BIDS 2̶.̶0̶1.0: flex BIDS layout (bids-2-devel/issues/54) #29
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| name: validate_datasets | |
| on: | |
| push: | |
| branches: ['master'] | |
| pull_request: | |
| branches: ['**'] | |
| # create: | |
| # branches: [master] | |
| # tags: ['**'] | |
| # schedule: | |
| # - cron: "0 4 * * 1" | |
| concurrency: | |
| group: ${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| build: | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| platform: [ubuntu-latest] # , macos-latest, windows-latest] | |
| bids-validator: [master-deno] | |
| python-version: ["3.11"] | |
| runs-on: ${{ matrix.platform }} | |
| env: | |
| TZ: Europe/Berlin | |
| FORCE_COLOR: 1 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: "Apply patches for BIDS-2.0" | |
| run: | | |
| set -o pipefail | |
| tools/bids-2.0/apply_all 2>&1 | tee /tmp/patch.log | |
| - name: "Show differences after patching" | |
| run: | | |
| git add . | |
| git diff --cached | |
| - name: "Commit and push patched version online for possible introspection" | |
| # Run only on a non-merge commit for the PR | |
| if: > | |
| github.repository == 'bids-standard/bids-specification' && | |
| github.event.pull_request.head.ref == 'bids-2.0' && | |
| github.event.pull_request.merge_commit_sha != github.sha | |
| run: | | |
| set -x | |
| commit=$(git rev-parse HEAD) | |
| branch=${GITHUB_HEAD_REF}-patched | |
| git config --global user.email "[email protected]" | |
| git config --global user.name "BIDS 2.0 GitHub CI" | |
| git checkout -b "$branch" | |
| { | |
| echo -e "Applied patches for ${GITHUB_HEAD_REF} to ${commit}\n"; | |
| cat /tmp/patch.log; | |
| } | git commit -F - | |
| git push -f origin "$branch" | |
| # Setup Python with bst | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: "Install build dependencies" | |
| run: pip install --upgrade build twine | |
| - name: "Build source distribution and wheel" | |
| run: python -m build tools/schemacode | |
| - name: "Check distribution metadata" | |
| run: twine check tools/schemacode/dist/* | |
| - name: "Install bst tools from the build" | |
| run: pip install $( ls tools/schemacode/dist/*.whl )[all] | |
| - name: "Produce dump of the schema as schema.json" | |
| run: bst -v export --output src/schema.json | |
| - uses: denoland/[email protected] | |
| if: "matrix.bids-validator == 'master-deno'" | |
| with: | |
| deno-version: v1.x | |
| - name: Install BIDS validator (master deno build) | |
| if: "matrix.bids-validator == 'master-deno'" | |
| run: | | |
| pushd .. | |
| # Let's use specific commit for now | |
| # TODO: progress it once in a while | |
| commit=a7b291b882a8c6184219ccb84faae255ba96203a | |
| git clone --depth 1 https://github.com/bids-standard/bids-validator | |
| cd bids-validator | |
| git fetch --depth 1 origin $commit; | |
| echo -e '#!/bin/sh\n'"$PWD/bids-validator/bids-validator-deno \"\$@\"" >| /usr/local/bin/bids-validator | |
| chmod a+x /usr/local/bin/bids-validator | |
| which -a bids-validator | |
| bids-validator --help | |
| popd | |
| - name: Display versions and environment information | |
| run: | | |
| echo $TZ | |
| date | |
| echo -n "npm: "; npm --version | |
| echo -n "node: "; node --version | |
| echo -n "bids-validator: "; bids-validator --version | |
| echo -n "python: "; python --version | |
| # Checkout bids-examples | |
| - uses: actions/checkout@v4 | |
| with: | |
| # repository: bids-standard/bids-examples | |
| # For now use the forked repository with support for deno validator | |
| # from https://github.com/bids-standard/bids-examples/pull/435 | |
| repository: yarikoptic/bids-examples | |
| ref: deno-validator | |
| path: bids-examples | |
| - name: Mark known not yet to be deno-legit BIDS datasets | |
| run: touch {ds000117,ds000246,ds000247,ds000248,eeg_ds003645s_hed_demo,ieeg_motorMiller2007,ieeg_visual}/.SKIP_VALIDATION | |
| shell: bash | |
| working-directory: bids-examples | |
| - name: Validate using bids-validator without migration | |
| run: ./run_tests.sh | |
| working-directory: bids-examples | |
| - name: Migrate all BIDS datasets | |
| run: /bin/ls */dataset_description.json | sed -e 's,/.*,,g' | xargs bst migrate-datasets | |
| shell: bash | |
| working-directory: bids-examples | |
| - name: Show migrated datasets diff | |
| run: git diff HEAD | |
| working-directory: bids-examples | |
| # TODO: commit as a merge from current state of bids-examples | |
| # and prior bids-2.0 branch there, but overloading with new updated | |
| # state and recording commit hash of bids-specification used. | |
| - name: Validate all BIDS datasets using bids-validator after migration | |
| run: VALIDATOR_ARGS="--schema file://$PWD/../src/schema.json" bash ./run_tests.sh | |
| working-directory: bids-examples |