Fix installation instructions

[johnbradley]

When installing kabr-tools in a clean environment as described in the README:

pip install git+https://github.com/Imageomics/kabr-tools

The following error occurs:

...
Collecting detectron2@ git+https://github.com/facebookresearch/detectron2.git@2a420edb307c9bdf640f036d3b196bed474b8593 (from kabr_tools==0.1.0)
...
ModuleNotFoundError: No module named 'torch'

[johnbradley]

The issue is that our detectron2 dependency uses the torch library as part of setup.py:
https://github.com/facebookresearch/detectron2/blob/8d85329aed8506ea3672e3e208971345973ea761/setup.py#L10-L11
So before we can install detectron2 pytorch must be installed.

Perhaps the simplest solution is to change our README to specify that pytorch is a requirement and reference the detectron2 docs: https://detectron2.readthedocs.io/en/latest/tutorials/install.html#requirements

Potential new installation instructions:

pip install torch torchvision
pip install git+https://github.com/Imageomics/kabr-tools

[johnbradley]

Even with the above steps on a Mac I still hit the error.
It did print a more helpful instruction:

  Caused by: This error likely indicates that detectron2 @ git+https://github.com/facebookresearch/detectron2.git@2a420edb307c9bdf640f036d3b196bed474b8593 
depends on torch, but doesn't declare it as a build dependency.
 If detectron2 @ git+https://github.com/facebookresearch/detectron2.git@2a420edb307c9bdf640f036d3b196bed474b8593 is a first-party package, consider adding torch to its `build-system.requires`. 
Otherwise, `uv pip install torch` into the environment and re-run with `--no-build-isolation`.

Unfortunately --no-build-isolation doesn't seem to work with hatchling our current build system. Adding "torch" to build-system-requires still has the same error. Perhaps we could switch to setuptools.

[zhong-al]

Can you check if enhancement/setuptools fixes this? python -m pip install git+https://github.com/Imageomics/kabr-tools@138d170e7b5ed9ce76b3846d2f01b8d015cfa608 works for me (just tried with a new conda environment on Mac).

[johnbradley]

@zhong-al After deleting the ~/.cache directory install from this branch still fails for me. Even adding 'torch' to build-system.requires in addition to your changes doesn't fix the issue. I think instead we need to update the README to include two steps for installation of the software: 1) Install pytorch 2) install kabr-tools. We could reference the detectron2 Requirements in our README:https://detectron2.readthedocs.io/en/latest/tutorials/install.html#requirements. Alternatively we could referencing the pytorch documentation: https://pytorch.org/get-started/locally/. On the pytorch page users can pick the version of CUDA and other options based on their environment.

[zhong-al]

@johnbradley I updated the instructions here. I can update it again if it doesn't fix the issue. Should I close the setuptools PR since it fails to fix the issue?

[johnbradley]

@zhong-al These instructions look good to me. The instructions worked fine for me using pip within a conda environment on my Mac.

I still had a problem trying to use uv pip after deleting ~/.cache/uv/, but I think that's a problem with uv: astral-sh/uv#2252.

I would close the setuptools PR - there are quite a few more changes necessary to switch over to setuptools. Since it doesn't fix this issue I'm not aware of any advantage we would get to switching from hatch to setuptools.