[INFRA] Use linkchecker to verify URLs

.circleci/config.yml

@@ -2,18 +2,18 @@ version: 2
 jobs:
   build:
     docker:
-      - image: circleci/python:3.6.6
+      - image: circleci/python:2.7
     steps:
       - checkout
       - run: sudo chown -R circleci:circleci /usr/local/bin
-      - run: sudo chown -R circleci:circleci /usr/local/lib/python3.6/site-packages
+      - run: sudo chown -R circleci:circleci /usr/local/lib/python*/site-packages
       - restore_cache:  # ensure this step occurs *before* installing dependencies
           key: deps9-{{ .Branch }}-{{ checksum "Pipfile.lock" }}
       - run:
           command: |
             sudo pip install pip==18.0
             sudo pip install pipenv==2018.7.1
-            pipenv install
+            pipenv install -d
       - save_cache:
           key: deps9-{{ .Branch }}-{{ checksum "Pipfile.lock" }}
           paths:
@@ -23,5 +23,14 @@ jobs:
       - run:
           name: generate docs
           command: pipenv run mkdocs build --clean --strict --verbose
+      - run:
+          name: quick check URLs
+          command: |
+            mkdir -p ~/.linkchecker/ && echo '[AnchorCheck]' >| ~/.linkchecker/linkcheckerrc
+            pipenv run linkchecker site/
+      # TODO: ATM 38 errors (and locally got also 43 internal errors)
+      #- run:
+      #    name: thorough check of external URLs
+      #    command: pipenv run linkchecker --check-extern site/
       - store_artifacts:
           path: site

Pipfile

@@ -8,6 +8,15 @@ mkdocs = "==1.0.4"
 mkdocs-material = "==3.0.4"
 
 [dev-packages]
+# Custom version with the fix for anchors
+linkchecker = {file = "https://github.com/yarikoptic/linkchecker/archive/9.4.0.anchorfix1.zip"}
+# Installing from a file seems to not pull in all the dependencies linkchecker needs,
+# so installing them manually here
+requests = "*"
+pyxdg = "*"
+dnspython = "*"
+
 
 [requires]
-python_version = "3.6"
+# linkchecker doesn't support python3 yet
+# python_version = "3.6"

src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md

@@ -171,9 +171,9 @@ inplaneT1, referenced by a defacemask image. E.g.,
 `sub-01_mod-T1w_defacemask.nii.gz`.
 
 Some meta information about the acquisition MAY be provided in an additional
-JSON file. See Common MR metadata fields for a list of terms and their
-definitions. There are also some OPTIONAL JSON fields specific to anatomical
-scans:
+JSON file. See [Common metadata fields](#common-metadata-fields) for a
+list of terms and their definitions. There are also some OPTIONAL JSON
+fields specific to anatomical scans:
 
 | Field name              | Definition                                                                                                                                         |
 | :---------------------- | :------------------------------------------------------------------------------------------------------------------------------------------------- |
@@ -287,7 +287,7 @@ combined image rather than an image from each coil.
 | CogAtlasID      | RECOMMENDED. URL of the corresponding [Cognitive Atlas](http://www.cognitiveatlas.org/) Task term.                                                                                                         |
 | CogPOID         | RECOMMENDED. URL of the corresponding [CogPO](http://www.cogpo.org/) term.                                                                                                                                 |
 
-See [8.3.1. Common MR metadata fields](#heading=h.5u721tt1h9pe) for a list of
+See [Common metadata fields](#common-metadata-fields) for a list of
 additional terms and their definitions.
 
 Example:
@@ -360,7 +360,7 @@ dwi.nii file) and not the magnet’s coordinate system, which means that any
 rotations applied to dwi.nii also need to be applied to the corresponding bvec
 file.
 
-<sup>4</sup>[http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/fdt/fdt_dtifit.html](hhttp://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/fdt/fdt_dtifit.html)
+<sup>4</sup>[http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/fdt/fdt_dtifit.html](http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/fdt/fdt_dtifit.html)
 
 bvec example:
 
@@ -384,8 +384,8 @@ bval example:
 and thus define those values for all sessions and/or subjects in one place (see
 Inheritance principle).
 
-See Common MR metadata fields for a list of additional terms that can be
-included in the corresponding JSON file.
+See [Common metadata fields](#common-metadata-fields) for a list of
+additional terms that can be included in the corresponding JSON file.
 
 JSON example: