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pyproject.toml
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pyproject.toml
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[tool.setuptools.packages.find]
include = ["cneuromax"]
[project]
name = "cneuromax"
requires-python = ">=3.10" # Did not test with lower versions
authors = [{ name = "The SIMEXP Laboratory", email = "[email protected]" }]
description = "The CNeuromod project's centralized Machine Learning repository"
version = "0.0.1"
# The following assumes that we build on top of the NGC PyTorch Docker image.
dependencies = [
# MANDATORY for cneuromax/
"torch==2.5.1+cu124", # Tensor manipulation
"hydra-core==1.3.2", # Configuration management
"hydra-zen==0.13.0", # Cleaner Hydra configs
"beartype==0.19.0", # Dynamic type checking
"wandb==0.19.0", # Logging
"""
submitit@git+https://github.com/courtois-neuromod/submitit@\
b289f81004ab063b185dc97982934c266e605fad""", # Local & SLURM job launcher
# CNeuroMod fork that launches the `tasks_per_node` with `mpi` rather
# than the original `submitit` method. Used for
# `cneuromax/fitting/neuroevolution/`.
"""
hydra-submitit-launcher@git+https://github.com/courtois-neuromod/hydra@\
4c84b7185f496fe201e7ae8e48b7cae9e66df5f3\
#subdirectory=plugins/hydra_submitit_launcher/""", # Launcher config
# CNeuroMod fork that implements the missing connecting feature to
# `submitit`'s `python` option. Also modifies the `local` launcher
# so that it queues the jobs sequentially rather than in parallel.
# OPTIONAL for cneuromax/
"matplotlib==3.9.3", # Plotting
"hydra-orion-sweeper==1.6.4", # Hyperparameter optimization
"hydra-optuna-sweeper==1.2.0", # Hyperparameter optimization
"""
autorl-sweepers@git+https://github.com/courtois-neuromod/autorl-sweepers@\
c7bc16f133031950b73cf38140367e75775b261b""", # Hyperparameter optimization
"jaxtyping==0.2.36", # Torch tensor annotations
"nptyping==2.5.0", # Numpy array annotations
"einops==0.8.0", # Makes shape transformations more readable
"jupyterlab==4.3.2", # Jupyter notebook
"jupyterlab-code-formatter==3.0.2", # Jupyter code formatter
"ipywidgets==8.1.5", # Jupyter widgets
# Replaces `pytorch_lightning` w/ `lightning.pytorch` to adress
# https://github.com/Lightning-AI/pytorch-lightning/issues/17485
# Also loops while an epoch is not done syncing.
"h5py==3.12.1", # HDF5 file format load/save
"opencv-python==4.10.0.84", # Image processing
# MANDATORY for cneuromax/fitting/deeplearning/
"lightning==2.4.0", # PyTorch wrapper to decrease boilerplate
# OPTIONAL for cneuromax/fitting/deeplearning/
"torchaudio==2.5.1+cu124", # Tensor manipulation on audio data
"torchvision==0.20.1+cu124", # Tensor manipulation on vision data
"transformers==4.47.0", # Pre-trained models published on Hugging Face
"diffusers==0.31.0", # Diffusion models published on Hugging Face
"timm==1.0.12", # Image models
"datasets==3.1.0", # Datasets published on Hugging Face
"x-transformers==1.42.24", # Transformer utils
"mambapy==1.2.0", # Mamba
"denoising-diffusion-pytorch==2.1.1", # Diffusion models
"vector-quantize-pytorch==1.20.11", # Vector quantization utils
"accelerate==1.2.0", # PEFT crashing w/ 0.30.0
"peft==0.14.0", # Fine-tuning
# fMRI libraries
"nibabel==5.3.2", # Neuroimaging format accessor
"nilearn==0.11.0", # ML for neuroimaging
# Audio libraries
"librosa==0.10.2.post1",
# MANDATORY for cneuromax/fitting/neuroevolution/
"mpi4py==4.0.1", # Inter-process communication
"torchrl==0.6.0", # For reinforcement/imitation Learning tasks
"gymnasium[mujoco]==0.29.1", # RL/IL environments
"ordered-set==4.1.0", # Sets w/ deterministic order
# MANDATORY for docs/
"sphinx==8.1.3", # Documentation generator
"esbonio==0.16.5", # Language server to render sphinx
"furo==2024.8.6", # Documentation theme
"sphinx-copybutton==0.5.2", # Copy button for code blocks
