Merge pull request #19 from cds-astro/fix-docs-notebook #3

Workflow file for this run

.github/workflows/deploy_pypi.yml at 02940e9

	# 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

	name: publish-cdshealpix-wheels

	# Exec only if a tag starting by 'v' is pushed
	# see: https://docs.github.com/en/actions/reference/workflow-syntax-for-github-actions
	on:
	push:
	tags:
	- v*
	# Allows to run this workflow manually from the Actions tab
	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:

	# Linux is specifi because of manylinux, we have to use a docker file
	build-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
	# We are now in CentOS 7 64 bits
	steps:
	- name: "Checkout the full project"
	uses: actions/checkout@v4
	# 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 publish wheels"
	shell: bash
	env:
	MATURIN_USERNAME: ${{ secrets.PYPI_USERNAME_FXP }}
	MATURIN_PASSWORD: ${{ secrets.PYPI_PASSWORD_FXP }}
	run: \|
	source $HOME/.cargo/env
	for PYBIN in /opt/python/cp3{8,9,10,11,12}-*/bin; do
	"${PYBIN}/pip" install --upgrade pip
	"${PYBIN}/pip" install maturin
	"${PYBIN}/maturin" -V
	rustc -vV
	echo "${PYBIN}/python"
	"${PYBIN}/maturin" publish -i "${PYBIN}/python" --no-sdist --skip-existing --compatibility manylinux2014 --username "$MATURIN_USERNAME"
	"${PYBIN}/maturin" publish -i "${PYBIN}/python" --no-sdist --skip-existing --compatibility musllinux_1_2 --username "$MATURIN_USERNAME"
	done

	# Linux is specifi because of manylinux, we have to use a docker file
	# Replace because last version was generating x86_64 wheels :o/
	#build-linux32-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_i686
	# # We are now in CentOS 7 32 bits
	# steps:
	# # Checkout the project
	# - name: "Checkout the full project"
	# uses: actions/checkout@v1
	# # 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 -- --default-host i686-unknown-linux-gnu -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 publish wheels"
	# shell: bash
	# env:
	# MATURIN_USERNAME: ${{ secrets.PYPI_USERNAME_FXP }}
	# MATURIN_PASSWORD: ${{ secrets.PYPI_PASSWORD_FXP }}
	# run: \|
	# source $HOME/.cargo/env
	# for PYBIN in /opt/python/cp3[78910]*/bin; do
	# "${PYBIN}/pip" install --upgrade pip
	# "${PYBIN}/pip" install maturin
	# "${PYBIN}/maturin" -V
	# rustc -vV
	# echo "${PYBIN}/python"
	# echo "CARGO_BUILD_TARGET: ${CARGO_BUILD_TARGET}"
	# "${PYBIN}/maturin" publish -i "${PYBIN}/python" --no-sdist --skip-existing --compatibility manylinux2014 --username "$MATURIN_USERNAME" --target i686-unknown-linux-gnu
	# done

	# Comming in large parts from @odidev in MOCPy pull request
	build-linux32-wheels:
	runs-on: ubuntu-latest
	env:
	MATURIN_USERNAME: ${{ secrets.PYPI_USERNAME_FXP }}
	MATURIN_PASSWORD: ${{ secrets.PYPI_PASSWORD_FXP }}
	img: quay.io/pypa/manylinux2014_i686
	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 ${{ github.workspace }}:/ws:rw --workdir=/ws \
	-e MATURIN_USERNAME=${{ env.MATURIN_USERNAME }} \
	-e MATURIN_PASSWORD=${{ env.MATURIN_PASSWORD}} \
	${{ env.img }} \
	bash -exc 'curl --proto "=https" --tlsv1.2 -sSf https://sh.rustup.rs \| sh -s -- -y && \
	source $HOME/.cargo/env && \
	for PYBIN in /opt/python/cp3{8,9,10,11,12}-*/bin; do
	echo "Loop on PYBIN: $PYBIN"
	"${PYBIN}/pip" install --upgrade pip
	"${PYBIN}/pip" install maturin
	"${PYBIN}/maturin" -V
	rustc -vV
	echo "${PYBIN}/python"
	"${PYBIN}/maturin" publish -i "${PYBIN}/python" -v --no-sdist --skip-existing --compatibility manylinux2014 --username "$MATURIN_USERNAME"
	"${PYBIN}/maturin" publish -i "${PYBIN}/python" -v --no-sdist --skip-existing --compatibility musllinux_1_2 --username "$MATURIN_USERNAME"
	done'



	# Comming in large parts from @odidev in MOCPy pull request
	build-aarch64-wheels:
	runs-on: ubuntu-latest
	env:
	MATURIN_USERNAME: ${{ secrets.PYPI_USERNAME_FXP }}
	MATURIN_PASSWORD: ${{ secrets.PYPI_PASSWORD_FXP }}
	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 ${{ github.workspace }}:/ws:rw --workdir=/ws \
	-e MATURIN_USERNAME=${{ env.MATURIN_USERNAME }} \
	-e MATURIN_PASSWORD=${{ env.MATURIN_PASSWORD}} \
	${{ 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{8,9,10,11,12}-*/bin; do
	echo "Loop on PYBIN: $PYBIN"
	"${PYBIN}/pip" install maturin
	"${PYBIN}/maturin" -V
	rustc -vV
	echo "${PYBIN}/python"
	"${PYBIN}/maturin" publish -i "${PYBIN}/python" -v --skip-existing --compatibility manylinux2014 --username "$MATURIN_USERNAME" --target aarch64-unknown-linux-gnu --config "net.git-fetch-with-cli = true"
	"${PYBIN}/maturin" publish -i "${PYBIN}/python" -v --skip-existing --compatibility musllinux_1_2 --username "$MATURIN_USERNAME" --target aarch64-unknown-linux-gnu --config "net.git-fetch-with-cli = true"
	done'


	build-windows-wheels:
	runs-on: ${{ matrix.os }}
	strategy:
	# See https://docs.github.com/en/actions/reference/workflow-syntax-for-github-actions#jobsjob_idstrategyfail-fast
	# run all matrix jobs even if on is failling (default behaviour is to stop all jobs)
	fail-fast: false
	matrix:
	os: [windows-latest]
	python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
	steps:
	# Checkout the project
	- uses: actions/checkout@v4
	# Set up python, see https://docs.github.com/en/actions/guides/building-and-testing-python
	- name: Set up Python ${{ matrix.python-version }} on ${{ matrix.os }}
	uses: actions/setup-python@v4
	with:
	python-version: ${{ matrix.python-version }}
	# For secrets, see https://docs.github.com/en/actions/reference/encrypted-secrets
	- name: Build and publish wheel for Python ${{ matrix.python-version }} on ${{ matrix.os }}
	# We do not use environement variable for user, because it seems that the way of providing it in the command
	# line is not the same for macos and for windows. We should create 2 different actions (see
	# https://docs.github.com/en/actions/reference/encrypted-secrets )
	env:
	MATURIN_USERNAME: ${{ secrets.PYPI_USERNAME_FXP }}
	MATURIN_PASSWORD: ${{ secrets.PYPI_PASSWORD_FXP }}
	run: \|
	#python3 -m pip install maturin
	pip install --upgrade pip
	pip install maturin
	#maturin build --release --no-sdist
	#maturin publish --no-sdist --skip-existing --username fxpineau
	maturin -V
	rustc -vV
	maturin publish --interpreter python${{matrix.python_version}} --no-sdist --skip-existing --username fxpineau

	build-macos-wheels:
	runs-on: ${{ matrix.os }}
	strategy:
	# See https://docs.github.com/en/actions/reference/workflow-syntax-for-github-actions#jobsjob_idstrategyfail-fast
	# run all matrix jobs even if on is failling (default behaviour is to stop all jobs)
	fail-fast: false
	matrix:
	os: [macOS-latest]
	python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
	steps:
	# Checkout the project
	- uses: actions/checkout@v4
	# Set up python, see https://docs.github.com/en/actions/guides/building-and-testing-python
	- name: Set up Python ${{ matrix.python-version }} on ${{ matrix.os }}
	uses: actions/setup-python@v4
	with:
	python-version: ${{ matrix.python-version }}
	# For secrets, see https://docs.github.com/en/actions/reference/encrypted-secrets
	- name: Build and publish wheel for Python ${{ matrix.python-version }} on ${{ matrix.os }}
	# We do not use environement variable for user, because it seems that the way of providing it in the command
	# line is not the same for macos and for windows. We should create 2 different actions (see
	# https://docs.github.com/en/actions/reference/encrypted-secrets )
	env:
	MATURIN_USERNAME: ${{ secrets.PYPI_USERNAME_FXP }}
	MATURIN_PASSWORD: ${{ secrets.PYPI_PASSWORD_FXP }}
	run: \|
	#python3 -m pip install maturin
	rustup target add aarch64-apple-darwin
	pip install --upgrade pip
	pip install maturin
	maturin -V
	rustc -vV
	echo "${PYBIN}/python"
	maturin publish --interpreter python${{matrix.python_version}} --no-sdist --universal2 --skip-existing --username "$MATURIN_USERNAME"
	maturin publish --interpreter python${{matrix.python_version}} --no-sdist --skip-existing --username "$MATURIN_USERNAME"

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Merge pull request #19 from cds-astro/fix-docs-notebook #3

Workflow file

Merge pull request #19 from cds-astro/fix-docs-notebook #3

Jobs

Run details

Workflow file for this run