requirements-dev.lock

# generated by rye
# use `rye lock` or `rye sync` to update this lockfile
#
# last locked with the following flags:
#   pre: false
#   features: []
#   all-features: true
#   with-sources: false
#   generate-hashes: false
#   universal: false

-e file:.
asttokens==3.0.0
    # via stack-data
attrs==24.2.0
    # via jsonschema
    # via referencing
babel==2.16.0
    # via mkdocs-material
beautifulsoup4==4.12.3
    # via nbconvert
biopython==1.84
    # via pymsaviz
black==24.10.0
bleach==6.2.0
    # via nbconvert
certifi==2024.8.30
    # via requests
cfgv==3.4.0
    # via pre-commit
charset-normalizer==3.4.0
    # via requests
click==8.1.7
    # via black
    # via mkdocs
    # via mkdocstrings
colorama==0.4.6
    # via griffe
    # via mkdocs-material
comm==0.2.2
    # via ipykernel
contourpy==1.3.0
    # via matplotlib
coverage==7.6.8
    # via pytest-cov
cycler==0.12.1
    # via matplotlib
debugpy==1.8.9
    # via ipykernel
decorator==5.1.1
    # via ipython
defusedxml==0.7.1
    # via nbconvert
distlib==0.3.9
    # via virtualenv
exceptiongroup==1.2.2
    # via ipython
    # via pytest
executing==2.1.0
    # via stack-data
fastjsonschema==2.21.0
    # via nbformat
filelock==3.16.1
    # via virtualenv
fonttools==4.55.0
    # via matplotlib
ghp-import==2.1.0
    # via mkdocs
griffe==1.5.1
    # via mkdocstrings-python
identify==2.6.3
    # via pre-commit
idna==3.10
    # via requests
importlib-metadata==8.5.0
    # via jupyter-client
    # via markdown
    # via mkdocs
    # via mkdocs-get-deps
    # via mkdocstrings
    # via nbconvert
importlib-resources==6.4.5
    # via matplotlib
iniconfig==2.0.0
    # via pytest
ipykernel==6.29.5
    # via mkdocs-jupyter
ipython==8.18.1
    # via ipykernel
jedi==0.19.2
    # via ipython
jinja2==3.1.4
    # via mkdocs
    # via mkdocs-material
    # via mkdocstrings
    # via nbconvert
jsonschema==4.23.0
    # via nbformat
jsonschema-specifications==2024.10.1
    # via jsonschema
jupyter-client==8.6.3
    # via ipykernel
    # via nbclient
jupyter-core==5.7.2
    # via ipykernel
    # via jupyter-client
    # via nbclient
    # via nbconvert
    # via nbformat
jupyterlab-pygments==0.3.0
    # via nbconvert
jupytext==1.16.4
    # via mkdocs-jupyter
kiwisolver==1.4.7
    # via matplotlib
markdown==3.7
    # via mkdocs
    # via mkdocs-autorefs
    # via mkdocs-material
    # via mkdocstrings
    # via pymdown-extensions
markdown-it-py==3.0.0
    # via jupytext
    # via mdit-py-plugins
markupsafe==3.0.2
    # via jinja2
    # via mkdocs
    # via mkdocs-autorefs
    # via mkdocstrings
    # via nbconvert
matplotlib==3.9.3
    # via pymsaviz
matplotlib-inline==0.1.7
    # via ipykernel
    # via ipython
mdit-py-plugins==0.4.2
    # via jupytext
mdurl==0.1.2
    # via markdown-it-py
mergedeep==1.3.4
    # via mkdocs
    # via mkdocs-get-deps
mistune==3.0.2
    # via nbconvert
mkdocs==1.6.1
    # via mkdocs-autorefs
    # via mkdocs-jupyter
    # via mkdocs-material
    # via mkdocstrings
mkdocs-autorefs==1.2.0
    # via mkdocstrings
