refactor jsonld snippets out of doc

.github/workflows/pythonpackage.yml

@@ -16,10 +16,10 @@ jobs:
 
     steps:
     - uses: actions/checkout@v2
-    - name: Set up Python 3.10
+    - name: Set up Python
       uses: actions/setup-python@v5
       with:
-        python-version: "3.10"
+        python-version: 3.12
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip setuptools

.github/workflows/validate.yml

@@ -0,0 +1,53 @@
+name: validate protocol and activities
+
+# describes when this workfllow is triggered
+on:
+    push: # when pushing to a branch
+        branches: [master] # on which branch
+    pull_request: # when opening a new pull request
+        branches: "*" # * refers to all branches
+
+jobs:
+    build:
+        # describes the operating system that will #be used
+        runs-on: ubuntu-latest
+
+        # Steps represent a sequence of tasks executed as part of the job
+        steps:
+        -   name: Setup Node # installing Node.js for all the javascript part
+            uses: actions/[email protected]
+
+        # Checks-out your repository under $GITHUB_WORKSPACE,
+        #  so your job can access it
+        - uses: actions/checkout@v2
+
+        # Checks that our JSON are valid
+        # Installing `jsonlint` to validate the JSON files
+        # Looking recursively through the directories `protocol`
+        # and `activities` for any file with "@context" in them
+        # (that makes them JSON-LD files) and validate their content
+        # with jsonlint
+        -   name: Check for syntax errors
+            run: |
+                npm install -g jsonlint
+                grep -r  "@context" activities | cut -d: -f1 | xargs -I fname jsonlint -q fname
+                grep -r  "@context" protocols | cut -d: -f1 | xargs -I fname jsonlint -q fname
+
+        # Checks that the schemas are valid
+        # Using python and the installing the reproschema tools
+        # from the reproschema-py repository to then validate
+        # the content of the `activities` and `protocols` folders.
+        -   name: Set up Python
+            uses: actions/setup-python@v5
+            with:
+                python-version: 3.12
+
+        -   name: Install dependencies
+            run: |
+                python -m pip install --upgrade pip setuptools
+                pip install reproschema requests_cache
+
+        -   name: Test with pyshacl
+            run: |
+                reproschema -l DEBUG validate activities
+                reproschema -l DEBUG validate protocols

.pre-commit-config.yaml

@@ -19,3 +19,17 @@ repos:
     rev: v2.2.6
     hooks:
     -   id: codespell
+# Check formatting of CSS and HTML
+# prettier: https://prettier.io/
+-   repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v4.0.0-alpha.8
+    hooks:
+    -   id: prettier
+        types_or: [json]
+        # exclude files that
+        #  - are skipped for other hooks
+        #  - are still involved in some PR
+        exclude: |
+            (?x)^(
+                releases/.*
+            )$

docs/glossary.md

@@ -4,8 +4,5 @@
 -   compute specification
 -   input type
 -   item
--   JSON
--   JSON-LD
 -   protocol
--   SHACL
 -   visibility

docs/introduction.md

@@ -1,6 +1,6 @@
 # Introduction
 
-??? example "Tl;DR - Advantages of the current schema representation"
+!!! example "Tl;DR - Advantages of the current schema representation"
 
     -   Rich contexts for a questionnaire with JSON-LD rather than a "flat" csv file.
     -   A single source of curated assessments from [ReproSchema Library](https://github.com/ReproNim/reproschema-library)