From c013d28851d461961df44df24272cf21d9ccb05a Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Fri, 6 Oct 2023 11:06:47 +0200 Subject: [PATCH] clean up --- .github/workflows/check_md_links.yml | 27 +++++++++++++++++++++++++++ md_link_check_config.json | 4 ++++ src/CONTRIBUTING.md | 4 ++-- src/examples.md | 1 - src/index.md | 2 +- src/inputs.md | 5 +++-- src/outputs.md | 16 +++++++--------- src/specification.md | 6 +++--- 8 files changed, 47 insertions(+), 18 deletions(-) create mode 100644 .github/workflows/check_md_links.yml create mode 100644 md_link_check_config.json diff --git a/.github/workflows/check_md_links.yml b/.github/workflows/check_md_links.yml new file mode 100644 index 0000000..96a8249 --- /dev/null +++ b/.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 diff --git a/md_link_check_config.json b/md_link_check_config.json new file mode 100644 index 0000000..4270344 --- /dev/null +++ b/md_link_check_config.json @@ -0,0 +1,4 @@ +{ + "timeout": "20s", + "retryOn429": true +} diff --git a/src/CONTRIBUTING.md b/src/CONTRIBUTING.md index 3bd6860..8340b23 100644 --- a/src/CONTRIBUTING.md +++ b/src/CONTRIBUTING.md @@ -11,10 +11,10 @@ - Pierre Rioux: [pierre.rioux@mcgill.ca](mailto:pierre.rioux@mcgill.ca) - Yaroslav O. Halchenko [yoh@dartmouth.edu](mailto:yoh@dartmouth.edu) - Eric Earl [eric.earl@nih.gov](mailto:eric.earl@nih.gov) -- Pradeep Reddy Raamana raamanap@pitt.edu +- Pradeep Reddy Raamana [raamanap@pitt.edu](mailto:raamanap@pitt.edu) - Aki Nikolaidis [aki.nikolaidis@childmind.org](mailto:aki.nikolaidis@childmind.org) - Guiomar Niso [guiomar.niso@ctb.upm.es](mailto:guiomar.niso@ctb.upm.es), - Lennart Walger [lennart.walger@ukbonn.de](mailto:lennart.walger@ukbonn.de) - Sebastien Tourbier [sebastien.tourbier1@gmail.com](mailto:sebastien.tourbier1@gmail.com) - Alejandro de la Vega [delavega@utexas.edu](mailto:delavega@utexas.edu) -- Robert Luke robert.luke@mq.edu.au +- Robert Luke [robert.luke@mq.edu.au](mailto:robert.luke@mq.edu.au) diff --git a/src/examples.md b/src/examples.md index b50ee44..8fae307 100644 --- a/src/examples.md +++ b/src/examples.md @@ -1,4 +1,3 @@ - # Example BIDS App This section describes a BIDS Application named bids-app that can only operate diff --git a/src/index.md b/src/index.md index 1ae52e6..9bf12a2 100644 --- a/src/index.md +++ b/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? diff --git a/src/inputs.md b/src/inputs.md index f85b607..e8c013d 100644 --- a/src/inputs.md +++ b/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 diff --git a/src/outputs.md b/src/outputs.md index aaa9365..3155e90 100644 --- a/src/outputs.md +++ b/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. -#### 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 diff --git a/src/specification.md b/src/specification.md index 500c973..3049372 100644 --- a/src/specification.md +++ b/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: