# This file was autogenerated by uv via the following command:
#    uv pip compile --python-version=3.11 ../../pyproject.toml --extra docs --extra release --extra testing --extra jit -o requirements-all.txt
alabaster==1.0.0
    # via sphinx
alifedata-phyloinformatics-convert==0.17.0
    # via hstrat (../../pyproject.toml)
annotated-types==0.7.0
    # via pydantic
anytree==2.12.1
    # via
    #   hstrat (../../pyproject.toml)
    #   alifedata-phyloinformatics-convert
asttokens==2.4.1
    # via stack-data
attrs==24.2.0
    # via
    #   jsonschema
    #   referencing
babel==2.16.0
    # via sphinx
backcall==0.2.0
    # via ipython
beautifulsoup4==4.12.3
    # via nbconvert
biopython==1.84
    # via
    #   hstrat (../../pyproject.toml)
    #   alifedata-phyloinformatics-convert
bitarray==3.0.0
    # via hstrat (../../pyproject.toml)
bitstring==4.0.2
    # via hstrat (../../pyproject.toml)
bleach==6.2.0
    # via nbconvert
bumpver==2022.1120
    # via hstrat (../../pyproject.toml)
certifi==2024.8.30
    # via requests
charset-normalizer==3.4.0
    # via requests
click==8.1.7
    # via
    #   alifedata-phyloinformatics-convert
    #   bumpver
    #   keyname
colorama==0.4.6
    # via bumpver
comm==0.2.2
    # via ipykernel
contexttimer==0.3.3
    # via hstrat (../../pyproject.toml)
contourpy==1.3.1
    # via matplotlib
coverage==6.4.4
    # via hstrat (../../pyproject.toml)
cppimport==22.8.2
    # via hstrat (../../pyproject.toml)
cycler==0.12.1
    # via matplotlib
debugpy==1.8.9
    # via ipykernel
decorator==5.1.1
    # via ipython
defusedxml==0.7.1
    # via nbconvert
dendropy==5.0.1
    # via
    #   hstrat (../../pyproject.toml)
    #   alifedata-phyloinformatics-convert
deprecated==1.2.15
    # via
    #   hstrat (../../pyproject.toml)
    #   alifedata-phyloinformatics-convert
distlib==0.3.9
    # via virtualenv
docutils==0.21.2
    # via
    #   nbsphinx
    #   readme-renderer
    #   sphinx
    #   sphinx-rtd-theme
downstream==1.4.0
    # via hstrat (../../pyproject.toml)
entrypoints==0.3
    # via flake8
ete3==3.1.3
    # via alifedata-phyloinformatics-convert
execnet==2.1.1
    # via pytest-xdist
executing==2.1.0
    # via stack-data
fastjsonschema==2.21.0
    # via nbformat
filelock==3.16.1
    # via
    #   cppimport
    #   tox
    #   virtualenv
flake8==3.7.8
    # via hstrat (../../pyproject.toml)
fonttools==4.55.0
    # via matplotlib
idna==3.10
    # via
    #   requests
    #   yarl
imagesize==1.4.1
    # via sphinx
iniconfig==2.0.0
    # via pytest
interval-search==0.5.2
    # via hstrat (../../pyproject.toml)
ipykernel==6.26.0
    # via hstrat (../../pyproject.toml)
ipython==8.12.3
    # via
    #   hstrat (../../pyproject.toml)
    #   ipykernel
iterify==0.1.0
    # via hstrat (../../pyproject.toml)
iterpop==0.4.1
    # via
    #   hstrat (../../pyproject.toml)
    #   alifedata-phyloinformatics-convert
jedi==0.19.2
    # via ipython
jinja2==3.1.4
    # via
    #   nbconvert
    #   nbsphinx
    #   sphinx
joinem==0.9.1
    # via
    #   hstrat (../../pyproject.toml)
    #   downstream
jsonschema==4.23.0
    # via nbformat
jsonschema-specifications==2024.10.1
    # via jsonschema
jupyter-client==8.6.3
    # via
    #   ipykernel
    #   nbclient
jupyter-core==5.7.2
    # via
    #   ipykernel
    #   jupyter-client
    #   nbclient
    #   nbconvert
    #   nbformat
jupyterlab-pygments==0.3.0
    # via nbconvert
keyname==0.4.1
    # via
    #   hstrat (../../pyproject.toml)
    #   teeplot
kiwisolver==1.4.7
    # via matplotlib
lazy-loader==0.4
    # via
    #   hstrat (../../pyproject.toml)
    #   downstream
lexid==2021.1006
    # via bumpver
