Add L-H threshold comparison plot and improve bootstrap comparison la… #2419

Workflow file for this run

.github/workflows/process.yml at c9564c5

	---
	name: PROCESS main/develop testing

	on:
	pull_request:
	push:

	permissions:
	contents: read
	pages: write
	id-token: write

	jobs:
	make:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v3
	- uses: actions/setup-python@v4
	with:
	python-version: '3.10'
	- name: Build PROCESS
	run: \|
	git config --global --add safe.directory '*'
	cmake -S. -Bbuild
	cmake --build build
	- name: Archive build artifacts in process
	uses: actions/upload-artifact@v3
	with:
	name: process-build-artifacts
	path: \|
	process/*/.so
	process/io/python_fortran_dicts.json
	- name: Archive coverage data
	uses: actions/upload-artifact@v3
	with:
	name: coverage-artifacts
	path: \|
	build/CMakeFiles/process.dir/source/fortran/*.gcno
	lcov_results
	- name: Archive ford artifacts
	uses: actions/upload-artifact@v3
	with:
	name: ford-artifact
	path: build/ford_project.pickle

	unit-test:
	runs-on: ubuntu-latest
	needs: make
	steps:
	- uses: actions/checkout@v3
	- uses: actions/setup-python@v4
	with:
	python-version: '3.10'
	- name: Download build artifacts
	uses: actions/download-artifact@v3
	with:
	name: process-build-artifacts
	path: process/
	- name: Install PROCESS
	# Editable install to match default install
	run: \|
	pip install -e '.[test, examples]'
	pip install -r requirements_dev.txt
	- name: Run unit tests
	run: \|
	pytest --cov=process tests/unit -v \
	--cov-report xml
	- name: Archive unit test coverage data
	uses: actions/upload-artifact@v3
	with:
	name: unit-coverage-artifacts
	path: .coverage
	- name: Upload coverage to Codecov
	uses: codecov/codecov-action@v4
	env:
	CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
	with:
	fail_ci_if_error: ${{ github.ref_name == 'main' }}

	integration-test:
	runs-on: ubuntu-latest
	needs: make
	steps:
	- uses: actions/checkout@v3
	- uses: actions/setup-python@v4
	with:
	python-version: '3.10'
	- name: Download build artifacts
	uses: actions/download-artifact@v3
	with:
	name: process-build-artifacts
	path: process/
	- name: Install PROCESS
	# Editable install to match default install
	run: \|
	pip install -e '.[test, examples]'
	pip install -r requirements_dev.txt
	- name: Install poppler
	run: \|
	sudo apt update
	sudo apt install poppler-utils
	- name: Run integration tests
	run: pytest tests/integration -n auto -v


	regression-test:
	runs-on: ubuntu-latest
	needs: [make, tracking]
	# depend on make and tracking job, check make job was successful
	# but dont skip if tracking was skipped
	if: always() && needs.make.result == 'success'
	continue-on-error: true
	strategy:
	matrix:
	tolerance: [0, 5]
	steps:
	- uses: actions/checkout@v3
	with:
	fetch-depth: 0
	- uses: actions/setup-python@v4
	with:
	python-version: '3.10'
	- name: Download build artifacts
	uses: actions/download-artifact@v3
	with:
	name: process-build-artifacts
	path: process/
	- name: Install PROCESS
	# Editable install to match default install
	run: \|
	pip install -e '.[test, examples]'
	pip install -r requirements_dev.txt
	- name: Allow git commands to be run
	run: git config --global --add safe.directory '*'
	- name: Run regression tests
	run: pytest tests/regression -sv --reg-tolerance=${{ matrix.tolerance }}

	run-tracking-inputs:
	runs-on: ubuntu-latest
	needs: make
	if: github.ref == 'refs/heads/main'
	steps:
	- uses: actions/checkout@v3
	- name: Download build artifacts
	uses: actions/download-artifact@v3
	with:
	name: process-build-artifacts
	path: process/
	- name: Install PROCESS
	run: pip install -e .
	- name: Install dev dependencies
	run: pip install -r requirements_dev.txt
	- name: Run regression input files
	run: python tracking/run_tracking_inputs.py run tests/regression/input_files
	- name: Archive tracked MFILEs
	uses: actions/upload-artifact@v3
	with:
	name: tracked-mfiles
	path: tracking/*_MFILE.DAT