    # via mkdocstrings-python
mkdocs-get-deps==0.2.0
    # via mkdocs
mkdocs-jupyter==0.25.1
mkdocs-material==9.5.46
    # via mkdocs-jupyter
mkdocs-material-extensions==1.3.1
    # via mkdocs-material
mkdocstrings==0.27.0
    # via mkdocstrings-python
mkdocstrings-python==1.12.2
    # via mkdocstrings
mypy-extensions==1.0.0
    # via black
nbclient==0.10.1
    # via nbconvert
nbconvert==7.16.4
    # via mkdocs-jupyter
nbformat==5.10.4
    # via jupytext
    # via nbclient
    # via nbconvert
nest-asyncio==1.6.0
    # via ipykernel
nodeenv==1.9.1
    # via pre-commit
numpy==2.0.2
    # via biopython
    # via contourpy
    # via matplotlib
packaging==24.2
    # via black
    # via ipykernel
    # via jupytext
    # via matplotlib
    # via mkdocs
    # via nbconvert
    # via pytest
paginate==0.5.7
    # via mkdocs-material
pandocfilters==1.5.1
    # via nbconvert
parso==0.8.4
    # via jedi
pathspec==0.12.1
    # via black
    # via mkdocs
pexpect==4.9.0
    # via ipython
pillow==11.0.0
    # via matplotlib
platformdirs==4.3.6
    # via black
    # via jupyter-core
    # via mkdocs-get-deps
    # via mkdocstrings
    # via virtualenv
pluggy==1.5.0
    # via pytest
pre-commit==4.0.1
prompt-toolkit==3.0.48
    # via ipython
psutil==6.1.0
    # via ipykernel
ptyprocess==0.7.0
    # via pexpect
pure-eval==0.2.3
    # via stack-data
pygments==2.18.0
    # via ipython
    # via mkdocs-jupyter
    # via mkdocs-material
    # via nbconvert
pymdown-extensions==10.12
    # via mkdocs-material
    # via mkdocstrings
pyparsing==3.2.0
    # via matplotlib
pytest==8.3.3
    # via pytest-cov
pytest-cov==6.0.0
python-dateutil==2.9.0.post0
    # via ghp-import
    # via jupyter-client
    # via matplotlib
pyyaml==6.0.2
    # via jupytext
    # via mkdocs
    # via mkdocs-get-deps
    # via pre-commit
    # via pymdown-extensions
    # via pyyaml-env-tag
pyyaml-env-tag==0.1
    # via mkdocs
pyzmq==26.2.0
    # via ipykernel
    # via jupyter-client
referencing==0.35.1
    # via jsonschema
    # via jsonschema-specifications
regex==2024.11.6
    # via mkdocs-material
requests==2.32.3
    # via mkdocs-material
rpds-py==0.21.0
    # via jsonschema
    # via referencing
ruff==0.8.1
six==1.16.0
    # via python-dateutil
soupsieve==2.6
    # via beautifulsoup4
stack-data==0.6.3
    # via ipython
tinycss2==1.4.0
    # via nbconvert
tomli==2.2.1
    # via black
    # via coverage
    # via jupytext
    # via pytest
tornado==6.4.2
    # via ipykernel
    # via jupyter-client
traitlets==5.14.3
    # via comm
    # via ipykernel
    # via ipython
    # via jupyter-client
    # via jupyter-core
    # via matplotlib-inline
    # via nbclient
    # via nbconvert
    # via nbformat
typing-extensions==4.12.2
    # via black
    # via ipython
    # via mkdocstrings
urllib3==2.2.3
    # via requests
virtualenv==20.28.0
    # via pre-commit
watchdog==6.0.0
    # via mkdocs
wcwidth==0.2.13
    # via prompt-toolkit
webencodings==0.5.1
    # via bleach
    # via tinycss2
zipp==3.21.0
    # via importlib-metadata
    # via importlib-resources