# This file was autogenerated by uv via the following command:
#    uv pip compile --python-version=3.8 ../../pyproject.toml --extra pinned_dependencies_py38 --extra pinned_jit --extra docs --extra release --extra testing_py38 -o requirements-all.txt
alabaster>=0.7.13
    # via sphinx
alifedata-phyloinformatics-convert>=0.16.4
    # via hstrat (../../pyproject.toml)
annotated-types>=0.7.0
    # via pydantic
anytree>=2.8.0
    # via
    #   hstrat (../../pyproject.toml)
    #   alifedata-phyloinformatics-convert
asttokens>=2.4.1
    # via stack-data
attrs>=24.2.0
    # via
    #   jsonschema
    #   pytest
    #   referencing
babel>=2.16.0
    # via sphinx
backcall>=0.2.0
    # via ipython
beautifulsoup4>=4.12.3
    # via nbconvert
biopython>=1.79
    # via
    #   hstrat (../../pyproject.toml)
    #   alifedata-phyloinformatics-convert
bitarray>=2.6.2
    # via hstrat (../../pyproject.toml)
bitstring>=3.1.9
    # via hstrat (../../pyproject.toml)
bleach>=6.1.0
    # 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)
coverage>=6.4.4
    # via hstrat (../../pyproject.toml)
cycler>=0.12.1
    # via matplotlib
debugpy>=1.8.8
    # via ipykernel
decorator>=5.1.1
    # via ipython
defusedxml>=0.7.1
    # via nbconvert
dendropy>=4.5.2
    # via
    #   hstrat (../../pyproject.toml)
    #   alifedata-phyloinformatics-convert
deprecated>=1.2.13
    # via
    #   hstrat (../../pyproject.toml)
    #   alifedata-phyloinformatics-convert
distlib>=0.3.9
    # via virtualenv
docutils>=0.17.1
    # via
    #   nbsphinx
    #   readme-renderer
    #   sphinx
    #   sphinx-rtd-theme
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>=2.20.0
    # via nbformat
filelock>=3.16.1
    # via
    #   tox
    #   virtualenv
flake8>=3.7.8
    # via hstrat (../../pyproject.toml)
fonttools>=4.54.1
    # via matplotlib
idna>=3.10
    # via
    #   requests
    #   yarl
imagesize>=1.4.1
    # via sphinx
importlib-metadata>=8.5.0
    # via
    #   jupyter-client
    #   nbconvert
    #   numba
    #   sphinx
importlib-resources>=6.4.5
    # via
    #   jsonschema
    #   jsonschema-specifications
iniconfig>=2.0.0
    # via pytest
interval-search>=0.3.1
    # 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>=0.19.1
    # via ipython
jinja2>=3.1.4
    # via
    #   nbconvert
    #   nbsphinx
    #   sphinx
jsonschema>=4.23.0
    # via nbformat
jsonschema-specifications>=2023.12.1
    # 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)
lexid>=2021.1006
    # via bumpver
llvmlite>=0.39.1
    # via numba
lru-dict>=1.1.8
    # via hstrat (../../pyproject.toml)
markupsafe>=2.1.5
    # via
    #   jinja2
    #   nbconvert
matplotlib>=3.5.2
    # 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>=3.0.0
    # via hstrat (../../pyproject.toml)
more-itertools>=8.13.0
    # via hstrat (../../pyproject.toml)
mpmath>=1.2.1
    # via hstrat (../../pyproject.toml)
multidict>=6.1.0
    # via yarl
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>=0.10.0
    # 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>=2.6.3
    # via
    #   hstrat (../../pyproject.toml)
    #   alifedata-phyloinformatics-convert
nh3>=0.2.18
    # via readme-renderer
numba>=0.56.4
    # via hstrat (../../pyproject.toml)
numpy<2,>=1.21.6
    # via
    #   hstrat (../../pyproject.toml)
    #   alifedata-phyloinformatics-convert
    #   biopython
    #   matplotlib
    #   numba
    #   pandas
    #   pandera
    #   patsy
    #   scipy
    #   seaborn
    #   statsmodels
    #   teeplot
opytional>=0.1.0
    # via
    #   hstrat (../../pyproject.toml)
    #   alifedata-phyloinformatics-convert
ordered-set>=4.1.0
    # via hstrat (../../pyproject.toml)
packaging>=23.0
    # via
    #   hstrat (../../pyproject.toml)
    #   ipykernel
    #   lazy-loader
    #   matplotlib
    #   nbconvert
    #   pandera
    #   pytest
    #   setuptools-scm
    #   sphinx
    #   statsmodels
    #   tox
pandas<2,>=1.3.5
    # via
    #   hstrat (../../pyproject.toml)
    #   alifedata-phyloinformatics-convert
