRIX_COMPILER: gcc8
	GH_YML_MATRIX_PARALLEL: serial
	permissions:
	actions: read
	contents: read
	security-events: write

	strategy:
	fail-fast: false
	matrix:
	language: [ 'cpp' ]

	steps:
	- uses: actions/checkout@v4
	with:
	path: gha
	- uses: actions/checkout@v4
	with:
	ref: ${{ github.event.pull_request.head.sha }}
	path: source
	- name: Initialize CodeQL
	uses: github/codeql-action/init@v2
	with:
	languages: ${{ matrix.language }}
	config: \|
	paths:
	- source
	paths-ignore:
	- source/thirdparty
	- name: Setup
	run: gha/scripts/ci/gh-actions/linux-setup.sh
	- name: Update
	run: gha/scripts/ci/gh-actions/run.sh update
	- name: Configure
	run: gha/scripts/ci/gh-actions/run.sh configure
	- name: Build
	run: gha/scripts/ci/gh-actions/run.sh build
	- name: Perform CodeQL Analysis
	uses: github/codeql-action/analyze@v2
	with:
	category: "/language:${{matrix.language}}"

	#######################################
	# Workaround for skipping matrix jobs
	#######################################

	build_and_test:
	needs: [linux_el8, linux_ubuntu, macos, docker, contract]
	runs-on: ubuntu-latest
	steps:
	- run: echo "All required jobs complete"

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fix and work for fully contained and partial first -> integrate #5

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fix and work for fully contained and partial first -> integrate #5

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