update requirements

Author: poshul

requirements.txt

@@ -1,5 +1,5 @@
 #
-# This file is autogenerated by pip-compile with Python 3.12
+# This file is autogenerated by pip-compile with Python 3.13
 # by the following command:
 #
 #    pip-compile --all-extras --output-file=requirements.txt
@@ -8,99 +8,145 @@ accessible-pygments==0.0.5
     # via pydata-sphinx-theme
 alabaster==1.0.0
     # via sphinx
-attrs==24.3.0
+asttokens==3.0.0
+    # via stack-data
+attrs==25.3.0
     # via
     #   jsonschema
     #   referencing
-babel==2.16.0
+babel==2.17.0
     # via
     #   pydata-sphinx-theme
     #   sphinx
-beautifulsoup4==4.12.3
+beautifulsoup4==4.13.4
     # via
     #   nbconvert
     #   pydata-sphinx-theme
-bleach==6.2.0
+bleach[css]==6.2.0
     # via nbconvert
-bokeh==3.6.0
+bokeh==3.7.3
     # via pyopenms_viz (pyproject.toml)
-certifi==2024.12.14
+cairocffi==1.7.1
+    # via cairosvg
+cairosvg==2.8.2
+    # via pyopenms_viz (pyproject.toml)
+certifi==2025.8.3
     # via requests
-charset-normalizer==3.4.0
+cffi==1.17.1
+    # via cairocffi
+charset-normalizer==3.4.3
     # via requests
-contourpy==1.3.0
+comm==0.2.3
+    # via ipykernel
+contourpy==1.3.3
     # via
     #   bokeh
     #   matplotlib
+cssselect2==0.8.0
+    # via cairosvg
 cycler==0.12.1
     # via matplotlib
+debugpy==1.8.16
+    # via ipykernel
+decorator==5.2.1
+    # via ipython
 defusedxml==0.7.1
-    # via nbconvert
+    # via
+    #   cairosvg
+    #   nbconvert
 docutils==0.21.2
     # via
     #   nbsphinx
     #   pydata-sphinx-theme
     #   sphinx
+executing==2.2.0
+    # via stack-data
 fastjsonschema==2.21.1
     # via nbformat
-fonttools==4.54.1
+fonttools==4.59.0
     # via matplotlib
 idna==3.10
     # via requests
 imagesize==1.4.1
     # via sphinx
-iniconfig==2.0.0
+iniconfig==2.1.0
     # via pytest
-jinja2==3.1.4
+ipykernel==6.30.1
+    # via pyopenms_viz (pyproject.toml)
+ipython==9.4.0
+    # 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==4.23.0
+jsonschema==4.25.0
     # via nbformat
-jsonschema-specifications==2024.10.1
+jsonschema-specifications==2025.4.1
     # via jsonschema
 jupyter-client==8.6.3
-    # via nbclient
-jupyter-core==5.7.2
     # via
+    #   ipykernel
+    #   nbclient
+jupyter-core==5.8.1
+    # via
+    #   ipykernel
     #   jupyter-client
     #   nbclient
     #   nbconvert
     #   nbformat
 jupyterlab-pygments==0.3.0
     # via nbconvert
-kiwisolver==1.4.7
+kiwisolver==1.4.9
     # via matplotlib
 markupsafe==3.0.2
     # via
     #   jinja2
     #   nbconvert
-matplotlib==3.9.2
+matplotlib==3.10.5
     # via pyopenms_viz (pyproject.toml)
-mistune==3.1.0
+matplotlib-inline==0.1.7
+    # via
+    #   ipykernel
+    #   ipython
+mistune==3.1.3
     # via nbconvert
+narwhals==2.0.1
+    # via
+    #   bokeh
+    #   plotly
 nbclient==0.10.2
     # via nbconvert
-nbconvert==7.16.4
+nbconvert==7.16.6
     # via nbsphinx
 nbformat==5.10.4
     # via
     #   nbclient
     #   nbconvert
     #   nbsphinx
-nbsphinx==0.9.6
+nbsphinx==0.9.7
     # via pyopenms_viz (pyproject.toml)
+nest-asyncio==1.6.0
+    # via ipykernel
 numpy==2.1.2
     # via
     #   bokeh
     #   contourpy
     #   matplotlib
     #   pandas
-packaging==24.1
+    #   pymzml
+    #   rdkit
+packaging==25.0
     # via
     #   bokeh
+    #   ipykernel
     #   matplotlib
     #   nbconvert
     #   plotly
