Add M+theta arg error and test #8153

Workflow file for this run

.github/workflows/workflow.yml at d351fea

	name: ASPIRE Python Pip CI

	on:
	pull_request:
	types: [opened, synchronize, reopened, ready_for_review]
	push:


	jobs:
	check:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	- name: Set up Python
	uses: actions/setup-python@v5
	with:
	python-version: '3.9'
	- name: Install dependencies
	run: \|
	pip install tox tox-gh-actions
	- name: Run Tox Check
	run: tox -e check

	data-cache:
	needs: check
	runs-on: ubuntu-latest
	outputs:
	cache_hash: ${{ steps.compute-cache-hash.outputs.cache_hash }}
	steps:
	- uses: actions/checkout@v4
	- name: Setup Python
	uses: actions/setup-python@v5
	with:
	python-version: '3.9'
	- name: Install Dependencies
	run: \|
	python -m pip install --upgrade pip
	pip install -e ".[dev]"
	- name: Restore Cache
	uses: actions/cache@v4
	with:
	key: cached-data-${{ hashFiles('/registry.py', '/*workflow.yml') }}
	restore-keys: \|
	cached-data-
	path: .github_cache/ASPIRE-data
	enableCrossOsArchive: true
	- name: Create Cache Directory
	run: \|
	# Create cache and config directories
	mkdir -p .github_cache/ASPIRE-data
	chmod -R 777 .github_cache/ASPIRE-data
	echo "cache:" > config.yaml
	echo " cache_dir: .github_cache/ASPIRE-data" >> config.yaml
	echo "Logging config.yaml for verification:"
	cat config.yaml
	- name: Download Cache Files
	run: \|
	export ASPIREDIR=.
	python -c "
	from aspire.downloader import emdb_2660, simulated_channelspin
	emdb_2660()
	simulated_channelspin()
	"
	- name: Compute Cache Directory Hash
	id: compute-cache-hash
	run: \|
	echo "Computing hash for .github_cache/ASPIRE-data..."
	# Compute a hash on the sorted file listing.
	cache_hash=$(ls -1 .github_cache/ASPIRE-data/** \| md5sum)
	echo "Computed cache hash: $cache_hash"
	# Expose the computed hash to subsequent steps/jobs.
	echo "cache_hash=${cache_hash}" >> $GITHUB_OUTPUT
	- name: Verify Cache Directory Before Saving
	run: \|
	ls -lhR .github_cache/ASPIRE-data
	[ -f config.yaml ]
	- name: Save Cache
	uses: actions/cache@v4
	with:
	key: cached-data-${{ hashFiles('/registry.py', '/*workflow.yml') }}
	path: .github_cache/ASPIRE-data
	enableCrossOsArchive: true

	build:
	needs: [check, data-cache]
	runs-on: ubuntu-latest
	# Run on every code push, but only on review ready PRs
	if: ${{ github.event_name == 'push' \|\| github.event.pull_request.draft == false }}
	strategy:
	matrix:
	python-version: ['3.9', '3.10', '3.11', '3.12']
	pyenv: [pip]
	exclude:
	# Exclude 3.9-pip so we can add pre/post tasks to that environment.
	- python-version: '3.9'
	pyenv: pip
	include:
	# Re-include 3.9 with additional tox tasks.
	- python-version: '3.9'
	pyenv: pip,docs

	steps:
	- uses: actions/checkout@v4
	- name: Set up Python ${{ matrix.python-version }} ${{ matrix.pyenv }}
	uses: actions/setup-python@v5
	with:
	python-version: ${{ matrix.python-version }}
	- name: Install dependencies
	run: \|
	pip install tox tox-gh-actions
	# Optional packages
	pip install pyfftw # `test_fft` runs for pyfftw when installed
	- name: Restore Cache
	uses: actions/cache@v4
	with:
	key: cached-data-${{ hashFiles('/registry.py', '/*workflow.yml') }}
	restore-keys: \|
	cached-data-
	path: .github_cache/ASPIRE-data
	enableCrossOsArchive: true
	- name: Set Cache Directory
	run: \|
	echo "cache:" > config.yaml
	echo " cache_dir: .github_cache/ASPIRE-data" >> config.yaml
	- name: Verify Restored Cache Directory
	run: \|
	ls -lhR .github_cache/ASPIRE-data
	[ -f config.yaml ]
	- name: Test with tox
	run: \|
	tox --override testenv.set_env=ASPIREDIR=${{ github.workspace }} \
	--skip-missing-interpreters false \
	-e py${{ matrix.python-version }}-${{ matrix.pyenv }}
	- name: Validate Cache Directory Hash
	run: \|
	echo "Computing hash for .github_cache/ASPIRE-data..."
	new_hash=$(ls -1 .github_cache/ASPIRE-data/** \| md5sum)
	echo "Hash from data-cache job: ${{ needs.data-cache.outputs.cache_hash }}"
	echo "Computed hash now: $new_hash"
	if [ "${{ needs.data-cache.outputs.cache_hash }}" != "$new_hash" ]; then
	echo "Error: Cache directory hash has changed!"
	exit 1
	fi
	- name: Upload Coverage to CodeCov
	uses: codecov/codecov-action@v4
	with:
	token: ${{ secrets.CODECOV_TOKEN }}

	conda-build:
	needs: [check, data-cache]
	runs-on: ${{ matrix.os }}
	# Only run on review ready pull_requests
	if: ${{ github.event_name == 'pull_request' && github.event.pull_request.draft == false }}
	defaults:
	run:
	shell: bash -el {0}
	strategy:
	matrix:
	os: [ubuntu-latest, ubuntu-22.04, macOS-latest, macOS-14]
	backend: [default, openblas]
	python-version: ['3.9']
	include:
	- os: ubuntu-latest
	backend: intel
	- os: macOS-latest
	backend: accelerate
	- os: windows-2022
	backend: win64

	steps:
	- uses: actions/checkout@v4
	- name: Set up Conda ${{ matrix.os }} Python ${{ matrix.python-version }}
	uses: conda-incubator/setup-miniconda@v2.3.0
	with:
	miniconda-version: "latest"
	auto-update-conda: true
	python-version: ${{ matrix.python-version }}
	activate-environment: aspire
	environment-file: environment-${{ matrix.backend }}.yml
	auto-activate-base: false
	- name: Complete Install and Log Environment ${{ matrix.os }} Python ${{ matrix.python-version }}
	run: \|
	conda info
	conda list
	pip install -e ".[dev]"
	pip freeze
	python -c "import numpy; numpy.show_config()"
	- name: Restore Cache
	uses: actions/cache@v4
	with:
	key: cached-data-${{ hashFiles('/registry.py', '/*workflow.yml') }}
	restore-keys: \|
	cached-data-
	path: .github_cache/ASPIRE-data
	enableCrossOsArchive: true
	- name: Set Cache Directory
	run: \|
	echo "cache:" > config.yaml
	echo " cache_dir: .github_cache/ASPIRE-data" >> config.yaml
	- name: Execute Pytest Conda ${{ matrix.os }} Python ${{ matrix.python-version }}
	run: \|
	export ASPIREDIR=.
	export OMP_NUM_THREADS=2
	# -n runs test in parallel using pytest-xdist
	pytest -n2 --durations=50 -s

	# Build and Deploy production (main) docs.
	docs_deploy:
	if: github.ref == 'refs/heads/main'
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	- name: Setup Python
	uses: actions/setup-python@v5
	with:
	python-version: '3.9'
	- name: Install Dependencies
	run: \|
	pip install -e ".[dev]"
	- name: Run Sphinx doc build script
	env:
	GITHUB_ACTOR: ${{ github.actor }}
	GITHUB_REPOSITORY: ${{ github.repository }}
	GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
	run: "docs/buildsite.sh"
	shell: bash

