tests

Fixed an incorrectly indented block in pytest.yml #493

Workflow file for this run

	name: tests

	on:
	push:
	branches: ["**"]
	pull_request:
	types:
	- opened
	- reopened
	- ready_for_review

	jobs:
	pytest-unit:
	runs-on: ubuntu-24.04
	strategy:
	matrix:
	python-version: ["3.9"]
	steps:
	- name: System Dependencies
	run: \|
	sudo apt-get update
	sudo apt install -y build-essential \
	libcairo2-dev \
	pkg-config \
	python3-dev \
	python3-openssl
	- uses: actions/checkout@v3
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v4
	with:
	python-version: ${{ matrix.python-version }}

	- name: Cache Python dependencies
	uses: actions/cache@v3
	with:
	path: ~/.cache/pip
	key: ${{ runner.os }}-pip-${{ hashFiles('pip/*.txt') }}
	restore-keys: \|
	${{ runner.os }}-pip-

	- name: Install dependencies
	run: \|
	python3.9 -m pip install --upgrade pip
	pip install -e .
	if [ -f pip/cpu_requirements.txt ]; then pip install -r pip/cpu_requirements.txt; fi
	if [ -f pip/dev_requirements.txt ]; then pip install -r pip/dev_requirements.txt; fi

	- name: pytest
	run: \|
	# python3.9 -m pytest --capture=sys --capture=fd --cov=atomsci/ -vv atomsci/ddm/test/unit
	cd atomsci/modac/test/unit && python3.9 -m pytest --capture=sys --capture=fd --cov=atomsci/ -vv
	cd ../../../../atomsci/ddm/test/unit && python3.9 -m pytest -m "not moe_required" -n 2 --capture=sys --capture=fd --cov=atomsci -vv
	env:
	ENV: test

	- name: Save coverage
	uses: actions/upload-artifact@v4
	with:
	name: coverage-pytest-unit
	path: .coverage*
	pytest-integrative-1:
	runs-on: ubuntu-24.04
	strategy:
	matrix:
	python-version: ["3.9"]
	steps:
	- name: System Dependencies
	run: \|
	sudo apt-get update
	sudo apt install -y build-essential \
	libcairo2-dev \
	pkg-config \
	python3-dev \
	python3-openssl
	- uses: actions/checkout@v3
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v4
	with:
	python-version: ${{ matrix.python-version }}

	- name: Cache Python dependencies
	uses: actions/cache@v3
	with:
	path: ~/.cache/pip
	key: ${{ runner.os }}-pip-${{ hashFiles('pip/*.txt') }}
	restore-keys: \|
	${{ runner.os }}-pip-

	- name: Install dependencies
	run: \|
	python3.9 -m pip install --upgrade pip
	pip install -e .
	if [ -f pip/cpu_requirements.txt ]; then pip install -r pip/cpu_requirements.txt; fi
	if [ -f pip/dev_requirements.txt ]; then pip install -r pip/dev_requirements.txt; fi

	- name: pytest
	run: \|
	# TODO: Run this test with pytest for paralell testing
	# python3.9 -m pytest -n 2 --capture=sys --capture=fd --cov=atomsci -vv atomsci/ddm/test/integrative
	cd atomsci/ddm/test/integrative && ./integrative_batch_chunk_tests 0
	env:
	ENV: test

	- name: Save coverage
	uses: actions/upload-artifact@v4
	with:
	name: coverage-pytest-integrative-1
	path: .coverage*
	pytest-integrative-2:
	runs-on: ubuntu-24.04
	strategy:
	matrix:
	python-version: ["3.9"]
	steps:
	- name: System Dependencies
	run: \|
	sudo apt-get update
	sudo apt install -y build-essential \
	libcairo2-dev \
	pkg-config \
	python3-dev \
	python3-openssl
	- uses: actions/checkout@v3
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v4
	with:
	python-version: ${{ matrix.python-version }}

	- name: Cache Python dependencies
	uses: actions/cache@v3
	with:
	path: ~/.cache/pip
	key: ${{ runner.os }}-pip-${{ hashFiles('pip/*.txt') }}
	restore-keys: \|
	${{ runner.os }}-pip-

	- name: Install dependencies
	run: \|
	python3.9 -m pip install --upgrade pip
	pip install -e .
	if [ -f pip/cpu_requirements.txt ]; then pip install -r pip/cpu_requirements.txt; fi
	if [ -f pip/dev_requirements.txt ]; then pip install -r pip/dev_requirements.txt; fi

