Merge pull request #3 from bids-standard/migrate

Migrate to top-level layout
bids-standard · Oct 31, 2024 · 7d88eea · 7d88eea
2 parents 7f69dec + 0574977
commit 7d88eea
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Showing 623 changed files with 112 additions and 563 deletions.
diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml
@@ -3,9 +3,9 @@ name: Codespell
 
 on:
   push:
-    branches: [master]
+    branches: [master, main]
   pull_request:
-    branches: [master]
+    branches: [master, main]
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
@@ -21,4 +21,4 @@ jobs:
       - uses: codespell-project/actions-codespell@master
         with:
           ignore_words_list: ro,anser,te,tage,afterall,nwe,nin,nd,falsy
-          skip: package-lock.json, deps*, deno.lock
+          skip: deno.lock
diff --git a/.github/workflows/deno_tests.yml b/.github/workflows/deno_tests.yml
@@ -3,10 +3,10 @@ name: Deno build
 
 on:
   push:
-    branches: [master]
+    branches: [master, main]
     tags: ['*']
   pull_request:
-    branches: [master]
+    branches: [master, main]
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}

diff --git a/.github/workflows/schema_web_build.yml b/.github/workflows/schema_web_build.yml
@@ -3,10 +3,10 @@ name: Schema validator web build
 
 on:
   push:
-    branches: [master]
+    branches: [master, main]
     tags: ['*']
   pull_request:
-    branches: [master]
+    branches: [master, main]
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}

diff --git a/.gitmodules b/.gitmodules
@@ -1,3 +1,3 @@
 [submodule "bids-examples"]
-	path = bids-validator/tests/data/bids-examples
+	path = tests/data/bids-examples
 	url = https://github.com/bids-standard/bids-examples.git
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -60,7 +60,7 @@ To participate, be sure you know how to
 1. [Make a GitHub account][link_signupinstructions]
 1. Install the required software:
    - [git](https://git-scm.com/book/en/v2/Getting-Started-Installing-Git)
-   - [NodeJS](https://nodejs.org/en/download/), including `npm` of version 7 or higher (check existing version with `npm -v`, to update an existing nodejs, we can suggest [this guide](https://phoenixnap.com/kb/update-node-js-version).)
+   - [Deno](https://deno.com/)
 1. In the GitHub interface, [make a fork][link_fork] of
    https://github.com/bids-standard/bids-validator to your own user (called `USER` for the
    sake of the example)
@@ -71,18 +71,9 @@ To participate, be sure you know how to
    - You will now have a new directory called `bids-validator`
    - navigate to that directory and run `git status` to verify that it's a `git`
      directory
-   - run `npm install` to install the BIDS validator
-1. Upon inspection of the `bids-validator` repository we can find the
-   "executable" BIDS validator, located in `<...>/bids-validator/bin`, where
-   `<...>` is the path to your `bids-validator` repository
-   - To make this executable available from the command line, we have to add it
-     to the path. On Unix systems with bash as their default shell, this means
-     editing the `.bashrc` file by adding the following line to the bottom of
-     it: `export PATH="$PATH:<...>/bids-validator/bin"` ... Note that `<...>`
-     again needs to be replaced by the path to your BIDS validator repository
-   - Now whenever you open a new command line, we will have the `bids-validator`
-     executable available. You can verify by opening a new command line and
-     typing `bids-validator --version`, and it should print the version number
+1. Install `bids-validator` with: `deno install -Agf --reload ./bids-validator/src/bids-validator.ts`
+   - Deno will install the file to its `bin` directory. On Unix systems,
+     this should be `$HOME/.deno/bin`. You may need to add this to your `PATH`.
 
 Now your development version of BIDS validator is set up and you can use it.
 Whenever you _checkout_ a new branch in your git repository, the

diff --git a/README.md b/README.md
diff --git a/bids-validator/.gitattributes b/bids-validator/.gitattributes
diff --git a/bids-validator/.npmignore b/bids-validator/.npmignore
diff --git a/bids-validator/README.md b/bids-validator/README.md
diff --git a/bids-validator/bids-validator-deno b/bids-validator/bids-validator-deno
diff --git a/bids-validator/deno.json b/bids-validator/deno.json
diff --git a/bids-validator/build.ts → build.ts b/bids-validator/build.ts → build.ts
diff --git a/deno.json b/deno.json
@@ -1,3 +1,57 @@
 {
-  "lock": false
+  "name": "@bids/validator",
+  "version": "1.14.14",
+  "exports": {
+    ".": "./src/bids-validator.ts",
+    "./main": "./src/main.ts",
+    "./output": "./src/utils/output.ts",
+    "./files": "./src/files/deno.ts",
+    "./options": "./src/setup/options.ts",
+    "./issues": "./src/issues/datasetIssues.ts"
+  },
+  "publish": {
+    "exclude": [
+      "bids_validator/",
+      "bin/",
+      "tests/",
+      "docs/",
+      "utils/",
+      "validators/",
+      "bids-validator-deno",
+      "build.ts",
+      "cli.js",
+      "esbuild.mjs",
+      "index.js",
+      "package.json",
+      ".npmignore",
+      ".gitattributes"
+    ]
+  },
+  "imports": {
+    "@ajv": "npm:[email protected]",
+    "@bids/schema": "jsr:@bids/[email protected]+6e2874ce",
+    "@cliffy/command": "jsr:@cliffy/[email protected]",
+    "@cliffy/table": "jsr:@cliffy/[email protected]",
+    "@hed/validator": "npm:[email protected]",
+    "@ignore": "npm:[email protected]",
+    "@libs/xml": "jsr:@libs/[email protected]",
+    "@mango/nifti": "npm:@bids/[email protected]",
+    "@std/assert": "jsr:@std/[email protected]",
+    "@std/fmt": "jsr:@std/[email protected]",
+    "@std/fs": "jsr:@std/[email protected]",
+    "@std/io": "jsr:@std/[email protected]",
+    "@std/log": "jsr:@std/[email protected]",
+    "@std/path": "jsr:@std/[email protected]",
+    "@std/yaml": "jsr:@std/yaml@^1.0.4"
+  },
+  "tasks": {
+    "test": "deno test -A src/tests/"
+  },
+  "fmt": {
+    "lineWidth": 99,
+    "semiColons": false,
+    "singleQuote": true,
+    "proseWrap": "preserve",
+    "include": ["src/"]
+  }
 }
diff --git a/bids-validator/deno.lock → deno.lock b/bids-validator/deno.lock → deno.lock
diff --git a/local-run b/local-run
@@ -0,0 +1,4 @@
+#!/usr/bin/env -S deno run --allow-read --allow-write --allow-env --allow-net --allow-run 
+// This script runs the local copy of the validator, intended as a development aid.
+// You generally should run `deno run -A jsr:@bids/validator`
+import './src/bids-validator.ts'
diff --git a/bids-validator/src/.git-meta.json → src/.git-meta.json b/bids-validator/src/.git-meta.json → src/.git-meta.json
diff --git a/bids-validator/src/bids-validator.ts → src/bids-validator.ts b/bids-validator/src/bids-validator.ts → src/bids-validator.ts
diff --git a/bids-validator/src/files/browser.test.ts → src/files/browser.test.ts b/bids-validator/src/files/browser.test.ts → src/files/browser.test.ts
diff --git a/bids-validator/src/files/browser.ts → src/files/browser.ts b/bids-validator/src/files/browser.ts → src/files/browser.ts
diff --git a/bids-validator/src/files/deno.test.ts → src/files/deno.test.ts b/bids-validator/src/files/deno.test.ts → src/files/deno.test.ts
diff --git a/bids-validator/src/files/deno.ts → src/files/deno.ts b/bids-validator/src/files/deno.ts → src/files/deno.ts
diff --git a/bids-validator/src/files/dwi.ts → src/files/dwi.ts b/bids-validator/src/files/dwi.ts → src/files/dwi.ts
