Optimize downsample-tips, add CLI #1118

Workflow file for this run

	name: ci

	on:
	push:
	branches:
	- master
	tags:
	- '*'
	pull_request:
	branches:
	- '*'
	schedule:
	- cron: '0 0 * * 1' # weekly
	workflow_dispatch:
	jobs:
	test:
	runs-on: ubuntu-24.04
	strategy:
	fail-fast: false
	matrix:
	python-version: ["3.10", "3.11", "3.12"]
	subdivision:
	- "test_auxiliary_lib"
	- "test_dataframe"
	- "test_frozen_instrumentation"
	- "test_genome_instrumentation"
	- "test_juxtaposition"
	- "test_phylogenetic_inference/test_estimators"
	- "test_phylogenetic_inference/test_pairwise"
	- "test_phylogenetic_inference/test_population"
	- "test_phylogenetic_inference/test_priors"
	- "test_phylogenetic_inference/test_tree"
	- "test_serialization"
	- "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_depth_proportional_resolution_algo"
	- "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_depth_proportional_resolution_tapered_algo"
	- "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_fixed_resolution_algo"
	- "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_geom_seq_nth_root_algo"
	- "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_geom_seq_nth_root_tapered_algo"
	- "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_nominal_resolution_algo"
	- "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_perfect_resolution_algo"
	- "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_pseudostochastic_algo"
	- "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_recency_proportional_resolution_algo"
	- "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_recency_proportional_resolution_curbed_algo"
	- "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_stochastic_algo"
	- "test_stratum_retention_strategy/test_stratum_retention_policy_evaluators"
	- "test_stratum_retention_viz"
	- "test_test_drive"

	steps:
	- uses: actions/checkout@v1
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v2
	with:
	python-version: ${{ matrix.python-version }}
	- name: Install dependencies
	run: \|
	sudo sed -i 's/azure\.//' /etc/apt/sources.list
	sudo apt-get update -o Acquire::Retries=3
	sudo apt-get install -y ffmpeg -o Acquire::Retries=3
	python -m pip install --upgrade pip setuptools
	pip install tox tox-gh-actions
	- name: Test with tox
	run: \|
	export HSTRAT_TESTS_SUBDIVISION=${{ matrix.subdivision }}
	tox

	cli:
	runs-on: ubuntu-24.04
	steps:
	- uses: actions/checkout@v1
	- name: Set up Python 3.10
	uses: actions/setup-python@v2
	with:
	python-version: "3.10"
	- name: Install Python dependencies
	uses: py-actions/py-dependency-install@v4
	with:
	path: "requirements-dev/requirements-testing.txt"
	- name: Run examples
	run: \|
	python3 -m hstrat
	python3 -m hstrat.dataframe.surface_unpack_reconstruct --help

	examples:
	runs-on: ubuntu-24.04
	steps:
	- uses: actions/checkout@v1
	- name: Set up Python 3.10
	uses: actions/setup-python@v2
	with:
	python-version: "3.10"
	- name: Install Python dependencies
	uses: py-actions/py-dependency-install@v4
	with:
	path: "requirements-dev/requirements-jit.txt"
	- name: Install Python dependencies
	uses: py-actions/py-dependency-install@v4
	with:
	path: "requirements-dev/requirements-testing.txt"
	- name: Run examples
	run: ./examples/run_all.sh

	build-script:
	runs-on: ubuntu-24.04
	steps:
	- uses: actions/checkout@v1
	- run: \|
	sudo sed -i 's/azure\.//' /etc/apt/sources.list
	sudo apt-get update -o Acquire::Retries=3
	sudo apt-get install -y python3-pybind11 -o Acquire::Retries=3
	- run: ./build.sh

