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Update run workflows (#215)
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.github/workflows/run_linux_cuda.yml

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name: run-linux-cuda
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name: Run notebook (Linux, CUDA)
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on:
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workflow_dispatch:
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runs-on: [self-hosted, Linux, X64, CUDA]
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container:
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image: martinkim0/scvi-tools:py${{ inputs.python-version }}-cu${{ inputs.cuda-version }}-devel-${{ inputs.scvi-tools-version }}
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image: scverse/scvi-tools:py${{ inputs.python-version }}-cu${{ inputs.cuda-version }}-tutorials-${{ inputs.scvi-tools-version }}
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options: --user root --gpus all
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timeout-minutes: 600 # lenient timeout for scbasset tutorial
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steps:
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- name: Checkout
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uses: actions/checkout@v3
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uses: actions/checkout@v4
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- name: Install Python kernel
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run: |
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run: |
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python -m jupyter nbconvert --execute --inplace ${{ inputs.notebook-path }}
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- name: Submit pull request with changes
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- name: Submit PR changes
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uses: peter-evans/create-pull-request@v5
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with:
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commit-message: Rerun ${{ inputs.notebook-path }}

.github/workflows/run_linux_cuda_branch.yml

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name: run-linux-cuda-branch
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name: Run notebook (Linux, CUDA, branch)
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on:
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workflow_dispatch:
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runs-on: [self-hosted, Linux, X64, CUDA]
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container:
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image: martinkim0/scvi-tools:py${{ inputs.python-version }}-cu${{ inputs.cuda-version }}-tutorials-${{ inputs.branch-name}}
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image: scverse/scvi-tools:py${{ inputs.python-version }}-cu${{ inputs.cuda-version }}-tutorials-${{ inputs.branch-name}}
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options: --user root --gpus all
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timeout-minutes: 600 # lenient timeout for scbasset tutorial
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run: |
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python -m jupyter nbconvert --execute --inplace ${{ inputs.notebook-path }}
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- name: Submit pull request with changes
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- name: Submit PR with changes
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uses: peter-evans/create-pull-request@v5
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with:
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commit-message: Execute ${{ inputs.notebook-path }}

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