# This file was autogenerated by uv via the following command:
#    uv pip compile --python-version=3.14 pyproject.toml --extra docs --extra release --extra testing --extra jit -o requirements-dev/py314/requirements-all.txt -c /tmp/constraints-all-314.txt
alabaster==1.0.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   sphinx
alifedata-phyloinformatics-convert==0.19.3
    # via
    #   -c /tmp/constraints-all-314.txt
    #   phyloframe (pyproject.toml)
anytree==2.13.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   alifedata-phyloinformatics-convert
asttokens==3.0.1
    # via
    #   -c /tmp/constraints-all-314.txt
    #   stack-data
attrs==25.4.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   jsonschema
    #   referencing
babel==2.18.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   sphinx
backcall==0.2.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   ipython
beautifulsoup4==4.14.3
    # via
    #   -c /tmp/constraints-all-314.txt
    #   nbconvert
biopython==1.86
    # via
    #   -c /tmp/constraints-all-314.txt
    #   alifedata-phyloinformatics-convert
black==22.10.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   phyloframe (pyproject.toml)
bleach==6.3.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   nbconvert
bumpver==2022.1120
    # via
    #   -c /tmp/constraints-all-314.txt
    #   phyloframe (pyproject.toml)
certifi==2026.2.25
    # via
    #   -c /tmp/constraints-all-314.txt
    #   requests
charset-normalizer==3.4.6
    # via
    #   -c /tmp/constraints-all-314.txt
    #   requests
click==8.3.1
    # via
    #   -c /tmp/constraints-all-314.txt
    #   alifedata-phyloinformatics-convert
    #   black
    #   bumpver
colorama==0.4.6
    # via
    #   -c /tmp/constraints-all-314.txt
    #   bumpver
comm==0.2.3
    # via
    #   -c /tmp/constraints-all-314.txt
    #   ipykernel
contexttimer==0.3.3
    # via
    #   -c /tmp/constraints-all-314.txt
    #   phyloframe (pyproject.toml)
contourpy==1.3.3
    # via matplotlib
coverage==7.13.5
    # via
    #   -c /tmp/constraints-all-314.txt
    #   phyloframe (pyproject.toml)
cycler==0.12.1
    # via matplotlib
debugpy==1.8.20
    # via
    #   -c /tmp/constraints-all-314.txt
    #   ipykernel
decorator==5.2.1
    # via
    #   -c /tmp/constraints-all-314.txt
    #   ipython
defusedxml==0.7.1
    # via
    #   -c /tmp/constraints-all-314.txt
    #   nbconvert
dendropy==5.0.8
    # via
    #   -c /tmp/constraints-all-314.txt
    #   alifedata-phyloinformatics-convert
deprecated==1.3.1
    # via
    #   -c /tmp/constraints-all-314.txt
    #   phyloframe (pyproject.toml)
    #   alifedata-phyloinformatics-convert
distlib==0.4.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   virtualenv
docutils==0.21.2
    # via
    #   -c /tmp/constraints-all-314.txt
    #   nbsphinx
    #   readme-renderer
    #   sphinx
    #   sphinx-rtd-theme
ete3==3.1.3
    # via
    #   -c /tmp/constraints-all-314.txt
    #   alifedata-phyloinformatics-convert
execnet==2.1.2
    # via
    #   -c /tmp/constraints-all-314.txt
    #   pytest-xdist
executing==2.2.1
    # via
    #   -c /tmp/constraints-all-314.txt
    #   stack-data
fastjsonschema==2.21.2
    # via
    #   -c /tmp/constraints-all-314.txt
    #   nbformat
filelock==3.25.2
    # via
    #   -c /tmp/constraints-all-314.txt
    #   python-discovery
    #   tox
    #   virtualenv
fishersrc==0.1.15
    # via
    #   -c /tmp/constraints-all-314.txt
    #   phyloframe (pyproject.toml)
fonttools==4.62.1
    # via matplotlib
idna==3.11
    # via
    #   -c /tmp/constraints-all-314.txt
    #   requests
    #   yarl
imagesize==2.0.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   sphinx
iniconfig==2.3.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   pytest
iplotx==1.7.1
    # via phyloframe (pyproject.toml)
ipykernel==6.26.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   phyloframe (pyproject.toml)
ipython==8.12.3
    # via