diff --git a/bids-validator/src/files/filetree.test.ts → src/files/filetree.test.ts b/bids-validator/src/files/filetree.test.ts → src/files/filetree.test.ts
diff --git a/bids-validator/src/files/filetree.ts → src/files/filetree.ts b/bids-validator/src/files/filetree.ts → src/files/filetree.ts
diff --git a/bids-validator/src/files/gzip.test.ts → src/files/gzip.test.ts b/bids-validator/src/files/gzip.test.ts → src/files/gzip.test.ts
diff --git a/bids-validator/src/files/gzip.ts → src/files/gzip.ts b/bids-validator/src/files/gzip.ts → src/files/gzip.ts
diff --git a/bids-validator/src/files/ignore.test.ts → src/files/ignore.test.ts b/bids-validator/src/files/ignore.test.ts → src/files/ignore.test.ts
diff --git a/bids-validator/src/files/ignore.ts → src/files/ignore.ts b/bids-validator/src/files/ignore.ts → src/files/ignore.ts
diff --git a/bids-validator/src/files/inheritance.test.ts → src/files/inheritance.test.ts b/bids-validator/src/files/inheritance.test.ts → src/files/inheritance.test.ts
diff --git a/bids-validator/src/files/inheritance.ts → src/files/inheritance.ts b/bids-validator/src/files/inheritance.ts → src/files/inheritance.ts
diff --git a/bids-validator/src/files/json.test.ts → src/files/json.test.ts b/bids-validator/src/files/json.test.ts → src/files/json.test.ts
diff --git a/bids-validator/src/files/json.ts → src/files/json.ts b/bids-validator/src/files/json.ts → src/files/json.ts
diff --git a/bids-validator/src/files/nifti.test.ts → src/files/nifti.test.ts b/bids-validator/src/files/nifti.test.ts → src/files/nifti.test.ts
diff --git a/bids-validator/src/files/nifti.ts → src/files/nifti.ts b/bids-validator/src/files/nifti.ts → src/files/nifti.ts
diff --git a/bids-validator/src/files/tiff.test.ts → src/files/tiff.test.ts b/bids-validator/src/files/tiff.test.ts → src/files/tiff.test.ts
diff --git a/bids-validator/src/files/tiff.ts → src/files/tiff.ts b/bids-validator/src/files/tiff.ts → src/files/tiff.ts
diff --git a/bids-validator/src/files/tsv.ts → src/files/tsv.ts b/bids-validator/src/files/tsv.ts → src/files/tsv.ts
diff --git a/...alidator/src/issues/datasetIssues.test.ts → src/issues/datasetIssues.test.ts b/...alidator/src/issues/datasetIssues.test.ts → src/issues/datasetIssues.test.ts
diff --git a/bids-validator/src/issues/datasetIssues.ts → src/issues/datasetIssues.ts b/bids-validator/src/issues/datasetIssues.ts → src/issues/datasetIssues.ts
diff --git a/bids-validator/src/issues/list.test.ts → src/issues/list.test.ts b/bids-validator/src/issues/list.test.ts → src/issues/list.test.ts
diff --git a/bids-validator/src/issues/list.ts → src/issues/list.ts b/bids-validator/src/issues/list.ts → src/issues/list.ts
diff --git a/bids-validator/src/main.ts → src/main.ts b/bids-validator/src/main.ts → src/main.ts
diff --git a/bids-validator/src/schema/applyRules.test.ts → src/schema/applyRules.test.ts b/bids-validator/src/schema/applyRules.test.ts → src/schema/applyRules.test.ts
diff --git a/bids-validator/src/schema/applyRules.ts → src/schema/applyRules.ts b/bids-validator/src/schema/applyRules.ts → src/schema/applyRules.ts
diff --git a/bids-validator/src/schema/associations.ts → src/schema/associations.ts b/bids-validator/src/schema/associations.ts → src/schema/associations.ts
diff --git a/bids-validator/src/schema/context.test.ts → src/schema/context.test.ts b/bids-validator/src/schema/context.test.ts → src/schema/context.test.ts
diff --git a/bids-validator/src/schema/context.ts → src/schema/context.ts b/bids-validator/src/schema/context.ts → src/schema/context.ts
diff --git a/bids-validator/src/schema/entities.test.ts → src/schema/entities.test.ts b/bids-validator/src/schema/entities.test.ts → src/schema/entities.test.ts
