Merge pull request #932 from effigies/linkchecker

[INFRA] Run linkchecker in stock docker image
bids-standard · Nov 17, 2021 · 4ee5928 · 4ee5928
2 parents bade5e8 + ddca51d
commit 4ee5928
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diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -21,18 +21,18 @@ jobs:
 
   linkchecker:
     docker:
-      - image: yarikoptic/linkchecker:9.4.0.anchorfix1-1
+      - image: circleci/python:3.8
     steps:
       # checkout code to default ~/project
       - checkout
       - attach_workspace:
           # mkdocs build outputs will be in ~/project/site
           at: ~/project
       - run:
-          name: install git
+          name: install linkchecker
           command: |
-            apt update -y
-            apt install git-all -y
+            python -m ensurepip
+            python -m pip install linkchecker
       - run:
           name: check links
           command: |

diff --git a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
@@ -3,9 +3,11 @@
 ## Common metadata fields
 
 MR Data described in the following sections share the following RECOMMENDED metadata
-fields (stored in sidecar JSON files). MRI acquisition parameters are divided
-into several categories based on
-["A checklist for fMRI acquisition methods reporting in the literature"](https://thewinnower.com/papers/977-a-checklist-for-fmri-acquisition-methods-reporting-in-the-literature)
+fields (stored in sidecar JSON files).
+MRI acquisition parameters are divided into several categories based on
+"A checklist for fMRI acquisition methods reporting in the literature"
+([article](https://winnower-production.s3.amazonaws.com/papers/977/v4/pdf/977-a-checklist-for-fmri-acquisition-methods-reporting-in-the-literature.pdf),
+[checklist](https://winnower-production.s3.amazonaws.com/papers/977/assets/993e199d-6bc3-4418-be3a-f620af1188b7-Parameter_Reporting_V1p3.pdf))
 by Ben Inglis.
 
 ### Scanner Hardware

diff --git a/src/04-modality-specific-files/04-intracranial-electroencephalography.md b/src/04-modality-specific-files/04-intracranial-electroencephalography.md
@@ -24,7 +24,7 @@ stored in one of the following formats:
 | [BrainVision Core Data Format](https://www.brainproducts.com/productdetails.php?id=21&tab=5) | `.vhdr`, `.vmrk`, `.eeg` | Each recording consists of a  `.vhdr`, `.vmrk`, `.eeg` file triplet.                                                                                                       |
 | [EEGLAB](https://sccn.ucsd.edu/eeglab)                                                       | `.set`, `.fdt`           | The format used by the MATLAB toolbox [EEGLAB](https://sccn.ucsd.edu/eeglab). Each recording consists of a `.set` file with an optional `.fdt` file.                       |
 | [Neurodata Without Borders](https://nwb-schema.readthedocs.io)                               | `.nwb`                   | Each recording consists of a single `.nwb` file.                                                                                                                           |
-| [MEF3](https://msel.mayo.edu/files/codes/MEF%203%20Specification.pdf)                        | `.mefd`                  | Each recording consists of a `.mefd` directory.                                                                                                                            |
+| [MEF3](https://osf.io/e3sf9/)                                                                | `.mefd`                  | Each recording consists of a `.mefd` directory.                                                                                                                            |
 
 It is RECOMMENDED to use the European data format, or the BrainVision data
 format. It is furthermore discouraged to use the other accepted formats over

diff --git a/tools/linkchecker-docker/neurodocker-build.sh b/tools/linkchecker-docker/neurodocker-build.sh