    #   -c /tmp/constraints-all-314.txt
    #   phyloframe (pyproject.toml)
    #   ipykernel
isort==8.0.1
    # via
    #   -c /tmp/constraints-all-314.txt
    #   phyloframe (pyproject.toml)
iterify==0.1.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   phyloframe (pyproject.toml)
iterpop==0.4.1
    # via
    #   -c /tmp/constraints-all-314.txt
    #   alifedata-phyloinformatics-convert
jedi==0.19.2
    # via
    #   -c /tmp/constraints-all-314.txt
    #   ipython
jinja2==3.1.6
    # via
    #   -c /tmp/constraints-all-314.txt
    #   nbconvert
    #   nbsphinx
    #   sphinx
joblib==1.5.3
    # via
    #   -c /tmp/constraints-all-314.txt
    #   phyloframe (pyproject.toml)
    #   scikit-learn
joinem==0.11.1
    # via
    #   -c /tmp/constraints-all-314.txt
    #   phyloframe (pyproject.toml)
jsonschema==4.26.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   nbformat
jsonschema-specifications==2025.9.1
    # via
    #   -c /tmp/constraints-all-314.txt
    #   jsonschema
jupyter-client==8.8.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   ipykernel
    #   nbclient
jupyter-core==5.9.1
    # via
    #   -c /tmp/constraints-all-314.txt
    #   ipykernel
    #   jupyter-client
    #   nbclient
    #   nbconvert
    #   nbformat
jupyterlab-pygments==0.3.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   nbconvert
kiwisolver==1.5.0
    # via matplotlib
lazy-loader==0.5
    # via
    #   -c /tmp/constraints-all-314.txt
    #   phyloframe (pyproject.toml)
lexid==2021.1006
    # via
    #   -c /tmp/constraints-all-314.txt
    #   bumpver
llvmlite==0.46.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   numba
markupsafe==3.0.3
    # via
    #   -c /tmp/constraints-all-314.txt
    #   jinja2
    #   nbconvert
matplotlib==3.10.8
    # via iplotx
matplotlib-inline==0.2.1
    # via
    #   -c /tmp/constraints-all-314.txt
    #   ipykernel
    #   ipython
mistune==3.2.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   nbconvert
more-itertools==10.8.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   phyloframe (pyproject.toml)
multidict==6.7.1
    # via
    #   -c /tmp/constraints-all-314.txt
    #   yarl
mypy-extensions==1.1.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   black
nanto==0.1.1
    # via
    #   -c /tmp/constraints-all-314.txt
    #   alifedata-phyloinformatics-convert
nbclient==0.10.4
    # via
    #   -c /tmp/constraints-all-314.txt
    #   nbconvert
nbconvert==7.17.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   nbsphinx
nbformat==5.10.4
    # via
    #   -c /tmp/constraints-all-314.txt
    #   nbclient
    #   nbconvert
    #   nbsphinx
nbsphinx==0.9.3
    # via
    #   -c /tmp/constraints-all-314.txt
    #   phyloframe (pyproject.toml)
nest-asyncio==1.6.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   ipykernel
networkx==3.6.1
    # via
    #   -c /tmp/constraints-all-314.txt
    #   alifedata-phyloinformatics-convert
nh3==0.3.3
    # via
    #   -c /tmp/constraints-all-314.txt
    #   readme-renderer
numba==0.64.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   phyloframe (pyproject.toml)
numpy==2.4.3
    # via
    #   -c /tmp/constraints-all-314.txt
    #   phyloframe (pyproject.toml)
    #   alifedata-phyloinformatics-convert
    #   biopython
    #   contourpy
    #   fishersrc
    #   iplotx
    #   matplotlib
    #   numba
    #   pandas
    #   patsy
    #   scikit-learn
    #   scipy
    #   statsmodels
opytional==0.1.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   phyloframe (pyproject.toml)
    #   alifedata-phyloinformatics-convert
ordered-set==4.1.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   phyloframe (pyproject.toml)
packaging==26.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   phyloframe (pyproject.toml)
    #   ipykernel
    #   lazy-loader
    #   matplotlib
    #   nbconvert
    #   pytest
    #   setuptools-scm
    #   sphinx
    #   statsmodels