diff --git a/bids-validator/src/schema/entities.ts → src/schema/entities.ts b/bids-validator/src/schema/entities.ts → src/schema/entities.ts
diff --git a/...tor/src/schema/expressionLanguage.test.ts → src/schema/expressionLanguage.test.ts b/...tor/src/schema/expressionLanguage.test.ts → src/schema/expressionLanguage.test.ts
diff --git a/...alidator/src/schema/expressionLanguage.ts → src/schema/expressionLanguage.ts b/...alidator/src/schema/expressionLanguage.ts → src/schema/expressionLanguage.ts
diff --git a/bids-validator/src/schema/fixtures.test.ts → src/schema/fixtures.test.ts b/bids-validator/src/schema/fixtures.test.ts → src/schema/fixtures.test.ts
diff --git a/bids-validator/src/schema/modalities.ts → src/schema/modalities.ts b/bids-validator/src/schema/modalities.ts → src/schema/modalities.ts
diff --git a/bids-validator/src/schema/tables.test.ts → src/schema/tables.test.ts b/bids-validator/src/schema/tables.test.ts → src/schema/tables.test.ts
diff --git a/bids-validator/src/schema/tables.ts → src/schema/tables.ts b/bids-validator/src/schema/tables.ts → src/schema/tables.ts
diff --git a/bids-validator/src/schema/walk.test.ts → src/schema/walk.test.ts b/bids-validator/src/schema/walk.test.ts → src/schema/walk.test.ts
diff --git a/bids-validator/src/schema/walk.ts → src/schema/walk.ts b/bids-validator/src/schema/walk.ts → src/schema/walk.ts
diff --git a/bids-validator/src/setup/loadSchema.test.ts → src/setup/loadSchema.test.ts b/bids-validator/src/setup/loadSchema.test.ts → src/setup/loadSchema.test.ts
diff --git a/bids-validator/src/setup/loadSchema.ts → src/setup/loadSchema.ts b/bids-validator/src/setup/loadSchema.ts → src/setup/loadSchema.ts
diff --git a/bids-validator/src/setup/options.test.ts → src/setup/options.test.ts b/bids-validator/src/setup/options.test.ts → src/setup/options.test.ts
diff --git a/bids-validator/src/setup/options.ts → src/setup/options.ts b/bids-validator/src/setup/options.ts → src/setup/options.ts
diff --git a/...validator/src/setup/requestPermissions.ts → src/setup/requestPermissions.ts b/...validator/src/setup/requestPermissions.ts → src/setup/requestPermissions.ts
diff --git a/...tor/src/summary/collectSubjectMetadata.ts → src/summary/collectSubjectMetadata.ts b/...tor/src/summary/collectSubjectMetadata.ts → src/summary/collectSubjectMetadata.ts
diff --git a/bids-validator/src/summary/summary.test.ts → src/summary/summary.test.ts b/bids-validator/src/summary/summary.test.ts → src/summary/summary.test.ts
diff --git a/bids-validator/src/summary/summary.ts → src/summary/summary.ts b/bids-validator/src/summary/summary.ts → src/summary/summary.ts
diff --git a/bids-validator/src/tests/README.md → src/tests/README.md b/bids-validator/src/tests/README.md → src/tests/README.md
diff --git a/bids-validator/src/tests/bom-utf16.tsv → src/tests/bom-utf16.tsv b/bids-validator/src/tests/bom-utf16.tsv → src/tests/bom-utf16.tsv
diff --git a/bids-validator/src/tests/bom-utf8.json → src/tests/bom-utf8.json b/bids-validator/src/tests/bom-utf8.json → src/tests/bom-utf8.json
diff --git a/...validator/src/tests/generate-filenames.ts → src/tests/generate-filenames.ts b/...validator/src/tests/generate-filenames.ts → src/tests/generate-filenames.ts
diff --git a/...tor/src/tests/local/bids_examples.test.ts → src/tests/local/bids_examples.test.ts b/...tor/src/tests/local/bids_examples.test.ts → src/tests/local/bids_examples.test.ts
diff --git a/bids-validator/src/tests/local/common.ts → src/tests/local/common.ts b/bids-validator/src/tests/local/common.ts → src/tests/local/common.ts
