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Major refactoring to support more thorough conversion of dandischema pydantic models #1

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Major refactoring to support more thorough conversion of dandischema pydantic models #1

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yarikoptic
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@candleindark
Outline the basic structure of the LinkML generator
75e210a
@candleindark
Ensure no name collection in initiating LinkmlGenerator
76e052f
@candleindark
Change the signature of tools.ensure_unique_names
2a59078 
Allow classes to be input as positional argument makes
the function more portable
@candleindark
Add all enums to the schema
dce98dd
@candleindark
Define func to normalized whitespace
7974869 
This func is intended to be used for converting
a docstring to description in metadata in a
LinkML schema
@candleindark
Include description in EnumDefinition
1328950
@candleindark
Define interfaces to add slots and classes
23f1a05
@candleindark
Rearrange comments
eda50a7
@candleindark
Define internal map of models to their locally defined fields
dd4888c
@candleindark
Implement LinkmlGenerator._add_slots
8cfe73b 
A method that adds the slots construed from
the models in `self._models` to the schema
@candleindark
Provide a function to bucketize items
36f5cc6
@candleindark
Utilize bucketize
3f783b0
@candleindark
Add support of transforming values in bucketize
1d6a711
@candleindark
Adopt the new support in bucketize
1607e0c
@candleindark
Change slot generation to be handled by a class
f9025d2
@candleindark
Implement SlotGenerator.__init__
58135c1
@candleindark
Outline SlotGenerator.generate
22ef7b0
@candleindark
Specifies interfaces of Pydantic core schema handler functions in `Sl…
c515b05 
…otGenerator`
@candleindark
Reformat generate_linkml_from_aind.py with Black
bcfff9a
@candleindark
Remove unused imports
af93dce 
In generate_linkml_from_aind.py
@candleindark
Replace use of not and in with not in
0423fb8
@candleindark
Remove unused variable in generate_linkml_from_aind.main()
2f9b121
@candleindark
Correct type annotation in populate_enum and populate_basemodel
be16880
@candleindark
Move get_all_modules() to tools.py
674ad72
@candleindark
Use inner function to simplify the interface of get_all_modules()
ce5476e
@candleindark
Implement fetch_defs() and provided needed tests
afeecc9 
`fetch_defs()` is a function for fetching Python objects
from given modules that provide schema definitions
@candleindark
Corret import statement for CoreSchemaOrField
cb68232
@candleindark
Rename local variables
c17f55e
@candleindark
Correct retrieval of corresponding core_schema.ModelSchema of a Pyd…
268700b 
…antic model
@candleindark
Remove limitation of not supporting multi inheritance in Pydantic models
87c7ef0
@candleindark
Outline class generation process
717205b
@candleindark
Define slots in ClassDefinition objects
a2b1169
@candleindark
Eliminate use of from __future__ import annotations in tools.py
6975a5a 
The use of `from __future__ import annotations` solicit hard to
predict behaviors from Pydantic and Typer in older Python versions
@candleindark
Eliminate use of from __future__ import annotations in test_tools.py
ec092b7 
The use of `from __future__ import annotations` solicit hard to
predict behaviors from Pydantic and Typer in older Python versions
@candleindark
Merge branch 'enh' into add-classes
b36e30a
@candleindark
Simply the key function for sorting slots by names
46ef009
@candleindark
Remove unneeded comment
134e685
@candleindark
Define SlotExtensionError
73f5815
@candleindark
Define get_non_empty_meta_slots()
b5155fd
@candleindark
Raise ValueError in SlotExtensionError creation
647ebda
@candleindark
Define get_slot_usage_entry
3af3e4e
@candleindark
RF: Introduce sort_dict_by_ikeys()
e736339
@candleindark
Introduce a dict for slot representation of new fields
3cab658
@candleindark
Add slot usage entries for new slots
cfc7261
@candleindark
Ensure slot usage entries are sorted
160a7d4
@candleindark
Delay sorting of slots
843d145
@candleindark
Rename variable
959b5e3
@candleindark
Improve docstring of SlotExtensionError
1e4a16b
@candleindark
Handling overriding fields in class generation
cf45afb
@candleindark
Set parent class of a class definition
4a6ab7c
@candleindark
Rename test_get_parent_model to test_get_parent_models
dd50a66
@candleindark
Make pydantic.BaseModel an invalid input to get_parent_models
c003aea 
`pydantic.BaseModel` doesn't really model anything. It is merely
a template to specify a model.
@candleindark
Specify mixins in generating a ClassDefinition
0810e8d
@candleindark
Specify mixins in generating a ClassDefinition
f839ad8
@candleindark
Add the interface for translating complex number specs
3ec2098 
Pydantic 2.9 adds support of validation of complex numbers.
To be compatible with Pydantic 2.9, We need this interface
defined.
@candleindark
Restrict pydantic to ~=2.9
f8e1491 
Pydantic 2.8 doesn't have "core_schema.ComplexSchema"
needed in the current code. Let's support Pydantic 2.8
only when needed
@candleindark
Update .gitignore to ignore __pycache__ folders
8bab6d1
@candleindark
Update README.md
640f9c6
@candleindark
Update project urls
27ec216 
Due to the transfer of the project to the DANDI
organization on github
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@yarikoptic @candleindark