# ================================
# Indexes and extra repositories
# ================================
-i https://pypi.org/simple
--extra-index-url https://download.pytorch.org/whl/cpu

# For LC developers: comment out PyPI index url and use internal repo instead
# -i https://wci-repo.llnl.gov/repository/pypi/simple
# --extra-index-url https://wci-repo.llnl.gov/repository/$
# or define variables to get the CERT
# $ export REQUESTS_CA_BUNDLE=/etc/pki/tls/cert.pem
# $ export SSL_CERT_FILE=/etc/pki/tls/cert.pem

# DGL wheels (generic and torch-version specific)
--find-links https://data.dgl.ai/wheels/repo.html
--find-links https://data.dgl.ai/wheels/torch-2.1/repo.html

# =============================
# Core deep learning frameworks
# =============================

# PyTorch CPU; Python 3.10 compatible; aligned with DGL torch-2.1 wheels
torch==2.1.2+cpu
torchdata==0.7.1

# Lightning; pin to a recent stable series to avoid breaking changes
lightning==2.2.5

# TensorFlow CPU; compatible with DeepChem 2.8
tensorflow-cpu~=2.14.0


# ==========================
# Graph / GNN related stack
# ==========================

# DGL stack; 2.1.0 has matching wheels for torch 2.1.x
dgl==2.1.0
dgllife==0.3.2

# PyTorch Geometric; works with torch 2.1.x on CPU
torch_geometric==2.7.0

# DGL currently imports pydantic but does not declare it.
# Stay on pydantic 1.x for maximum compatibility.
pydantic>=1.10,<2


# ==================
# Numeric / ML stack
# ==================

# Constrained for broad compatibility (esp. with DeepChem, scikit-learn)
numpy<2
scipy>=1.10

scikit-learn==1.2.2
optuna

xgboost
lightgbm

umap-learn


# ============================
# Visualization and plotting
# ============================

bokeh
matplotlib
matplotlib-venn
seaborn>=0.13.0


# =========================
# Data / IO / misc tooling
# =========================

pyarrow
pyyaml>=6.0
bravado

# imbalanced-learn is the canonical package name on PyPI
imbalanced-learn

maestrowf


# ==========================
# Cheminformatics / domain
# ==========================

deepchem==2.8
rdkit==2024.3.5
mordred

# ==========================
# Dev / runtime utilities
# ==========================

pytest
ipykernel