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Docs: Sphinx → properdocs migration + descending-drive Poisson fix (+ Optuna parallelization) #214

Workflow file for this run

.github/workflows/build-wheels.yml at 9d9e7dd

	name: Build Wheels

	on:
	push:
	branches:
	- main
	tags:
	- 'v*'
	pull_request:
	branches:
	- main
	release:
	types: [published]
	workflow_dispatch:

	jobs:
	build_wheels:
	name: Build wheels on ${{ matrix.os }}
	runs-on: ${{ matrix.os }}
	strategy:
	fail-fast: false
	matrix:
	# macos-latest = arm64 (Apple Silicon). Intel (x86_64) macos-13
	# runner dropped — GitHub is retiring it.
	os: [ubuntu-latest, macos-latest]

	steps:
	- uses: actions/checkout@v5

	- name: Build wheels
	uses: pypa/cibuildwheel@v2.21
	env:
	# Build for Python 3.12 and 3.13
	CIBW_BUILD: "cp312-* cp313-*"

	# Skip 32-bit builds and musl (Alpine) on Linux
	CIBW_SKIP: "-win32 -manylinux_i686 -musllinux_"

	# Install system dependencies before building (Linux).
	# On manylinux_2_28 scipy installs from a prebuilt wheel, so the
	# openblas-devel that the old source-build fallback needed (and which
	# lives in the PowerTools repo on AlmaLinux 8) is no longer required.
	CIBW_BEFORE_ALL_LINUX: \|
	yum install -y openmpi-devel

	# Install system dependencies before building (macOS)
	CIBW_BEFORE_ALL_MACOS: \|
	brew install open-mpi
	# Ensure command line tools are available
	xcode-select --install 2>/dev/null \|\| true

	# Install NEURON for nrnivmodl, set NMODL_PYLIB to skip find_libpython() which fails in manylinux
	# Run nrnivmodl from within nmodl_files directory so compiled output stays there
	CIBW_BEFORE_BUILD_LINUX: \|
	pip install neuron==8.2.7
	cd myogen/simulator/nmodl_files && NMODL_PYLIB="" nrnivmodl .

	CIBW_BEFORE_BUILD_MACOS: \|
	pip install neuron==8.2.7
	cd myogen/simulator/nmodl_files && nrnivmodl .

	# manylinux_2_28 (glibc >= 2.28) so scipy >= 1.17 prebuilt wheels are
	# available in the build container (scipy dropped manylinux2014).
	CIBW_MANYLINUX_X86_64_IMAGE: manylinux_2_28

	# Custom repair to preserve NEURON mechanisms while adding proper platform tags
	# Standard tools (auditwheel/delocate) strip the architecture directories
	CIBW_REPAIR_WHEEL_COMMAND_LINUX: \|
	python -c "
	import shutil, sys
	from pathlib import Path
	wheel = Path(sys.argv[1])
	dest = Path(sys.argv[2])
	# Rename to manylinux without modifying contents
	new_name = wheel.name.replace('linux_', 'manylinux_2_28_').replace('manylinux2014_', 'manylinux_2_28_')
	shutil.copy2(wheel, dest / new_name)
	" {wheel} {dest_dir}

	# macOS: Just copy wheel as-is (already has correct platform tag)
	CIBW_REPAIR_WHEEL_COMMAND_MACOS: "cp {wheel} {dest_dir}/"

	- name: Show built wheel names
	run: ls -lh wheelhouse/

	- name: Upload wheels
	uses: actions/upload-artifact@v6
	with:
	name: wheels-${{ matrix.os }}
	path: wheelhouse/*.whl
	retention-days: 7

	build_sdist:
	name: Build source distribution
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v5

	- name: Set up Python
	uses: actions/setup-python@v6
	with:
	python-version: "3.12"

	- name: Install build dependencies
	run: \|
	python -m pip install --upgrade pip
	pip install build

	- name: Build sdist
	run: python -m build --sdist --outdir dist/

	- name: Upload sdist
	uses: actions/upload-artifact@v6
	with:
	name: sdist
	path: dist/*.tar.gz
	retention-days: 7

	test_wheels:
	name: Test wheel on ${{ matrix.os }}
	needs: [build_wheels]
	runs-on: ${{ matrix.os }}
	strategy:
	matrix:
	os: [ubuntu-latest, macos-latest] # Match build_wheels matrix
	python-version: ["3.12", "3.13"]

	steps:
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v6
	with:
	python-version: ${{ matrix.python-version }}

	- name: Download wheels
	uses: actions/download-artifact@v7
	with:
	name: wheels-${{ matrix.os }}
	path: dist/

	- name: Install system dependencies (Ubuntu)
	if: runner.os == 'Linux'
	run: \|
	sudo apt-get update
	sudo apt-get install -y openmpi-bin libopenmpi-dev

	- name: Install system dependencies (macOS)
	if: runner.os == 'macOS'
	run: \|
	brew install open-mpi

	- name: Install NEURON
	run: \|
	python -m pip install --upgrade pip
	pip install neuron==8.2.7

	- name: Install wheel
	run: \|
	# dist/ now holds both cp312 and cp313 wheels; install only the one
	# matching this runner's Python so pip doesn't reject the other ABI.
	tag="cp$(echo '${{ matrix.python-version }}' \| tr -d .)"
	pip install dist/"${tag}-${tag}".whl

	- name: Test import
	run: \|
	python -c "import myogen; print('MyoGen imported successfully')"
	python -c "from myogen.simulator import Muscle, SurfaceEMG; print('Core components OK')"

	- name: Test NEURON components (Linux only)
	if: runner.os == 'Linux'
	run: \|
	python -c "from myogen.simulator.neuron.populations import AlphaMN__Pool; print('NEURON components OK')"

	publish:
	name: Publish to PyPI
	needs: [build_wheels, build_sdist, test_wheels]
	runs-on: ubuntu-latest
	if: github.event_name == 'release' \|\| (github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v'))
	permissions:
	id-token: write # Required for OIDC publishing
	contents: write # Required for uploading release assets

	steps:
	- name: Download all artifacts
	uses: actions/download-artifact@v7
	with:
	path: dist/
	merge-multiple: true

	- name: Upload artifacts to GitHub Release
	if: github.event_name == 'release'
	uses: softprops/action-gh-release@v3
	with:
	files: dist/*

	- name: Publish to PyPI
	uses: pypa/gh-action-pypi-publish@release/v1
	with:
	skip-existing: true

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Docs: Sphinx → properdocs migration + descending-drive Poisson fix (+ Optuna parallelization) #214

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Docs: Sphinx → properdocs migration + descending-drive Poisson fix (+ Optuna parallelization) #214

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