Fix STAMP Build / Update Installation Instruction

[FWao]

This PR enables to install STAMP with all slide encoders on CPU-only and CUDA systems.

With #75 it happened that dependencies like flash-attn, causal-conv1d or mamba-ssm were installed / compiled using a different version of PyTorch than in the environment which caused errors.

Some changes in this PR are temporary measurements to simplify the installation process. They can be reverted as soon as the underlying issues have been resolved.

The triton version has been fixed until this is resolved. This caused torch to downgrade to 2.6.0. As the flash-attn wheels for 2.6.0 are broken for my setups, I had to make sure to force flash-attn to build. Unfortunately the no-binary-package statement in the pyproject.toml file does not ensure that. That is the reason for the flash-attention fork. Can be reverted as soon as fixed.

This PR bumps the default python version to 3.12 (but is still compatible with 3.11).

• Update the uv install URLs before merging this PR

closes #81

Follow-up: #94 (publish PyPI package)

[georg-wolflein]

Wow, thanks for fixing this Fabi!

[EzicStar]

Wow!!! Great job Fabi. The installation steps are clear and also the PR description. Unfortunately, I reproduced the steps for installation using the repository with gpu (updated uv and ran the commands one by one) and the models that require flash-attention fail:

    # Copyright (c) 2023, Tri Dao.
    
    from typing import Optional, Sequence, Tuple, Union
    
    import torch
    import torch.nn as nn
    import os
    
    # isort: off
    # We need to import the CUDA kernels after importing torch
    USE_TRITON_ROCM = os.getenv("FLASH_ATTENTION_TRITON_AMD_ENABLE", "FALSE") == "TRUE"
    if USE_TRITON_ROCM:
        from .flash_attn_triton_amd import interface_fa as flash_attn_gpu
    else:
>       import flash_attn_2_cuda as flash_attn_gpu
E       ImportError: /mnt/bulk-sirius/juan/pap_screening/STAMP/.venv/lib/python3.12/site-packages/flash_attn_2_cuda.cpython-312-x86_64-linux-gnu.so: undefined symbol: _ZN3c105ErrorC2ENS_14SourceLocationENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE

.venv/lib/python3.12/site-packages/flash_attn/flash_attn_interface.py:15: ImportError

Tried it on sirius, on this branch, removed previous .venv and ran uv sync step with --refresh. Also took around 20 minutes to build flash-attn. Hope this info helps!

[EzicStar]

LGTM! Thank you so much for fixing this :)