Fix clippy warnings and add some code factorization #153

Workflow file for this run

	# The starting point of this script are the links provided on the maturing doc:
	# * https://github.com/nanoporetech/fast-ctc-decode/blob/b226ea0f2b2f4f474eff47349703d57d2ea4801b/.github/workflows/publish.yml
	# * https://github.com/konstin/complex-manylinux-maturin-docker/blob/main/.github/workflows/build.yml

	# Description of the usage of virtual env:
	# * https://packaging.python.org/guides/installing-using-pip-and-virtual-environments/

	name: test-cdshealpix

	on: [push, workflow_dispatch]


	# Jobs run in parallel, see https://docs.github.com/en/actions/reference/workflow-syntax-for-github-actions#jobs
	# Github hosted runner are: see https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners
	jobs:
	test-linux64-wheels:
	# Containers run in Linux
	runs-on: ubuntu-latest
	# Docker Hub image that 'build-linux-wheels' executes in.
	# See https://github.com/pypa/manylinux for this particular container:
	# * CPython 3.8, 3.9, ... installed in /opt/python/<python tag>-<abi tag>
	container: quay.io/pypa/manylinux2014_x86_64
	env: {ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION: true} # Allow using Node16 actions required for CentOS7
	# We are now in CentOS 7 64 bits
	steps:
	- name: "Checkout the full project"
	uses: actions/checkout@v3
	# We need to install rust in the docker image (else, cargo is already available in github action)
	- name: "Install Rust"
	run: \|
	curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs \| sh -s -- -y
	# Build wheels for all pre-installed python version (in /opt/python/, see docker image comment)
	# installing first maturin and using maturin: https://github.com/PyO3/maturin#pypy
	# For secrets, see https://docs.github.com/en/actions/reference/encrypted-secrets
	- name: "Build and run tests"
	shell: bash
	run: \|
	source $HOME/.cargo/env
	for PYBIN in /opt/python/cp3{8,9,10,11,12}-*/bin; do
	"${PYBIN}/pip" install virtualenv
	"${PYBIN}/virtualenv" cdshealpixenv
	source cdshealpixenv/bin/activate
	pip install --upgrade pip
	pip install maturin
	maturin build --release --compatibility manylinux2014
	maturin develop --release
	pip install -r requirements-dev.txt
	python -m pytest -v
	deactivate
	rm -r cdshealpixenv
	done

	## So far desactivated because too long to build astropy wheels
	#test-aarch64-wheels:
	# runs-on: ubuntu-latest
	# env:
	# img: quay.io/pypa/manylinux2014_aarch64
	# steps:
	# - name: Checkout
	# uses: actions/checkout@v4
	# - name: "Set up QEMU"
	# id: qemu
	# uses: docker/setup-qemu-action@v1
	# - name: Install dependencies
	# run: \|
	# docker run --rm -v ${{ github.workspace }}:/ws:rw --workdir=/ws \
	# ${{ env.img }} \
	# bash -exc 'curl --proto "=https" --tlsv1.2 -sSf https://sh.rustup.rs \| sh -s -- --default-host aarch64-unknown-linux-gnu -y && \
	# source $HOME/.cargo/env && \
	# for PYBIN in /opt/python/cp3[78910]*/bin; do
	# echo "Loop on PYBIN: $PYBIN"
	# "${PYBIN}/pip" install virtualenv
	# "${PYBIN}/virtualenv" cdshealpixenv
	# source cdshealpixenv/bin/activate
	# pip install --upgrade pip
	# pip install maturin
	# cargo build --release --config "net.git-fetch-with-cli = true"
	# maturin build --release --compatibility manylinux2014 --target aarch64-unknown-linux-gnu --config "net.git-fetch-with-cli = true"
	# maturin develop --release --target aarch64-unknown-linux-gnu --config "net.git-fetch-with-cli = true"
	# pip install -r requirements-dev.txt
	# cd python
	# python -m pytest -v -s cdshealpix/tests/test_nested_healpix.py
	# python -m pytest -v -s cdshealpix/tests/test_ring_healpix.py
	# cd ..
	# pip freeze > requirements-uninstall.txt
	# pip uninstall -r requirements-uninstall.txt -y
	# deactivate
	# rm -r cdshealpixenv/
	# done'

	test-macos-wheels:
	runs-on: macos-latest
	strategy:
	matrix:
	python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
	steps:
	# Checkout the project
	- name: "Checkout branch"
	uses: actions/checkout@v4
	# Test Rust code
	#- name: Run rust wrapper tests
	# run: cargo test --verbose -- --nocapture
	# Set up python, see https://docs.github.com/en/actions/guides/building-and-testing-python
	- name: "Set up Python ${{ matrix.python-version }} on MacOS"
	uses: actions/setup-python@v4
	with:
	python-version: ${{ matrix.python-version }}
	# Test python code
	- name: "Build and test wheel for Python ${{ matrix.python-version }} on MacOS"
	run: \|
	# Install, create and activate a python virtualenv
	rustup target add x86_64-apple-darwin
	pip install virtualenv
	virtualenv cdshealpixenv
	source cdshealpixenv/bin/activate
	# Install and use maturin
	pip install --upgrade pip
	pip install maturin
	maturin -V
	maturin build --release --target universal2-apple-darwin
	maturin develop --release
	# Install dependencies
	pip install -r requirements-dev.txt
	# Run tests
	python -m pytest -v
	# Clean
	#pip freeze > requirements-uninstall.txt
	#pip uninstall -r requirements-uninstall.txt -y
	deactivate
	#rm -r cdshealpixenv/

	test-windows-wheels:
	runs-on: windows-latest
	strategy:
	matrix:
	python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
	steps:
	# Checkout the project
	- name: "Checkout branch"
	uses: actions/checkout@v4
	# Test Rust code
	#- name: Run rust wrapper tests
	# run: cargo test --verbose -- --nocapture
	# Set up python, see https://docs.github.com/en/actions/guides/building-and-testing-python
	- name: "Set up Python ${{ matrix.python-version }} on Windows"
	uses: actions/setup-python@v4
	with:
	python-version: ${{ matrix.python-version }}
	# Test python code
	- name: "Build and test wheel for Python ${{ matrix.python-version }} on Windows"
	run: \|
	# Install, create and activate a python virtualenv
	# See: https://mothergeo-py.readthedocs.io/en/latest/development/how-to/venv-win.html
	pip install virtualenv
	virtualenv cdshealpixenv
	.\cdshealpixenv\Scripts\activate
	pip install --upgrade pip
	# Install and use maturin
	pip install maturin
	maturin -V
	maturin develop --release
	# Install dependencies
	pip install -r requirements-dev.txt
	# Run tests
	python -m pytest -v
	deactivate

	# Build the doc and run the tests in the doc (only for python 3.11 on ubuntu)
	test-doc:
	runs-on: ubuntu-latest
	steps:
	- name: "Checkout branch"
	uses: actions/checkout@v4
	- name: "Set up Python 3.11 on Ubuntu"
	uses: actions/setup-python@v4
	with:
	python-version: '3.11'
	- name: "Build and test doc"
	run: \|
	# Install virtualenv
	pip install virtualenv
	# Create and activate a new virtualenv
	virtualenv cdshealpixenv
	source cdshealpixenv/bin/activate
	# Install maturin
	pip install --upgrade pip
	pip install maturin
	sudo apt-get install pandoc
	maturin -V
	# Build and install cdshealpix
	maturin develop --release
	# Install dependencies needed to build the docs
	pip install -r requirements-doc.txt
	# Compile the docs and run the test examples
	cd ./docs
	# * Generate the HTML files
	make html
	# * Run the API test examples
	make doctest
	cd ..
	# Switch of the virtualenv
	deactivate

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Fix clippy warnings and add some code factorization #153

Workflow file

Fix clippy warnings and add some code factorization #153

Jobs

Run details

Workflow file for this run