	- name: pytest
	run: \|
	# TODO: Run this test with pytest for paralell testing
	cd atomsci/ddm/test/integrative && ./integrative_batch_chunk_tests 1
	echo 'done'
	env:
	ENV: test

	- name: Save coverage
	uses: actions/upload-artifact@v4
	with:
	name: coverage-pytest-integrative-2
	path: .coverage*
	pytest-integrative-3:
	runs-on: ubuntu-24.04
	strategy:
	matrix:
	python-version: ["3.9"]
	steps:
	- name: System Dependencies
	run: \|
	sudo apt-get update
	sudo apt install -y build-essential \
	libcairo2-dev \
	pkg-config \
	python3-dev \
	python3-openssl
	- uses: actions/checkout@v3
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v4
	with:
	python-version: ${{ matrix.python-version }}

	- name: Cache Python dependencies
	uses: actions/cache@v3
	with:
	path: ~/.cache/pip
	key: ${{ runner.os }}-pip-${{ hashFiles('pip/*.txt') }}
	restore-keys: \|
	${{ runner.os }}-pip-

	- name: Install dependencies
	run: \|
	python3.9 -m pip install --upgrade pip
	pip install -e .
	if [ -f pip/cpu_requirements.txt ]; then pip install -r pip/cpu_requirements.txt; fi
	if [ -f pip/dev_requirements.txt ]; then pip install -r pip/dev_requirements.txt; fi

	- name: pytest
	run: \|
	# TODO: Run this test with pytest for paralell testing
	# python3.9 -m pytest -n 2 --capture=sys --capture=fd --cov=atomsci -vv atomsci/ddm/test/integrative
	cd atomsci/ddm/test/integrative && ./integrative_batch_chunk_tests 2
	env:
	ENV: test

	- name: Save coverage
	uses: actions/upload-artifact@v4
	with:
	name: coverage-pytest-integrative-3
	path: .coverage*
	pytest-integrative-4:
	runs-on: ubuntu-24.04
	strategy:
	matrix:
	python-version: ["3.9"]
	steps:
	- name: System Dependencies
	run: \|
	sudo apt-get update
	sudo apt install -y build-essential \
	libcairo2-dev \
	pkg-config \
	python3-dev \
	python3-openssl
	- uses: actions/checkout@v3
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v4
	with:
	python-version: ${{ matrix.python-version }}

	- name: Cache Python dependencies
	uses: actions/cache@v3
	with:
	path: ~/.cache/pip
	key: ${{ runner.os }}-pip-${{ hashFiles('pip/*.txt') }}
	restore-keys: \|
	${{ runner.os }}-pip-

	- name: Install dependencies
	run: \|
	python3.9 -m pip install --upgrade pip
	pip install -e .
	if [ -f pip/cpu_requirements.txt ]; then pip install -r pip/cpu_requirements.txt; fi
	if [ -f pip/dev_requirements.txt ]; then pip install -r pip/dev_requirements.txt; fi

	- name: pytest
	run: \|
	# TODO: Run this test with pytest for paralell testing
	# python3.9 -m pytest -n 2 --capture=sys --capture=fd --cov=atomsci -vv atomsci/ddm/test/integrative
	cd atomsci/ddm/test/integrative && ./integrative_batch_chunk_tests 3
	env:
	ENV: test

	- name: Save coverage
	uses: actions/upload-artifact@v4
	with:
	name: coverage-pytest-integrative-4
	path: .coverage*

	coverage-merge:
	runs-on: ubuntu-24.04
	needs: [pytest-unit, pytest-integrative-1, pytest-integrative-2, pytest-integrative-3, pytest-integrative-4]
	steps:
	- uses: actions/checkout@v3
	- name: Set up Python
	uses: actions/setup-python@v4
	with:
	python-version: "3.9"

	- name: Install coverage
	run: pip install coverage

	- name: Download all coverage artifacts
	uses: actions/download-artifact@v5
	with:
	path: coverage-reports

	- name: Merge coverage reports
	run: \|
	# List directory structure for debugging
	ls -la
	ls -la coverage-reports/ \|\| echo "coverage-reports directory not found"

	# Find and combine all coverage files
	find coverage-reports -name ".coverage*" -type f

	# Combine all coverage files
	coverage combine coverage-reports/*/.coverage

	# Generate XML report for codecov
	coverage xml

	- name: Upload merged coverage to Codecov
	uses: codecov/codecov-action@v4
	with:
	files: ./coverage.xml
	flags: unittests
	name: codecov-umbrella
	env:
	CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

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Fixed an incorrectly indented block in pytest.yml #493

Workflow file

Fixed an incorrectly indented block in pytest.yml #493

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Workflow file for this run