"sphinx-paramlinks==0.6.0", # Links to parameters in other pages
"sphinx-autodoc-typehints==2.5.0", # More type hint customization
"myst-parser==4.0.0", # Embeds markdown in sphinx
# DEVELOPMENT
"black[jupyter]==24.10.0", # Python Formatter
"ruff==0.8.2", # Python Linter
"doc8==1.1.2", # Documentation linter
"yamllint==1.35.1", # YAML linter
"pre-commit==4.0.1", # Git commit hooks
"mypy==1.13.0", # Static type checker
"pytest==8.3.4", # Testing framework
"pytest-cov==6.0.0", # Test coverage
]
[tool.uv.sources]
torch = { index = "pytorch" }
torchaudio = { index = "pytorch" }
torchvision = { index = "pytorch" }
[[tool.uv.index]]
name = "pytorch"
url = "https://download.pytorch.org/whl/cu124"
explicit = true
[tool.black]
line-length = 79
[tool.ruff]
line-length = 79
[tool.ruff.lint]
select = ["ALL"]
ignore = [
"D107", # `undocumented-public-init`
# Missing docstring in public `__init__`
# https://docs.astral.sh/ruff/rules/undocumented-public-init/
# Disabled as we combine the docstring of the class and the
# `__init__` method because 1) `__init__` docstrings are
# often redundant and 2) Our auto-documentation tool
# renders better when the full docstring is in the class.
"D417", # `undocumented-param`
# Missing argument description in the docstring for {definition}: {name} Missing docstring in public `__init__`
# https://docs.astral.sh/ruff/rules/undocumented-param/
# This warning pops up even when the argument is simply
# mentioned in the argument section but not given a description.
# Disabled for flexibility of not giving a description for
# every argument.
"F722", # `forward-annotation-syntax-error`
# Syntax error in forward annotation: {body}.
# https://docs.astral.sh/ruff/rules/forward-annotation-syntax-error/
# Disabled to be able to utilize Jaxtyping, see:
# https://docs.kidger.site/jaxtyping/faq/#flake8-or-ruff-are-throwing-an-error
"G004", # `logging-f-string`
# Logging statement uses f-string.
# https://docs.astral.sh/ruff/rules/logging-f-string/
# Disabled to make it less verbose to log since printing is
# disabled, see: https://docs.astral.sh/ruff/rules/print/
"NPY002", # `numpy-legacy-random`
# Replace legacy np.random.{method_name} call with
# np.random.Generator
# Disabled for legacy purposes.
"S301", # `suspicious-pickle-usage`
# `pickle` and modules that wrap it can be unsafe when used to
# deserialize untrusted data, possible security issue
# https://docs.astral.sh/ruff/rules/suspicious-pickle-usage/
# Disabled due to current implementation of checkpointing
# in `cneuromax.fitting.neuroevolution`.
"TC001", # `typing-only-first-party-import`
# Move application import {} into a type-checking block
# https://docs.astral.sh/ruff/rules/typing-only-first-party-import/
# Disabled as we use Beartype for dynamic type checking.
"TC002", # `typing-only-third-party-import`
# Move third-party import {} into a type-checking block
# https://docs.astral.sh/ruff/rules/typing-only-third-party-import/
# Disabled as we use Beartype for dynamic type checking.
]
[tool.ruff.lint.pycodestyle]
max-doc-length = 72
[tool.ruff.lint.pydocstyle]
convention = "google"
[tool.ruff.lint.per-file-ignores]
"*_test.py" = [
"S101", # `assert`
# Use of assert detected.
# https://docs.astral.sh/ruff/rules/assert/
# Disabled to be able to use assertions in test files.
"PLR2004", # `magic-value-comparison`
# Magic value used in comparison, consider replacing {value}
# with a constant variable.
# https://docs.astral.sh/ruff/rules/magic-value-comparison/
# Disabled to be able to use magic values in test files.
]
[tool.doc8]
max-line-length = 79
# docs/index.rst:1: D000 Error in "include" directive:
# invalid option value: (option: "parser"; value: 'myst_parser.sphinx_')
# Parser "myst_parser.sphinx_" not found. No module named 'myst_parser'.
ignore = ["D000"]
[tool.mypy]
strict = true
allow_redefinition = true
ignore_missing_imports = true