	ampere_gpu:
	needs: check
	runs-on: self-hosted
	# Run on every code push, but only on review ready PRs
	if: ${{ github.event_name == 'push' \|\| github.event.pull_request.draft == false }}
	steps:
	- uses: actions/checkout@v4
	- name: Install dependencies
	run: \|
	pip install -e ".[dev,gpu-12x]"
	- name: Customize config
	run: \|
	echo "Setup tmp dirs and chmod so others can cleanup."
	CI_TMP_DIR=/var/ci/tmp
	mkdir -p ${CI_TMP_DIR}
	chmod g+rwx ${CI_TMP_DIR}
	CI_CACHE_DIR=${CI_TMP_DIR}/cache
	mkdir -p ${CI_CACHE_DIR}
	chmod g+rwx ${CI_CACHE_DIR}
	echo "Create and assign a unique temp dir to hold our config."
	WORK_DIR=$(mktemp -d -p "${CI_TMP_DIR}")
	echo "WORK_DIR=${WORK_DIR}"
	echo "Stash the WORK_DIR to GitHub env so we can clean it up later."
	echo "WORK_DIR=${WORK_DIR}" >> $GITHUB_ENV
	echo -e "common:" >> ${WORK_DIR}/config.yaml
	echo -e " numeric: cupy" >> ${WORK_DIR}/config.yaml
	echo -e " fft: cupy\n" >> ${WORK_DIR}/config.yaml
	echo -e "cache:" >> ${WORK_DIR}/config.yaml
	echo -e " cache_dir: ${CI_CACHE_DIR}" >> ${WORK_DIR}/config.yaml
	echo "Log the config: ${WORK_DIR}/config.yaml"
	cat ${WORK_DIR}/config.yaml
	- name: Cache Data
	run: \|
	ASPIREDIR=${{ env.WORK_DIR }} python -c \
	"import aspire; print(aspire.config['cache']['cache_dir']); import aspire.downloader; aspire.downloader.emdb_2660()"
	- name: Run
	run: \|
	ASPIREDIR=${{ env.WORK_DIR }} PYTHONWARNINGS=error python -m pytest --durations=50 --cov=aspire --cov-report=xml
	- name: Upload Coverage to CodeCov
	uses: codecov/codecov-action@v4
	with:
	token: ${{ secrets.CODECOV_TOKEN }}
	- name: Cleanup
	run: rm -rf ${{ env.WORK_DIR }}

	# Build branch's docs and gallery.
	docs:
	needs: [check, data-cache]
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	- name: Setup Python
	uses: actions/setup-python@v5
	with:
	python-version: '3.9'
	- name: Install Dependencies
	run: \|
	python -m pip install --upgrade pip
	pip install -e ".[dev]"
	- name: Restore Cache
	uses: actions/cache@v4
	with:
	key: cached-data-${{ hashFiles('/registry.py', '/*workflow.yml') }}
	restore-keys: \|
	cached-data-
	path: .github_cache/ASPIRE-data
	enableCrossOsArchive: true
	- name: Set Cache Directory
	run: \|
	echo "cache:" > config.yaml
	echo " cache_dir: .github_cache/ASPIRE-data" >> config.yaml
	- name: Build Sphinx docs
	run: \|
	export ASPIREDIR=${{ github.workspace }}
	make distclean
	sphinx-apidoc -f -o ./source ../src -H Modules
	make html
	working-directory: ./docs
	- name: Archive Sphinx docs
	uses: actions/upload-artifact@v4
	with:
	name: sphinx-docs
	path: docs/build
	retention-days: 7
	- name: Validate Cache Directory Hash
	run: \|
	echo "Computing hash for .github_cache/ASPIRE-data..."
	new_hash=$(ls -1 .github_cache/ASPIRE-data/** \| md5sum)
	echo "Hash from data-cache job: ${{ needs.data-cache.outputs.cache_hash }}"
	echo "Computed hash now: $new_hash"
	if [ "${{ needs.data-cache.outputs.cache_hash }}" != "$new_hash" ]; then
	echo "Error: Cache directory hash has changed!"
	exit 1
	fi

	osx_arm:
	needs: [check, data-cache]
	runs-on: macos-14
	# Run on every code push, but only on review ready PRs
	if: ${{ github.event_name == 'push' \|\| github.event.pull_request.draft == false }}
	steps:
	- uses: actions/checkout@v4
	- uses: actions/setup-python@v5
	with:
	python-version: '3.12'
	- name: Complete Install and Log Environment
	run: \|
	python --version
	pip install -e ".[dev]" # install aspire
	pip freeze
	- name: Restore Cache
	uses: actions/cache@v4
	with:
	key: cached-data-${{ hashFiles('/registry.py', '/*workflow.yml') }}
	restore-keys: \|
	cached-data-
	path: .github_cache/ASPIRE-data
	enableCrossOsArchive: true
	- name: Set Cache Directory
	run: \|
	echo "cache:" > config.yaml
	echo " cache_dir: .github_cache/ASPIRE-data" >> config.yaml
	- name: Verify Restored Cache Directory
	run: \|
	ls -lhR .github_cache/ASPIRE-data
	[ -f config.yaml ]
	- name: Test
	run: \|
	export ASPIREDIR=.
	python -m pytest -n3 --durations=50

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Add M+theta arg error and test #8153

Workflow file

Add M+theta arg error and test #8153

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Workflow file for this run