Deno 2 upgrades and project reorganization.

.circleci/config.yml

@@ -4,11 +4,12 @@ jobs:
   test:
     docker:
       - image: node:18-alpine
+    working_directory: ~/project/legacy
     steps:
       - checkout
       - restore_cache:
           keys:
-            - npm-deps-{{ checksum "package.json" }}-{{ checksum "./bids-validator/package.json" }}-{{ checksum "./bids-validator-web/package.json" }}-v1
+            - npm-deps-{{ checksum "./package.json" }}-{{ checksum "./bids-validator/package.json" }}-{{ checksum "./bids-validator-web/package.json" }}-v1
       - run: apk --no-cache add git
       - run: npm install -g npm@^7
       - run: npm install
@@ -37,6 +38,7 @@ jobs:
       # Ubuntu 20.04, Docker v20.10.11, Docker Compose v1.29.2
       # see: https://circleci.com/docs/2.0/configuration-reference/#available-machine-images
       image: ubuntu-2004:202111-02
+    working_directory: ~/project/legacy
     steps:
       - checkout
       - run: docker build -t $IMAGE_NAME:latest .
@@ -55,21 +57,22 @@ jobs:
   githubPagesTest:
     docker:
       - image: node:18-alpine
+    working_directory: ~/project/legacy
     steps:
       - run: npm install --global npm
       - run: apk --no-cache add ca-certificates git openssh-client rsync
       - checkout
       - restore_cache:
           keys:
-            - npm-deps-{{ checksum "package.json" }}-{{ checksum "./bids-validator/package.json" }}-{{ checksum "./bids-validator-web/package.json" }}-v1
+            - npm-deps-{{ checksum "./package.json" }}-{{ checksum "./bids-validator/package.json" }}-{{ checksum "./bids-validator-web/package.json" }}-v1
       - run:
           name: Install bids-validator and bids-validator-web dependencies
           command: npm install
       - run:
           name: Build and export web-validator
           command: npm run web-export && rsync -av ./bids-validator-web/out/ ~/web_version
       - save_cache:
-          key: npm-deps-{{ checksum "package.json" }}-{{ checksum "./bids-validator/package.json" }}-{{ checksum "./bids-validator-web/package.json" }}-v1
+          key: npm-deps-{{ checksum "./package.json" }}-{{ checksum "./bids-validator/package.json" }}-{{ checksum "./bids-validator-web/package.json" }}-v1
           paths:
             - ./node_modules
             - ./.next/cache
@@ -78,22 +81,4 @@ jobs:
 workflows:
   version: 2
   build-deploy:
-    jobs:
-      - test:
-          filters:
-            branches:
-              only: /.*/
-            tags:
-              only: /.*/
-      - test_docker:
-          filters:
-            tags:
-              only: /.*/
-      - githubPagesTest:
-          requires:
-            - test
-          filters:
-            branches:
-              only: /.*/
-            tags:
-              only: /.*/
+    jobs: []

.dockerignore

@@ -1,3 +1,2 @@
 tests
-.git
 node_modules

.github/workflows/deno_tests.yml

@@ -22,10 +22,10 @@ jobs:
       - name: Save describe stamp
         id: describe
         run: echo version=$( git describe ) >> $GITHUB_OUTPUT
-      - uses: denoland/setup-deno@v1
+      - uses: denoland/setup-deno@v2
         with:
-          deno-version: v1.x
-      - run: ./build.ts
+          deno-version: v2.x
+      - run: deno --node-modules-dir=auto -A ./build.ts
         working-directory: ./bids-validator
       - run: deno run -A ./bids-validator/dist/validator/bids-validator.js --version
       - uses: actions/upload-artifact@v4
@@ -52,14 +52,14 @@ jobs:
           submodules: true
       - uses: denoland/setup-deno@v1
         with:
-          deno-version: v1.x
+          deno-version: v2.x
       - name: Set permissions with network access
         run: echo 'PERMS=--allow-read --allow-write --allow-env --allow-run --allow-net' >> $GITHUB_ENV
         if: ${{ matrix.allow-net }}
       - name: Set permissions without network access
         run: echo 'PERMS=--allow-read --allow-write --allow-env --allow-run --deny-net' >> $GITHUB_ENV
         if: ${{ ! matrix.allow-net }}
-      - run: deno test $PERMS --coverage=cov/ src/
+      - run: deno test --node-modules-dir=auto $PERMS --coverage=cov/ src/
       - name: Collect coverage
         run: deno coverage cov/ --lcov --output=coverage.lcov
         if: ${{ always() }}

