build: migrate dependency management from requirements.txt to uv

[ganow]

Overview

Migrate dependency management from requirements.txt to uv (pyproject.toml + uv.lock). Along the way, this also fixes a few issues found in README.md, data/files.json, and evaluation.ipynb.

Changes

Migration to uv (main)

Replace requirements.txt with pyproject.toml + uv.lock, and update the README setup instructions to use uv sync. Dependencies are carried over as-is from requirements.txt, with jupyter / pycortex added under an optional visualization group.

Incidental fixes

Clean up minor issues found while running the examples (outdated script name in the README, a JSON syntax error, unused imports in the notebook). As part of this, I restored the pycortex download entry in data/files.json by recovering it from the commit history; I'm not certain about its details yet and have asked the previous maintainer in #2, but restored it for now so the Pycortex visualization works.

Verification

Verified end-to-end by running the Examples section of the README:

# Download example data (in the ./data directory)
python download.py fmri_deeprecon_fmriprep_hcpvc
python download.py features_imagenet_training_vgg19_random5000
python download.py features_imagenet_test_vgg19_random5000
python download.py pycortex  # Optional, required for Pycortex visualization

# Training and test
python train_encoder_fastl2lir.py config/example_encoding_deeprecon_hcp_rois_vgg19_random5000_pyfastl2lir_alpha100_select500units.yaml
python predict_fmri_fastl2lir.py config/example_encoding_deeprecon_hcp_rois_vgg19_random5000_pyfastl2lir_alpha100_select500units.yaml

# Evaluation
jupyter notebook evaluation.ipynb

🤖 Generated with Claude Code

[KenyaOtsuka]

I left one inline comment about a typo.

Also, since jupyter and pycortex are included as optional dependencies under the visualization extra, I think it would be helpful to mention in the README that users need to run uv sync --extra visualization before running evaluation.ipynb.

Other than that, the changes look good to me.

[KenyaOtsuka]

Nonaki should be Nonaka

[ganow]

@KenyaOtsuka Thank you for reviewing this PR! All of your comments make sense. I'll apply them later