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🔖 v1.8.7 to conincide with FCP-INDI/C-PAC#2100 (#76)
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‎.coveragerc‎

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‎.github/Dockerfiles/c-pac_api.latest.Dockerfile‎

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# Copyright (C) 2023-2024 C-PAC Developers
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# This file is modified from a file that is part of C-PAC.
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# C-PAC is free software: you can redistribute it and/or modify it under
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# the terms of the GNU Lesser General Public License as published by the
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# Free Software Foundation, either version 3 of the License, or (at your
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# option) any later version.
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# C-PAC is distributed in the hope that it will be useful, but WITHOUT
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# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
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# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
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# License for more details.
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# You should have received a copy of the GNU Lesser General Public
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# License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
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FROM ghcr.io/fcp-indi/c-pac/ubuntu:jammy-non-free as src
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LABEL org.opencontainers.image.description "NOT INTENDED FOR USE OTHER THAN AS A DRY-RUN TESTING IMAGE \
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Dry-run C-PAC latest API."
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LABEL org.opencontainers.image.source https://github.com/FCP-INDI/cpac
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USER root
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COPY --from=fcpindi/c-pac:latest /code /code
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RUN mkdir -p /home/user/c-pac_user \
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&& chown -R c-pac_user:c-pac /home/user/c-pac_user \
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&& chown -R c-pac_user:c-pac /code \
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&& apt-get update && apt-get install -y \
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git \
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python3-pip \
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python3.10 \
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python-is-python3 \
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&& rm -rf /var/lib/apt/lists/*
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ENV PYTHONUSERBASE=/home/c-pac_user/.local
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ENV PATH=$PATH:/home/c-pac_user/.local/bin \
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PYTHONPATH=$PYTHONPATH:$PYTHONUSERBASE/lib/python3.10/site-packages
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USER c-pac_user
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RUN pip install -r /code/requirements.txt && pip install -e /code
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ENV FSLDIR="/FSLDIR"
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ENTRYPOINT [ "/code/run.py" ]

‎.github/Dockerfiles/c-pac_api.nightly.Dockerfile‎

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# Copyright (C) 2023-2024 C-PAC Developers
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# This file is modified from a file that is part of C-PAC.
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# C-PAC is free software: you can redistribute it and/or modify it under
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# the terms of the GNU Lesser General Public License as published by the
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# Free Software Foundation, either version 3 of the License, or (at your
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# option) any later version.
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# C-PAC is distributed in the hope that it will be useful, but WITHOUT
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# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
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# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
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# License for more details.
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# You should have received a copy of the GNU Lesser General Public
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# License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
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FROM ghcr.io/fcp-indi/c-pac/ubuntu:jammy-non-free as src
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LABEL org.opencontainers.image.description "NOT INTENDED FOR USE OTHER THAN AS A DRY-RUN TESTING IMAGE \
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Dry-run C-PAC nightly API."
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LABEL org.opencontainers.image.source https://github.com/FCP-INDI/cpac
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USER root
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COPY --from=fcpindi/c-pac:nightly /code /code
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RUN mkdir -p /home/user/c-pac_user \
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&& chown -R c-pac_user:c-pac /home/user/c-pac_user \
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&& chown -R c-pac_user:c-pac /code \
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&& apt-get update && apt-get install -y \
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git \
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python3-pip \
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python3.10 \
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python-is-python3 \
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&& rm -rf /var/lib/apt/lists/*
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ENV PYTHONUSERBASE=/home/c-pac_user/.local
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ENV PATH=$PATH:/home/c-pac_user/.local/bin \
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PYTHONPATH=$PYTHONPATH:$PYTHONUSERBASE/lib/python3.10/site-packages
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USER c-pac_user
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RUN pip install -r /code/requirements.txt && pip install -e /code
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ENV FSLDIR="/FSLDIR"
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ENTRYPOINT [ "/code/run.py" ]

‎.github/workflows/pythonpublish.yml‎ renamed to ‎.github/workflows/pythonpublish.yaml‎

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# This workflows will upload a Python Package using Twine when a release is created
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# This workflow will upload a Python Package using Twine when a release is created
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# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
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name: Upload Python Package