.github/workflows/docker-build-push.yml

@@ -1,6 +1,8 @@
 name: Build & publish containers
 
 on:
+  pull_request:
+    branches: [master]
   push:
     tags:
       - 'v[0-9]+.[0-9]+.[0-9]+'
@@ -29,61 +31,8 @@ jobs:
         uses: docker/build-push-action@v6
         with:
           context: .
-          push: true
+          push: false
+          target: base
           tags: ${{ steps.meta.outputs.tags }}
           labels: ${{ steps.meta.outputs.labels }}
-
-  push_singularity_to_registry:
-    runs-on: ubuntu-latest
-    needs:
-      - push_docker_to_registry
-    steps:
-      - name: Set up Go 1.13
-        uses: actions/setup-go@v5
-        with:
-          go-version: 1.13
-        id: go
-      - name: Install Dependencies
-        run: |
-          sudo apt-get update && sudo apt-get install -y \
-            build-essential \
-            libssl-dev \
-            uuid-dev \
-            libgpgme11-dev \
-            squashfs-tools \
-            libseccomp-dev \
-            pkg-config
-      - name: Install Singularity
-        env:
-          SINGULARITY_VERSION: 3.8.0
-          GOPATH: /tmp/go
-        run: |
-          mkdir -p $GOPATH
-          sudo mkdir -p /usr/local/var/singularity/mnt && \
-          mkdir -p $GOPATH/src/github.com/sylabs && \
-          cd $GOPATH/src/github.com/sylabs && \
-          wget -qO- https://github.com/sylabs/singularity/releases/download/v${SINGULARITY_VERSION}/singularity-ce-${SINGULARITY_VERSION}.tar.gz | \
-          tar xzv && \
-          cd singularity-ce-${SINGULARITY_VERSION} && \
-          ./mconfig -p /usr/local && \
-          make -C builddir && \
-          sudo make -C builddir install
-      - name: Check out code for the container build
-        uses: actions/checkout@v4
-      - name: Extract metadata (tags, labels) for Docker
-        id: meta
-        uses: docker/metadata-action@v5
-        with:
-          images: bids/validator
-      - name: Build Container
-        run: |
-          tags=${{ steps.meta.outputs.tags }}
-          echo $tags
-          singularity pull container.sif docker://${tags%,*}
-      - name: Login and Deploy Container
-        if: (github.event_name != 'pull_request')
-        run: |
-          tags=${{ steps.meta.outputs.tags }}
-          echo ${{ secrets.GITHUB_TOKEN }} |  singularity remote login -u ${{ github.actor }} --password-stdin oras://ghcr.io
-          for tag in $(echo $tags | sed "s/,/ /g" | sed "s/bids\/validator/bids-standard\/bids-validator/g"); 
-            do echo $tag; singularity push container.sif oras://ghcr.io/$tag; done
+          outputs: type=cacheonly

.github/workflows/node_tests.yml

@@ -35,20 +35,26 @@ jobs:
           git config --global user.email "[email protected]"
           git config --global user.name "bids-maintenance"
       - name: Set up Node
+        working-directory: ./legacy
         run: |
           npm install -g npm@^7
           npm install
       - name: Eslint
+        working-directory: ./legacy
         run: npm run lint
       - name: Get bids-examples data
+        working-directory: ./legacy
         run: git submodule update --init
       - name: Jest tests
+        working-directory: ./legacy
         run: npm run coverage -- --maxWorkers=2 --testTimeout=10000 --colors
       - name: Upload to codecov
+        working-directory: ./legacy
         uses: codecov/codecov-action@v4
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
       - name: Smoke tests
+        working-directory: ./legacy
         run: |
           bids-validator/bin/bids-validator bids-validator/tests/data/valid_headers/ --ignoreNiftiHeaders
           bids-validator/bin/bids-validator bids-validator/tests/data/valid_headers/ --ignoreNiftiHeaders --json

.github/workflows/schema_web_build.yml

@@ -17,9 +17,9 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: denoland/setup-deno@v1
+      - uses: denoland/setup-deno@v2
         with:
-          deno-version: v1.x
+          deno-version: v2.x
       - run: deno task build
         working-directory: ./web
       - uses: actions/upload-artifact@v4

