# ==========================================================================
# QBioCode core runtime dependencies
# ==========================================================================
# This is the SINGLE SOURCE OF TRUTH for the package's install_requires:
# pyproject.toml declares `dynamic = ["version", "dependencies"]` and reads
# this file via [tool.setuptools.dynamic]. It therefore MUST ship in the
# sdist (see MANIFEST.in) or building from an sdist yields an empty
# dependency list.
#
# Keep this list to what `import qbiocode` and the console scripts actually
# need. Optional tiers live in sibling files:
#   requirements-quvine.txt  -> the [quvine] extra (QuVINE embeddings)
#   requirements-docs.txt    -> the [docs] extra (Sphinx toolchain)
#   requirements.txt         -> everything, for development environments
#
# Do NOT add build-time tooling here (e.g. setuptools). A build-time pin
# declared as a runtime dependency is a published-metadata bug; see the
# docstring in setup.py.
# ==========================================================================

dill
h5py
hfda
hydra-core
ipykernel
joblib
matplotlib
networkx
numpy
optuna
pandas
pyyaml
qiskit==2.2.0
qiskit-aer==0.17.0
qiskit-algorithms==0.4.0
qiskit-ibm-runtime==0.44.0
qiskit-ibm-transpiler==0.11.0
qiskit-machine-learning==0.9.0
qiskit-nature==0.7.2
scikit-dimension
scikit-learn
scipy
seaborn
torch
tqdm
umap-learn
xgboost

# Single-cell / multi-omics tutorials (sc-qc preprocessing, QProfiler single-cell)
scanpy
anndata
leidenalg
igraph
