Update phonons.py #12692

Workflow file for this run

	name: tests
	on:
	push:
	branches: [main]
	pull_request:

	concurrency:
	group: ${{ github.workflow }}-${{ github.ref }}
	cancel-in-progress: true

	jobs:
	tests-core:
	strategy:
	fail-fast: true
	matrix:
	python-version: ["3.9", "3.12"]
	os: [ubuntu-latest, windows-latest]
	exclude:
	- os: windows-latest
	python-version: "3.9"

	runs-on: ${{ matrix.os }}
	defaults:
	run:
	shell: bash -l {0}

	steps:
	- name: Check out repo
	uses: actions/checkout@v4

	- name: Set up Python
	uses: actions/setup-python@v5
	with:
	python-version: ${{ matrix.python-version }}
	cache: pip
	cache-dependency-path: tests/requirements**.txt

	- name: Install pip packages
	run: \|
	pip install uv
	uv pip install --system -r tests/requirements.txt -r tests/requirements-mp.txt "quacc[dev] @ ."

	- name: Run tests with pytest (w/ coverage)
	if: matrix.python-version != '3.12'
	run: pytest --durations=10 --cov=quacc --cov-report=xml

	- name: Run tests with pytest (w/o coverage)
	if: matrix.python-version == '3.12'
	run: pytest --durations=10

	- name: Upload code coverage report to Artifact
	uses: actions/upload-artifact@v4
	with:
	name: ${{ github.job }} ${{ matrix.python-version }} ${{ matrix.os }} coverage report
	path: "coverage.xml"
	retention-days: 1

	tests-engines-covalent:
	runs-on: ubuntu-latest
	strategy:
	fail-fast: true

	defaults:
	run:
	shell: bash -l {0}

	steps:
	- name: Check out repo
	uses: actions/checkout@v4

	- name: Set up Python
	uses: actions/setup-python@v5
	with:
	python-version: "3.10"
	cache: pip
	cache-dependency-path: tests/requirements**.txt

	- name: Install pip packages
	run: \|
	pip install uv
	uv pip install --system -r tests/requirements.txt -r tests/requirements-covalent.txt -r tests/requirements-phonopy.txt "quacc[dev] @ ."

	- name: Start Covalent server
	run: covalent start

	- name: Run tests with pytest
	run: pytest --durations=10 tests/covalent --cov=quacc --cov-report=xml

	- name: Upload code coverage report to Artifact
	uses: actions/upload-artifact@v4
	with:
	name: ${{ github.job }} coverage report
	path: "coverage.xml"
	retention-days: 1

	tests-engines:
	runs-on: ubuntu-latest
	strategy:
	fail-fast: true
	matrix:
	wflow_engine: [dask, parsl, redun, jobflow]

	defaults:
	run:
	shell: bash -l {0}

	steps:
	- name: Check out repo
	uses: actions/checkout@v4

	- name: Set up Python
	uses: actions/setup-python@v5
	with:
	python-version: "3.11"
	cache: pip
	cache-dependency-path: tests/requirements**.txt

	- name: Set up conda
	if: matrix.wflow_engine == 'dask'
	uses: conda-incubator/setup-miniconda@v3
	with:
	python-version: "3.11"
	activate-environment: quacc-env

	- name: Install conda packages
	if: matrix.wflow_engine == 'dask'
	run: conda install -c conda-forge qe

	- name: Install pip packages
	run: \|
	pip install uv
	uv pip install --system -r tests/requirements.txt -r tests/requirements-${{ matrix.wflow_engine }}.txt -r tests/requirements-phonopy.txt "quacc[dev] @ ."

