Use my fork of bids-examples, mark known to fail, run deno validator

.github/workflows/validate_bids-examples.yml

@@ -21,7 +21,7 @@ jobs:
       fail-fast: false
       matrix:
         platform: [ubuntu-latest] # , macos-latest, windows-latest]
-        bids-validator: [master, stable]
+        bids-validator: [master-deno]
         python-version: ["3.11"]
 
     runs-on: ${{ matrix.platform }}
@@ -48,33 +48,20 @@ jobs:
     - name: "Produce dump of the schema as schema.json"
       run: bst -v export --output src/schema.json
 
-    # Setup validator
-    - name: Set up Node.js
-      uses: actions/setup-node@v4
+    - uses: denoland/[email protected]
+      if: "matrix.bids-validator == 'master-deno'"
       with:
-        node-version: 18
+        deno-version: v1.x
 
-    - name: Install BIDS validator (stable)
-      if: "matrix.bids-validator == 'stable'"
-      run: |
-        npm install -g bids-validator
-
-    - name: Install BIDS validator (master)
-      if: "matrix.bids-validator == 'master'"
+    - name: Install BIDS validator (master deno build)
+      if: "matrix.bids-validator == 'master-deno'"
       run: |
         pushd ..
-        # Get npm 7+
-        npm install -g npm
         git clone --depth 1 https://github.com/bids-standard/bids-validator
-        cd bids-validator
-        # Generate the full development node_modules
-        npm clean-install
-        # Build & bundle the bids-validator CLI package
-        npm -w bids-validator run build
-        # Generate a package to install globally
-        npm -w bids-validator pack
-        # Install the package globally
-        bash -c "npm install -g bids-validator-*.tgz"
+        echo -e '#!/bin/sh\n'"$PWD/bids-validator/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
@@ -89,18 +76,24 @@ jobs:
     # Checkout bids-examples
     - uses: actions/checkout@v4
       with:
-        repository: bids-standard/bids-examples
+        # 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
+        branch: deno-validator
         path: bids-examples
 
-    - name: Validate all BIDS datasets using bids-validator without migration
-      run: |
-        cat ./run_tests.sh
-        bash ./run_tests.sh
+    - name: Mark known not yet to be deno-legit BIDS datasets
+      run: touch {ds000117,ds000248,eeg_ds003645s_hed_demo,ieeg_epilepsy,ieeg_epilepsy_ecog,ieeg_epilepsyNWB,ieeg_visual_multimodal}/.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
+      run: /bin/ls */dataset_description.json | sed -e 's,/.*,,g' | xargs bst migrate-datasets
       shell: bash
       working-directory: bids-examples
 
@@ -109,6 +102,5 @@ jobs:
       working-directory: bids-examples
 
     - name: Validate all BIDS datasets using bids-validator after migration
-      run: |
-        VALIDATOR_ARGS="-s local" bash ./run_tests.sh
+      run: VALIDATOR_ARGS="-s local" bash ./run_tests.sh
       working-directory: bids-examples