.github/workflows/schema_web_deploy.yml

@@ -18,17 +18,19 @@ jobs:
       - uses: actions/setup-node@v4
         with:
           node-version: 18
-      - uses: denoland/setup-deno@v1
+      - uses: denoland/setup-deno@v2
         with:
-          deno-version: v1.x
+          deno-version: v2.x
       - run: deno task build
         working-directory: ./web
       - name: Install NPM deps
         run: npm install
+        working-directory: ./legacy
       - name: Build legacy validator website
         run: npm run web-export
+        working-directory: ./legacy
       - name: Move legacy validator build into deno website
-        run: mv bids-validator-web/out web/dist/legacy
+        run: mv legacy/bids-validator-web/out web/dist/legacy
       - name: Upload GitHub Pages artifact
         uses: actions/upload-pages-artifact@v3
         with:

.github/workflows/test-bids-examples.yml

@@ -37,16 +37,19 @@ jobs:
         run: npm install --global npm
 
       - name: Install bids-validator
+        working-directory: ./legacy
         run: |
           npm install
           npm link ./bids-validator
           echo "./node_modules/.bin" >> $GITHUB_PATH
 
       - name: Get bids-examples data
+        working-directory: ./legacy
         run: |
           git clone --depth 1 https://github.com/bids-standard/bids-examples
 
       - name: Display versions and environment information
+        working-directory: ./legacy
         run: |
           echo $TZ
           export PATH="../node_modules/.bin:$PATH"
@@ -58,15 +61,17 @@ jobs:
           ls -a $(which bids-validator)
 
       - name: Ignore examples not supported by legacy validator
+        working-directory: ./legacy
         run: |
           for DS in bids-examples/mrs_*; do
             touch $DS/.SKIP_VALIDATION
           done
 
       - name: Validate all BIDS datasets using bids-validator
+        working-directory: ./legacy
         run: |
           export PATH="../node_modules/.bin:$PATH"
           cat ./run_tests.sh
           bash ./run_tests.sh
         shell: bash
-        working-directory: ./bids-examples
+        working-directory: /bids-examples

.gitignore

@@ -11,7 +11,7 @@ coverage/
 __pycache__/
 dist/
 *.egg-info/
-bids-validator-web/out/
+legacy/bids-validator-web/out/
 .next/
 
 # Only use global yarn.lock

.gitmodules

@@ -1,3 +1,3 @@
 [submodule "bids-examples"]
-	path = bids-validator/tests/data/bids-examples
+	path = legacy/bids-validator/tests/data/bids-examples
 	url = https://github.com/bids-standard/bids-examples.git

Dockerfile

@@ -1,16 +1,30 @@
-FROM node:18-alpine as build
-RUN npm install -g npm
-
-COPY . /src
+ARG BASE_IMAGE=denoland/deno:2.0.1
+FROM ${BASE_IMAGE} AS build
 WORKDIR /src
 
-RUN npm install 
-RUN npm -w bids-validator run build
-RUN npm -w bids-validator pack
+RUN apt-get update && \
+    apt-get install -y git jq && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+ADD . .
+RUN export VERSION=`git -C . -c safe.directory=* describe --tags --always` && \
+    jq -r ".version|=\"$VERSION\"" bids-validator/deno.json > ._deno.json
 
-FROM node:18-alpine
+WORKDIR /src/bids-validator
+RUN deno cache ./bids-validator-deno
+RUN ./build.ts
 
-COPY --from=build /src/bids-validator-*.tgz /tmp
-RUN npm install -g /tmp/bids-validator-*.tgz
+FROM ${BASE_IMAGE} AS base
+WORKDIR /src
+COPY . .
+COPY --from=build /src/._deno.json /src/bids-validator/deno.json
+WORKDIR /src/bids-validator
+RUN deno cache ./bids-validator-deno
+ENTRYPOINT ["./bids-validator-deno"]
+
+FROM ${BASE_IMAGE} AS min
+WORKDIR /src
+COPY --from=build /src/bids-validator/dist/validator/* .
 
-ENTRYPOINT ["/usr/local/bin/bids-validator"]
+ENTRYPOINT ["deno", "-A", "./bids-validator.js"]