# =====================================================================
# AUTO-GENERATED FILE -- DO NOT EDIT BY HAND.
#
# Regenerate with:  python scripts/generate_requirements.py
# Source of truth:  pyproject.toml  ([project.dependencies] and extras)
#
# This file mirrors the packaging metadata for convenience
# (`pip install -r requirements.txt`). For a proper install prefer:
#     pip install .            (core)
#     pip install .[all]       (core + optional features)
#     pip install .[msm]       (core + Markov State Models)
# =====================================================================

# --- core runtime dependencies -----------------------------------
MDAnalysis>=2.4.0
networkx>=2.8
numpy>=1.23
scipy>=1.11
matplotlib>=3.6
seaborn>=0.12
pandas>=1.5
scikit-learn>=1.1
tqdm>=4.62

# --- optional features -------------------------------------------
# Install these via extras rather than uncommenting, e.g.:
#   pip install .[all]
#       deeptime>=0.4.4
#       python-igraph>=0.10.0
#       leidenalg>=0.9.0
#       plotly>=5.0.0
#       ipywidgets>=7.6.0
#       joblib>=1.1.0
#   pip install .[dev]
#       pytest>=7.0.0
#       pytest-cov>=4.0.0
#       black>=23.0.0
#       ruff>=0.1.0
#       mypy>=1.0.0
#       statsmodels>=0.14
#       build>=1.0.0
#       twine>=4.0.0
#   pip install .[docs]
#       sphinx>=5.0.0
#       sphinx-rtd-theme>=1.2.0
#       myst-parser>=1.0.0
#   pip install .[leiden]
#       python-igraph>=0.10.0
#       leidenalg>=0.9.0
#   pip install .[ml]
#       joblib>=1.1.0
#   pip install .[msm]
#       deeptime>=0.4.4
#   pip install .[viz]
#       plotly>=5.0.0
#       ipywidgets>=7.6.0

