bring in changes from nexusformat/1428

Author: lukaspie

dev_tools/docs/nxdl_index.py

@@ -66,16 +66,21 @@ def nxdl_indices() -> Dict[str, dict]:
         else:
             file = ""
             print("---------++++++++-", section)
-        if file.endswith("contributed_definitions/index.rst"):
+        if file.endswith("applications/index.rst"):
+            rst_lines.append(f"{indentation}apm-structure\n")
             rst_lines.append(f"{indentation}em-structure\n")
+            rst_lines.append(f"{indentation}mpes-structure\n")
             rst_lines.append(f"{indentation}optical-spectroscopy-structure\n")
+        if file.endswith("base_classes/index.rst"):
+            rst_lines.append(f"{indentation}apm-structure\n")
+            rst_lines.append(f"{indentation}cgms-structure\n")
+            rst_lines.append(f"{indentation}em-structure\n")
             rst_lines.append(f"{indentation}mpes-structure\n")
+            rst_lines.append(f"{indentation}optical-spectroscopy-structure\n")
+        if file.endswith("contributed_definitions/index.rst"):
             rst_lines.append(f"{indentation}apm-structure\n")
+            rst_lines.append(f"{indentation}optical-spectroscopy-structure\n")
             rst_lines.append(f"{indentation}transport-structure\n")
-            rst_lines.append(f"{indentation}spm-structure\n")
-            rst_lines.append(f"{indentation}cgms-structure\n")
-            rst_lines.append(f"{indentation}icme-structure\n")
-
         for cname in sorted(classes):
             rst_lines.append(f"{indentation}{cname}\n")
 
@@ -112,6 +117,20 @@ def get_nxclass_description(nxdl_file: Path, namespaces) -> str:
 *might* be used in an instance of that class.
 Consider the base classes as a set of *components*
 that are used to construct a data file.
+
+Some base classes are grouped together:
+  :ref:`Atom Probe Microscopy <BC-Apm-Structure>`
+
+  :ref:`Computational Geometry and Microstructures <BC-Cgms-Structure>`
+
+  :ref:`Electron Microscopy <BC-Em-Structure>`
+
+  :ref:`Multi-dimensional Photoemission Spectroscopy <BC-Mpes-Structure>`
+
+  :ref:`Optical Spectroscopy <BC-Opt-Spec-Structure>`
+
+and others are simply listed here:
+
     """,
     # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     "applications": """
@@ -140,6 +159,18 @@ def get_nxclass_description(nxdl_file: Path, namespaces) -> str:
 In application definitions involving raw data,
 write the raw data in the :ref:`NXinstrument` tree and then link to it
 from the location(s) defined in the relevant application definition.
+
+Some application definitions are grouped together:
+  :ref:`Atom Probe Microscopy <AppDef-Apm-Structure>`
+
+  :ref:`Electron Microscopy <AppDef-Em-Structure>`
+
+  :ref:`Multi-dimensional Photoemission Spectroscopy <AppDef-Mpes-Structure>`
+
+  :ref:`Optical Spectroscopy <AppDef-Opt-Spec-Structure>`
+
+and others are simply listed here:
+
     """,
     # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     "contributed_definitions": """
@@ -162,18 +193,9 @@ def get_nxclass_description(nxdl_file: Path, namespaces) -> str:
 and acceptance as either a base class or application definition.
 
 Some contributions are grouped together:
-  :ref:`Optical Spectroscopy <Optical-Spectroscopy-Structure>`
-
-  :ref:`Multi-dimensional Photoemission Spectroscopy <Mpes-Structure>`
-
-  :ref:`Atom Probe Microscopy <Apm-Structure>`
-
-  :ref:`Electron Microscopy <Em-Structure>`
-
-  :ref:`Transport Measurements <Transport-Structure>`
-
-  :ref:`Geometry and Microstructures  <CgmsFeatures-Structure>`
+  :ref:`Optical Spectroscopy <Contributed-Opt-Spec-Structure>`
 
+  :ref:`Transport Measurements <Contributed-Transport-Structure>`
 
 and others are simply listed here: