chore: Last minute cleanups

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/"
+    ]
   }
 }

src/files/deno.test.ts

@@ -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/dwi.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/filetree.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.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/gzip.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/tiff.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/issues/datasetIssues.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/list.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 = {

src/main.ts

@@ -28,9 +28,9 @@ export async function main(): Promise<ValidationResult> {
   // Run the schema based validator
   const schemaResult = await validate(tree, options, config)
 
-  let output_string = ""
+  let output_string = ''
   if (options.json) {
-      output_string = resultToJSONStr(schemaResult)
+    output_string = resultToJSONStr(schemaResult)
   } else {
     output_string = consoleFormat(schemaResult, {
       verbose: options.verbose ? options.verbose : false,
@@ -41,7 +41,7 @@ export async function main(): Promise<ValidationResult> {
     if (globalThis.Deno) {
       Deno.writeTextFileSync(options.outfile, output_string)
     } else {
-      console.error("Output to file only supported in Deno runtime")
+      console.error('Output to file only supported in Deno runtime')
       console.log(output_string)
     }
   } else {

src/schema/associations.ts

@@ -163,7 +163,10 @@ export async function buildAssociations(
     try {
       file = walkBack(source, inherit, extensions, suffix).next().value
     } catch (error) {
-      if (error && typeof error === 'object' && 'code' in error && error.code === 'MULTIPLE_INHERITABLE_FILES') {
+      if (
+        error && typeof error === 'object' && 'code' in error &&
+        error.code === 'MULTIPLE_INHERITABLE_FILES'
+      ) {
         // @ts-expect-error
         issues.add(error)
         break

src/schema/context.ts

@@ -184,7 +184,10 @@ export class BIDSContext implements Context {
     try {
       sidecars = [...walkBack(this.file)]
     } catch (error) {
-      if (error && typeof error === 'object' && 'code' in error && error.code === 'MULTIPLE_INHERITABLE_FILES') {
+      if (
+        error && typeof error === 'object' && 'code' in error &&
+        error.code === 'MULTIPLE_INHERITABLE_FILES'
+      ) {
         // @ts-expect-error
         this.dataset.issues.add(error)
       } else {

src/schema/fixtures.test.ts

@@ -1,4 +1,4 @@
-import { BIDSFile, FileTree } from '../types/filetree.ts'
+import type { BIDSFile, FileTree } from '../types/filetree.ts'
 import { pathsToTree } from '../files/filetree.ts'
 import { nullReadBytes } from '../tests/nullReadBytes.ts'
 

src/schema/tables.ts

@@ -1,5 +1,5 @@
-import { GenericRule, GenericSchema, SchemaType, SchemaTypeLike } from '../types/schema.ts'
-import { BIDSContext } from './context.ts'
+import type { GenericRule, GenericSchema, SchemaType, SchemaTypeLike } from '../types/schema.ts'
+import type { BIDSContext } from './context.ts'
 
 interface ColumnDefinition {
   Levels?: Record<string, unknown>

src/setup/options.ts

@@ -32,7 +32,7 @@ export type ValidatorOptions = {
 }
 
 const modalityType = new EnumType<string>(
-  Object.keys(schema.rules.modalities)
+  Object.keys(schema.rules.modalities),
 )
 
 /** Extendable Cliffy Command with built in BIDS validator options */

src/validators/citation.test.ts

@@ -3,7 +3,7 @@ import { pathsToTree } from '../files/filetree.ts'
 import { BIDSFileDeno } from '../files/deno.ts'
 import { citationValidate } from './citation.ts'
 import { BIDSContextDataset } from '../schema/context.ts'
-import { GenericSchema } from '../types/schema.ts'
+import type { GenericSchema } from '../types/schema.ts'
 import { loadSchema } from '../setup/loadSchema.ts'
 
 Deno.test('citation validation', async (t) => {

src/validators/filenameValidate.test.ts

@@ -1,4 +1,4 @@
-import { FileTree } from '../types/filetree.ts'
+import type { FileTree } from '../types/filetree.ts'
 import type { GenericSchema } from '../types/schema.ts'
 import { assertEquals } from '@std/assert'
 import { BIDSContext } from '../schema/context.ts'

src/version.ts

@@ -34,14 +34,14 @@ export async function getVersion(): Promise<string> {
 async function getLocalVersion(path: string): Promise<string> {
   // safe.directory setting so we could still operate from another user
   try {
-    const command = new Deno.Command("git", {
+    const command = new Deno.Command('git', {
       args: ['-C', path, '-c', 'safe.directory=*', 'describe', '--tags', '--always'],
     })
-    const { success, stdout } = await command.output();
+    const { success, stdout } = await command.output()
     const description = new TextDecoder().decode(stdout).trim()
     return description
-  } catch(err) {
-    return ""
+  } catch (err) {
+    return ''
   }
 }