stroke/requirements.txt at main · max-talanov/stroke · GitHub

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# Core numerical and scientific computing
numpy>=2.0.0
scipy>=1.17.0
matplotlib>=3.10.0

# Data I/O
h5py>=3.16.0
pandas>=3.0.0

# The Virtual Brain framework and components
tvb-framework>=2.10.0
tvb-library>=2.10.0
tvb-data>=3.0.0
tvb-gdist>=2.9.2
tvb-storage>=2.10.0

# Neuroimaging tools
nibabel>=5.4.0
nilearn>=0.13.0

# Graph analysis
networkx>=3.6.0

# Scientific computing utilities
scikit-learn>=1.8.0
scikit-image>=0.26.0
pandas>=3.0.0

# Performance
numba>=0.65.0
numexpr>=2.14.0
Cython>=3.2.0

# Development and utilities
IPython>=9.13.0
Jupyter>=1.0.0

# ─────────────────────────────────────────────────────────────────────────
#  BigStroke-MN5 stack (Stage 1+)
# ─────────────────────────────────────────────────────────────────────────
# NEST spiking neural simulator — primary engine for M1 microcircuit
# and (later) spinal CPG.  pip install works on most Linux x86_64; on
# macOS / Apple Silicon use:  conda install -c conda-forge nest-simulator
# On MareNostrum 5:  module load nest/3.7
nest-simulator>=3.7 ; platform_system == "Linux"

# Workflow management for ~1,400-run pipeline (MN5 production batch)
snakemake>=8.0

# Test runner
pytest>=8.0

# Optional (Stage 3+): TVB ↔ NEST coupling.  Install separately as it
# pulls a large dependency tree; see bigstroke_mn5/README.md.
# tvb-multiscale  ; install from github.com/the-virtual-brain/tvb-multiscale