Installing SCDL raises a missing dependency

[edawson]

When installing SCDL for local development purposes, there is a missing dependency:

git clone https://github.com/nvidia/bionemo-framework.git

cd bionemo-framework/sub-packages/bionemo-scdl

pip install -e .

Running the above raises the following:

Traceback (most recent call last):
  File "/home/edawson/miniconda3/envs/scdl/lib/python3.11/site-packages/pydantic/networks.py", line 865, in import_email_validator
    import email_validator
ModuleNotFoundError: No module named 'email_validator'

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/home/edawson/nv/bionemo-framework/sub-packages/bionemo-scdl/src/bionemo/scdl/scripts/convert_multiread.py", line 3, in <module>
    from bionemo.core.data.load import load
  File "/home/edawson/miniconda3/envs/scdl/lib/python3.11/site-packages/bionemo/core/data/load.py", line 33, in <module>
    from bionemo.core.data.resource import Resource, get_all_resources
  File "/home/edawson/miniconda3/envs/scdl/lib/python3.11/site-packages/bionemo/core/data/resource.py", line 39, in <module>
    class Resource(pydantic.BaseModel):
  File "/home/edawson/miniconda3/envs/scdl/lib/python3.11/site-packages/pydantic/_internal/_model_construction.py", line 226, in __new__
    complete_model_class(
  File "/home/edawson/miniconda3/envs/scdl/lib/python3.11/site-packages/pydantic/_internal/_model_construction.py", line 658, in complete_model_class
    schema = cls.__get_pydantic_core_schema__(cls, handler)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/edawson/miniconda3/envs/scdl/lib/python3.11/site-packages/pydantic/main.py", line 702, in __get_pydantic_core_schema__
    return handler(source)
           ^^^^^^^^^^^^^^^
  File "/home/edawson/miniconda3/envs/scdl/lib/python3.11/site-packages/pydantic/_internal/_schema_generation_shared.py", line 84, in __call__
    schema = self._handler(source_type)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/edawson/miniconda3/envs/scdl/lib/python3.11/site-packages/pydantic/_internal/_generate_schema.py", line 612, in generate_schema
    schema = self._generate_schema_inner(obj)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/edawson/miniconda3/envs/scdl/lib/python3.11/site-packages/pydantic/_internal/_generate_schema.py", line 881, in _generate_schema_inner
    return self._model_schema(obj)
           ^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/edawson/miniconda3/envs/scdl/lib/python3.11/site-packages/pydantic/_internal/_generate_schema.py", line 693, in _model_schema
    {k: self._generate_md_field_schema(k, v, decorators) for k, v in fields.items()},
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/edawson/miniconda3/envs/scdl/lib/python3.11/site-packages/pydantic/_internal/_generate_schema.py", line 693, in <dictcomp>
    {k: self._generate_md_field_schema(k, v, decorators) for k, v in fields.items()},
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/edawson/miniconda3/envs/scdl/lib/python3.11/site-packages/pydantic/_internal/_generate_schema.py", line 1073, in _generate_md_field_schema
    common_field = self._common_field_schema(name, field_info, decorators)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/edawson/miniconda3/envs/scdl/lib/python3.11/site-packages/pydantic/_internal/_generate_schema.py", line 1261, in _common_field_schema
    schema = self._apply_annotations(
             ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/edawson/miniconda3/envs/scdl/lib/python3.11/site-packages/pydantic/_internal/_generate_schema.py", line 2061, in _apply_annotations
    schema = get_inner_schema(source_type)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/edawson/miniconda3/envs/scdl/lib/python3.11/site-packages/pydantic/_internal/_schema_generation_shared.py", line 84, in __call__
    schema = self._handler(source_type)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/edawson/miniconda3/envs/scdl/lib/python3.11/site-packages/pydantic/_internal/_generate_schema.py", line 2040, in inner_handler
    from_property = self._generate_schema_from_property(obj, source_type)
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/edawson/miniconda3/envs/scdl/lib/python3.11/site-packages/pydantic/_internal/_generate_schema.py", line 761, in _generate_schema_from_property
    schema = get_schema(
             ^^^^^^^^^^^
  File "/home/edawson/miniconda3/envs/scdl/lib/python3.11/site-packages/pydantic/networks.py", line 980, in __get_pydantic_core_schema__
    import_email_validator()
  File "/home/edawson/miniconda3/envs/scdl/lib/python3.11/site-packages/pydantic/networks.py", line 867, in import_email_validator
    raise ImportError('email-validator is not installed, run `pip install pydantic[email]`') from e
ImportError: email-validator is not installed, run `pip install pydantic[email]`

Installing pydantic[email] fixes the issue. However, we shouldn't need the email parser is my assumption.

In addition, SCDL now has a dependency on bionemo-core, meaning it requires all of that package's dependencies. Is there a way to minimize the dependency surface so that users could easily install standalone SCDL without having to install all of bionemo-core, torch, nccl, etc?