Simplify typing, remove uses of the Algorithm class #122

Workflow file for this run

	# This workflow will install Python dependencies, run tests and lint with a single version of Python
	# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python

	name: Python application

	on:
	push:
	branches:
	- master
	pull_request:
	paths-ignore:
	- 'docs/**'

	permissions:
	contents: read

	# https://stackoverflow.com/a/72408109/6388696
	# https://docs.github.com/en/actions/using-jobs/using-concurrency#example-using-concurrency-to-cancel-any-in-progress-job-or-run
	concurrency:
	group: ${{ github.workflow }}-${{ github.event.pull_request.number \|\| github.ref }}
	cancel-in-progress: true

	jobs:
	linting:
	name: Run linting/pre-commit checks
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	- uses: actions/setup-python@v4
	with:
	python-version: '3.12'
	- run: pip install pre-commit
	- run: pre-commit --version
	- run: pre-commit install
	- run: pre-commit run --all-files

	unit_tests:
	needs: [linting]
	runs-on: ${{ matrix.platform }}
	strategy:
	max-parallel: 4
	matrix:
	platform: [ubuntu-latest]
	python-version: ['3.12']
	steps:
	- uses: actions/checkout@v4
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v5
	with:
	python-version: ${{ matrix.python-version }}
	- run: pip install pdm
	- name: Install dependencies
	run: pdm install
	- name: Test with pytest (very fast)
	env:
	JAX_PLATFORMS: cpu
	run: pdm run pytest -v --shorter-than=1.0 --cov=project --cov-report=xml --cov-append
	- name: Test with pytest (fast)
	env:
	JAX_PLATFORMS: cpu
	run: pdm run pytest -v --cov=project --cov-report=xml --cov-append

	- name: Store coverage report as an artifact
	uses: actions/upload-artifact@v4
	with:
	name: coverage-reports-unit-tests-${{ matrix.platform }}-${{ matrix.python-version }}
	path: ./coverage.xml

	local_integration_tests:
	needs: [unit_tests]
	runs-on: self-hosted
	strategy:
	max-parallel: 1
	matrix:
	python-version: ['3.12']
	steps:
	- uses: actions/checkout@v4
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v5
	with:
	python-version: ${{ matrix.python-version }}
	- run: pip install pdm
	- name: Install dependencies
	run: pdm config install.cache true && pdm install

	- name: Test with pytest
	run: pdm run pytest -v --cov=project --cov-report=xml --cov-append

	# TODO: this is taking too long to run, and is failing consistently. Need to debug this before making it part of the CI again.
	# - name: Test with pytest (only slow tests)
	# run: pdm run pytest -v -m slow --slow --cov=project --cov-report=xml --cov-append

	- name: Store coverage report as an artifact
	uses: actions/upload-artifact@v4
	with:
	name: coverage-reports-integration-tests-${{ matrix.python-version }}
	path: ./coverage.xml

	launch-slurm-actions-runner:
	needs: [local_integration_tests]
	runs-on: self-hosted
	strategy:
	max-parallel: 5
	matrix:
	cluster: ['mila'] #, 'narval', 'beluga']
	outputs:
	job_id: ${{ steps.sbatch.outputs.stdout }}
	steps:
	- name: Copy job script to the cluster
	run: "scp actions-runner-job.sh ${{ matrix.cluster }}:actions-runner-job.sh"

	- name: Launch Slurm Actions Runner
	id: sbatch
	# TODO: for DRAC clusters, the account needs to be set somehow (and obviously not be hard-coded here).
	# Output the job ID to a file so that the next step can use it.
	# NOTE: Could also use the --wait flag to wait for the job to finish (and have this run at the same time as the other step).
	run: \|
	job_id=`ssh ${{ matrix.cluster }} 'cd $SCRATCH && sbatch --parsable $HOME/actions-runner-job.sh'`
	echo "Submitted job $job_id on the ${{ matrix.cluster }} cluster!"
	echo "job_id=$job_id" >> "$GITHUB_OUTPUT"

	# This step runs in a self-hosted Github Actions runner inside a SLURM job on the compute node of the cluster.
	slurm_integration_tests:
	name: Run integration tests on the ${{ matrix.cluster }} cluster in job ${{ needs.launch-slurm-actions-runner.outputs.job_id}}
	needs: [launch-slurm-actions-runner]
	runs-on: ${{ matrix.cluster }}
	strategy:
	max-parallel: 5
	matrix:
	# TODO: this should be tied to the same setting in the `launch-slurm-actions-runner` job.
	# cluster: ${{ needs.launch-slurm-actions-runner.strategy.matrix.cluster }}
	cluster: ['mila']
	steps:
	- uses: actions/checkout@v4
	- name: Set up Python 3.12
	uses: actions/setup-python@v5
	with:
	python-version: 3.12
	- run: pip install pdm
	- name: Install dependencies
	run: pdm install

	- name: Test with pytest
	run: pdm run pytest -v --cov=project --cov-report=xml --cov-append

	# TODO: Re-enable this later
	# - name: Test with pytest (only slow tests)
	# run: pdm run pytest -v -m slow --slow --cov=project --cov-report=xml --cov-append

	- name: Store coverage report as an artifact
	uses: actions/upload-artifact@v4
	with:
	name: coverage-reports-slurm-integration-tests-${{ matrix.cluster }}
	path: ./coverage.xml

	# https://about.codecov.io/blog/uploading-code-coverage-in-a-separate-job-on-github-actions/
	upload-coverage-codecov:
	needs: [local_integration_tests, slurm_integration_tests]
	runs-on: ubuntu-latest
	name: Upload coverage reports to Codecov
	steps:
	- name: Checkout
	uses: actions/checkout@v4
	- name: Download artifacts
	uses: actions/download-artifact@v4
	with:
	pattern: coverage-reports-*
	merge-multiple: false
	# download all the artifacts in this directory (each .coverage.xml will be in a subdirectory)
	# Next step if this doesn't work would be to give the coverage files a unique name and use merge-multiple: true
	path: coverage_reports
	- name: Upload coverage reports to Codecov
	uses: codecov/codecov-action@v4
	with:
	token: ${{ secrets.CODECOV_TOKEN }}
	directory: coverage_reports
	fail_ci_if_error: true

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Simplify typing, remove uses of the Algorithm class #122

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Simplify typing, remove uses of the Algorithm class #122

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Workflow file for this run