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Merge remote-tracking branch 'refs/remotes/upstream/main' into on-error-abort
# Conflicts: # cwltool/executors.py
2 parents 1e4b9ca + 048eb55 commit 5de80a1

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‎.circleci/config.yml

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version: 2.1
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parameters:
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REF:
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type: string
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default: ''
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description: Optional tag to build
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jobs:
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arm-wheels:
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parameters:
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build:
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type: string
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image:
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type: string
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machine:
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image: ubuntu-2404:current
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resource_class: arm.medium # 2 vCPUs
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environment:
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CIBW_ARCHS: "aarch64"
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CIBW_MANYLINUX_AARCH64_IMAGE: "<< parameters.image >>"
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CIBW_MUSLLINUX_AARCH64_IMAGE: "<< parameters.image >>"
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CIBW_BUILD: "<< parameters.build >>"
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steps:
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- checkout
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- when:
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condition: << pipeline.parameters.REF >>
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steps:
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- run:
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name: Checkout branch/tag << pipeline.parameters.REF >>
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command: |
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echo "Switching to branch/tag << pipeline.parameters.REF >> if it exists"
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git checkout << pipeline.parameters.REF >> || true
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git pull origin << pipeline.parameters.REF >> || true
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- run:
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name: install cibuildwheel and other build reqs
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command: |
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python3 -m pip install --upgrade pip setuptools setuptools_scm[toml]
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python3 -m pip install -rcibw-requirements.txt
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- run:
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name: pip freeze
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command: |
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python3 -m pip freeze
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- run:
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name: list wheels
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command: |
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python3 -m cibuildwheel . --print-build-identifiers
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- run:
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name: cibuildwheel
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command: |
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python3 -m cibuildwheel .
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- store_test_results:
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path: test-results/
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- store_artifacts:
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path: wheelhouse/
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# - when:
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# condition:
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# or:
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# - matches:
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# pattern: ".+"
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# value: "<< pipeline.git.tag >>"
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# - << pipeline.parameters.REF >>
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# steps:
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# - run:
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# environment:
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# TWINE_NONINTERACTIVE: "1"
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# command: |
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# python3 -m pip install twine
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# python3 -m twine upload --verbose --skip-existing wheelhouse/*
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workflows:
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wheels: # This is the name of the workflow, feel free to change it to better match your workflow.
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# Inside the workflow, you define the jobs you want to run.
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jobs:
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- arm-wheels:
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name: arm-wheels-manylinux_2_28
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filters:
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branches:
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only: main
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tags:
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only: /.*/
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build: "*manylinux*"
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image: quay.io/pypa/manylinux_2_28_aarch64
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- arm-wheels:
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name: arm-wheels-musllinux_1_2
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filters:
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branches:
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only: main
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tags:
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only: /.*/
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build: "*musllinux*"
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image: quay.io/pypa/musllinux_1_2_aarch64

‎.github/workflows/ci-tests.yml

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with:
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fetch-depth: 0
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- name: Set up Singularity
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- name: Set up Singularity and environment-modules
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if: ${{ matrix.step == 'unit' || matrix.step == 'mypy' }}
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run: |
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wget --no-verbose https://github.com/sylabs/singularity/releases/download/v3.10.4/singularity-ce_3.10.4-focal_amd64.deb
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sudo apt-get install -y ./singularity-ce_3.10.4-focal_amd64.deb
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sudo apt-get install -y ./singularity-ce_3.10.4-focal_amd64.deb environment-modules
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- name: Give the test runner user a name to make provenance happy.
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if: ${{ matrix.step == 'unit' || matrix.step == 'mypy' }}
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with:
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fetch-depth: 0
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- name: Set up Singularity
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- name: Set up Singularity and environment-modules
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run: |
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wget --no-verbose https://github.com/sylabs/singularity/releases/download/v3.10.4/singularity-ce_3.10.4-focal_amd64.deb
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sudo apt-get install -y ./singularity-ce_3.10.4-focal_amd64.deb
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sudo apt-get install -y ./singularity-ce_3.10.4-focal_amd64.deb environment-modules
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- name: Give the test runner user a name to make provenance happy.
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run: sudo usermod -c 'CI Runner' "$(whoami)"
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steps:
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- uses: actions/checkout@v4
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- name: Set up Singularity
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- name: Set up Singularity and environment-modules
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if: ${{ matrix.container == 'singularity' }}
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run: |
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wget --no-verbose https://github.com/sylabs/singularity/releases/download/v3.10.4/singularity-ce_3.10.4-jammy_amd64.deb
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sudo apt-get install -y ./singularity-ce_3.10.4-jammy_amd64.deb
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sudo apt-get install -y ./singularity-ce_3.10.4-jammy_amd64.deb environment-modules
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- name: Singularity cache
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if: ${{ matrix.container == 'singularity' }}
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steps:
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- uses: actions/checkout@v4
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- name: Set up Singularity
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- name: Set up Singularity and environment-modules
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run: |
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wget --no-verbose https://github.com/sylabs/singularity/releases/download/v3.10.4/singularity-ce_3.10.4-jammy_amd64.deb
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sudo apt-get install -y ./singularity-ce_3.10.4-jammy_amd64.deb
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sudo apt-get install -y ./singularity-ce_3.10.4-jammy_amd64.deb environment-modules
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- name: Set up Python
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uses: actions/setup-python@v5

‎.github/workflows/wheels.yml

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name: Python package build and publish
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on:
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release:
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types: [published]
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workflow_dispatch: {}
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repository_dispatch: {}
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push:
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branches:
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- main
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concurrency:
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group: wheels-${{ github.event.pull_request.number || github.ref }}
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cancel-in-progress: true
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jobs:
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build_wheels:
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name: ${{ matrix.image }} wheels
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runs-on: ubuntu-24.04
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strategy:
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matrix:
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include:
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- image: manylinux_2_28_x86_64
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build: "*manylinux*"
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- image: musllinux_1_2_x86_64
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build: "*musllinux*"
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steps:
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- uses: actions/checkout@v4
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if: ${{ github.event_name != 'repository_dispatch' }}
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with:
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fetch-depth: 0 # slow, but gets all the tags
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- uses: actions/checkout@v4
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if: ${{ github.event_name == 'repository_dispatch' }}
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with:
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fetch-depth: 0 # slow, but gets all the tags
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ref: ${{ github.event.client_payload.ref }}
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# - name: Set up QEMU
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# if: runner.os == 'Linux'
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# uses: docker/setup-qemu-action@v2
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# with:
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# platforms: all
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- name: Build wheels
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uses: pypa/[email protected]
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env:
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CIBW_BUILD: ${{ matrix.build }}
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CIBW_MANYLINUX_X86_64_IMAGE: quay.io/pypa/${{ matrix.image }}
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CIBW_MUSLLINUX_X86_64_IMAGE: quay.io/pypa/${{ matrix.image }}
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# configure cibuildwheel to build native 64-bit archs ('auto64'), and some
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# emulated ones
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# Linux arm64 wheels are built on circleci
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CIBW_ARCHS_LINUX: auto64 # ppc64le s390x
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- uses: actions/upload-artifact@v4
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with:
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name: artifact-${{ matrix.image }}
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path: ./wheelhouse/*.whl
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build_sdist:
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name: Build source distribution
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runs-on: ubuntu-24.04
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steps:
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- uses: actions/checkout@v4
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if: ${{ github.event_name != 'repository_dispatch' }}
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with:
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fetch-depth: 0 # slow, but gets all the tags
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- uses: actions/checkout@v4
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if: ${{ github.event_name == 'repository_dispatch' }}
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with:
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fetch-depth: 0 # slow, but gets all the tags
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ref: ${{ github.event.client_payload.ref }}
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- name: Build sdist
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run: pipx run build --sdist
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- uses: actions/upload-artifact@v4
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with:
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name: artifact-source
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path: dist/*.tar.gz
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build_wheels_macos:
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name: Build wheels on ${{ matrix.os }}
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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# macos-13 is an intel runner, macos-14 is apple silicon
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os: [macos-13, macos-14]
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steps:
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- uses: actions/checkout@v4
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if: ${{ github.event_name != 'repository_dispatch' }}
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with:
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fetch-depth: 0 # slow, but gets all the tags
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- uses: actions/checkout@v4
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if: ${{ github.event_name == 'repository_dispatch' }}
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with:
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fetch-depth: 0 # slow, but gets all the tags
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ref: ${{ github.event.client_payload.ref }}
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- name: Build wheels
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uses: pypa/[email protected]
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- uses: actions/upload-artifact@v4
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with:
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name: artifact-${{ matrix.os }}-${{ strategy.job-index }}
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path: ./wheelhouse/*.whl
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# upload_pypi:
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# needs: [build_wheels, build_sdist]
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# runs-on: ubuntu-24.04
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# environment: deploy
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# permissions:
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# id-token: write
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# if: (github.event_name == 'release' && github.event.action == 'published') || (github.event_name == 'repository_dispatch' && github.event.client_payload.publish_wheel == true)
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# steps:
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# - uses: actions/download-artifact@v4
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# with:
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# # unpacks default artifact into dist/
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# pattern: artifact-*
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# merge-multiple: true
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# path: dist
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# - name: Publish package distributions to PyPI
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# uses: pypa/gh-action-pypi-publish@release/v1
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# with:
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# skip-existing: true