	- name: Run tests with pytest
	run: pytest --durations=10 tests/${{ matrix.wflow_engine }} --cov=quacc --cov-report=xml

	- name: Combine Coverage Reports
	if: matrix.wflow_engine == 'dask'
	run: \|
	coverage combine -a
	coverage xml

	- name: Upload code coverage report to Artifact
	uses: actions/upload-artifact@v4
	with:
	name: ${{ github.job }} ${{ matrix.wflow_engine }} coverage report
	path: "coverage.xml"
	retention-days: 1

	tests-engines2:
	runs-on: ubuntu-latest
	strategy:
	fail-fast: true
	matrix:
	wflow_engine: [prefect]

	defaults:
	run:
	shell: bash -l {0}

	steps:
	- name: Check out repo
	uses: actions/checkout@v4

	- name: Set up Python
	uses: actions/setup-python@v5
	with:
	python-version: "3.11"
	cache: pip
	cache-dependency-path: tests/requirements**.txt

	- name: Install pip packages
	run: \|
	pip install uv
	uv pip install --system -r tests/requirements.txt -r tests/requirements-${{ matrix.wflow_engine }}.txt -r tests/requirements-phonopy.txt "quacc[dev] @ ."

	- name: Run tests with pytest
	run: pytest --durations=10 tests/${{ matrix.wflow_engine }} --cov=quacc --cov-report=xml

	- name: Upload code coverage report to Artifact
	uses: actions/upload-artifact@v4
	with:
	name: ${{ github.job }} ${{ matrix.wflow_engine }} coverage report
	path: "coverage.xml"
	retention-days: 1

	tests-psi4:
	strategy:
	fail-fast: true
	runs-on: ubuntu-latest

	defaults:
	run:
	shell: bash -l {0}

	steps:
	- name: Check out repo
	uses: actions/checkout@v4

	- name: Set up Python
	uses: actions/setup-python@v5
	with:
	python-version: "3.11"
	cache: pip
	cache-dependency-path: tests/requirements**.txt

	- name: Set up conda
	uses: conda-incubator/setup-miniconda@v3
	with:
	python-version: ${{ matrix.python-version }}
	activate-environment: quacc-env

	- name: Install conda packages
	run: \|
	conda install -n base conda-libmamba-solver
	conda install psi4 -c conda-forge --solver libmamba

	- name: Install pip packages
	run: \|
	pip install uv
	uv pip install --system -r tests/requirements.txt "quacc[dev] @ ."

	- name: Run tests with pytest
	run: pytest -k 'psi4' --durations=10 --cov=quacc --cov-report=xml

	- name: Upload code coverage report to Artifact
	uses: actions/upload-artifact@v4
	with:
	name: ${{ github.job }} coverage report
	path: "coverage.xml"
	retention-days: 1

	tests-defects-phonons-espresso:
	strategy:
	fail-fast: true
	runs-on: ubuntu-latest

	defaults:
	run:
	shell: bash -l {0}

	steps:
	- name: Check out repo
	uses: actions/checkout@v4

	- name: Set up Python
	uses: actions/setup-python@v5
	with:
	python-version: "3.11"
	cache: pip
	cache-dependency-path: tests/requirements**.txt

	- name: Set up conda
	uses: conda-incubator/setup-miniconda@v3
	with:
	python-version: ${{ matrix.python-version }}
	activate-environment: quacc-env

	- name: Install conda packages
	run: conda install -c conda-forge qe

	- name: Install pip packages
	run: \|
	pip install uv
	uv pip install --system -r tests/requirements.txt -r tests/requirements-defects.txt -r tests/requirements-phonopy.txt "quacc[dev] @ ."