diff --git a/...dator/src/tests/local/derivatives.test.ts → src/tests/local/derivatives.test.ts b/...dator/src/tests/local/derivatives.test.ts → src/tests/local/derivatives.test.ts
diff --git a/...dator/src/tests/local/empty_files.test.ts → src/tests/local/empty_files.test.ts b/...dator/src/tests/local/empty_files.test.ts → src/tests/local/empty_files.test.ts
diff --git a/...r/src/tests/local/hed-integration.test.ts → src/tests/local/hed-integration.test.ts b/...r/src/tests/local/hed-integration.test.ts → src/tests/local/hed-integration.test.ts
diff --git a/...tor/src/tests/local/valid_dataset.test.ts → src/tests/local/valid_dataset.test.ts b/...tor/src/tests/local/valid_dataset.test.ts → src/tests/local/valid_dataset.test.ts
diff --git a/...r/src/tests/local/valid_filenames.test.ts → src/tests/local/valid_filenames.test.ts b/...r/src/tests/local/valid_filenames.test.ts → src/tests/local/valid_filenames.test.ts
diff --git a/...tor/src/tests/local/valid_headers.test.ts → src/tests/local/valid_headers.test.ts b/...tor/src/tests/local/valid_headers.test.ts → src/tests/local/valid_headers.test.ts
diff --git a/bids-validator/src/tests/nullReadBytes.ts → src/tests/nullReadBytes.ts b/bids-validator/src/tests/nullReadBytes.ts → src/tests/nullReadBytes.ts
diff --git a/.../tests/schema-expression-language.test.ts → src/tests/schema-expression-language.test.ts b/.../tests/schema-expression-language.test.ts → src/tests/schema-expression-language.test.ts
diff --git a/bids-validator/src/tests/simple-dataset.ts → src/tests/simple-dataset.ts b/bids-validator/src/tests/simple-dataset.ts → src/tests/simple-dataset.ts
diff --git a/bids-validator/src/types/check.ts → src/types/check.ts b/bids-validator/src/types/check.ts → src/types/check.ts
diff --git a/bids-validator/src/types/columns.test.ts → src/types/columns.test.ts b/bids-validator/src/types/columns.test.ts → src/types/columns.test.ts
diff --git a/bids-validator/src/types/columns.ts → src/types/columns.ts b/bids-validator/src/types/columns.ts → src/types/columns.ts
diff --git a/bids-validator/src/types/filetree.ts → src/types/filetree.ts b/bids-validator/src/types/filetree.ts → src/types/filetree.ts
diff --git a/bids-validator/src/types/issues.ts → src/types/issues.ts b/bids-validator/src/types/issues.ts → src/types/issues.ts
diff --git a/bids-validator/src/types/schema.ts → src/types/schema.ts b/bids-validator/src/types/schema.ts → src/types/schema.ts
diff --git a/...-validator/src/types/validation-result.ts → src/types/validation-result.ts b/...-validator/src/types/validation-result.ts → src/types/validation-result.ts
diff --git a/bids-validator/src/utils/errors.ts → src/utils/errors.ts b/bids-validator/src/utils/errors.ts → src/utils/errors.ts
diff --git a/bids-validator/src/utils/logger.test.ts → src/utils/logger.test.ts b/bids-validator/src/utils/logger.test.ts → src/utils/logger.test.ts
diff --git a/bids-validator/src/utils/logger.ts → src/utils/logger.ts b/bids-validator/src/utils/logger.ts → src/utils/logger.ts
diff --git a/bids-validator/src/utils/memoize.ts → src/utils/memoize.ts b/bids-validator/src/utils/memoize.ts → src/utils/memoize.ts
diff --git a/...-validator/src/utils/objectPathHandler.ts → src/utils/objectPathHandler.ts b/...-validator/src/utils/objectPathHandler.ts → src/utils/objectPathHandler.ts
diff --git a/bids-validator/src/utils/output.ts → src/utils/output.ts b/bids-validator/src/utils/output.ts → src/utils/output.ts
diff --git a/bids-validator/src/validators/bids.test.ts → src/validators/bids.test.ts b/bids-validator/src/validators/bids.test.ts → src/validators/bids.test.ts
diff --git a/bids-validator/src/validators/bids.ts → src/validators/bids.ts b/bids-validator/src/validators/bids.ts → src/validators/bids.ts