	coverage:
	runs-on: ubuntu-24.04
	strategy:
	fail-fast: false
	matrix:
	subdivision:
	- "test_auxiliary_lib"
	- "test_dataframe"
	- "test_frozen_instrumentation"
	- "test_genome_instrumentation"
	- "test_juxtaposition"
	- "test_phylogenetic_inference/test_estimators"
	- "test_phylogenetic_inference/test_pairwise"
	- "test_phylogenetic_inference/test_population"
	- "test_phylogenetic_inference/test_priors"
	- "test_phylogenetic_inference/test_tree"
	- "test_serialization"
	- "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_depth_proportional_resolution_algo"
	- "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_depth_proportional_resolution_tapered_algo"
	- "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_fixed_resolution_algo"
	- "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_geom_seq_nth_root_algo"
	- "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_geom_seq_nth_root_tapered_algo"
	- "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_nominal_resolution_algo"
	- "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_perfect_resolution_algo"
	- "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_pseudostochastic_algo"
	- "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_recency_proportional_resolution_algo"
	- "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_recency_proportional_resolution_curbed_algo"
	- "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_stochastic_algo"
	- "test_stratum_retention_strategy/test_stratum_retention_policy_evaluators"
	- "test_stratum_retention_viz"
	- "test_test_drive"
	steps:
	- uses: actions/checkout@v1
	- name: Set up Python 3.10
	uses: actions/setup-python@v2
	with:
	python-version: "3.10"
	- name: Install dependencies
	run: \|
	sudo sed -i 's/azure\.//' /etc/apt/sources.list
	sudo apt-get update -o Acquire::Retries=3
	sudo apt-get install -y ffmpeg -o Acquire::Retries=3
	python -m pip install --upgrade pip setuptools
	python -m pip install -r requirements-dev/py310/requirements-testing.txt
	- name: Log coverage configuration
	run: coverage debug sys
	- name: Run tests with coverage report
	run: coverage run -m pytest tests/test_hstrat/${{ matrix.subdivision }}
	- uses: codecov/codecov-action@v4
	with:
	token: ${{ secrets.CODECOV_TOKEN }} # required
	flags: tests # optional
	fail_ci_if_error: true # optional (default = false)
	verbose: true # optional (default = false)

	tidy:
	runs-on: ubuntu-24.04
	steps:
	- name: Install apt dependencies
	run: sudo apt-get install -y rename
	- uses: actions/checkout@v1
	- name: Set up Python 3.10
	uses: actions/setup-python@v2
	with:
	python-version: "3.10"
	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip setuptools
	python -m pip install -r requirements-dev/py310/requirements-testing.txt
	- name: Test isort tidyness
	uses: jamescurtin/isort-action@master
	with:
	requirementsFiles: "requirements-dev/py310/requirements-testing.txt"
	- name: Test Black tidyness
	uses: psf/black@27d20144a7517594e24a1649451177b2a11284be
	with:
	version: "22.10.0"
	- uses: editorconfig-checker/action-editorconfig-checker@main
	- name: Test editorconfig tidyness
	run: editorconfig-checker
	- name: Test tidy/ tidyness
	run: ./tidy/test_tidy.sh

	paper:
	runs-on: ubuntu-24.04
	steps:
	- name: Checkout
	uses: actions/checkout@v2
	- name: Build draft PDF
	uses: openjournals/openjournals-draft-action@master
	with:
	journal: joss
	# This should be the path to the paper within your repo.
	paper-path: joss/paper.md
	- name: Upload
	uses: actions/upload-artifact@v4
	with:
	name: paper
	# This is the output path where Pandoc will write the compiled
	# PDF. Note, this should be the same directory as the input
	# paper.md
	path: joss/paper.pdf

	# regression test for https://github.com/mmore500/hstrat/commit/c276530
	packaging-bdist:
	runs-on: ubuntu-24.04
	steps:
	- name: Checkout
	uses: actions/checkout@v2
	- name: Build bdist
	run: \|
	python3 -m venv env
	source env/bin/activate
	python3 -m pip install -r requirements-dev/requirements-release.txt
	python3 setup.py bdist_wheel
	tree dist
	deactivate
	- name: Upgrade pip
	run: python3 -m pip install pip --upgrade
	- name: Install from bdist
	run: python3 -m pip install dist/*.whl
	- name: Test install
	run: \|
	find . -type f -name '*.py' -exec rm {} \;
	find . -type f -name '*.pyi' -exec rm {} \;
	python3 -c "import hstrat; print(hstrat.__version__)"

	# regression test for https://github.com/mmore500/hstrat/commit/c276530
	packaging-sdist:
	runs-on: ubuntu-24.04
	steps:
	- name: Checkout
	uses: actions/checkout@v2
	- name: Build sdist
	run: \|
	python3 -m venv env
	source env/bin/activate
	python3 -m pip install -r requirements-dev/requirements-release.txt
	python3 setup.py sdist
	tree dist
	deactivate
	- name: Upgrade pip
	run: python3 -m pip install pip --upgrade
	- name: Install from sdist
	run: python3 -m pip install dist/*.tar.gz
	- name: Test install
	run: \|
	find . -type f -name '*.py' -exec rm {} \;
	find . -type f -name '*.pyi' -exec rm {} \;
	python3 -c "import hstrat; print(hstrat.__version__)"

	# regression test for https://github.com/mmore500/hstrat/commit/c276530
	packaging-source:
	runs-on: ubuntu-24.04
	steps:
	- name: Checkout
	uses: actions/checkout@v2
	- name: Upgrade pip
	run: python3 -m pip install pip --upgrade
	- name: Install from source
	run: python3 -m pip install .
	- name: Test install
	run: \|
	rm -rf *
	cd
	python3 -c "import hstrat; print(hstrat.__version__)"

	deploy-ghcr:
	name: Docker Image Deploy
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v2
	- name: Set Tags
	id: set_tags
	run: \|
	if [[ "${GITHUB_REF_NAME}" != *merge ]]; then
	echo "TAGS=latest,${GITHUB_REF_NAME}" >> $GITHUB_ENV
	else
	echo "TAGS=latest" >> $GITHUB_ENV
	fi
	- name: Build and Push to GitHub Container Registry
	uses: docker/build-push-action@v1
	with:
	push: ${{ github.ref == 'refs/heads/master' \|\| startsWith(github.ref, 'refs/tags/v') }}
	tags: ${{ env.TAGS }}
	username: ${{ github.actor }}
	password: ${{ secrets.GITHUB_TOKEN }}
	repository: mmore500/hstrat
	registry: ghcr.io
	add_git_labels: true

	build_wheels:
	name: Build wheels on ${{ matrix.os }}
	runs-on: ${{ matrix.os }}
	strategy:
	fail-fast: false
	matrix:
	os: [ubuntu-24.04, windows-latest, macos-14]

	steps:
	- uses: actions/checkout@v4
	with:
	submodules: "recursive"
	- name: Set up Ubuntu Dependecies
	if: matrix.os == 'ubuntu-24.04'
	run: \|
	sudo sed -i 's/azure\.//' /etc/apt/sources.list
	sudo apt-get update -o Acquire::Retries=3
	sudo apt-get install -y python3.12-dev python3-dev python3-pybind11 -o Acquire::Retries=3
	- name: Build wheels
	uses: pypa/[email protected]
	env:
	CIBW_TEST_COMMAND: python3 -m hstrat.dataframe.surface_unpack_reconstruct --help
	CIBW_TEST_SKIP: "313- pp* win i686 musllinux"
	CIBW_SKIP: "*-win32"
	- uses: actions/upload-artifact@v4
	with:
	name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
	path: ./wheelhouse/*.whl

	build_sdist:
	name: Build source distribution
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	with:
	submodules: "recursive"
	- name: Build sdist
	run: pipx run build --sdist

	- uses: actions/upload-artifact@v4
	with:
	name: cibw-sdist
	path: dist/*.tar.gz

	deploy-test:
	runs-on: ubuntu-24.04
	steps:
	- uses: actions/checkout@v1
	- name: Set up Python 3.10
	uses: actions/setup-python@v2
	with:
	python-version: "3.10"
	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip
	python -m pip install -r requirements-dev/py310/requirements-release.txt
	- name: Build package
	run: python setup.py egg_info --tag-build="${{github.run_number}}" sdist bdist_wheel
	- name: Test publish package
	uses: pypa/gh-action-pypi-publish@release/v1
	with:
	user: __token__
	password: ${{ secrets.TEST_PYPI_API_TOKEN }}
	repository-url: https://test.pypi.org/legacy/
	- name: Install from test PyPI
	run: \|
	rm -rf *
	python3 -m pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple/ hstrat
	- name: Test install
	run: \|
	python3 -c "import hstrat; print(hstrat.__version__)"

	deploy:
	if: startsWith(github.ref, 'refs/tags/v')
	needs:
	- build_sdist
	- build_wheels
	- build-script
	- coverage
	- cli
	- deploy-test
	- examples
	- packaging-bdist
	- packaging-sdist
	- packaging-source
	- test
	- tidy
	runs-on: ubuntu-24.04
	steps:
	- uses: actions/checkout@v1
	- name: Set up Python 3.10
	uses: actions/setup-python@v2
	with:
	python-version: "3.10"
	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip setuptools
	python -m pip install -r requirements-dev/py310/requirements-release.txt
	- uses: actions/download-artifact@v4
	with:
	# unpacks default artifact into dist/
	# if `name: artifact` is omitted, the action will create extra parent dir
	pattern: cibw-*
	path: dist
	merge-multiple: true
	- name: Publish package
	uses: pypa/gh-action-pypi-publish@release/v1
	with:
	user: __token__
	password: ${{ secrets.PYPI_API_TOKEN }}

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Optimize downsample-tips, add CLI #1118

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Optimize downsample-tips, add CLI #1118

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