Add manual corrections for spinal canal (#182) #234
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| name: Dataset Validator | |
| on: | |
| push: | |
| branches: [ master ] | |
| pull_request: | |
| branches: [ master ] | |
| jobs: | |
| Validate: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Gain disk space by remapping temp disk (`/dev/sdb1`) | |
| uses: easimon/maximize-build-space@master | |
| # We use the above action instead of removing unwanted packages because it only takes about 2s; | |
| # by comparison, removing lots of small file is very time-consuming. | |
| with: | |
| # After freeing up space we could have as much as 87GB available, which is overkill. | |
| # So, we set root == 10GB to save room for installing dependencies (leaving us with ~77GB) | |
| root-reserve-mb: 10240 | |
| swap-size-mb: 1024 | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| 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 git-annex | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get --yes install git-annex | |
| # the user name and email is needed by git-annex to write to | |
| # the local git-annex branch | |
| git config --global user.name "gh-actions" | |
| git config --global user.email "gh-actions" | |
| # save space by using hard links to annexed files | |
| git config --global annex.thin true | |
| # retry for transient failures when downloading annexed file contents | |
| git config --global annex.retry 2 | |
| - name: Download dataset | |
| run: | | |
| git fetch --depth=1 origin git-annex:git-annex | |
| git annex get --jobs 8 | |
| - name: Install Deno | |
| uses: denoland/setup-deno@v2 | |
| - name: Install Python 3.13 | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.13 | |
| - name: Install spine-generic | |
| run: | | |
| pip install spinegeneric@git+https://github.com/spine-generic/[email protected] | |
| - name: Run bids-validator | |
| # If the explicit whitelist of allowed environment variables gets too annoying to update, | |
| # we can loosen it to just a blanket `--allow-env`. This will let bids-validator and all of its | |
| # dependencies access any credentials that github CI exposes in environment variables, but at | |
| # least we're not giving it any network access, so exfiltrating them would require more effort. | |
| run: | | |
| deno run --no-prompt --allow-env=BIDS_SCHEMA,FORCE_COLOR,IGNORE_TEST_WIN32 --allow-read=. jsr:@bids/validator . || echo '::warning title=bids-validator::Errors found by bids-validator' | |
| - name: Run acquisition parameter validator | |
| run: | | |
| sg_params_checker -path-in . || echo '::warning title=bids-validator::Errors found by sg_params_checker' | |
| - name: Run data consistency validator | |
| run: | | |
| sg_check_data_consistency -path-in . || echo '::warning title=bids-validator::Errors found by sg_check_data_consistency' |