    #   pandera
    #   seaborn
    #   statsmodels
    #   teeplot
pandera>=0.13.4
    # via hstrat (../../pyproject.toml)
pandocfilters>=1.5.1
    # via nbconvert
parso>=0.8.4
    # via jedi
pathlib2>=2.3.7.post1
    # via bumpver
patsy>=0.5.6
    # via statsmodels
pexpect>=4.9.0
    # via ipython
phylotrackpy>=0.2.2
    # via alifedata-phyloinformatics-convert
pickleshare>=0.7.5
    # via ipython
pillow>=10.4.0
    # via matplotlib
pip>=22.0.4
    # via hstrat (../../pyproject.toml)
pkginfo>=1.11.2
    # via twine
pkgutil-resolve-name>=1.3.10
    # via jsonschema
platformdirs>=4.3.6
    # via
    #   jupyter-core
    #   virtualenv
pluggy>=1.5.0
    # via
    #   pytest
    #   tox
prettytable>=3.5.0
    # 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
    #   pytest-forked
    #   tox
pycodestyle>=2.5.0
    # via flake8
pydantic>=2.9.2
    # via pandera
pydantic-core>=2.23.4
    # via pydantic
pyflakes>=2.1.1
    # via flake8
pygments>=2.18.0
    # via
    #   ipython
    #   nbconvert
    #   readme-renderer
    #   sphinx
pyparsing>=3.1.4
    # via matplotlib
pytest>=7.1.2
    # 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>=6.1.2
    # via
    #   hstrat (../../pyproject.toml)
    #   teeplot
pytz>=2024.2
    # via
    #   babel
    #   pandas
pyyaml>=6.0.1
    # via hstrat (../../pyproject.toml)
pyzmq>=26.2.0
    # via
    #   ipykernel
    #   jupyter-client
readme-renderer>=43.0
    # 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>=0.20.1
    # via
    #   jsonschema
    #   referencing
ruff>=0.1.11
    # via hstrat (../../pyproject.toml)
safe-assert>=0.2.0
    # via hstrat (../../pyproject.toml)
scipy>=1.7.3
    # via
    #   hstrat (../../pyproject.toml)
    #   seaborn
    #   statsmodels
seaborn>=0.11.0
    # via hstrat (../../pyproject.toml)
setuptools>=65.6.3
    # via
    #   hstrat (../../pyproject.toml)
    #   bumpver
    #   dendropy
    #   numba
    #   setuptools-scm
    #   twine
setuptools-scm>=8.1.0
    # via hstrat (../../pyproject.toml)
six>=1.16.0
    # via
    #   anytree
    #   asttokens
    #   bleach
    #   pathlib2
    #   patsy
    #   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>=4.4.0
    # via
    #   hstrat (../../pyproject.toml)
    #   nbsphinx
    #   sphinx-rtd-theme
sphinx-rtd-theme>=1.0.0
    # via hstrat (../../pyproject.toml)
sphinxcontrib-applehelp>=1.0.4
    # via sphinx
sphinxcontrib-devhelp>=1.0.2
    # via sphinx
sphinxcontrib-htmlhelp>=2.0.1
    # via sphinx
sphinxcontrib-jsmath>=1.0.1
    # via sphinx
sphinxcontrib-qthelp>=1.0.3
    # via sphinx
sphinxcontrib-serializinghtml>=1.1.5
    # via sphinx
stack-data>=0.6.3
    # via ipython
statsmodels>=0.14.1
    # 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
tomli>=2.0.2
    # via
    #   mypy
    #   pytest
    #   setuptools-scm
tornado>=6.4.1
    # via
    #   ipykernel
    #   jupyter-client
tox>=3.24.0
    # via hstrat (../../pyproject.toml)
tqdist>=1.0
    # via hstrat (../../pyproject.toml)
tqdm>=4.62.3
    # via
    #   hstrat (../../pyproject.toml)
    #   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)
typing-extensions>=4.12.2
    # via
    #   hstrat (../../pyproject.toml)
    #   alifedata-phyloinformatics-convert
    #   annotated-types
    #   ipython
    #   multidict
    #   mypy
    #   pydantic
    #   pydantic-core
    #   setuptools-scm
    #   typing-inspect
typing-inspect>=0.9.0
    # via pandera
urllib3>=2.2.3
    # via requests
uv>=0.4.18
    # via hstrat (../../pyproject.toml)
validators>=0.34.0
    # via alifedata-phyloinformatics-convert
virtualenv>=20.27.1
    # via tox
wcwidth>=0.2.13
    # via
    #   prettytable
    #   prompt-toolkit
webencodings>=0.5.1
    # via
    #   bleach
    #   tinycss2
wheel>=0.33.6
    # via hstrat (../../pyproject.toml)
wrapt>=1.16.0
    # via
    #   deprecated
    #   pandera
yarl>=1.15.2
    # via alifedata-phyloinformatics-convert
zipp>=3.20.2
    # via
    #   importlib-metadata
    #   importlib-resources
