# This file was autogenerated by uv via the following command:
#    uv pip compile pyproject.toml -o requirements-py311.txt --python-version=3.11
annoy==1.17.3
    # via pacmap
appdirs==1.4.4
    # via bioservices
asttokens==3.0.0
    # via stack-data
attrs==25.3.0
    # via
    #   cattrs
    #   requests-cache
beautifulsoup4==4.13.4
    # via bioservices
bioservices==1.12.1
    # via protspace (pyproject.toml)
cattrs==25.1.1
    # via requests-cache
certifi==2025.6.15
    # via requests
charset-normalizer==3.4.2
    # via requests
click==8.2.1
    # via
    #   bioservices
    #   rich-click
colorama==0.4.6
    # via easydev
colorlog==6.9.0
    # via
    #   bioservices
    #   easydev
contourpy==1.3.1
    # via matplotlib
cycler==0.12.1
    # via matplotlib
decorator==5.2.1
    # via ipython
easydev==0.13.3
    # via bioservices
executing==2.2.0
    # via stack-data
fonttools==4.55.0
    # via matplotlib
gevent==25.5.1
    # via grequests
greenlet==3.2.3
    # via gevent
grequests==0.7.0
    # via bioservices
h5py==3.12.1
    # via protspace (pyproject.toml)
idna==3.10
    # via
    #   requests
    #   url-normalize
ipython==8.37.0
    # via pymmseqs
jedi==0.19.2
    # via ipython
joblib==1.4.2
    # via
    #   pynndescent
    #   scikit-learn
kiwisolver==1.4.7
    # via matplotlib
line-profiler==4.2.0
    # via easydev
llvmlite==0.43.0
    # via
    #   numba
    #   pynndescent
lxml==5.4.0
    # via bioservices
markdown-it-py==3.0.0
    # via rich
matplotlib==3.9.2
    # via
    #   protspace (pyproject.toml)
    #   bioservices
matplotlib-inline==0.1.7
    # via ipython
mdurl==0.1.2
    # via markdown-it-py
numba==0.60.0
    # via
    #   pacmap
    #   pynndescent
    #   umap-learn
numpy==2.0.2
    # via
    #   protspace (pyproject.toml)
    #   contourpy
    #   h5py
    #   matplotlib
    #   numba
    #   pacmap
    #   pandas
    #   pymmseqs
    #   scikit-learn
    #   scipy
    #   umap-learn
packaging==24.2
    # via matplotlib
pacmap==0.8.0
    # via protspace (pyproject.toml)
pandas==2.2.3
    # via
    #   protspace (pyproject.toml)
    #   bioservices
    #   pymmseqs
parso==0.8.4
    # via jedi
pexpect==4.9.0
    # via
    #   easydev
    #   ipython
pillow==11.0.0
    # via matplotlib
platformdirs==4.3.8
    # via
    #   easydev
    #   requests-cache
prompt-toolkit==3.0.51
    # via ipython
ptyprocess==0.7.0
    # via pexpect
pure-eval==0.2.3
    # via stack-data
pyarrow==20.0.0
    # via protspace (pyproject.toml)
pygments==2.19.2
    # via
    #   ipython
    #   rich
pymmseqs==1.0.4
    # via protspace (pyproject.toml)
pynndescent==0.5.13
    # via umap-learn
pyparsing==3.2.0
    # via matplotlib
python-dateutil==2.9.0.post0
    # via
    #   matplotlib
    #   pandas
pytz==2024.2
    # via pandas
pyyaml==6.0.2
    # via pymmseqs
requests==2.32.4
    # via
    #   bioservices
    #   grequests
    #   requests-cache
requests-cache==1.2.1
    # via bioservices
rich==14.0.0
    # via rich-click
rich-click==1.8.9
    # via bioservices
scikit-learn==1.7.0
    # via
    #   protspace (pyproject.toml)
    #   pacmap
    #   pynndescent
    #   umap-learn
scipy==1.14.1
    # via
    #   pynndescent
    #   scikit-learn
    #   umap-learn
setuptools==80.9.0
    # via
    #   zope-event
    #   zope-interface
six==1.16.0
    # via python-dateutil
soupsieve==2.7
    # via beautifulsoup4
stack-data==0.6.3
    # via ipython
suds-community==1.2.0
    # via bioservices
taxopy==0.14.0
    # via protspace (pyproject.toml)
threadpoolctl==3.5.0
    # via scikit-learn
tqdm==4.67.1
    # via
    #   protspace (pyproject.toml)
    #   bioservices
    #   umap-learn
traitlets==5.14.3
    # via
    #   ipython
    #   matplotlib-inline
typing-extensions==4.14.0
    # via
    #   beautifulsoup4
    #   cattrs
    #   ipython
    #   rich-click
tzdata==2024.2
    # via pandas
umap-learn==0.5.7
    # via protspace (pyproject.toml)
url-normalize==2.2.1
    # via requests-cache
urllib3==2.5.0
    # via
    #   requests
    #   requests-cache
wcwidth==0.2.13
    # via prompt-toolkit
wrapt==1.17.2
    # via bioservices
xmltodict==0.14.2
    # via bioservices
zope-event==5.1
    # via gevent
zope-interface==7.2
    # via gevent