‎.github/workflows/test_cpac.yaml‎

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# This workflow will test cpac
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name: Test cpac
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on:
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push:
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paths-ignore:
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- README.rst
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jobs:
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set_docker_image:
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outputs:
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docker_image: ${{ steps.set_docker_image.outputs.docker_image }}
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runs-on: ubuntu-latest
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steps:
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- id: set_docker_image
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name: set tag name
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run: |
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DOCKER_IMAGE="ghcr.io/${{ github.repository }}/api-test"
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DOCKER_IMAGE="${DOCKER_IMAGE@L}"
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echo "docker_image=${DOCKER_IMAGE}" >> "${GITHUB_OUTPUT}"
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build_dry_run_image:
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needs: set_docker_image
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runs-on: ubuntu-latest
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steps:
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- name: Set up Docker Buildx
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uses: docker/[email protected]
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- name: Log in to GitHub Container Registry
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uses: docker/[email protected]
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with:
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registry: ghcr.io
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username: ${{ github.actor }}
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password: ${{ secrets.GITHUB_TOKEN }}
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- uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- name: Build and push
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uses: docker/[email protected]
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with:
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context: .
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file: ./.github/Dockerfiles/c-pac_api.${{ matrix.tag }}.Dockerfile
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provenance: false
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sbom: false
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push: true
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tags: |
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${{ needs.set_docker_image.outputs.docker_image }}:${{ matrix.tag }}
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strategy:
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matrix:
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tag: [latest, nightly]
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test_cpac:
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env:
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APPTAINER_CACHEDIR: ${{ github.workspace }}/.apptainer/cache
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APPTAINER_TMPDIR: ${{ github.workspace }}/.apptainer/tmp
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needs:
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- build_dry_run_image
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- set_docker_image
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runs-on: ubuntu-latest
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strategy:
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matrix:
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apptainer: [1.0.0, 1.3.0]
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go: [1.14]
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platform: [apptainer, docker]
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python: ['3.10', 3.11, 3.12]
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tag: [latest, nightly]
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exclude:
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- platform: apptainer
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python: 3.11
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- platform: apptainer
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python: 3.12
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steps:
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- name: Clear up some space on runner
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run: |
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sudo rm -rf /usr/share/dotnet
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sudo rm -rf /opt/ghc
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sudo rm -rf "/usr/local/share/boost"
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- uses: actions/checkout@v4
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- name: Set up Go
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uses: actions/setup-go@v5
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with:
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cache: false
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go-version: ${{ matrix.go }}
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python }}
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- name: Install --upgrade pip setuptools wheel
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run: python -m pip install --upgrade pip setuptools wheel
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- name: Setup apptainer
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if: ${{ matrix.platform == 'apptainer' }}
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uses: eWaterCycle/setup-apptainer@v2
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with:
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apptainer-version: ${{ matrix.apptainer }}
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- name: Install cpac
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run: cd $GITHUB_WORKSPACE && pip install -e ".[dev,testing,tsconcat]"
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- name: Pull images
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if: ${{ matrix.platform == 'apptainer' }}
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run: |
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mkdir -p ${{ env.APPTAINER_CACHEDIR }}
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mkdir -p ${{ env.APPTAINER_TMPDIR }}
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export APPTAINER_CACHEDIR=${{ env.APPTAINER_CACHEDIR }}
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export SINGULARITY_CACHEDIR=${{ env.APPTAINER_CACHEDIR }}
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export APPTAINER_TMPDIR=${{ env.APPTAINER_TMPDIR }}
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export SINGULARITY_TMPDIR=${{ env.APPTAINER_TMPDIR }}
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cpac --platform ${{ matrix.platform }} pull --image ${{ needs.set_docker_image.outputs.docker_image }} --tag ${{ matrix.tag }}
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- name: Test cpac, platform and tag specified
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run: |
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coverage run --append -m pytest --basetemp=${PWD}/tmp --doctest-modules --image=${{ needs.set_docker_image.outputs.docker_image }} --platform ${{ matrix.platform }} --tag ${{ matrix.tag }} .
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coverage report -m
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- name: Test cpac, platform specified, tag unspecified
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if: ${{ matrix.tag == 'latest' }} and ${{ matrix.platform == 'docker' }}
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run: |
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coverage run --append -m pytest --basetemp=${PWD}/tmp --doctest-modules --image=${{ needs.set_docker_image.outputs.docker_image }} --platform ${{ matrix.platform }} .
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coverage report -m
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- name: Test cpac, platform unspecified, tag specified
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if: ${{ matrix.platform == 'docker' }}
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run: |
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coverage run --append -m pytest --basetemp=${PWD}/tmp --doctest-modules --image=${{ needs.set_docker_image.outputs.docker_image }} --tag ${{ matrix.tag }} .
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coverage report -m
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- name: Test cpac, platform and tag unspecified
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if: ${{ matrix.platform == 'docker' }} && ${{ matrix.tag }} == 'latest'
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run: |
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coverage run --append -m pytest --basetemp=${PWD}/tmp --doctest-modules --image=${{ needs.set_docker_image.outputs.docker_image }} .
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coverage report -m
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- name: Report coverage
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uses: AndreMiras/coveralls-python-action@v20201129
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with:
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parallel: true
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flag-name: Test cpac ${{ matrix.platform }} with Python ${{ matrix.python }}
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continue-on-error: true
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finalize_coverage-report:
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needs:
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- test_cpac
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runs-on: ubuntu-latest
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steps:
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- name: Finalize coverage report
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uses: AndreMiras/coveralls-python-action@v20201129
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with:
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parallel-finished: true
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continue-on-error: true
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update_README:
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# Only update README if tests succeed
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needs:
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- test_cpac
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- name: Install cpac
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run: |
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export DEB_PYTHON_INSTALL_LAYOUT=deb_system
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cd $GITHUB_WORKSPACE
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pip install .
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- name: Configure Git credentials
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uses: oleksiyrudenko/[email protected]
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with:
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global: true
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token: ${{ secrets.GITHUB_TOKEN }}
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- name: Update README
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run: |
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(head -n $(read -d : <<< $(less README.rst | grep ".. BEGIN USAGE" -n); expr $REPLY + 1) README.rst; \
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printf ".. code-block:: shell\n\n cpac --help\n"; \
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cpac --help | sed 's/^/ /'; \
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tail --lines=+$(read -d : <<< $(less README.rst | grep ".. END USAGE" -n); expr $REPLY - 1) README.rst\
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) > tempREADME &&
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mv tempREADME README.rst &
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wait %1
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if [[ $(git diff --numstat README.rst) ]]; then
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git add README.rst
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git commit -m ":memo: Update usage from helpstring"
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git push origin HEAD:${GITHUB_REF}
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fi
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shell: bash

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