llvmlite==0.43.0
    # via numba
lru-dict==1.3.0
    # via hstrat (../../pyproject.toml)
mako==1.3.6
    # via cppimport
markupsafe==3.0.2
    # via
    #   jinja2
    #   mako
    #   nbconvert
matplotlib==3.9.2
    # via
    #   hstrat (../../pyproject.toml)
    #   seaborn
    #   teeplot
matplotlib-inline==0.1.7
    # via
    #   ipykernel
    #   ipython
mccabe==0.6.1
    # via flake8
mistune==3.0.2
    # via nbconvert
mmh3==5.0.1
    # via hstrat (../../pyproject.toml)
more-itertools==8.13.0
    # via hstrat (../../pyproject.toml)
mpmath==1.3.0
    # via hstrat (../../pyproject.toml)
multidict==6.1.0
    # via yarl
multimethod==1.12
    # via pandera
mypy==0.991
    # via hstrat (../../pyproject.toml)
mypy-extensions==1.0.0
    # via
    #   mypy
    #   typing-inspect
nanto==0.1.1
    # via alifedata-phyloinformatics-convert
nbclient==0.10.1
    # via nbconvert
nbconvert==7.16.4
    # via nbsphinx
nbformat==5.10.4
    # via
    #   nbclient
    #   nbconvert
    #   nbsphinx
nbsphinx==0.9.3
    # via hstrat (../../pyproject.toml)
nest-asyncio==1.6.0
    # via ipykernel
networkx==3.4.2
    # via
    #   hstrat (../../pyproject.toml)
    #   alifedata-phyloinformatics-convert
nh3==0.2.19
    # via readme-renderer
numba==0.60.0
    # via hstrat (../../pyproject.toml)
numpy==2.0.2
    # via
    #   hstrat (../../pyproject.toml)
    #   alifedata-phyloinformatics-convert
    #   biopython
    #   contourpy
    #   downstream
    #   matplotlib
    #   numba
    #   pandas
    #   pandera
    #   patsy
    #   scipy
    #   seaborn
    #   statsmodels
    #   teeplot
opytional==0.1.0
    # via
    #   hstrat (../../pyproject.toml)
    #   alifedata-phyloinformatics-convert
    #   downstream
ordered-set==4.1.0
    # via hstrat (../../pyproject.toml)
packaging==24.2
    # via
    #   hstrat (../../pyproject.toml)
    #   ipykernel
    #   lazy-loader
    #   matplotlib
    #   nbconvert
    #   pandera
    #   pytest
    #   setuptools-scm
    #   sphinx
    #   statsmodels
    #   tox
pandas==2.2.3
    # via
    #   hstrat (../../pyproject.toml)
    #   alifedata-phyloinformatics-convert
    #   pandera
    #   seaborn
    #   statsmodels
    #   teeplot
pandera==0.21.0
    # via hstrat (../../pyproject.toml)
pandocfilters==1.5.1
    # via nbconvert
parso==0.8.4
    # via jedi
pathlib2==2.3.7.post1
    # via bumpver
patsy==1.0.1
    # via statsmodels
pexpect==4.9.0
    # via ipython
phylotrackpy==0.2.4
    # via hstrat (../../pyproject.toml)
pickleshare==0.7.5
    # via ipython
pillow==11.0.0
    # via matplotlib
pkginfo==1.11.2
    # via twine
platformdirs==4.3.6
    # via
    #   jupyter-core
    #   virtualenv
pluggy==1.5.0
    # via
    #   pytest
    #   tox
polars==1.16.0
    # via
    #   hstrat (../../pyproject.toml)
    #   downstream
    #   joinem
prettytable==3.12.0
    # via hstrat (../../pyproject.toml)
prompt-toolkit==3.0.48
    # via ipython
propcache==0.2.0
    # via yarl
psutil==6.1.0
    # via ipykernel
ptyprocess==0.7.0
    # via pexpect
pure-eval==0.2.3
    # via stack-data
py==1.11.0
    # via
    #   pytest-forked
    #   tox
pyarrow==18.1.0
    # via polars
pybind11==2.13.6
    # via
    #   hstrat (../../pyproject.toml)
    #   cppimport
pycodestyle==2.5.0
    # via flake8
pydantic==2.10.2
    # via pandera
pydantic-core==2.27.1
    # via pydantic
pyflakes==2.1.1
    # via flake8
pygments==2.18.0
    # via
    #   ipython
    #   nbconvert
    #   readme-renderer
    #   sphinx
pyparsing==3.2.0
    # via matplotlib
pytest==8.3.3
    # via
    #   hstrat (../../pyproject.toml)
    #   pytest-forked
    #   pytest-xdist
pytest-forked==1.6.0