    #   tox
    # via
    #   -c /tmp/constraints-all-314.txt
    #   phyloframe (pyproject.toml)
    #   alifedata-phyloinformatics-convert
    #   iplotx
    #   statsmodels
pandocfilters==1.5.1
    # via
    #   -c /tmp/constraints-all-314.txt
    #   nbconvert
parso==0.8.6
    # via
    #   -c /tmp/constraints-all-314.txt
    #   jedi
pathlib2==2.3.7.post1
    # via
    #   -c /tmp/constraints-all-314.txt
    #   bumpver
pathspec==1.0.4
    # via
    #   -c /tmp/constraints-all-314.txt
    #   black
patsy==1.0.2
    # via
    #   -c /tmp/constraints-all-314.txt
    #   statsmodels
pexpect==4.9.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   ipython
pickleshare==0.7.5
    # via
    #   -c /tmp/constraints-all-314.txt
    #   ipython
pillow==12.2.0
    # via matplotlib
pkginfo==1.12.1.2
    # via
    #   -c /tmp/constraints-all-314.txt
    #   twine
platformdirs==4.9.4
    # via
    #   -c /tmp/constraints-all-314.txt
    #   black
    #   jupyter-core
    #   python-discovery
    #   virtualenv
pluggy==1.6.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   pytest
    #   tox
polars==1.39.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   phyloframe (pyproject.toml)
    #   joinem
polars-runtime-32==1.39.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   polars
polars-runtime-64==1.39.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   polars
prompt-toolkit==3.0.52
    # via
    #   -c /tmp/constraints-all-314.txt
    #   ipython
propcache==0.4.1
    # via
    #   -c /tmp/constraints-all-314.txt
    #   yarl
psutil==7.2.2
    # via
    #   -c /tmp/constraints-all-314.txt
    #   ipykernel
ptyprocess==0.7.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   pexpect
pure-eval==0.2.3
    # via
    #   -c /tmp/constraints-all-314.txt
    #   stack-data
py==1.11.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   pytest-forked
    #   tox
pyarrow==23.0.1
    # via
    #   -c /tmp/constraints-all-314.txt
    #   phyloframe (pyproject.toml)
    #   polars
pygments==2.19.2
    # via
    #   -c /tmp/constraints-all-314.txt
    #   ipython
    #   nbconvert
    #   readme-renderer
    #   sphinx
pyparsing==3.3.2
    # via matplotlib
pytest==8.3.3
    # via
    #   -c /tmp/constraints-all-314.txt
    #   phyloframe (pyproject.toml)
    #   pytest-forked
    #   pytest-xdist
pytest-forked==1.6.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   pytest-xdist
pytest-xdist==2.5.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   phyloframe (pyproject.toml)
python-dateutil==2.9.0.post0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   jupyter-client
    #   matplotlib
    #   pandas
python-discovery==1.1.3
    # via
    #   -c /tmp/constraints-all-314.txt
    #   virtualenv
pyyaml==6.0.1
    # via
    #   -c /tmp/constraints-all-314.txt
    #   phyloframe (pyproject.toml)
pyzmq==27.1.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   ipykernel
    #   jupyter-client
readme-renderer==44.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   twine
referencing==0.37.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   jsonschema
    #   jsonschema-specifications
requests==2.32.5
    # via
    #   -c /tmp/constraints-all-314.txt
    #   requests-toolbelt
    #   sphinx
    #   twine
requests-toolbelt==1.0.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   twine
rpds-py==0.30.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   jsonschema
    #   referencing
ruff==0.15.6
    # via
    #   -c /tmp/constraints-all-314.txt
    #   phyloframe (pyproject.toml)
safe-assert==0.2.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   phyloframe (pyproject.toml)
scikit-learn==1.8.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   phyloframe (pyproject.toml)
scipy==1.17.1
    # via
    #   -c /tmp/constraints-all-314.txt
    #   phyloframe (pyproject.toml)
    #   scikit-learn
    #   statsmodels
setuptools==75.5.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   phyloframe (pyproject.toml)
    #   bumpver
    #   dendropy
    #   setuptools-scm
    #   twine
setuptools-scm==8.1.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   phyloframe (pyproject.toml)
six==1.17.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   pathlib2
    #   python-dateutil
    #   tox
snowballstemmer==3.0.1
    # via
    #   -c /tmp/constraints-all-314.txt
    #   sphinx
sortedcontainers==2.4.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   phyloframe (pyproject.toml)
    #   alifedata-phyloinformatics-convert
soupsieve==2.8.3
    # via
    #   -c /tmp/constraints-all-314.txt
    #   beautifulsoup4
sphinx==8.1.3
    # via
    #   -c /tmp/constraints-all-314.txt
    #   phyloframe (pyproject.toml)
    #   nbsphinx
    #   sphinx-rtd-theme
    #   sphinxcontrib-jquery
sphinx-rtd-theme==3.0.2
    # via
    #   -c /tmp/constraints-all-314.txt
    #   phyloframe (pyproject.toml)
sphinxcontrib-applehelp==2.0.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   sphinx
sphinxcontrib-devhelp==2.0.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   sphinx
sphinxcontrib-htmlhelp==2.1.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   sphinx
sphinxcontrib-jquery==4.1
    # via
    #   -c /tmp/constraints-all-314.txt
    #   sphinx-rtd-theme
sphinxcontrib-jsmath==1.0.1
    # via
    #   -c /tmp/constraints-all-314.txt
    #   sphinx
sphinxcontrib-qthelp==2.0.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   sphinx
sphinxcontrib-serializinghtml==2.0.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   sphinx
stack-data==0.6.3
    # via
    #   -c /tmp/constraints-all-314.txt
    #   ipython
statsmodels==0.14.6
    # via
    #   -c /tmp/constraints-all-314.txt
    #   phyloframe (pyproject.toml)
threadpoolctl==3.6.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   scikit-learn
tinycss2==1.4.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   bleach
toml==0.10.2
    # via
    #   -c /tmp/constraints-all-314.txt
    #   bumpver
    #   tox
tornado==6.5.5
    # via
    #   -c /tmp/constraints-all-314.txt
    #   ipykernel
    #   jupyter-client
tox==3.24.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   phyloframe (pyproject.toml)
tqdist==1.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   phyloframe (pyproject.toml)
tqdm==4.67.3
    # via
    #   -c /tmp/constraints-all-314.txt
    #   phyloframe (pyproject.toml)
    #   joinem
    #   twine
traitlets==5.14.3
    # via
    #   -c /tmp/constraints-all-314.txt
    #   ipykernel
    #   ipython
    #   jupyter-client
    #   jupyter-core
    #   matplotlib-inline
    #   nbclient
    #   nbconvert
    #   nbformat
    #   nbsphinx
treeswift==1.1.45
    # via
    #   -c /tmp/constraints-all-314.txt
    #   alifedata-phyloinformatics-convert
twine==1.14.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   phyloframe (pyproject.toml)
typing-extensions==4.15.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   phyloframe (pyproject.toml)
    #   alifedata-phyloinformatics-convert
    #   beautifulsoup4
urllib3==2.6.3
    # via
    #   -c /tmp/constraints-all-314.txt
    #   requests
uv==0.4.18
    # via
    #   -c /tmp/constraints-all-314.txt
    #   phyloframe (pyproject.toml)
validators==0.35.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   alifedata-phyloinformatics-convert
virtualenv==21.2.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   tox
wcwidth==0.6.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   prompt-toolkit
webencodings==0.5.1
    # via
    #   -c /tmp/constraints-all-314.txt
    #   bleach
    #   tinycss2
wheel==0.45.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   phyloframe (pyproject.toml)
wrapt==2.1.2
    # via
    #   -c /tmp/constraints-all-314.txt
    #   deprecated
yarl==1.23.0
    # via
    #   -c /tmp/constraints-all-314.txt
    #   alifedata-phyloinformatics-convert