	pre-commit-quality-check:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v3
	- uses: actions/setup-python@v4
	with:
	python-version: '3.10'
	- name: Install dev dependencies
	run: pip install -r requirements_dev.txt
	- name: Run pre-commit
	run: pre-commit run --all-files

	tracking:
	concurrency:
	group: tracking-jobs
	cancel-in-progress: false
	runs-on: ubuntu-latest
	needs: run-tracking-inputs
	if: github.ref == 'refs/heads/main'
	env:
	COMMIT_MESSAGE: ${{ github.event.head_commit.message }}
	steps:
	- uses: actions/checkout@v3
	- name: Download build artifacts
	uses: actions/download-artifact@v3
	with:
	name: process-build-artifacts
	path: process/
	- name: Install PROCESS
	run: pip install -e .
	- name: Install dev dependencies
	run: pip install -r requirements_dev.txt
	- name: Setup SSH identity
	uses: webfactory/[email protected]
	with:
	ssh-private-key: ${{ secrets.SSH_PRIVATE_KEY }}
	- name: Download tracking data
	run: git clone [email protected]:timothy-nunn/process-tracking-data.git process-tracking-data
	- name: Download large tokamak MFILE
	uses: actions/download-artifact@v3
	with:
	name: tracked-mfiles
	path: tracking/
	- name: Create new tracking entries
	shell: bash
	run: \|
	MSG=$(printf "%q " $COMMIT_MESSAGE)
	git config --global --add safe.directory '*'
	python tracking/run_tracking_inputs.py track process-tracking-data "${MSG}" ${{ github.sha }}
	- name: Create the tracking dashboard
	run: python tracking/tracking_data.py plot process-tracking-data --out tracking.html
	- name: Archive tracking dashboard
	uses: actions/upload-artifact@v3
	with:
	name: tracking-html
	path: tracking.html
	- name: Setup Git identity
	run: \|
	git config --global user.email "${{ github.triggering_actor }}@github.runner"
	git config --global user.name "${{ github.job }}"
	- name: Commit and push tracking data
	run: \|
	cd process-tracking-data
	git add .
	git commit -m "${{ github.run_id }}-${{ github.run_number }}-${{ github.run_attempt }}"
	git push

	docs:
	concurrency:
	group: docs-jobs
	cancel-in-progress: false
	runs-on: ubuntu-latest
	needs: tracking
	if: github.ref == 'refs/heads/main'
	steps:
	- uses: actions/checkout@v3
	with:
	fetch-depth: 0
	- name: Download build artifacts
	uses: actions/download-artifact@v3
	with:
	name: process-build-artifacts
	path: process/
	- name: Install PROCESS
	run: pip install -e .
	- name: Install dev dependencies
	run: pip install -r requirements_dev.txt
	- name: Install ford
	run: pip install git+https://github.com/jonmaddock/ford
	- run: ford documentation/ford/index.md
	- name: Download ford project
	uses: actions/download-artifact@v3
	with:
	name: ford-artifact
	path: build/
	- run: python scripts/document_fortran_interface.py
	- run: python scripts/vardes.py
	- run: git config --global --add safe.directory '*'
	- run: mkdocs build
	- run: mv ford_site site
	- name: Download tracking html
	uses: actions/download-artifact@v3
	with:
	name: tracking-html
	- run: mv tracking.html site \|\| cp site/404.html site/tracking.html
	- name: Upload documentation page
	uses: actions/upload-pages-artifact@v1
	with:
	path: site/
	- name: Deploy GitHub pages
	id: deployment
	uses: actions/deploy-pages@v2

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Add L-H threshold comparison plot and improve bootstrap comparison la… #2419

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Add L-H threshold comparison plot and improve bootstrap comparison la… #2419

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