Merge pull request #106 from effigies/fix/pre-publish

chore: Last minute cleanups

Author: effigies

deno.json

@@ -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,

src/files/tiff.ts

@@ -1,6 +1,6 @@
 import { nonSchemaIssues } from './list.ts'
-import type { Issue, Severity, IssueDefinition, IssueFile } from '../types/issues.ts'
-export type { Issue, Severity, IssueDefinition, IssueFile }
+import type { Issue, IssueDefinition, IssueFile, Severity } from '../types/issues.ts'
+export type { Issue, IssueDefinition, IssueFile, Severity }
 
 // Code is deprecated, return something unusual but JSON serializable
 const CODE_DEPRECATED = Number.MIN_SAFE_INTEGER

src/issues/datasetIssues.ts

@@ -168,14 +168,13 @@ export const bidsIssues: IssueDefinitionRecord = {
   },
   CITATION_CFF_VALIDATION_ERROR: {
     severity: 'error',
-    reason: 
-      "The file does not pass validation using the citation.cff standard's schema." +
-      'https://github.com/citation-file-format/citation-file-format/blob/main/schema-guide.md'
+    reason: "The file does not pass validation using the citation.cff standard's schema." +
+      'https://github.com/citation-file-format/citation-file-format/blob/main/schema-guide.md',
   },
   FILE_READ: {
     severity: 'error',
-    reason: 'We were unable to read this file.'
-  }
+    reason: 'We were unable to read this file.',
+  },
 }
 
 const hedIssues: IssueDefinitionRecord = {