add relpath for suffix tables

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

@@ -276,7 +276,8 @@ and a guide for using macros can be found at
          "PDT2",
          "UNIT1",
          "angio",
-      ]
+      ],
+      ".."
    )
 }}
 
@@ -412,7 +413,8 @@ and a guide for using macros can be found at
          "RB1map",
          "S0map",
          "M0map",
-      ]
+      ],
+      ".."
    )
 }}
 
@@ -449,7 +451,8 @@ and a guide for using macros can be found at
          "T2star",
          "FLASH",
          "PD",
-      ]
+      ],
+      ".."
    )
 }}
 
@@ -469,7 +472,8 @@ and a guide for using macros can be found at
          "bold",
          "cbv",
          "phase",
-      ]
+      ],
+      ".."
    )
 }}
 
@@ -736,7 +740,8 @@ and a guide for using macros can be found at
       [
          "dwi",
          "sbref",
-      ]
+      ],
+      ".."
    )
 }}
 
@@ -1172,7 +1177,8 @@ and a guide for using macros can be found at
          "phasediff",
          "fieldmap",
          "epi",
-      ]
+      ],
+      ".."
    )
 }}
 

src/04-modality-specific-files/10-microscopy.md

@@ -90,7 +90,8 @@ and a guide for using macros can be found at
          "NLO",
          "OCT",
          "SPIM",
-      ]
+      ],
+      ".."
    )
 }}
 

src/schema/objects/suffixes.yaml

@@ -463,7 +463,7 @@ blood:
   name: Blood recording data
   description: |
     Blood measurements of radioactivity stored in
-    [tabular files](/02-common-principles.html#tabular-files)
+    [tabular files](PATH_TO_SRC/02-common-principles.html#tabular-files)
     and located in the `pet/` directory along with the corresponding PET data.
 bold:
   name: Blood-Oxygen-Level Dependent image
@@ -579,11 +579,11 @@ pet:
 phase:
   name: Phase image
   description: |
-    [DEPRECATED](/02-common-principles.html#definitions).
+    [DEPRECATED](PATH_TO_SRC/02-common-principles.html#definitions).
     Phase information associated with magnitude information stored in BOLD
     contrast.
     This suffix should be replaced by the
-    [`part-phase`](/99-appendices/09-entities.html#part)
+    [`part-phase`](PATH_TO_SRC/99-appendices/09-entities.html#part)
     in conjunction with the `bold` suffix.
   anyOf:
   - unit: arbitrary

tools/mkdocs_macros_bids/macros.py

@@ -91,13 +91,16 @@ def make_glossary(relpath=None):
     return text
 
 
-def make_suffix_table(suffixes):
+def make_suffix_table(suffixes, relpath=None):
     """Generate a markdown table of suffix information.
 
     Parameters
     ----------
     suffixes : list of str
         A list of the suffixes to include in the table.
+    relpath : str | None
+        path from file where this func is called to src/
+
 
     Returns
     -------
@@ -107,7 +110,7 @@ def make_suffix_table(suffixes):
     """
     schemapath = utils.get_schema_path()
     schema_obj = schema.load_schema(schemapath)
-    table = render.make_suffix_table(schema_obj, suffixes)
+    table = render.make_suffix_table(schema_obj, suffixes, relpath)
     return table
 
 

tools/schemacode/schemacode/render.py

@@ -408,13 +408,15 @@ def _remove_numeric_suffixes(string):
     return table_str
 
 
-def make_suffix_table(schema, suffixes, tablefmt="github"):
+def make_suffix_table(schema, suffixes, relpath=None, tablefmt="github"):
     """Produce suffix table (markdown) based on requested suffixes.
 
     Parameters
     ----------
     schema : dict
     suffixes : list of str
+    relpath : str | None
+        path from file where this func is called to src/
     tablefmt : str
 
     Returns
@@ -445,6 +447,9 @@ def make_suffix_table(schema, suffixes, tablefmt="github"):
         description = description.replace("\n\n", "<br>")
         # Otherwise a newline corresponds to a space
         description = description.replace("\n", " ")
+        # Spec internal links need to be replaced
+        if relpath is not None:
+            description = description.replace("PATH_TO_SRC", relpath)
 
         df.loc[suffix] = [suffix_info["name"], description]