Merge remote-tracking branch 'upstream/main' into dev

Author: effigies

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

@@ -0,0 +1,53 @@
+name: Docker
+
+on:
+  push:
+    branches: [main, dev]
+    tags: ['*']
+  pull_request:
+    branches: [main, dev]
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+defaults:
+  run:
+    shell: bash
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out the repo
+        uses: actions/checkout@v5
+        with:
+          fetch-depth: 200
+          filter: blob:none
+          # fetch-tags: true breaks on tags
+          fetch-tags: ${{ !startsWith(github.ref, 'refs/tags/') }}
+
+      - name: Log in to Docker Hub
+        if: github.event_name == 'push'
+        uses: docker/login-action@v3
+        with:
+          username: ${{ secrets.DOCKER_USERNAME }}
+          password: ${{ secrets.DOCKER_PASSWORD }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: bids/validator
+
+      - name: Build ${{ startsWith(github.ref, 'refs/tags/') && 'and push' || '' }} ${{ steps.meta.outputs.tags }}
+        uses: docker/build-push-action@v6
+        with:
+          context: .
+          push: ${{ startsWith(github.ref, 'refs/tags/') }}
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+
+      - name: Verify Docker image
+        run: docker run --rm ${{ fromJSON(steps.meta.outputs.json).tags[0] }} --version

CHANGELOG.md

@@ -1,4 +1,54 @@
 
+<a id='changelog-2.0.11'></a>
+# 2.0.11 — 2025-08-29
+
+## Fixed
+
+- Docker build workflow should now run correctly on releases.
+
+<a id='changelog-2.0.10'></a>
+# 2.0.10 — 2025-08-29
+
+## Added
+
+- Added a [FAQ] to the user guide. ([#215])
+
+[FAQ]: https://bids-validator.readthedocs.io/en/latest/user_guide/faq.html
+[#215]: https://github.com/bids-standard/bids-validator/issues/215
+
+## Changed
+
+- Improved handling of TSV columns with sidecar definitions.
+  `"Format"`, `"Minimum"` and `"Maximum"` keys are now supported.
+
+- `--datasetTypes` and `--blacklistModalities` options now accept a string array (`--datasetTypes raw,derivative`) and can be combined.
+
+## Fixed
+
+- A crash in the web validator prevented validation from taking place.
+
+## Infrastructure
+
+- Docker images will once again be pushed to [bids/validator][].
+
+[bids/validator]: https://hub.docker.com/r/bids/validator/
+
+<a id='changelog-"2.0.9"'></a>
+# "2.0.9" — 2025-08-26
+
+## Added
+
+- Display version in web app
+
+- The `--datasetTypes` flag accepts a list of `DatasetType`s,
+  allowing applications to restrict the datasets they accept.
+
+## Changed
+
+- Upgraded to BIDS schema version 1.0.13.
+
+- Raise error when JSON files are parsed and their root value is anything other than an object
+
 <a id='changelog-"2.0.8"'></a>
 # "2.0.8" — 2025-08-07
 

Dockerfile

@@ -1,30 +1,18 @@
-ARG BASE_IMAGE=denoland/deno:2.0.1
+ARG BASE_IMAGE=denoland/deno:alpine-2.4.5
 FROM ${BASE_IMAGE} AS build
 WORKDIR /src
 
-RUN apt-get update && \
-    apt-get install -y git jq && \
-    apt-get clean && \
-    rm -rf /var/lib/apt/lists/*
+RUN apk add --no-cache git jq
 
 ADD . .
 RUN export VERSION=`git -C . -c safe.directory=* describe --tags --always` && \
-    jq -r ".version|=\"$VERSION\"" bids-validator/deno.json > ._deno.json
+    jq -r ".version|=\"$VERSION\"" deno.json > ._deno.json && \
+    mv ._deno.json deno.json
 
-WORKDIR /src/bids-validator
-RUN deno cache ./bids-validator-deno
-RUN ./build.ts
-
-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"]
+RUN deno run -A ./build.ts
 
 FROM ${BASE_IMAGE} AS min
 WORKDIR /src
-COPY --from=build /src/bids-validator/dist/validator/* .
+COPY --from=build /src/dist/validator/bids-validator.js .
 
 ENTRYPOINT ["deno", "-A", "./bids-validator.js"]

changelog.d/20250807_170325_markiewicz_update_schema.md

@@ -33,6 +33,7 @@ deno run -A jsr:@bids/validator
 user_guide/web.md
 user_guide/command-line.md
 user_guide/issues.md
+user_guide/faq.md
 ```
 
 ```{toctree}

changelog.d/20250808_135941_rosswilsonblair_raise_error_on_non_object_json.md

@@ -0,0 +1,110 @@
+# Frequently Asked Questions
+
+This page is for questions about the Javascript validator that may not be
+well addressed elsewhere in the documentation.
+
+If you have a question, please [open an issue][new-issue].
+The answer may end up on this page!
+
+## Q: What does the validator actually check?
+
+The BIDS Validator aspires to check that a dataset meets the requirements of the BIDS Standard.
+The primary way it does this is by interpreting the [BIDS Schema][schema-description].
+
+The general categories of rules include:
+
+- Filename rules: These rules indicate valid combinations of [entities][], [suffixes][definitions]
+  [datatypes][definitions] and [extensions][definitions].
+  Every file in a dataset must match a filename rule.
+- Sidecar and JSON rules: These rules indicate whether fields are REQUIRED, RECOMMENDED
+  or OPTIONAL in a JSON file.
+  REQUIRED fields produce errors on absence, while RECOMMENDED fields produce warnings on absence.
+  If the field is defined, then it also has a type (for example, numeric or textual);
+  type mismatches produce errors.
+- Tabular data rules: These rules indicate what columns are REQUIRED, RECOMMENDED or OPTIONAL
+  in a TSV file, and behave similarly to sidecar rules.
+  Additionally, tabular file rules may indicate that columns must appear in a certain order or
+  have unique values, and that additional columns are permitted or forbidden.
+  If JSON sidecar files provide definitions for columns,
+  the values in those columns are validated against those definitions.
+- Checks: These rules are conditional assertions, with the form of selectors and checks.
+  Selectors are expressions that determine whether the rule applies to the file or dataset,
+  and checks are expressions about the file or dataset that must evaluate to `true`.
+
+## Q: Why doesn't the validator warn/error about inconsistencies in some TSV columns?
+
+A specific question we've received is why the validator does not ensure that a
+column like `sex` in `participants.tsv` will permit both `f` and `F`,
+rather than enforce consistency.
+
+The reason for this is that `sex` (like `age`) is not rigorously defined by the BIDS Standard,
+but is provided as an example with a default definition.
+Default definitions are loose and often accept a wide range of values that would be
+understandable by humans while still allowing some amount of machine validation.
+As of BIDS 1.10.0, the definition of `sex` in the schema is:
+
+```json
+{
+  "sex": {
+    "LongName": "sex",
+    "Description": "String value indicating phenotypical sex.",
+    "Levels": {
+      "F": "Female",
+      "FEMALE": "Female",
+      "Female": "Female",
+      "f": "Female",
+      "female": "Female",
+      "M": "Male",
+      "MALE": "Male",
+      "Male": "Male",
+      "m": "Male",
+      "male": "Male",
+      "O": "Other",
+      "OTHER": "Other",
+      "Other": "Other",
+      "o": "Other",
+      "other": "Other"
+    }
+  }
+}
+```
+
+Data curators are encouraged to refine this definition in their `participants.json` sidecar file,
+for example, if you use the SNOMEDCT ontology:
+
+```json
+{
+  "sex": {
+    "LongName": "sex",
+    "Description": "Finding related to biological sex",
+    "TermURL": "http://purl.bioontology.org/ontology/SNOMEDCT/429019009",
+    "Levels": {
+      "F": {
+        "Description": "Female",
+        "TermURL": "http://purl.bioontology.org/ontology/SNOMEDCT/248152002",
+      },
+      "M": {
+        "Description": "Male",
+        "TermURL": "http://purl.bioontology.org/ontology/SNOMEDCT/248153007",
+      },
+      "I": {
+        "Description": "Intersex",
+        "TermURL": "http://purl.bioontology.org/ontology/SNOMEDCT/32570691000036108",
+      },
+      "X": {
+        "Description": "Indeterminate sex",
+        "TermURL": "http://purl.bioontology.org/ontology/SNOMEDCT/32570681000036106",
+      }
+    }
+  }
+}
+```
+
+If provided, the validator will check that all values in the column are `F`, `M`, `I`, `X`,
+or `n/a` (which is permitted in all columns, according to the BIDS Standard).
+
+
+[new-issue]: https://github.com/bids-standard/bids-validator/issues/new
+[schema-description]: https://bidsschematools.readthedocs.io/en/latest/description.html
+[entities]: https://bids-specification.readthedocs.io/en/stable/common-principles.html#entities
+[definitions]: https://bids-specification.readthedocs.io/en/stable/common-principles.html#definitions