fixing mermaid

.github/workflows/publishdocs.yaml

@@ -18,21 +18,13 @@ jobs:
           python-version: 3.9
 
       - name: Install the required python packages
-        run: python -m pip install linkml mkdocs-material mkdocs-mermaid2-plugin
-
-      - name: Other installations
-        run: |
-          sudo apt-get update
-          sudo apt-get install -y build-essential git wget curl
+        run: python -m pip install linkml
 
       - name: Generating docs
         run: |
           gen-doc -d docs/schema/doc-linkml-autogen linkml-schema/reproschema.yaml
           gen-erdiagram linkml-schema/reproschema.yaml > docs/schema/erdiagram-autogen.md
 
-      - name: Build MkDocs site
-        run: mkdocs build
-
       - name: Deploy docs
         uses: mhausenblas/mkdocs-deploy-gh-pages@master
         env:

.gitignore

@@ -4,8 +4,12 @@ protocols/.DS_Store
 
 .idea/
 
-node_modules
 local_data
 
+# ignore linkml auto generated doc
+docs/schema/doc-linkml-autogen
+docs/schema/erdiagram-autogen.md
+
+node_modules
 package-lock.json
 package.json

.pre-commit-config.yaml

@@ -7,6 +7,11 @@ repos:
     -   id: trailing-whitespace
     -   id: end-of-file-fixer
     -   id: check-yaml
+        exclude: |
+            (?x)^(
+                docs/specification/.*
+                | mkdocs.yml
+            )$
     -   id: check-json
     -   id: check-ast
     -   id: check-added-large-files

docs/index.md

@@ -17,7 +17,7 @@ things are to use the ReproSchema but some "big picture" conceptual understandin
 could save you from a lot of confusion. 😉
 
 -   Not sure how the project is organized? Check out the [project structure](./project-structure.md) page.
--   Want more details on how the `Reproschema` itself is structured: check out our [schema page](./schema.md)
+-   Want more details on how the `Reproschema` itself is structured: check out our [schema page](./schema/schema.md)
 
 <!-- - If you want to use the schema to create your own questionnaire: check out our
 

docs/project-structure.md

@@ -37,7 +37,7 @@ The ReproSchema is like a blueprint for research projects, ensuring everyone col
 
 There is also an [`example`](https://github.com/ReproNim/reproschema/tree/master/examples)
 schema that can help give you a quick overview of what the protocol and activity
-for a study might look like. For more details see the [schema section](./schema.md).
+for a study might look like. For more details see the [schema section](./schema/schema.md).
 
 ## [reproschema-library](https://github.com/ReproNim/reproschema-library)
 

mkdocs.yml

@@ -42,6 +42,7 @@ nav:
   - Schema:
       - Schema overview: "schema/schema.md"
       - Schema documentation: "schema/doc-linkml-autogen/index.md"
+      - Schema diagram: schema/erdiagram-autogen.md
   - User Guide:
       - Create a research protocol: "user-guide/create-new-protocol.md"
       - Adopt assessments from the library: "user-guide/adopt-assessments.md"
@@ -79,11 +80,15 @@ markdown_extensions:
         - includes/abbreviations.md
   - toc:
       anchorlink: true
+  - pymdownx.superfences:
+      custom_fences:
+        - name: mermaid
+          class: mermaid
+          format: !!python/name:pymdownx.superfences.fence_code_format
 
 watch:
   - includes
 
 plugins:
   - search
   - tags
-  - mermaid2