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

Author: effigies

.github/workflows/deno_tests.yml

@@ -95,6 +95,25 @@ jobs:
           deno-version: v2.x
       - run: deno publish --dry-run
 
+  publish:
+    runs-on: ubuntu-latest
+    needs: [test, publish-dry-run]
+    if: github.ref_type == 'tag'
+    permissions:
+      contents: read
+      id-token: write
+      attestations: write
+    steps:
+      - uses: actions/checkout@v4
+      - name: Check tag matches ${{ github.ref_name }}
+        run: jq -e ".version[:1] != \"v\" and .version==\"$TAG\"" deno.json
+        env:
+          TAG: ${{ github.ref_name }}
+      - uses: denoland/setup-deno@v2
+        with:
+          deno-version: v2.x
+      - run: deno publish
+
   deploy:
     needs: [build]
     runs-on: ubuntu-latest

.github/workflows/web_build.yml

@@ -3,9 +3,9 @@ name: Web validator
 
 on:
   push:
-    branches: [main, stable]
+    branches: [main, dev]
   pull_request:
-    branches: [main, stable]
+    branches: [main, dev]
   release:
     types: [published]
   workflow_dispatch:
@@ -42,24 +42,25 @@ jobs:
       - name: Checkout release/target
         uses: actions/checkout@v4
         with:
-          # Use the implicit ref, assuming it's stable
+          # Stable is whatever we're releasing. Should generally
+          # be the last release, but can be main.
           path: stable
-      - name: Checkout main
+      - name: Checkout dev
         uses: actions/checkout@v4
         with:
-          ref: main
-          path: main
+          ref: dev
+          path: dev
       - uses: denoland/setup-deno@v2
         with:
           deno-version: v2.x
       - name: Build release/target
         run: deno task build
         working-directory: stable/web
-      - name: Build main
+      - name: Build dev
         run: deno task build
-        working-directory: main/web
-      - name: Nest main inside stable
-        run: mv main/web/dist stable/web/dist/dev
+        working-directory: dev/web
+      - name: Nest dev inside stable
+        run: mv dev/web/dist stable/web/dist/dev
       - name: Upload GitHub Pages artifact
         uses: actions/upload-pages-artifact@v3
         with:

deno.json

@@ -1,6 +1,6 @@
 {
   "name": "@bids/validator",
-  "version": "2.0.0-dev",
+  "version": "2.1.0-dev",
   "exports": {
     ".": "./src/bids-validator.ts",
     "./main": "./src/main.ts",
@@ -9,17 +9,21 @@
     "./options": "./src/setup/options.ts",
     "./issues": "./src/issues/datasetIssues.ts"
   },
+  "exclude": [
+    "docs/",
+    "tools/",
+    "web/",
+    ".*",
+    "CITATION.cff",
+    "Dockerfile",
+    "build.ts",
+    "local-run"
+  ],
   "publish": {
     "exclude": [
       "**/tests/",
-      "tools/",
-      "web/",
-      ".*",
       "**/*.test.ts",
-      "Dockerfile",
-      "build.ts",
-      "deno.lock",
-      "local-run"
+      "deno.lock"
     ]
   },
   "imports": {
@@ -47,6 +51,8 @@
     "semiColons": false,
     "singleQuote": true,
     "proseWrap": "preserve",
-    "include": ["src/"]
+    "include": [
+      "src/"
+    ]
   }
 }

deno.lock

@@ -2,7 +2,7 @@ import { assert, assertEquals, assertRejects } from '@std/assert'
 import { readAll, readerFromStreamReader } from '@std/io'
 import { basename, dirname, fromFileUrl, join } from '@std/path'
 import { EOL } from '@std/fs'
-import { FileTree } from '../types/filetree.ts'
+import type { FileTree } from '../types/filetree.ts'
 import { BIDSFileDeno, readFileTree, UnicodeDecodeError } from './deno.ts'
 import { requestReadPermission } from '../setup/requestPermissions.ts'
 import { FileIgnoreRules } from './ignore.ts'

src/files/deno.test.ts

@@ -4,7 +4,7 @@ import { parseBvalBvec } from './dwi.ts'
 
 Deno.test('Test bval/bvec parsing', async (t) => {
   await t.step('Load 3 bvals', async () => {
-    const bvals = parseBvalBvec('0 1 2 \n')  // Typically ends with " \n"
+    const bvals = parseBvalBvec('0 1 2 \n') // Typically ends with " \n"
     assertEquals(bvals, [['0', '1', '2']])
   })
   await t.step('Load 3 bvals - missing newline', async () => {
@@ -32,4 +32,3 @@ Deno.test('Test bval/bvec parsing', async (t) => {
     assertEquals(bvecs, [['0', '1', '2'], ['0', '1', '2'], ['0', '1', '2']])
   })
 })
-

src/files/dwi.test.ts

@@ -1,6 +1,6 @@
 import { assert, assertEquals } from '@std/assert'
-import { FileIgnoreRules } from './ignore.ts'
-import { FileTree } from '../types/filetree.ts'
+import type { FileIgnoreRules } from './ignore.ts'
+import type { FileTree } from '../types/filetree.ts'
 import { filesToTree, pathsToTree } from './filetree.ts'
 
 Deno.test('FileTree generation', async (t) => {

src/files/filetree.test.ts

@@ -1,6 +1,6 @@
 import { parse, SEPARATOR_PATTERN } from '@std/path'
 import * as posix from '@std/path/posix'
-import { BIDSFile, FileTree } from '../types/filetree.ts'
+import { type BIDSFile, FileTree } from '../types/filetree.ts'
 
 const nullFile = {
   size: 0,

src/files/filetree.ts

@@ -2,8 +2,8 @@
  * GZIP
  * Module for extracting gzip metadata from a file
  */
-import { Gzip } from '@bids/schema/context'
-import { BIDSFile } from '../types/filetree.ts'
+import type { Gzip } from '@bids/schema/context'
+import type { BIDSFile } from '../types/filetree.ts'
 
 /**
  * Parse a gzip header from a file

src/files/gzip.ts

@@ -2,9 +2,9 @@
  * TIFF
  * Module for extracting Tiff metadata
  */
-import { Ome, Tiff } from '@bids/schema/context'
+import type { Ome, Tiff } from '@bids/schema/context'
 import * as XML from '@libs/xml'
-import { BIDSFile } from '../types/filetree.ts'
+import type { BIDSFile } from '../types/filetree.ts'
 
 function getImageDescription(
   dataview: DataView,