requirements.txt

#
# This file is autogenerated by pip-compile with Python 3.12
# by the following command:
#
#    pip-compile --all-extras --output-file=requirements.txt
#
accessible-pygments==0.0.5
    # via pydata-sphinx-theme
alabaster==1.0.0
    # via sphinx
asttokens==3.0.1
    # via stack-data
attrs==25.4.0
    # via
    #   jsonschema
    #   referencing
babel==2.17.0
    # via
    #   pydata-sphinx-theme
    #   sphinx
beautifulsoup4==4.14.3
    # via
    #   nbconvert
    #   pydata-sphinx-theme
bleach[css]==6.3.0
    # via nbconvert
bokeh==3.6.0
    # via pyopenms_viz (pyproject.toml)
cairocffi==1.7.1
    # via cairosvg
cairosvg==2.8.2
    # via pyopenms_viz (pyproject.toml)
certifi==2026.1.4
    # via requests
cffi==2.0.0
    # via cairocffi
charset-normalizer==3.4.4
    # via requests
comm==0.2.3
    # via ipykernel
contourpy==1.3.2
    # via
    #   bokeh
    #   matplotlib
cssselect2==0.8.0
    # via cairosvg
cycler==0.12.1
    # via matplotlib
debugpy==1.8.20
    # via ipykernel
decorator==5.2.1
    # via ipython
defusedxml==0.7.1
    # via
    #   cairosvg
    #   nbconvert
docstring-parser==0.17.0
    # via pyopenms_viz (pyproject.toml)
docutils==0.21.2
    # via
    #   nbsphinx
    #   pydata-sphinx-theme
    #   sphinx
executing==2.2.1
    # via stack-data
fastjsonschema==2.21.2
    # via nbformat
fonttools==4.61.1
    # via matplotlib
idna==3.11
    # via requests
imagesize==1.4.1
    # via sphinx
iniconfig==2.3.0
    # via pytest
ipykernel==7.1.0
    # via pyopenms_viz (pyproject.toml)
ipython==8.38.0
    # via
    #   ipykernel
    #   pyopenms_viz (pyproject.toml)
ipython-pygments-lexers==1.1.1
    # via ipython
jedi==0.19.2
    # via ipython
jinja2==3.1.6
    # via
    #   bokeh
    #   nbconvert
    #   nbsphinx
    #   sphinx
jsonschema==4.26.0
    # via nbformat
jsonschema-specifications==2025.9.1
    # via jsonschema
jupyter-client==8.8.0
    # via
    #   ipykernel
    #   nbclient
jupyter-core==5.9.1
    # via
    #   ipykernel
    #   jupyter-client
    #   nbclient
    #   nbconvert
    #   nbformat
jupyterlab-pygments==0.3.0
    # via nbconvert
kiwisolver==1.4.9
    # via matplotlib
markupsafe==3.0.3
    # via
    #   jinja2
    #   nbconvert
matplotlib==3.10.8
    # via pyopenms_viz (pyproject.toml)
matplotlib-inline==0.2.1
    # via
    #   ipykernel
    #   ipython
mistune==3.2.0
    # via nbconvert
narwhals==2.13.0
    # via
    #   bokeh
    #   plotly
nbclient==0.10.4
    # via nbconvert
nbconvert==7.16.6
    # via nbsphinx
nbformat==5.10.4
    # via
    #   nbclient
    #   nbconvert
    #   nbsphinx
nbsphinx==0.9.8
    # via pyopenms_viz (pyproject.toml)
nest-asyncio==1.6.0
    # via ipykernel
numpy==2.2.6
    # via
    #   bokeh
    #   contourpy
    #   matplotlib
    #   pandas
    #   pymzml
    #   rdkit
packaging==25.0
    # via
    #   bokeh
    #   ipykernel
    #   matplotlib
    #   nbconvert
    #   plotly
    #   pytest
    #   sphinx
pandas==2.3.3
    # via
    #   bokeh
    #   pyopenms_viz (pyproject.toml)
pandocfilters==1.5.1
    # via nbconvert
parso==0.8.5
    # via jedi
pexpect==4.9.0
    # via ipython
pillow==12.1.0
    # via
    #   bokeh
    #   cairosvg
    #   matplotlib
    #   rdkit
    #   sphinx-gallery
platformdirs==4.5.1
    # via jupyter-core
plotly==5.24.1
    # via pyopenms_viz (pyproject.toml)
pluggy==1.6.0
    # via pytest
prompt-toolkit==3.0.52
    # via ipython
psutil==7.2.2
    # via ipykernel
ptyprocess==0.7.0
    # via pexpect
pure-eval==0.2.3
    # via stack-data
pycparser==3.0
    # via cffi
pydata-sphinx-theme==0.16.1
    # via pyopenms_viz (pyproject.toml)
pygments==2.19.2
    # via
    #   accessible-pygments
    #   ipython
    #   ipython-pygments-lexers
    #   nbconvert
    #   pydata-sphinx-theme
    #   pytest
    #   sphinx
pymzml==2.6.0
    # via pyopenms_viz (pyproject.toml)
pyparsing==3.3.2
    # via matplotlib
pytest==9.0.2
    # via
    #   pyopenms_viz (pyproject.toml)
    #   syrupy
python-dateutil==2.9.0.post0
    # via
    #   jupyter-client
    #   matplotlib
    #   pandas
pytz==2025.2
    # via pandas
pyyaml==6.0.3
    # via bokeh
pyzmq==27.1.0
    # via
    #   ipykernel
    #   jupyter-client
rdkit==2025.9.3
    # via pyopenms_viz (pyproject.toml)
referencing==0.37.0
    # via
    #   jsonschema
    #   jsonschema-specifications
regex==2026.1.15
    # via pymzml
requests==2.32.5
    # via sphinx
roman-numerals==4.1.0
    # via sphinx
rpds-py==0.30.0
    # via
    #   jsonschema
    #   referencing
six==1.17.0
    # via python-dateutil
snowballstemmer==3.0.1
    # via sphinx
soupsieve==2.8.3
    # via beautifulsoup4
sphinx==9.0.4
    # via
    #   nbsphinx
    #   pydata-sphinx-theme
    #   pyopenms_viz (pyproject.toml)
    #   sphinx-copybutton
    #   sphinx-gallery
sphinx-copybutton==0.5.2
    # via pyopenms_viz (pyproject.toml)
sphinx-gallery==0.20.0
    # via pyopenms_viz (pyproject.toml)
sphinxcontrib-applehelp==2.0.0
    # via sphinx
sphinxcontrib-devhelp==2.0.0
    # via sphinx
sphinxcontrib-htmlhelp==2.1.0
    # via sphinx
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
syrupy==5.0.0
    # via pyopenms_viz (pyproject.toml)
tinycss2==1.4.0
    # via
    #   bleach
    #   cairosvg
    #   cssselect2
tornado==6.5.4
    # via
    #   bokeh
    #   ipykernel
    #   jupyter-client
traitlets==5.14.3
    # via
    #   ipykernel
    #   ipython
    #   jupyter-client
    #   jupyter-core
    #   matplotlib-inline
    #   nbclient
    #   nbconvert
    #   nbformat
    #   nbsphinx
typing-extensions==4.15.0
    # via
    #   beautifulsoup4
    #   pydata-sphinx-theme
    #   referencing
tzdata==2025.3
    # via pandas
urllib3==2.6.3
    # via requests
wcwidth==0.5.0
    # via prompt-toolkit
webencodings==0.5.1
    # via
    #   bleach
    #   cssselect2
    #   tinycss2
xyzservices==2025.11.0
    # via bokeh