fix imports being inside the any_of range, more manual inspection before finishing for the night

docs/meta/todo.md

@@ -11,6 +11,8 @@ NWB schema translation
 Cleanup
 - [ ] Update pydantic generator
 - [ ] Restore regressions from stripping the generator
+- [x] Make any_of with array ranges work
+- [ ] PR upstream `equals_string` and `ifabsent` (if existing PR doesnt fix)
 - [ ] Use the class rather than a string in _get_class_slot_range_origin:
       ```
       or inlined_as_list
@@ -43,6 +45,9 @@ Important things that are not implemented yet!
 Remove monkeypatches/overrides once PRs are closed
 - [ ] https://github.com/linkml/linkml-runtime/pull/330
 
+Tests
+- [ ] Ensure schemas and pydantic modules in repos are up to date
+
 ## Docs TODOs
 
 ```{todolist}

nwb_linkml/src/nwb_linkml/adapters/classes.py

@@ -246,7 +246,6 @@ class ClassAdapter(Adapter):
                 ifabsent=f"string({name})",
                 equals_string=equals_string,
                 range="string",
-                identifier=True,
             )
         else:
             name_slot = SlotDefinition(name="name", required=True, range="string", identifier=True)

nwb_linkml/src/nwb_linkml/generators/pydantic.py

@@ -30,6 +30,7 @@ The `serialize` method:
 
 import inspect
 import pdb
+import re
 import sys
 import warnings
 from copy import copy
@@ -40,7 +41,8 @@ from typing import ClassVar, Dict, List, Optional, Tuple, Type, Union
 
 from linkml.generators import PydanticGenerator
 from linkml.generators.pydanticgen.build import SlotResult
-from linkml.generators.pydanticgen.array import ArrayRepresentation
+from linkml.generators.pydanticgen.array import ArrayRepresentation, NumpydanticArray
+from linkml.generators.pydanticgen.template import PydanticModule
 from linkml_runtime.linkml_model.meta import (
     Annotation,
     AnonymousSlotExpression,
@@ -61,6 +63,8 @@ from pydantic import BaseModel
 from nwb_linkml.maps import flat_to_nptyping
 from nwb_linkml.maps.naming import module_case, version_module_case
 
+OPTIONAL_PATTERN = re.compile(r'Optional\[([\w\.]*)\]')
+
 @dataclass
 class NWBPydanticGenerator(PydanticGenerator):
 
@@ -86,7 +90,7 @@ class NWBPydanticGenerator(PydanticGenerator):
     gen_slots: bool = True
 
 
-    skip_meta: ClassVar[Tuple[str]] = ('domain_of',)
+    skip_meta: ClassVar[Tuple[str]] = ('domain_of','alias')
 
     def _check_anyof(
         self, s: SlotDefinition, sn: SlotDefinitionName, sv: SchemaView
@@ -111,18 +115,42 @@ class NWBPydanticGenerator(PydanticGenerator):
             if not base_range_subsumes_any_of:
                 raise ValueError("Slot cannot have both range and any_of defined")
 
-    def before_generate_schema(self):
-        pass
-
     def after_generate_slot(self, slot: SlotResult, sv: SchemaView) -> SlotResult:
         """
         - strip unwanted metadata
+        - generate range with any_of
         """
         for key in self.skip_meta:
             if key in slot.attribute.meta:
                 del slot.attribute.meta[key]
+
+        # make array ranges in any_of
+        if 'any_of' in slot.attribute.meta:
+            any_ofs = slot.attribute.meta['any_of']
+            if all(['array' in expr for expr in any_ofs]):
+                ranges = []
+                is_optional = False
+                for expr in any_ofs:
+                    # remove optional from inner type
+                    pyrange = slot.attribute.range
+                    is_optional = OPTIONAL_PATTERN.match(pyrange)
+                    if is_optional:
+                        pyrange = is_optional.groups()[0]
+                    range_generator = NumpydanticArray(ArrayExpression(**expr['array']), pyrange)
+                    ranges.append(range_generator.make().range)
+
+                slot.attribute.range = 'Union[' + ', '.join(ranges) + ']'
+                if is_optional:
+                    slot.attribute.range = 'Optional[' + slot.attribute.range + ']'
+                del slot.attribute.meta['any_of']
+
         return slot
 
+    def before_render_template(self, template: PydanticModule, sv: SchemaView) -> PydanticModule:
+        if 'source_file' in template.meta:
+            del template.meta['source_file']
+
+
     def compile_module(
         self, module_path: Path = None, module_name: str = "test", **kwargs
     ) -> ModuleType:  # pragma: no cover - replaced with provider

nwb_linkml/src/nwb_linkml/providers/pydantic.py

@@ -12,7 +12,7 @@ from types import ModuleType
 from typing import List, Optional, Type
 
 from linkml_runtime.linkml_model.meta import SchemaDefinition
-from linkml.generators.pydanticgen.pydanticgen import SplitMode, _import_to_path
+from linkml.generators.pydanticgen.pydanticgen import SplitMode, _import_to_path, _ensure_inits
 from pydantic import BaseModel
 
 from nwb_linkml.generators.pydantic import NWBPydanticGenerator
@@ -148,7 +148,9 @@ class PydanticProvider(Provider):
         force: bool,
         **kwargs
     ) -> List[str]:
+        # FIXME: This is messy as all fuck, we're just getting it to work again so we can start iterating on the models themselves
         res = []
+        module_paths = []
 
         # first make the namespace file we were given
 
@@ -170,6 +172,7 @@ class PydanticProvider(Provider):
             if dump:
                 with open(ns_file, 'w') as ofile:
                     ofile.write(serialized)
+                module_paths.append(ns_file)
         else:
             with open(ns_file, 'r') as ofile:
                 serialized = ofile.read()
@@ -203,6 +206,7 @@ class PydanticProvider(Provider):
                 if dump:
                     with open(import_file, 'w') as ofile:
                         ofile.write(serialized)
+                    module_paths.append(import_file)
 
             else:
                 with open(import_file, 'r') as ofile:
@@ -210,6 +214,10 @@ class PydanticProvider(Provider):
 
             res.append(serialized)
 
+        # make __init__.py files if we generated any files
+        if len(module_paths) > 0:
+            _ensure_inits(module_paths)
+
         return res
 
     def _make_inits(self, out_file: Path) -> None: