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chore(ci): Set FSLDIR in main environment
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.github/workflows/pythonpackage.yml

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@@ -69,14 +69,15 @@ jobs:
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with:
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python-version: ${{ matrix.python-version }}
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mamba-version: "*"
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channels: ${{ env.FSLCONDA }},conda-forge,defaults
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channels: ${{ env.FSLCONDA }},conda-forge
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channel-priority: true
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- name: Install FSL
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run: |
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mamba install fsl-avwutils
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mamba env config vars set FSLDIR="$CONDA_PREFIX" FSLOUTPUTTYPE="NIFTI_GZ"
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# Hack because we're not doing a full FSL install
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echo "6.0.7.9" > $CONDA_PREFIX/etc/fslversion
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- name: Set FSLDIR
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run: echo FSLDIR=$CONDA_PREFIX >> $GITHUB_ENV
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- name: Upgrade pip
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run: |
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python -m pip install --upgrade pip

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