diff --git a/...validator/src/validators/citation.test.ts → src/validators/citation.test.ts b/...validator/src/validators/citation.test.ts → src/validators/citation.test.ts
diff --git a/bids-validator/src/validators/citation.ts → src/validators/citation.ts b/bids-validator/src/validators/citation.ts → src/validators/citation.ts
diff --git a/...r/src/validators/filenameIdentify.test.ts → src/validators/filenameIdentify.test.ts b/...r/src/validators/filenameIdentify.test.ts → src/validators/filenameIdentify.test.ts
diff --git a/...idator/src/validators/filenameIdentify.ts → src/validators/filenameIdentify.ts b/...idator/src/validators/filenameIdentify.ts → src/validators/filenameIdentify.ts
diff --git a/...r/src/validators/filenameValidate.test.ts → src/validators/filenameValidate.test.ts b/...r/src/validators/filenameValidate.test.ts → src/validators/filenameValidate.test.ts
diff --git a/...idator/src/validators/filenameValidate.ts → src/validators/filenameValidate.ts b/...idator/src/validators/filenameValidate.ts → src/validators/filenameValidate.ts
diff --git a/bids-validator/src/validators/hed.ts → src/validators/hed.ts b/bids-validator/src/validators/hed.ts → src/validators/hed.ts
diff --git a/...ator/src/validators/internal/emptyFile.ts → src/validators/internal/emptyFile.ts b/...ator/src/validators/internal/emptyFile.ts → src/validators/internal/emptyFile.ts
diff --git a/...tor/src/validators/internal/unusedFile.ts → src/validators/internal/unusedFile.ts b/...tor/src/validators/internal/unusedFile.ts → src/validators/internal/unusedFile.ts
diff --git a/bids-validator/src/validators/json.ts → src/validators/json.ts b/bids-validator/src/validators/json.ts → src/validators/json.ts
diff --git a/...ator/src/validators/validateFiles.test.ts → src/validators/validateFiles.test.ts b/...ator/src/validators/validateFiles.test.ts → src/validators/validateFiles.test.ts
diff --git a/bids-validator/src/version.ts → src/version.ts b/bids-validator/src/version.ts → src/version.ts
diff --git a/bids-validator/tests/data/bids-examples → tests/data/bids-examples b/bids-validator/tests/data/bids-examples → tests/data/bids-examples
diff --git a/...brainvision_data/dataset_description.json → ...brainvision_data/dataset_description.json b/...brainvision_data/dataset_description.json → ...brainvision_data/dataset_description.json
diff --git a/..._data/sub-01/eeg/sub-01_task-test_eeg.eeg → ..._data/sub-01/eeg/sub-01_task-test_eeg.eeg b/..._data/sub-01/eeg/sub-01_task-test_eeg.eeg → ..._data/sub-01/eeg/sub-01_task-test_eeg.eeg
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diff --git a/.../data/broken_pet_example_2-pet_mri/README → .../data/broken_pet_example_2-pet_mri/README b/.../data/broken_pet_example_2-pet_mri/README → .../data/broken_pet_example_2-pet_mri/README
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diff --git a/...ata/broken_pet_example_3-pet_blood/README → ...ata/broken_pet_example_3-pet_blood/README b/...ata/broken_pet_example_3-pet_blood/README → ...ata/broken_pet_example_3-pet_blood/README
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diff --git a/bids-validator/tests/data/no_t1w/README → tests/data/no_t1w/README b/bids-validator/tests/data/no_t1w/README → tests/data/no_t1w/README
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diff --git a/...sk-rest_acq-fullbrain_run-2_physio.tsv.gz → ...sk-rest_acq-fullbrain_run-2_physio.tsv.gz b/...sk-rest_acq-fullbrain_run-2_physio.tsv.gz → ...sk-rest_acq-fullbrain_run-2_physio.tsv.gz
