Rename CSF segmentations in derivatives (#154) #177
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| name: Dataset Validator | |
| on: | |
| push: | |
| branches: [ master ] | |
| pull_request: | |
| branches: [ master ] | |
| jobs: | |
| Validate: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v2 | |
| with: | |
| # make sure to download directly from the PR's repo, whether that is this repo or a fork | |
| # By default github generates a merge commit for each PR in this repo, but only for the one branch under test | |
| # but `git-annex` needs access to *two* branches: the current branch and `git-annex` | |
| # this might be subtly buggy since it is testing the remote version, not the merged version | |
| # | |
| # *if* this is not a pull request, this will fall back to its default behaviour. | |
| repository: ${{github.event.pull_request.head.repo.full_name}} | |
| ref: ${{ github.event.pull_request.head.ref }} | |
| - name: Install dos2unix | |
| run: | | |
| # the easy way to do this: convert everything to unix and ask git if that changed anything | |
| sudo apt-get install -y dos2unix | |
| - name: Check line endings | |
| run: | | |
| # the easy way to do this: convert everything to unix and ask git if that changed anything | |
| find ./ -path ./.git -prune -o -type f -print0 | xargs -0 dos2unix -q | |
| # this version is safer, but more maintenance: | |
| #find ./ -path ./.git -prune -o -type f \( ! -name "*.nii" -a ! -name "*.nii.gz" \) -print0 | xargs -0 dos2unix -q | |
| git diff --stat --exit-code | |
| if [ "$?" -ne 0 ]; then | |
| echo "error: Windows line endings found." | |
| exit 1 | |
| fi | |
| - name: Lint participants.tsv | |
| run: .github/workflows/lint-tsv participants.tsv | |
| #- name: Update software | |
| # run: | | |
| # # do we want to do this? it's helpful to avoid testing against surprise out-of-date software, but also so slow. | |
| # sudo apt-get update && | |
| # sudo DEBIAN_FRONTEND=noninteractive apt-get -y dist-upgrade && | |
| # sudo DEBIAN_FRONTEND=noninteractive apt-get autoremove | |
| - name: Install git-annex | |
| run: | | |
| sudo apt-get install -y git-annex | |
| git config --global annex.thin true | |
| - name: Install bids-validator | |
| run: | | |
| # install proper NodeJS for bids-validator | |
| curl -sL https://deb.nodesource.com/setup_current.x | sudo -E bash - | |
| sudo apt-get install -y nodejs | |
| sudo npm install -g bids-validator | |
| - name: Set up Python | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.7 | |
| - name: Install spine-generic for acquisition parameters check | |
| run: pip install spinegeneric@git+https://github.com/spine-generic/spine-generic.git@master | |
| #- name: Increase free space | |
| # run: | | |
| # # this takes about 2 minutes but saves about 30GB, which is space we might need for git-annex. | |
| # # annex.thin saves a lot of space, but if the dataset grows beyond what Github can handle | |
| # # try enabling this. | |
| # # ref: https://github.com/actions/virtual-environments/issues/2606#issuecomment-772683150 | |
| # sudo rm -rf /usr/local/lib/android /usr/share/dotnet | |
| - name: git config | |
| run: | | |
| # this is needed by git-annex so that it can write to the local git-annex branch | |
| # the tracking information about the local copy | |
| git config --global user.name "gh-actions" | |
| git config --global user.email "gh-actions" | |
| # but actually, disable those writes. We don't need them because we're throwing away this copy immediately. | |
| # this might make the previous two lines unnecessary, but it's safer just to leave them both in | |
| git config annex.alwayscommit false | |
| - name: Download dataset | |
| run: | | |
| git fetch --depth=1 origin git-annex:git-annex # actions/checkout@v2 does a shallow checkout, so it is missing this important branch | |
| git annex init | |
| git annex get -J8 | |
| - name: Checking BIDS compliance | |
| run: bids-validator --verbose ./ | |
| - name: Checking acquisition parameters | |
| run: sg_params_checker -path-in ./ | |
| - name: Checking data consistency | |
| run: sg_check_data_consistency -path-in ./ |