	- name: Run tests with pytest
	run: pytest -k 'defects or phonon or espresso' --durations=10 --cov=quacc --cov-report=xml

	- name: Upload code coverage report to Artifact
	uses: actions/upload-artifact@v4
	with:
	name: ${{ github.job }} coverage report
	path: "coverage.xml"
	retention-days: 1

	tests-tblite-dftbplus:
	strategy:
	fail-fast: true
	runs-on: ubuntu-latest

	defaults:
	run:
	shell: bash -l {0}

	steps:
	- name: Check out repo
	uses: actions/checkout@v4

	- name: Set up Python
	uses: actions/setup-python@v5
	with:
	python-version: "3.11"
	cache: pip
	cache-dependency-path: tests/requirements**.txt

	- name: Set up conda
	uses: conda-incubator/setup-miniconda@v3
	with:
	python-version: ${{ matrix.python-version }}
	activate-environment: quacc-env

	- name: Install conda packages
	run: conda install -c conda-forge dftbplus

	- name: Install pip packages
	run: \|
	pip install uv
	uv pip install --system -r tests/requirements.txt -r tests/requirements-tblite.txt -r tests/requirements-phonopy.txt "quacc[dev] @ ."

	- name: Run tests with pytest
	run: pytest -k 'dftb or tblite' --durations=10 --cov=quacc --cov-report=xml

	- name: Upload code coverage report to Artifact
	uses: actions/upload-artifact@v4
	with:
	name: ${{ github.job }} coverage report
	path: "coverage.xml"
	retention-days: 1

	tests-qchem-sella:
	strategy:
	fail-fast: true
	runs-on: ubuntu-latest

	defaults:
	run:
	shell: bash -l {0}

	steps:
	- name: Check out repo
	uses: actions/checkout@v4

	- name: Set up Python
	uses: actions/setup-python@v5
	with:
	python-version: "3.11"
	cache: pip
	cache-dependency-path: tests/requirements**.txt

	- name: Set up conda
	uses: conda-incubator/setup-miniconda@v3
	with:
	python-version: ${{ matrix.python-version }}
	activate-environment: quacc-env

	- name: Install conda packages
	run: conda install -c conda-forge openbabel

	- name: Install pip packages
	run: \|
	pip install uv
	uv pip install --system -r tests/requirements.txt -r tests/requirements-sella.txt "quacc[dev] @ ."

	- name: Run tests with pytest
	run: pytest -k 'qchem or sella' --durations=10 --cov=quacc --cov-report=xml

	- name: Upload code coverage report to Artifact
	uses: actions/upload-artifact@v4
	with:
	name: ${{ github.job }} coverage report
	path: "coverage.xml"
	retention-days: 1

	tests-mlps:
	strategy:
	fail-fast: true
	runs-on: ubuntu-latest

	defaults:
	run:
	shell: bash -l {0}

	steps:
	- name: Check out repo
	uses: actions/checkout@v4

	- name: Set up Python
	uses: actions/setup-python@v5
	with:
	python-version: "3.11"
	cache: pip
	cache-dependency-path: tests/requirements**.txt

	- name: Install pip packages
	run: \|
	pip install uv
	uv pip install --system -r tests/requirements.txt -r tests/requirements-mlp.txt -r tests/requirements-newtonnet.txt -r tests/requirements-sella.txt -r tests/requirements-phonopy.txt "quacc[dev] @ ."

	- name: Run tests with pytest
	run: pytest -k 'mlp or newtonnet' --durations=10 --cov=quacc --cov-report=xml

	- name: Upload code coverage report to Artifact
	uses: actions/upload-artifact@v4
	with:
	name: ${{ github.job }} coverage report
	path: "coverage.xml"
	retention-days: 1

	codecov:
	needs:
	- tests-core
	- tests-engines-covalent
	- tests-engines
	- tests-engines2
	- tests-psi4
	- tests-defects-phonons-espresso
	- tests-tblite-dftbplus
	- tests-qchem-sella
	- tests-mlps
	runs-on: ubuntu-latest
	steps:
	- name: Checkout
	uses: actions/checkout@v4

	- name: Download coverage artifacts
	uses: actions/download-artifact@v4

	- name: Upload coverage to Codecov
	uses: codecov/codecov-action@v4
	env:
	CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
	with:
	fail_ci_if_error: true

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Update phonons.py #12692

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Update phonons.py #12692

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