[ENH] use macros for filename templates (#536)

* use files for templates

* fix

Author: Remi-Gau

.remarkignore

@@ -1,4 +1,3 @@
 docs/collaboration/bids_github/
 docs/datasets/index.md
-docs/getting_started/folders_and_files/files.md
 docs/specification/macros_doc.md

docs/faq/bids-extensions.md

@@ -1,3 +1,5 @@
+# BIDS extensions
+
 ## Can we introduce new entities / metadata in a BEP?
 
 > We need to introduce an entity to distinguish on-device preprocessing methods

docs/faq/eeg.md

@@ -1,3 +1,5 @@
+# EEG
+
 ## How to format Hardware and Software filter fields in a .json?
 
 In the modality specific sidecar file `_eeg.json`, we can specify the software

docs/faq/mri.md

@@ -1,3 +1,5 @@
+# MRI
+
 ## I only have nifti files and no dicom. Can I still create a BIDS dataset?
 
 In theory yes, but it is possible that you will be missing some metadata that is required by the BIDS specification.

docs/getting_started/folders_and_files/files.md

@@ -2,6 +2,7 @@
     generate_apps_table,
     generate_beps_table,
     generate_converter_table,
+    generate_filename_templates,
     generate_grants_table,
     generate_members_table,
     generate_tools_table,
@@ -18,4 +19,5 @@
     "generate_grants_table",
     "generate_apps_table",
     "generate_working_groups_table",
+    "generate_filename_templates",
 ]

macros/__init__.py

@@ -1,7 +1,9 @@
 from pathlib import Path
 
 import ruamel.yaml
+from bidsschematools import render, schema
 from jinja2 import Environment, FileSystemLoader, select_autoescape
+from rich import print
 
 yaml = ruamel.yaml.YAML()
 yaml.indent(mapping=2, sequence=4, offset=2)
@@ -78,8 +80,51 @@ def generate_apps_table():
     return template.render(include=content, type=type)
 
 
+def generate_filename_templates():
+    """Create filename templates for all datatypes of all modalities."""
+
+    schema_obj = schema.load_schema()
+
+    modalities = schema_obj.rules.modalities
+
+    to_render = [
+        {
+            "name": x,
+            "description": schema_obj.objects.modalities[x]["description"],
+            "datatypes": [
+                {
+                    "name": dt,
+                    "filenames": filename_template_for(schema_obj, dt),
+                }
+                for dt in modalities[x]["datatypes"]
+            ],
+        }
+        for x in modalities
+    ]
+
+    env = return_jinja_env()
+    template = env.get_template("filename_templates_md.jinja")
+    return template.render(include=to_render)
+
+
+def filename_template_for(schema_obj, datatype):
+    """Create filename templates for a single datatype."""
+    filenames = render.make_filename_template(
+        dstype="raw",
+        schema=schema_obj,
+        src_path=Path("https://bids-specification.readthedocs.io/en/latest/"),
+        pdf_format=False,
+        datatypes=[datatype],
+    )
+    filenames = filenames.replace(
+        "../../..",
+        "https://bids-specification.readthedocs.io/en/latest",
+    )
+    return filenames
+
+
 def main():
-    print(generate_converter_table(file="converters.yml", data_type="EEG"))
+    print(generate_filename_templates())
 
 
 if __name__ == "__main__":

macros/macros.py

@@ -41,3 +41,7 @@ def define_env(env):
         macros.generate_working_groups_table,
         "MACROS___generate_working_groups_table",
     )
+    env.macro(
+        macros.generate_filename_templates,
+        "MACROS___generate_filename_templates",
+    )

macros/main.py

@@ -12,5 +12,5 @@ rich
 ruamel.yaml
 tabulate
 pyzotero
-file:specification/tools/schemacode
+bidsschematools[render]
 -e file:tools

requirements.in

@@ -18,7 +18,7 @@ bibtexparser==1.4.1
     # via pyzotero
 bids-validator==1.14.6
     # via pybids
-file:specification/tools/schemacode
+bidsschematools==0.11.3
     # via -r requirements.in
 cairocffi==1.7.0
     # via cairosvg
@@ -90,7 +90,9 @@ markdown==3.6
     #   mkdocs-material
     #   pymdown-extensions
 markdown-it-py==3.0.0
-    # via -r requirements.in
+    # via
+    #   -r requirements.in
+    #   bidsschematools
 markupsafe==2.1.5
     # via
     #   jinja2
@@ -148,6 +150,7 @@ paginate==0.5.6
     # via mkdocs-material
 pandas==2.2.2
     # via
+    #   bidsschematools
     #   formulaic
     #   pybids
     #   seaborn
@@ -233,7 +236,9 @@ smmap==5.0.1
 sqlalchemy==2.0.30
     # via pybids
 tabulate==0.9.0
-    # via -r requirements.in
+    # via
+    #   -r requirements.in
+    #   bidsschematools
 tenacity==8.4.1
     # via plotly
 termcolor==2.4.0