diff --git a/...es-2_task-rest_acq-prefrontal_bold.nii.gz → ...es-2_task-rest_acq-prefrontal_bold.nii.gz b/...es-2_task-rest_acq-prefrontal_bold.nii.gz → ...es-2_task-rest_acq-prefrontal_bold.nii.gz
diff --git a/...-2_task-rest_acq-prefrontal_physio.tsv.gz → ...-2_task-rest_acq-prefrontal_physio.tsv.gz b/...-2_task-rest_acq-prefrontal_physio.tsv.gz → ...-2_task-rest_acq-prefrontal_physio.tsv.gz
diff --git a/...tude1/sub-01/ses-2/sub-01_ses-2_scans.tsv → ...tude1/sub-01/ses-2/sub-01_ses-2_scans.tsv b/...tude1/sub-01/ses-2/sub-01_ses-2_scans.tsv → ...tude1/sub-01/ses-2/sub-01_ses-2_scans.tsv
diff --git a/...out_magnitude1/sub-01/sub-01_sessions.tsv → ...out_magnitude1/sub-01/sub-01_sessions.tsv b/...out_magnitude1/sub-01/sub-01_sessions.tsv → ...out_magnitude1/sub-01/sub-01_sessions.tsv
diff --git a/...nitude1/task-rest_acq-fullbrain_bold.json → ...nitude1/task-rest_acq-fullbrain_bold.json b/...nitude1/task-rest_acq-fullbrain_bold.json → ...nitude1/task-rest_acq-fullbrain_bold.json
diff --git a/...task-rest_acq-fullbrain_run-1_physio.json → ...task-rest_acq-fullbrain_run-1_physio.json b/...task-rest_acq-fullbrain_run-1_physio.json → ...task-rest_acq-fullbrain_run-1_physio.json
diff --git a/...task-rest_acq-fullbrain_run-2_physio.json → ...task-rest_acq-fullbrain_run-2_physio.json b/...task-rest_acq-fullbrain_run-2_physio.json → ...task-rest_acq-fullbrain_run-2_physio.json
diff --git a/...itude1/task-rest_acq-prefrontal_bold.json → ...itude1/task-rest_acq-prefrontal_bold.json b/...itude1/task-rest_acq-prefrontal_bold.json → ...itude1/task-rest_acq-prefrontal_bold.json
diff --git a/...ude1/task-rest_acq-prefrontal_physio.json → ...ude1/task-rest_acq-prefrontal_physio.json b/...ude1/task-rest_acq-prefrontal_physio.json → ...ude1/task-rest_acq-prefrontal_physio.json
diff --git a/...ator/tests/data/symlinked_subject/CHANGES → tests/data/symlinked_subject/CHANGES b/...ator/tests/data/symlinked_subject/CHANGES → tests/data/symlinked_subject/CHANGES
diff --git a/...dator/tests/data/symlinked_subject/README → tests/data/symlinked_subject/README b/...dator/tests/data/symlinked_subject/README → tests/data/symlinked_subject/README
diff --git a/...ymlinked_subject/dataset_description.json → ...ymlinked_subject/dataset_description.json b/...ymlinked_subject/dataset_description.json → ...ymlinked_subject/dataset_description.json
diff --git a/...s/data/symlinked_subject/participants.tsv → ...s/data/symlinked_subject/participants.tsv b/...s/data/symlinked_subject/participants.tsv → ...s/data/symlinked_subject/participants.tsv
diff --git a/...dator/tests/data/symlinked_subject/sub-01 → tests/data/symlinked_subject/sub-01 b/...dator/tests/data/symlinked_subject/sub-01 → tests/data/symlinked_subject/sub-01
diff --git a/...nked_subject/task-rhymejudgment_bold.json → ...nked_subject/task-rhymejudgment_bold.json b/...nked_subject/task-rhymejudgment_bold.json → ...nked_subject/task-rhymejudgment_bold.json
diff --git a/...unused_data_dict/dataset_description.json → ...unused_data_dict/dataset_description.json b/...unused_data_dict/dataset_description.json → ...unused_data_dict/dataset_description.json
diff --git a/...ts/data/unused_data_dict/participants.tsv → tests/data/unused_data_dict/participants.tsv b/...ts/data/unused_data_dict/participants.tsv → tests/data/unused_data_dict/participants.tsv
diff --git a/...b-01/ses-1/anat/sub-01_ses-1_T1map.nii.gz → ...b-01/ses-1/anat/sub-01_ses-1_T1map.nii.gz b/...b-01/ses-1/anat/sub-01_ses-1_T1map.nii.gz → ...b-01/ses-1/anat/sub-01_ses-1_T1map.nii.gz
diff --git a/...sub-01/ses-1/anat/sub-01_ses-1_T1w.nii.gz → ...sub-01/ses-1/anat/sub-01_ses-1_T1w.nii.gz b/...sub-01/ses-1/anat/sub-01_ses-1_T1w.nii.gz → ...sub-01/ses-1/anat/sub-01_ses-1_T1w.nii.gz