ci: update FSL envvars in Dockerfile-ci #3204
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| name: Run Tests | |
| on: | |
| push: | |
| paths: | |
| - 'junifer/**' | |
| - '.github/workflows/**' | |
| pull_request: | |
| paths: | |
| - 'junifer/**' | |
| - '.github/workflows/**' | |
| jobs: | |
| run-tests: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ['3.9', '3.10', '3.11', '3.12', '3.13'] | |
| steps: | |
| - name: Set up system | |
| run: | | |
| bash -c "$(curl -fsSL http://neuro.debian.net/_files/neurodebian-travis.sh)" | |
| sudo apt-get -qq update | |
| sudo apt-get -qq install git-annex-standalone | |
| - name: Configure git for datalad | |
| run: | | |
| git config --global user.email "[email protected]" | |
| git config --global user.name "GitHub Runner" | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: true | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install Python dependencies | |
| run: | | |
| python -m pip install --upgrade pip setuptools wheel | |
| python -m pip install tox tox-gh-actions | |
| - name: Install AFNI | |
| run: | | |
| echo "++ Distro information" | |
| lsb_release -a | |
| echo "++ Add universe repo" | |
| sudo add-apt-repository -y universe | |
| echo "++ Add PPAs for R programs" | |
| sudo add-apt-repository -y "ppa:marutter/rrutter4.0" | |
| sudo add-apt-repository -y "ppa:c2d4u.team/c2d4u4.0+" | |
| echo "++ Update package manager info" | |
| sudo apt-get -qq update | |
| echo "++ Get main dependencies" | |
| sudo apt-get -qq install -y tcsh libssl-dev gsl-bin libjpeg62 vim curl \ | |
| build-essential libcurl4-openssl-dev libxml2-dev libgfortran-11-dev \ | |
| libgomp1 r-base cmake rsync libxm4 | |
| sudo ln -s /usr/lib/x86_64-linux-gnu/libgsl.so.27 /usr/lib/x86_64-linux-gnu/libgsl.so.19 | |
| curl -O https://afni.nimh.nih.gov/pub/dist/bin/misc/@update.afni.binaries | |
| sudo tcsh @update.afni.binaries -package linux_ubuntu_16_64 -bindir /afni | |
| echo "/afni" >> $GITHUB_PATH | |
| if: matrix.python-version == 3.12 | |
| # Bypass AFNI installation failure | |
| continue-on-error: true | |
| - name: Check AFNI | |
| run: | | |
| echo "Using AFNI : $(afni --version)" | |
| if: matrix.python-version == 3.12 | |
| # Bypass AFNI installation failure | |
| continue-on-error: true | |
| - name: Install ANTs | |
| run: | | |
| sudo apt-get install -y -qq unzip | |
| curl -fsSL -o ants.zip https://github.com/ANTsX/ANTs/releases/download/v2.5.2/ants-2.5.2-ubuntu-22.04-X64-gcc.zip | |
| unzip ants.zip -d /opt | |
| mv /opt/ants-2.5.2/bin/* /opt/ants-2.5.2 | |
| rm ants.zip | |
| echo "/opt/ants-2.5.2" >> $GITHUB_PATH | |
| if: matrix.python-version == 3.12 | |
| # Bypass ANTs installation failure | |
| continue-on-error: true | |
| - name: Check ANTs | |
| run: | | |
| echo "Using ANTs : $(antsRegistration --version)" | |
| if: matrix.python-version == 3.12 | |
| # Bypass ANTs installation failure | |
| continue-on-error: true | |
| - name: Install FSL | |
| run: | | |
| curl -fsSL https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fslinstaller.py | python - -d /opt/fsl/ --skip_registration | |
| echo "FSLDIR=/opt/fsl" >> $GITHUB_ENV | |
| echo "FSLOUTPUTTYPE=NIFTI_GZ" >> $GITHUB_ENV | |
| echo "FSLMULTIFILEQUIT=TRUE" >> $GITHUB_ENV | |
| echo "/opt/fsl/bin" >> $GITHUB_PATH | |
| if: matrix.python-version == 3.12 | |
| # Bypass FSL installation failure | |
| continue-on-error: true | |
| - name: Check FSL | |
| run: | | |
| echo "Using FSL : $(flirt -version)" | |
| if: matrix.python-version == 3.12 | |
| # Bypass FSL installation failure | |
| continue-on-error: true | |
| - name: Test with tox | |
| run: | | |
| tox | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| fail_ci_if_error: true | |
| flags: junifer | |
| if: success() && matrix.python-version == 3.12 |