@@ -112,28 +158,49 @@ pandas==2.2.3
     #   pyopenms_viz (pyproject.toml)
 pandocfilters==1.5.1
     # via nbconvert
-pillow==11.0.0
+parso==0.8.4
+    # via jedi
+pexpect==4.9.0
+    # via ipython
+pillow==11.3.0
     # via
     #   bokeh
+    #   cairosvg
     #   matplotlib
+    #   rdkit
     #   sphinx-gallery
-platformdirs==4.3.6
+platformdirs==4.3.8
     # via jupyter-core
-plotly==5.24.1
+plotly==6.2.0
     # via pyopenms_viz (pyproject.toml)
-pluggy==1.5.0
+pluggy==1.6.0
     # via pytest
+prompt-toolkit==3.0.51
+    # via ipython
+psutil==7.0.0
+    # via ipykernel
+ptyprocess==0.7.0
+    # via pexpect
+pure-eval==0.2.3
+    # via stack-data
+pycparser==2.22
+    # via cffi
 pydata-sphinx-theme==0.16.1
     # via pyopenms_viz (pyproject.toml)
-pygments==2.18.0
+pygments==2.19.2
     # via
     #   accessible-pygments
+    #   ipython
+    #   ipython-pygments-lexers
     #   nbconvert
     #   pydata-sphinx-theme
+    #   pytest
     #   sphinx
-pyparsing==3.2.0
+pymzml==2.5.11
+    # via pyopenms_viz (pyproject.toml)
+pyparsing==3.2.3
     # via matplotlib
-pytest==8.3.3
+pytest==8.4.1
     # via
     #   pyopenms_viz (pyproject.toml)
     #   syrupy
@@ -146,23 +213,29 @@ pytz==2024.2
     # via pandas
 pyyaml==6.0.2
     # via bokeh
-pyzmq==26.2.0
-    # via jupyter-client
-referencing==0.35.1
+pyzmq==27.0.1
+    # via
+    #   ipykernel
+    #   jupyter-client
+rdkit==2025.3.5
+    # via pyopenms_viz (pyproject.toml)
+referencing==0.36.2
     # via
     #   jsonschema
     #   jsonschema-specifications
-requests==2.32.3
+regex==2025.7.34
+    # via pymzml
+requests==2.32.4
     # via sphinx
-rpds-py==0.22.3
+rpds-py==0.27.0
     # via
     #   jsonschema
     #   referencing
 six==1.16.0
     # via python-dateutil
-snowballstemmer==2.2.0
+snowballstemmer==3.0.1
     # via sphinx
-soupsieve==2.6
+soupsieve==2.7
     # via beautifulsoup4
 sphinx==8.1.3
     # via
@@ -173,7 +246,7 @@ sphinx==8.1.3
     #   sphinx-gallery
 sphinx-copybutton==0.5.2
     # via pyopenms_viz (pyproject.toml)
-sphinx-gallery==0.18.0
+sphinx-gallery==0.19.0
     # via pyopenms_viz (pyproject.toml)
 sphinxcontrib-applehelp==2.0.0
     # via sphinx
@@ -187,37 +260,45 @@ sphinxcontrib-qthelp==2.0.0
     # via sphinx
 sphinxcontrib-serializinghtml==2.0.0
     # via sphinx
-syrupy==4.7.2
+stack-data==0.6.3
+    # via ipython
+syrupy==4.9.1
     # via pyopenms_viz (pyproject.toml)
-tenacity==9.0.0
-    # via plotly
 tinycss2==1.4.0
-    # via nbconvert
-tornado==6.4.2
+    # via
+    #   bleach
+    #   cairosvg
+    #   cssselect2
+tornado==6.5.2
     # via
     #   bokeh
+    #   ipykernel
     #   jupyter-client
 traitlets==5.14.3
     # via
+    #   ipykernel
+    #   ipython
     #   jupyter-client
     #   jupyter-core
+    #   matplotlib-inline
     #   nbclient
     #   nbconvert
     #   nbformat
     #   nbsphinx
-typing-extensions==4.12.2
-    # via pydata-sphinx-theme
+typing-extensions==4.14.1
+    # via
+    #   beautifulsoup4
+    #   pydata-sphinx-theme
 tzdata==2024.2
     # via pandas
-urllib3==2.2.3
+urllib3==2.5.0
     # via requests
+wcwidth==0.2.13
+    # via prompt-toolkit
 webencodings==0.5.1
     # via
     #   bleach
+    #   cssselect2
     #   tinycss2
-xyzservices==2024.9.0
+xyzservices==2025.4.0
     # via bokeh
-
-# pyopenms-viz
-git+https://github.com/OpenMS/pyopenms_viz.git
-