clean up

.github/workflows/check_md_links.yml

@@ -0,0 +1,27 @@
+---
+name: Check Markdown links
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: ['*']
+
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+
+jobs:
+  markdown-link-check:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@master
+    - uses: gaurav-nelson/github-action-markdown-link-check@v1
+      with:
+        use-quiet-mode: yes
+        use-verbose-mode: yes
+        config-file: md_link_check_config.json
+        folder-path: SRC
+        file-path: ./README.md

md_link_check_config.json

@@ -0,0 +1,4 @@
+{
+  "timeout": "20s",
+  "retryOn429": true
+}

src/CONTRIBUTING.md

@@ -11,10 +11,10 @@
 -   Pierre Rioux:  [[email protected]](mailto:[email protected])
 -   Yaroslav O. Halchenko [[email protected]](mailto:[email protected])
 -   Eric Earl [[email protected]](mailto:[email protected])
--   Pradeep Reddy Raamana [email protected]
+-   Pradeep Reddy Raamana [[email protected]](mailto:[email protected])
 -   Aki Nikolaidis [[email protected]](mailto:[email protected])
 -   Guiomar Niso [[email protected]](mailto:[email protected]),
 -   Lennart Walger [[email protected]](mailto:[email protected])
 -   Sebastien Tourbier [[email protected]](mailto:[email protected])
 -   Alejandro de la Vega [[email protected]](mailto:[email protected])
--   Robert Luke [email protected]
+-   Robert Luke [[email protected]](mailto:[email protected])

src/examples.md

@@ -1,4 +1,3 @@
-
 # Example BIDS App
 
 This section describes a BIDS Application named bids-app that can only operate

src/index.md

@@ -26,7 +26,7 @@ This document is a draft for the BIDS Application
 specification for the purposes of tool description, provenance and
 reproducibility. This is a working document in draft stage and any comments are
 welcome. This document inherits all components of the original specification
-(e.g. how to store imaging data, events, stimuli and behavioral data), and
+(for example how to store imaging data, events, stimuli and behavioral data), and
 should be seen as an extension of it, not a replacement.
 
 ## How can I help?

src/inputs.md

@@ -212,6 +212,7 @@ exhaustive list. The arguments may be specified as follows:
 -   The argument ID SHOULD be in CamelCase, with the form <entity>Label or
     <entity>Index, depending on whether the associated values are constrained
     to be alphanumeric or numeric, respectively.
+
 -   The argument MUST accept values referring to labels/indices, as consistent
     with the above, in either the form of a list or a file containing a
     line-delimited list. The items provided SHOULD NOT include the entity label in
@@ -226,14 +227,14 @@ CLI flag: `--subject-label`
 
 Acceptable and equivalent usages:
 
-```
+```bash
     --subject-label 01 02 03
     --subject-label subject_ids.txt
 ```
 
 Contents of `subject_ids.txt`:
 
-```
+```text
 01
 02
 03

src/outputs.md

@@ -1,8 +1,6 @@
+# Outputs
 
-
-### Outputs
-
-#### File formats for the application specification and report
+## File formats for the application specification and report
 
 BIDS Apps MUST be able to be called via the BIDS Application Boutiques
 descriptor and corresponding input parameter dictionary files, commonly referred
@@ -83,7 +81,7 @@ datasets.
   </tr>
 </table>
 
-#### Execution Report & Updating Dataset Description
+## Execution Report & Updating Dataset Description
 
 When generated, an execution report that completely describes the processing
 that was executed and the dataset MUST comply with the BIDS Provenance Extension
@@ -93,7 +91,7 @@ specified in the `output-files` section of the tool descriptor.
 Similarly, the dataset_description.json file SHOULD be updated to reflect the
 processing that has occurred by the BIDS Application.
 
-### Behaviors
+## Behaviors
 
 For a given set of arguments, the behavior of a BIDS Application will typically
 vary based on the contents of the input dataset. The dataset may be
@@ -102,7 +100,7 @@ requires, or it may not. This section describes the expected behavior under each
 combination of cases, and describes RECOMMENDED exit codes on systems that
 support them.
 
-#### Valid BIDS datasets
+### Valid BIDS datasets
 
 If the dataset is BIDS-compliant and contains the files required by the
 application, then the application should make a best effort to perform its task
@@ -113,7 +111,7 @@ application, then the application MAY fail immediately or when attempting to
 open a missing file. In this case, it is RECOMMENDED to use exit code 66
 (NOINPUT).
 
-#### Invalid BIDS datasets
+### Invalid BIDS datasets
 
 If the dataset is not BIDS-compliant, then the BIDS App MAY fail immediately
 with exit code 16.
@@ -122,7 +120,7 @@ If the dataset contains the required files but is not BIDS-compliant (for exampl
 "dirty" dataset that has more files than needed), then the BIDS App MAY treat
 the dataset as valid.
 
-#### Exit codes
+### Exit codes
 
 An exit code or [exit status](https://en.wikipedia.org/wiki/Exit_status) is an
 integer indicating the reason for termination for use by the parent program or

src/specification.md

@@ -9,9 +9,9 @@ There are three domains of requirements that BIDS Applications must specify:
 BIDS contains "required", "recommended" and "optional" fields. These are
 indicated throughout the document:
 
--   **REQUIRED**: essential to be BIDS compliant (i.e. MUST as per RFC2199)
--   **RECOMMENDED**: gives a warning if not present (i.e. SHOULD as per RFC2199)
--   **OPTIONAL**: no warning if missing (i.e. MAY as per RFC2199)
+-   **REQUIRED**: essential to be BIDS compliant (meaning MUST as per RFC2199)
+-   **RECOMMENDED**: gives a warning if not present (meaning SHOULD as per RFC2199)
+-   **OPTIONAL**: no warning if missing (meaning MAY as per RFC2199)
 
 Ultimately, through using Boutiques to define tools and their parameters, the
 goal is that each tool can be interacted with as follows: