Merge branch 'macro_doc' into doc

.gitignore

@@ -2,6 +2,8 @@
 activities/.DS_Store
 protocols/.DS_Store
 
+__pycache__
+
 .idea/
 
 node_modules

macros/__init__.py

@@ -0,0 +1,9 @@
+from .macros import (
+    schema_table,
+)
+from .main import define_env
+
+__all__ = [
+    "define_env",
+    "schema_table",
+]

macros/macros.py

@@ -0,0 +1,93 @@
+from pathlib import Path
+
+import ruamel.yaml
+from jinja2 import Environment, FileSystemLoader, select_autoescape
+
+yaml = ruamel.yaml.YAML()
+yaml.indent(mapping=2, sequence=4, offset=2)
+
+ROOT = Path(__file__).parents[1]
+
+TEMPLATES_DIR = ROOT / "templates"
+
+SCHEMA_DIR = ROOT / "linkml-schema"
+
+
+def return_jinja_env() -> Environment:
+    return Environment(
+        loader=FileSystemLoader(TEMPLATES_DIR),
+        autoescape=select_autoescape(),
+        lstrip_blocks=True,
+        trim_blocks=True,
+    )
+
+
+def schema_table() -> str:
+
+    target_classes = [
+        "Protocol",
+        "Activity",
+        "Item",
+        "AdditionalProperty",
+        "OverrideProperty",
+        "UnitOption",
+        "ResponseOption",
+        "Choice",
+        "ComputeSpecification",
+        "MessageSpecification",
+        "AdditionalNoteObj",
+        "ResponseActivity",
+        "Response",
+        "Participant",
+        "SoftwareAgent",
+    ]
+
+    input_file = SCHEMA_DIR / "reproschema.yaml"
+
+    reproschema = yaml.load(input_file)
+
+    env = return_jinja_env()
+    template = env.get_template("table.jinja")
+
+    content = []
+    for this_class in target_classes:
+
+        class_dict = reproschema["classes"][this_class]
+        class_dict["uri"] = class_dict["class_uri"].replace(
+            "reproschema:", reproschema["id"]
+        )
+
+        slots = []
+        for this_slot in class_dict["slots"]:
+
+            slot_dict = reproschema["slots"][this_slot]
+
+            slot_dict["name"] = this_slot
+
+            if "title" not in slot_dict:
+                slot_dict["title"] = "**TODO**"
+            if "description" not in slot_dict:
+                slot_dict["description"] = "**TODO**"
+
+            prefix = slot_dict["slot_uri"].split(":")[0]
+            value = reproschema["id"]
+            if prefix in reproschema["prefixes"]:
+                value = reproschema["prefixes"][prefix]
+
+            slot_dict["uri"] = slot_dict["slot_uri"].replace(f"{prefix}:", value)
+
+            slots.append(slot_dict)
+
+        class_dict["slots"] = slots
+
+        content.append(template.render(this_class=class_dict))
+
+    return "\n".join(content)
+
+
+def main():
+    print(schema_table())
+
+
+if __name__ == "__main__":
+    main()

macros/main.py

@@ -0,0 +1,32 @@
+"""This package is used to build elements from data into
+MarkDown format for the specification text.
+
+Functions decorated in "define_env()" are callable throughout the
+specification and are run/rendered with the mkdocs plugin "macros".
+"""
+
+import os
+import sys
+
+code_path = os.path.abspath(os.path.join(os.path.dirname(__file__)))
+sys.path.append(code_path)
+
+import macros  # noqa E402
+
+
+def define_env(env):
+    """Define variables, macros and filters for the mkdocs-macros plugin.
+
+    Parameters
+    ----------
+    env : :obj:`macros.plugin.MacrosPlugin`
+        An object in which to inject macros, variables, and filters.
+
+    Notes
+    -----
+    "variables" are the dictionary that contains the environment variables
+    "macro" is a decorator function, to declare a macro.
+
+    Macro aliases must start with "MACROS___"
+    """
+    env.macro(macros.schema_table, "MACROS___schema_table")

mkdocs.yml

@@ -76,12 +76,16 @@ markdown_extensions:
   - pymdownx.snippets:
       auto_append:
         - includes/abbreviations.md
+  - tables
   - toc:
       anchorlink: true
 
 watch:
   - includes
+  - linkml-schema
 
 plugins:
   - search
   - tags
+  - macros:
+      module_name: macros/main

requirements.txt

@@ -1,3 +1,5 @@
-rdflib==5.0.0
+mkdocs-macros-plugin
 mkdocs-material
 pymdown-extensions
+rdflib==5.0.0
+ruamel.yaml

templates/table.jinja

@@ -0,0 +1,13 @@
+
+
+### {{ this_class.title }}
+
+{{ this_class.description }}
+
+URI: [{{ this_class.uri }}]({{ this_class.uri }})
+
+| Property | Title | Description | URI |
+| :------- | :---- | :---------- | :-- |
+{% for slot in this_class.slots %}
+| {{ slot.name }} | {{ slot.title }} | {{ slot.description }} | [{{ slot.uri }}]({{ slot.uri }}) |
+{% endfor %}