fix: Markdown code environment not honored when generating description in glossary

Author: oesteban

src/schema/objects/metaentities.yaml

@@ -34,22 +34,22 @@ matches:
     `matches` is used as a placeholder in BIDS filenames templates to denote that several files
     share exactly the same sequence of entities and labels in their basename.
 
-        For example, in the following filename template:
+    For example, in the following filename template:
 
-        ```
-        <matches>_bold.nii.gz
-        <matches>_events.tsv
-        <matches>_events.json
-        ```
+    ```Text
+    <matches>_bold.nii.gz
+    <matches>_events.tsv
+    <matches>_events.json
+    ```
 
-        `<matches>` could correspond to `sub-control01_task-nback_run-1`.
+    `<matches>` could correspond to `sub-control01_task-nback_run-1`.
 
 source_entities:
   name: source_entities
   display_name: source entities
   description: |
     `source_entities` is used as a placeholder in BIDS derivatives filenames templates.
 
-        `source_entities` MUST be the entire source filename, with the omission of
-        the source suffix and extension.
-        One exception to this rule is filename entities that are no longer relevant.
+    `source_entities` MUST be the entire source filename, with the omission of
+    the source suffix and extension.
+    One exception to this rule is filename entities that are no longer relevant.

tools/schemacode/src/bidsschematools/render/text.py

@@ -151,12 +151,6 @@ def make_glossary(schema, src_path=None):
         obj_desc = obj_def.get("description", None)
         if obj_desc is None:
             raise ValueError(f"{obj_marker} has no description.")
-        # A backslash before a newline means continue a string
-        obj_desc = obj_desc.replace("\\\n", "")
-        # Two newlines should be respected
-        obj_desc = obj_desc.replace("\n\n", "<br>")
-        # Otherwise a newline corresponds to a space
-        obj_desc = obj_desc.replace("\n", " ")
 
         text += f'\n<a name="{obj_marker}"></a>'
         text += f"\n## {obj_key}\n\n"
@@ -184,7 +178,9 @@ def make_glossary(schema, src_path=None):
             levels = [level["name"] if isinstance(level, dict) else level for level in levels]
             text += f"**Allowed values**: `{'`, `'.join(levels)}`\n\n"
 
-        text += f"**Description**:\n{obj_desc}\n\n"
+        # Convert description into markdown and append to text
+        obj_desc = MarkdownIt().render(f"**Description**:\n{obj_desc}")
+        text += f"{obj_desc}\n\n"
 
         reduced_obj_def = {k: v for k, v in obj_def.items() if k not in keys_to_drop}