‎MANIFEST.in

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include tests/checker_wf/*
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include tests/subgraph/*
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include tests/input_deps/*
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recursive-include tests/test_deps_env
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include tests/trs/*
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include tests/wf/generator/*
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include cwltool/py.typed

‎README.rst

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$ cwl-runner --tmp-outdir-prefix=/Users/username/project --tmpdir-prefix=/Users/username/project wc-tool.cwl wc-job.json
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Docker default platform on macOS with Apple Silicon
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===================================================
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If macOS users want to run CWL tools/workflows using ``cwltool`` with Docker and their software containers only have support for amd64 (64-bit x86) CPUs, but they have an Apple Silicon (aarch64/arm64) CPU,
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they run into the error:
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WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested.
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To fix this, export the following environment variable before executing `cwltool`:
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``export DOCKER_DEFAULT_PLATFORM=linux/amd64``
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To automatically have this variable set in the future, add the same command to ones respective shell profile (e.g. ``~/.zshrc``, ``~/.bash_profile``).
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Using uDocker
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=============
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‎cibw-requirements.txt

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cibuildwheel==2.21.3

‎cwltool/executors.py

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self.pending_jobs_lock = threading.Lock()
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self.max_ram = int(psutil.virtual_memory().available / 2**20)
281-
self.max_cores = float(psutil.cpu_count())
281+
self.max_cores = float(psutil.cpu_count() or 1)
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self.max_cuda = cuda_version_and_device_count()[1]
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self.allocated_ram = float(0)
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self.allocated_cores = float(0)
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logger: logging.Logger,
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runtime_context: RuntimeContext,
441441
) -> None:
442-
self.taskqueue: TaskQueue = TaskQueue(threading.Lock(), psutil.cpu_count(), runtime_context)
442+
self.taskqueue: TaskQueue = TaskQueue(threading.Lock(), int(math.ceil(self.max_cores)), runtime_context)
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try:
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jobiter = process.job(job_order_object, self.output_callback, runtime_context)
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‎cwltool/software_requirements.py

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def __init__(self, args: argparse.Namespace) -> None:
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"""Initialize."""
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self.tool_dependency_dir: Optional[str] = None
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self.dependency_resolvers_config_file: Optional[str] = None
5355
conf_file = getattr(args, "beta_dependency_resolvers_configuration", None)
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tool_dependency_dir = getattr(args, "beta_dependencies_directory", None)
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conda_dependencies = getattr(args, "beta_conda_dependencies", None)

‎lint-requirements.txt

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flake8-bugbear<24.9
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flake8-bugbear<24.11
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black==24.*
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codespell

‎pyproject.toml

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"types-requests",
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"types-psutil",
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"importlib_resources>=1.4;python_version<'3.9'",
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"ruamel.yaml>=0.16.0,<0.18",
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"ruamel.yaml>=0.16.0,<0.19",
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"schema-salad>=8.7,<9",
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"cwl-utils>=0.32",
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"toml",
@@ -17,6 +17,19 @@ build-backend = "setuptools.build_meta"
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[tool.setuptools_scm]
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write_to = "cwltool/_version.py"
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[tool.cibuildwheel]
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test-command = "python -m pytest --ignore cwltool/schemas -n logical --dist worksteal --junitxml={project}/test-results/junit_$(python -V | awk '{print $2}')_${AUDITWHEEL_PLAT}.xml -k 'not (test_bioconda or test_env_filtering or test_udocker)' --pyargs cwltool"
22+
test-requires = "-r test-requirements.txt"
23+
test-extras = "deps"
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skip = "pp*"
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# ^ skip building wheels on PyPy (any version)
26+
build-verbosity = 1
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environment = { CWLTOOL_USE_MYPYC="1", MYPYPATH="$(pwd)/mypy-stubs" }
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# Install system library
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[tool.cibuildwheel.linux]
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before-all = "apk add libxml2-dev libxslt-dev nodejs || yum install -y libxml2-devel libxslt-devel nodejs environment-modules || apt-get install -y --no-install-recommends libxml2-dev libxslt-dev nodejs environment-modules"
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[tool.black]
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line-length = 100
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target-version = [ "py39" ]

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