    # via pytest-xdist
pytest-xdist==2.5.0
    # via hstrat (../../pyproject.toml)
python-dateutil==2.9.0.post0
    # via
    #   jupyter-client
    #   matplotlib
    #   pandas
python-slugify==8.0.4
    # via
    #   hstrat (../../pyproject.toml)
    #   teeplot
pytz==2024.2
    # via pandas
pyyaml==6.0.1
    # via hstrat (../../pyproject.toml)
pyzmq==26.2.0
    # via
    #   ipykernel
    #   jupyter-client
readme-renderer==44.0
    # via twine
referencing==0.35.1
    # via
    #   jsonschema
    #   jsonschema-specifications
requests==2.32.3
    # via
    #   requests-toolbelt
    #   sphinx
    #   twine
requests-toolbelt==1.0.0
    # via twine
rpds-py==0.21.0
    # via
    #   jsonschema
    #   referencing
ruff==0.1.11
    # via hstrat (../../pyproject.toml)
safe-assert==0.2.0
    # via hstrat (../../pyproject.toml)
scipy==1.14.1
    # via
    #   hstrat (../../pyproject.toml)
    #   statsmodels
seaborn==0.13.2
    # via hstrat (../../pyproject.toml)
setuptools==75.5.0
    # via
    #   hstrat (../../pyproject.toml)
    #   bumpver
    #   dendropy
    #   setuptools-scm
    #   twine
setuptools-scm==8.1.0
    # via hstrat (../../pyproject.toml)
six==1.16.0
    # via
    #   anytree
    #   asttokens
    #   pathlib2
    #   python-dateutil
    #   tox
snowballstemmer==2.2.0
    # via sphinx
sortedcontainers==2.4.0
    # via
    #   hstrat (../../pyproject.toml)
    #   alifedata-phyloinformatics-convert
soupsieve==2.6
    # via beautifulsoup4
sphinx==8.1.3
    # via
    #   hstrat (../../pyproject.toml)
    #   nbsphinx
    #   sphinx-rtd-theme
    #   sphinxcontrib-jquery
sphinx-rtd-theme==3.0.2
    # via hstrat (../../pyproject.toml)
sphinxcontrib-applehelp==2.0.0
    # via sphinx
sphinxcontrib-devhelp==2.0.0
    # via sphinx
sphinxcontrib-htmlhelp==2.1.0
    # via sphinx
sphinxcontrib-jquery==4.1
    # via sphinx-rtd-theme
sphinxcontrib-jsmath==1.0.1
    # via sphinx
sphinxcontrib-qthelp==2.0.0
    # via sphinx
sphinxcontrib-serializinghtml==2.0.0
    # via sphinx
stack-data==0.6.3
    # via ipython
statsmodels==0.14.4
    # via hstrat (../../pyproject.toml)
teeplot==0.4.0
    # via hstrat (../../pyproject.toml)
text-unidecode==1.3
    # via python-slugify
tinycss2==1.4.0
    # via nbconvert
toml==0.10.2
    # via
    #   bumpver
    #   tox
tornado==6.4.2
    # via
    #   ipykernel
    #   jupyter-client
tox==3.24.0
    # via hstrat (../../pyproject.toml)
tqdist==1.0
    # via hstrat (../../pyproject.toml)
tqdm==4.67.1
    # via
    #   hstrat (../../pyproject.toml)
    #   joinem
    #   twine
traitlets==5.14.3
    # via
    #   comm
    #   ipykernel
    #   ipython
    #   jupyter-client
    #   jupyter-core
    #   matplotlib-inline
    #   nbclient
    #   nbconvert
    #   nbformat
    #   nbsphinx
twine==1.14.0
    # via hstrat (../../pyproject.toml)
typeguard==4.4.1
    # via pandera
typing-extensions==4.12.2
    # via
    #   hstrat (../../pyproject.toml)
    #   alifedata-phyloinformatics-convert
    #   mypy
    #   pydantic
    #   pydantic-core
    #   typeguard
    #   typing-inspect
typing-inspect==0.9.0
    # via pandera
tzdata==2024.2
    # via pandas
urllib3==2.2.3
    # via requests
uv==0.4.18
    # via hstrat (../../pyproject.toml)
validators==0.34.0
    # via alifedata-phyloinformatics-convert
virtualenv==20.28.0
    # via tox
wcwidth==0.2.13
    # via
    #   prettytable
    #   prompt-toolkit
webencodings==0.5.1
    # via
    #   bleach
    #   tinycss2
wheel==0.45.0
    # via hstrat (../../pyproject.toml)
wrapt==1.17.0
    # via
    #   deprecated
    #   pandera
yarl==1.18.0
    # via alifedata-phyloinformatics-convert
