click>=8.1
cogent3==2025.7.10a10
gudhi>=3.11
landscapy-ml<2,>=1
networkx>=3.2
numpy>=1.24
pandas>=2.3
pyarrow>=17
ray>=2.48
scikit-learn>=1.3
scipy>=1.10
softalign>=1.0.0
torch>=2.1
torch-geometric>=2.6
transformers>=4.53.2
tqdm>=4.66

[:platform_system == "Darwin" and platform_machine == "arm64"]
faiss-cpu>=1.11

[:platform_system == "Darwin" and platform_machine == "x86_64"]
faiss-cpu>=1.11

[:platform_system == "Linux" and (platform_machine == "x86_64" or platform_machine == "aarch64")]
faiss-cpu>=1.11

[:platform_system == "Windows" and (platform_machine == "AMD64" or platform_machine == "ARM64" or platform_machine == "x86_64" or platform_machine == "arm64")]
faiss-cpu>=1.11

[:python_version < "3.12"]
piqtree<0.8,>=0.6.1

[:python_version >= "3.12"]
piqtree>=0.6.1

[alignment]
softalign>=1.0.0

[all]
click>=8.1
cogent3==2025.7.10a10
gudhi>=3.11
pyarrow>=17
ray>=2.48
scikit-learn>=1.3
softalign>=1.0.0
torch>=2.1
transformers>=4.53.2
tqdm>=4.66

[all:platform_system == "Darwin" and platform_machine == "arm64"]
faiss-cpu>=1.11

[all:platform_system == "Darwin" and platform_machine == "x86_64"]
faiss-cpu>=1.11

[all:platform_system == "Linux" and (platform_machine == "x86_64" or platform_machine == "aarch64")]
faiss-cpu>=1.11

[all:platform_system == "Windows" and (platform_machine == "AMD64" or platform_machine == "ARM64" or platform_machine == "x86_64" or platform_machine == "arm64")]
faiss-cpu>=1.11

[all:python_version < "3.12"]
piqtree<0.8,>=0.6.1

[all:python_version >= "3.12"]
piqtree>=0.6.1

[analysis]
gudhi>=3.11
scikit-learn>=1.3

[cli]
click>=8.1

[dev]
build>=1.2
matplotlib>=3.8
numpydoc>=1.8
pytest>=8
pytest-cov>=6
pytest-mock>=3.14
ruff>=0.5
twine>=5

[embeddings]
torch>=2.1
transformers>=4.53.2
tqdm>=4.66

[faiss]
scikit-learn>=1.3

[faiss:platform_system == "Darwin" and platform_machine == "arm64"]
faiss-cpu>=1.11

[faiss:platform_system == "Darwin" and platform_machine == "x86_64"]
faiss-cpu>=1.11

[faiss:platform_system == "Linux" and (platform_machine == "x86_64" or platform_machine == "aarch64")]
faiss-cpu>=1.11

[faiss:platform_system == "Windows" and (platform_machine == "AMD64" or platform_machine == "ARM64" or platform_machine == "x86_64" or platform_machine == "arm64")]
faiss-cpu>=1.11

[knn]
scikit-learn>=1.3

[ml]
torch>=2.1
torch-geometric>=2.6
transformers>=4.53.2
tqdm>=4.66

[parallel]
ray>=2.48

[parquet]
pyarrow>=17

[phylogeny]
cogent3==2025.7.10a10
softalign>=1.0.0

[phylogeny:python_version < "3.12"]
piqtree<0.8,>=0.6.1

[phylogeny:python_version >= "3.12"]
piqtree>=0.6.1

[tda]
gudhi>=3.11
scikit-learn>=1.3
