LISA/pyproject.toml at main · ivsemenkov/LISA · GitHub

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[build-system]
requires = ["setuptools>=61"]
build-backend = "setuptools.build_meta"

[project]
name = "lisa"
version = "0.1.0"
description = "Interpretable MEG-to-audio retrieval with explicit spatial and temporal filters"
readme = "README.md"
license = { file = "LICENSE" }
authors = [
  { name = "Ilia Semenkov", email = "iliasemenkov@gmail.com" },
]
maintainers = [
  { name = "Ilia Semenkov", email = "iliasemenkov@gmail.com" },
]
keywords = [
  "magnetoencephalography",
  "MEG",
  "speech perception",
  "neural decoding",
  "interpretable deep learning",
  "neuroimaging",
]
classifiers = [
  "Intended Audience :: Science/Research",
  "Natural Language :: English",
  "Programming Language :: Python :: 3",
  "Programming Language :: Python :: 3 :: Only",
  "Programming Language :: Python :: 3.11",
  "Topic :: Scientific/Engineering :: Artificial Intelligence",
]
requires-python = ">=3.11"
# Note: PyTorch is not included here because it requires --index-url for CUDA versions.
# Install PyTorch separately (see README or scripts/setup_main_env.sh).
dependencies = [
  "einops==0.8.1",
  "librosa==0.11.0",
  "matplotlib==3.10.0",
  "mne==1.9.0",
  "mne-bids==0.16.0",
  "nibabel==5.3.3",
  "numpy==1.26.4",
  "osfclient>=0.0.5",
  "pandas==2.2.3",
  "scikit-learn==1.6.1",
  "scipy==1.15.2",
  "seaborn==0.13.2",
  "soundfile==0.13.1",
  "soxr==0.5.0.post1",
  "textgrid==1.6.1",
  "tqdm==4.67.1",
  "transformers==4.53.1",
  "wordfreq==3.1.1",
]

[tool.setuptools]
package-dir = {"" = "src"}

[tool.setuptools.packages.find]
where = ["src"]
include = ["lisa*"]

[tool.ruff]
line-length = 88

[tool.ruff.format]
quote-style = "single"

[project.scripts]
lisa-train = "lisa.cli.train_model:main"
lisa-prepare-meg = "lisa.data.prepare_meg_data:main_cli"
lisa-generate-embeddings = "lisa.data.generate_all_embeddings:main_cli"
lisa-regen-windows = "lisa.data.regenerate_window_embeddings:main_cli"
lisa-precompute-pca = "lisa.data.audio_reduction:main_cli"
lisa-apply-ica = "lisa.data.apply_ica:main_cli"
lisa-meg-qc = "lisa.plots.meg_qc_check:main"
lisa-plot-metrics = "lisa.plots.plot_metrics:main_cli"
lisa-plot-branch-interpretations = "lisa.plots.plot_branch_interpretations:main_cli"
lisa-combined-cluster-branch-interpretations = "lisa.plots.combined_cluster_branch_interpretations:main"
lisa-plot-spatial-attention-maps = "lisa.plots.plot_spatial_attention_maps:main_cli"
lisa-plot-spatial-topography-svd = "lisa.plots.plot_spatial_topography_svd:main_cli"
lisa-occlusion-feature-analysis = "lisa.plots.occlusion_feature_analysis:main_cli"
lisa-plot-occlusion-seed-robustness = "lisa.plots.plot_occlusion_seed_robustness:main_cli"
lisa-plot-retrieval-ablations = "lisa.plots.retrieval_ablation_artifacts:main"
lisa-plot-segment-duration-ablation = "lisa.plots.plot_segment_duration_ablation:main_cli"
lisa-plot-temporal-filter-length-ablation = "lisa.plots.plot_temporal_filter_length_ablation:main"
lisa-scan-runs = "lisa.cli.scan_runs:main_cli"
lisa-export-parameter-counts = "lisa.cli.export_parameter_counts:main_cli"
lisa-precompute-word-features = "lisa.cli.precompute_word_features:main_cli"
lisa-download-osf = "lisa.utils.download_from_osf:main"

[project.optional-dependencies]
clearml = [
  "clearml==2.0.2",
]
dev = [
  "ruff>=0.6",
  "pytest>=7.0",
]

[project.urls]
Homepage = "https://ivsemenkov.github.io/LISA/"
Documentation = "https://ivsemenkov.github.io/LISA/"
Repository = "https://github.com/ivsemenkov/LISA"
Issues = "https://github.com/ivsemenkov/LISA/issues"