get_bottom_coords_for_each_lith in Subsurface does not support group_by parameter

[rexlintc]

Describe the bug
A clear and concise description of what the bug is. Include error messages /
tracebacks. If useful include screenshots.

When defining formations and colors following the borehole example notebook, I get an unexpected keyword argument group_by. See the error below.

Error

--> [128](https://file+.vscode-resource.vscode-cdn.net/Users/rex/notebooks/gempy/~/.pyenv/versions/3.12.9/envs/venv/lib/python3.12/site-packages/gempy/API/initialization_API.py:128) component_lith: dict[Hashable, np.ndarray] = borehole_set.get_bottom_coords_for_each_lith(group_by=group_by)
    [130](https://file+.vscode-resource.vscode-cdn.net/Users/rex/notebooks/gempy/~/.pyenv/versions/3.12.9/envs/venv/lib/python3.12/site-packages/gempy/API/initialization_API.py:130) for name, properties in elements_dict.items():
    [131](https://file+.vscode-resource.vscode-cdn.net/Users/rex/notebooks/gempy/~/.pyenv/versions/3.12.9/envs/venv/lib/python3.12/site-packages/gempy/API/initialization_API.py:131)     top_coordinates = component_lith.get(properties['id'])

TypeError: BoreholeSet.get_bottom_coords_for_each_lith() got an unexpected keyword argument 'group_by'

I believe this is because the usage of get_bottom_coords_for_each_lith was updated in Gempy Commit 519954e
but not updated in Subsurface Commit 218ec2f
.

To Reproduce
Provide detailed steps to reproduce the behavior:

1. Running the borehole notebook/code directly should lead to this error.
   ...

Expected behavior
A clear and concise description of what you expected to happen.

I believe the expected behavior is to update the Subsurface library so passing in a custom group_by parameter is optional with the current definition component lith as the default behavior.

Screenshots
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Desktop (please complete the following information):

• OS: (e.g. iOS) MacOS Sequoia 15.4.1
• GemPy Version: Version: 2025.2.0

Additional context
Add any other context about the problem here.

[javoha]

Hi @rexlintc,
thanks for reporting the bug. I think this is more a subsurface issue in this case - did you also open an issue on their github?

I will link @Leguark as he might have a better overview of the subsurface link.

Cheers,
Jan