Add Pydantic models for configuration validation #294

Workflow file for this run

.github/workflows/pipeline.yml at 143d18b

	name: Pipeline

	on:
	push:
	branches: [ main ]
	pull_request:

	jobs:
	black:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	- uses: psf/black@stable
	with:
	options: "--check --diff"
	src: ./src/${{ github.event.repository.name }}

	black_fix: # in most cases pre-commit is faster
	needs: [black]
	if: failure()
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	with:
	token: ${{ secrets.DEPENDABOT_WORKFLOW_TOKEN }}
	ref: ${{ github.event.pull_request.head.ref }} # Check out the head of the actual branch, not the PR
	fetch-depth: 0 # otherwise, you will fail to push refs to dest repo
	- name: format black
	uses: psf/black@stable
	with:
	options: ""
	src: "./src/${{ github.event.repository.name }}"
	- name: commit
	run: \|
	git config --local user.email "[email protected]"
	git config --local user.name "pyiron-runner"
	git commit -m "Format black" -a
	- name: push
	uses: ad-m/github-push-action@master
	with:
	github_token: ${{ secrets.DEPENDABOT_WORKFLOW_TOKEN }}
	branch: ${{ github.event.pull_request.head.ref }}

	mypy:
	needs: [black]
	runs-on: ubuntu-latest
	steps:
	- name: Setup Python
	uses: actions/setup-python@v5
	with:
	python-version: "3.14"
	architecture: x64
	- name: Checkout
	uses: actions/checkout@v4
	- name: Test
	run: \|
	pip install mypy types-PyYAML types-paramiko
	mypy --ignore-missing-imports src/${{ github.event.repository.name }}

	coverage:
	needs: [black]
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	- name: Setup environment
	run: \|
	cp .ci_support/environment.yml environment.yml
	echo "- flux-core =0.81.0" >> environment.yml
	echo -e "channels:\n - conda-forge\n" > .condarc
	mkdir -p /home/runner/.ssh
	echo "test.rebex.net,195.144.107.198 ecdsa-sha2-nistp256 AAAAE2VjZHNhLXNoYTItbmlzdHAyNTYAAAAIbmlzdHAyNTYAAABBBLZcZopPvkxYERubWeSrWOSHpxJdR14WFVES/Q3hFguTn6L+0EANqYcbRXhGBUV6SjR7SaxZACXSxOzgCtG4kwc=" > /home/runner/.ssh/known_hosts
	- name: Setup Mambaforge
	uses: conda-incubator/setup-miniconda@v3
	with:
	python-version: '3.13'
	miniforge-version: latest
	condarc-file: .condarc
	environment-file: environment.yml
	- name: Install
	shell: bash -l {0}
	run: pip install . --no-deps --no-build-isolation
	- name: Test
	shell: bash -l {0}
	run: >
	flux start
	coverage run
	- name: Collect Coverage
	shell: bash -l {0}
	run: coverage xml
	- name: Upload coverage reports to Codecov
	uses: codecov/codecov-action@v5
	with:
	token: ${{ secrets.CODECOV_TOKEN }}

	minimal:
	needs: [black]
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	- name: Setup environment
	run: \|
	cp .ci_support/environment.yml environment.yml
	sed -i '/defusedxml/d' environment.yml
	sed -i '/paramiko/d' environment.yml
	sed -i '/tqdm/d' environment.yml
	echo -e "channels:\n - conda-forge\n" > .condarc
	- name: Setup Mambaforge
	uses: conda-incubator/setup-miniconda@v3
	with:
	python-version: '3.14'
	miniforge-version: latest
	condarc-file: .condarc
	environment-file: environment.yml
	- name: Test
	shell: bash -l {0}
	run: \|
	pip install . --no-deps --no-build-isolation
	python -m unittest discover tests

	notebooks:
	needs: [black]
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	- name: Merge Notebook environment
	run: \|
	cp binder/environment.yml environment.yml
	tail --lines=+4 .ci_support/environment-notebooks.yml >> environment.yml
	echo -e "channels:\n - conda-forge\n" > .condarc
	- name: Setup Mambaforge
	uses: conda-incubator/setup-miniconda@v3
	with:
	python-version: "3.13"
	miniforge-version: latest
	condarc-file: .condarc
	environment-file: environment.yml
	- name: Install
	shell: bash -l {0}
	run: \|
	pip install . --no-deps --no-build-isolation
	mkdir config
	cp -r tests/static/flux config
	- name: Notebooks with config
	shell: bash -l {0}
	run: >
	flux start
	papermill notebooks/example_config.ipynb example-config-out.ipynb -k "python3"
	- name: Notebooks dynamic
	shell: bash -l {0}
	run: >
	flux start
	papermill notebooks/example_queue_type.ipynb example-queue-type-out.ipynb -k "python3"

	pip_check:
	needs: [black]
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	- name: Conda config
	run: echo -e "channels:\n - conda-forge\n" > .condarc
	- name: Setup Mambaforge
	uses: conda-incubator/setup-miniconda@v3
	with:
	python-version: '3.14'
	miniforge-version: latest
	condarc-file: .condarc
	environment-file: .ci_support/environment.yml
	- name: Pip check
	shell: bash -l {0}
	run: \|
	pip install tomlkit
	python .ci_support/check.py
	cat pyproject.toml
	pip install . --no-deps --no-build-isolation
	pip check

	uv_check:
	needs: [black]
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	- uses: astral-sh/setup-uv@v7
	- name: Install the project and pip check
	shell: bash -l {0}
	run: \|
	uv sync --all-extras --dev
	pip check

	unittest_matrix:
	needs: [black]
	runs-on: ${{ matrix.operating-system }}
	strategy:
	matrix:
	include:
	- operating-system: macos-latest
	python-version: '3.14'

	- operating-system: windows-latest
	python-version: '3.14'

	- operating-system: ubuntu-24.04-arm
	python-version: '3.14'

	- operating-system: ubuntu-22.04-arm
	python-version: '3.14'

	- operating-system: ubuntu-latest
	python-version: '3.14'

	- operating-system: ubuntu-latest
	python-version: '3.13'

	- operating-system: ubuntu-latest
	python-version: '3.12'

	- operating-system: ubuntu-latest
	python-version: '3.11'

	steps:
	- uses: actions/checkout@v4
	- name: Conda config
	shell: bash -l {0}
	run: echo -e "channels:\n - conda-forge\n" > .condarc
	- name: Setup Mambaforge
	uses: conda-incubator/setup-miniconda@v3
	with:
	python-version: ${{ matrix.python-version }}
	miniforge-version: latest
	condarc-file: .condarc
	environment-file: .ci_support/environment.yml
	- name: Test
	shell: bash -l {0}
	run: \|
	mkdir -p ~/.ssh
	echo "test.rebex.net,195.144.107.198 ecdsa-sha2-nistp256 AAAAE2VjZHNhLXNoYTItbmlzdHAyNTYAAAAIbmlzdHAyNTYAAABBBLZcZopPvkxYERubWeSrWOSHpxJdR14WFVES/Q3hFguTn6L+0EANqYcbRXhGBUV6SjR7SaxZACXSxOzgCtG4kwc=" > ~/.ssh/known_hosts
	pip install . --no-deps --no-build-isolation
	python -m unittest discover tests

	unittest_old:
	needs: [black]
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	- name: Conda config
	run: echo -e "channels:\n - conda-forge\n" > .condarc
	- name: Setup Mambaforge
	uses: conda-incubator/setup-miniconda@v3
	with:
	python-version: '3.9'
	miniforge-version: latest
	condarc-file: .condarc
	environment-file: .ci_support/environment-old.yml
	- name: Test
	shell: bash -l {0}
	run: \|
	mkdir -p ~/.ssh
	echo "test.rebex.net,195.144.107.198 ecdsa-sha2-nistp256 AAAAE2VjZHNhLXNoYTItbmlzdHAyNTYAAAAIbmlzdHAyNTYAAABBBLZcZopPvkxYERubWeSrWOSHpxJdR14WFVES/Q3hFguTn6L+0EANqYcbRXhGBUV6SjR7SaxZACXSxOzgCtG4kwc=" > ~/.ssh/known_hosts
	pip install . --no-deps --no-build-isolation
	python -m unittest discover tests

	unittest_slurm:
	needs: [black]
	runs-on: ubuntu-latest
	services:
	mysql:
	image: mysql:8.0
	env:
	MYSQL_ROOT_PASSWORD: root
	ports:
	- "8888:3306"
	options: --health-cmd="mysqladmin ping" --health-interval=10s --health-timeout=5s --health-retries=3
	steps:
	- uses: actions/checkout@v4
	- uses: koesterlab/setup-slurm-action@v1
	timeout-minutes: 5
	- name: Conda config
	run: echo -e "channels:\n - conda-forge\n" > .condarc
	- uses: conda-incubator/setup-miniconda@v3
	with:
	python-version: "3.13"
	miniforge-version: latest
	condarc-file: .condarc
	environment-file: .ci_support/environment.yml
	- name: Test
	shell: bash -l {0}
	timeout-minutes: 5
	run: \|
	pip install . --no-deps --no-build-isolation
	cd tests
	sinfo -o "%n %e %m %a %c %C"
	srun --mpi=list
	python -m unittest integration/test_slurm_integration.py

	unittest_flux:
	needs: [black]
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	- name: Conda config
	run: \|
	echo -e "channels:\n - conda-forge\n" > .condarc
	echo "- flux-core=0.81.0" >> .ci_support/environment.yml
	- uses: conda-incubator/setup-miniconda@v3
	with:
	python-version: "3.13"
	miniforge-version: latest
	condarc-file: .condarc
	environment-file: .ci_support/environment.yml
	- name: Test
	shell: bash -l {0}
	timeout-minutes: 5
	run: \|
	pip install . --no-deps --no-build-isolation
	cd tests
	flux start python -m unittest integration/test_flux_integration.py

	autobot:
	needs: [uv_check, unittest_old, unittest_matrix, pip_check, notebooks, minimal, coverage]
	permissions:
	contents: write
	pull-requests: write
	runs-on: ubuntu-latest
	if: (github.event.pull_request.user.login == 'dependabot[bot]' \|\| github.event.pull_request.user.login == 'pre-commit-ci[bot]')
	steps:
	- name: Enable auto-merge for bot PRs
	run: gh pr merge --auto --squash "$PR_URL"
	env:
	PR_URL: ${{github.event.pull_request.html_url}}
	GH_TOKEN: ${{secrets.GITHUB_TOKEN}}

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Add Pydantic models for configuration validation #294

Workflow file

Add Pydantic models for configuration validation #294

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Workflow file for this run