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GeezerVison is showing github.com — run modified notebooks (#117) · Project-MONAI/tutorials@a9eaf33

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  • .github/workflows
    • pep8.yml
    • test-modified.yml
  • modules
    • 2d_slices_from_3d_training.ipynb
  • runner.sh
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‎.github/workflows/pep8.yml‎

Copy file name to clipboardExpand all lines: .github/workflows/pep8.yml
+4-3Lines changed: 4 additions & 3 deletions
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@@ -15,24 +15,25 @@ jobs:
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pep8:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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- uses: actions/checkout@v3
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- name: Set up Python 3.8
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uses: actions/setup-python@v2
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uses: actions/setup-python@v3
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with:
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python-version: 3.8
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- name: cache weekly timestamp
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id: pip-cache
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run: |
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echo "::set-output name=datew::$(date '+%Y-%V')"
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- name: cache for pip
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uses: actions/cache@v2
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uses: actions/cache@v3
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id: cache
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with:
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path: ~/.cache/pip
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key: ${{ runner.os }}-pip-${{ steps.pip-cache.outputs.datew }}
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip wheel
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python -m pip install -r https://raw.githubusercontent.com/Project-MONAI/MONAI/dev/requirements-dev.txt
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python -m pip install -r requirements.txt
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- name: PEP8 check
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run: |
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‎.github/workflows/test-modified.yml‎

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name: build
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on:
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# quick tests of modified notebooks for every pull request
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push:
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branches:
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- main
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pull_request:
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concurrency:
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# automatically cancel the previously triggered workflows when there's a newer version
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group: build-gpu-${{ 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:
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if: github.repository == 'Project-MONAI/tutorials'
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container:
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image: nvcr.io/nvidia/pytorch:21.06-py3 # CUDA 11.3
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options: "--gpus 0"
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runs-on: [self-hosted, linux, x64]
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steps:
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- name: Install MONAI
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id: monai-install
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run: |
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which python
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python -m pip install --upgrade pip wheel
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BUILD_MONAI=0 python -m pip install git+https://github.com/Project-MONAI/MONAI#egg=MONAI
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python -m pip install -r https://raw.githubusercontent.com/Project-MONAI/MONAI/main/requirements-dev.txt
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- uses: actions/checkout@v3
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- name: Notebook quick check
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shell: bash
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run: |
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git fetch origin main
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python -m pip install -r requirements.txt; python -m pip list
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git diff --name-only origin/main | while read line; do if [[ $line == *.ipynb ]]; then ./runner.sh -p "-and -wholename './${line}'"; fi; done;
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# [[ $line == *.ipynb ]] && ./runner.sh --file "$line"
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‎modules/2d_slices_from_3d_training.ipynb‎

Copy file name to clipboardExpand all lines: modules/2d_slices_from_3d_training.ipynb
+1-1Lines changed: 1 addition & 1 deletion
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@@ -6,7 +6,7 @@
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"source": [
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"# Training with 2D slices from volumes\n",
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"\n",
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"This tutorial shows how to train a network with 2D samples from 3D inputs.\n",
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"This tutorial shows how to train a network with 2D slice samples from 3D inputs.\n",
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"\n",
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"It mainly demonstrates 2d slice dataset using `monai.data.PatchIterd` and `monai.data.GridPatchDataset`.\n",
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"\n",
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‎runner.sh‎

Copy file name to clipboardExpand all lines: runner.sh
+2-1Lines changed: 2 additions & 1 deletion
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failfast=true
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;;
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-p|--pattern)
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pattern="$2"
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pattern+="$2"
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echo $pattern
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shift
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;;
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-k|--kernelspec)

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