Merge branch 'main' into dependabot/pip/rdkit-2025.9.3

Author: jcharkow

.github/dependabot.yml

@@ -1,15 +1,25 @@
 version: 2
+
 updates:
   - package-ecosystem: "pip"
     directory: "/"
     schedule:
       interval: "weekly"
+
     commit-message:
       prefix: "deps"
-    open-pull-requests-limit: 10
+
+    open-pull-requests-limit: 5
+
     allow:
       - dependency-type: "all"
 
+    # --------------------------------------------------
+    # Explicit ignores to avoid unsatisfiable resolutions
+    # --------------------------------------------------
+    ignore:
+      - dependency-name: "tinycss2"
+
     groups:
       # ===============================
       # ABI / compiled scientific stack
@@ -143,7 +153,6 @@ updates:
           - "pygments"
           - "mistune"
           - "pandocfilters"
-          - "tinycss2"
           - "cssselect2"
 
       # ===============================

docs/requirements.txt

@@ -8,7 +8,7 @@ accessible-pygments==0.0.5
     # via pydata-sphinx-theme
 alabaster==1.0.0
     # via sphinx
-asttokens==3.0.0
+asttokens==3.0.1
     # via stack-data
 attrs==25.4.0
     # via
@@ -22,17 +22,17 @@ beautifulsoup4==4.14.3
     # via
     #   nbconvert
     #   pydata-sphinx-theme
-bleach[css]==6.2.0
+bleach[css]==6.3.0
     # via nbconvert
 bokeh==3.6.2
     # via pyopenms_viz (pyproject.toml)
 cairocffi==1.7.1
     # via cairosvg
-cairosvg==2.7.1
+cairosvg==2.8.2
     # via pyopenms_viz (pyproject.toml)
 certifi==2026.1.4
     # via requests
-cffi==1.17.1
+cffi==2.0.0
     # via cairocffi
 charset-normalizer==3.4.4
     # via requests
@@ -61,7 +61,7 @@ docutils==0.21.2
     #   nbsphinx
     #   pydata-sphinx-theme
     #   sphinx
-executing==2.1.0
+executing==2.2.1
     # via stack-data
 fastjsonschema==2.21.2
     # via nbformat
@@ -71,7 +71,7 @@ idna==3.11
     # via requests
 imagesize==1.4.1
     # via sphinx
-iniconfig==2.0.0
+iniconfig==2.3.0
     # via pytest
 ipykernel==7.1.0
     # via pyopenms_viz (pyproject.toml)
@@ -87,7 +87,7 @@ jinja2==3.1.6
     #   nbconvert
     #   nbsphinx
     #   sphinx
-jsonschema==4.23.0
+jsonschema==4.26.0
     # via nbformat
 jsonschema-specifications==2025.9.1
     # via jsonschema
@@ -116,7 +116,7 @@ matplotlib-inline==0.2.1
     # via
     #   ipykernel
     #   ipython
-mistune==3.1.0
+mistune==3.2.0
     # via nbconvert
 nbclient==0.10.4
     # via nbconvert
@@ -158,7 +158,7 @@ parso==0.8.5
     # via jedi
 pexpect==4.9.0
     # via ipython
-pillow==11.1.0
+pillow==12.1.0
     # via
     #   bokeh
     #   cairosvg
@@ -169,7 +169,7 @@ platformdirs==4.5.1
     # via jupyter-core
 plotly==5.24.1
     # via pyopenms_viz (pyproject.toml)
-pluggy==1.5.0
+pluggy==1.6.0
     # via pytest
 prompt-toolkit==3.0.52
     # via ipython
@@ -179,7 +179,7 @@ ptyprocess==0.7.0
     # via pexpect
 pure-eval==0.2.3
     # via stack-data
-pycparser==2.23
+pycparser==3.0
     # via cffi
 pydata-sphinx-theme==0.16.1
     # via pyopenms_viz (pyproject.toml)
@@ -192,9 +192,9 @@ pygments==2.19.2
     #   sphinx
 pymzml==2.6.0
     # via pyopenms_viz (pyproject.toml)
-pyparsing==3.3.1
+pyparsing==3.3.2
     # via matplotlib
-pytest==8.3.4
+pytest==9.0.2
     # via
     #   pyopenms_viz (pyproject.toml)
     #   syrupy
@@ -217,7 +217,7 @@ referencing==0.37.0
     # via
     #   jsonschema
     #   jsonschema-specifications
-regex==2024.11.6
+regex==2026.1.15
     # via pymzml
 requests==2.32.5
     # via sphinx
@@ -229,7 +229,7 @@ six==1.17.0
     # via python-dateutil
 snowballstemmer==3.0.1
     # via sphinx
-soupsieve==2.8.1
+soupsieve==2.8.3
     # via beautifulsoup4
 sphinx==8.1.3
     # via
@@ -256,9 +256,9 @@ sphinxcontrib-serializinghtml==2.0.0
     # via sphinx
 stack-data==0.6.3
     # via ipython
-syrupy==4.8.0
+syrupy==5.0.0
     # via pyopenms_viz (pyproject.toml)
-tenacity==9.0.0
+tenacity==9.1.2
     # via plotly
 tinycss2==1.4.0
     # via

pyopenms_viz/__init__.py

@@ -11,7 +11,7 @@
 from pathlib import Path
 from ._core import plot_chromatogram, plot_spectrum, plot_mobilogram, plot_peakmap
 
-__version__ = "1.0.0"
+__version__ = "1.0.1"
 
 
 def TEST_DATA_PATH():

pyproject.toml

@@ -7,7 +7,7 @@ name = "pyopenms_viz"
 authors = [
     {name = "OpenMS Team", email = "webmaster@openms.de"},
 ]
-version = "1.0.0"
+version = "1.0.1"
 description = "A package for visualizing mass spectrometry data using pandas dataframes"
 readme = "README.md"
 classifiers = [

requirements.txt

@@ -89,7 +89,7 @@ jinja2==3.1.6
     #   nbconvert
     #   nbsphinx
     #   sphinx
-jsonschema==4.25.1
+jsonschema==4.26.0
     # via nbformat
 jsonschema-specifications==2025.9.1
     # via jsonschema
@@ -118,7 +118,7 @@ matplotlib-inline==0.2.1
     # via
     #   ipykernel
     #   ipython
-mistune==3.1.4
+mistune==3.2.0
     # via nbconvert
 narwhals==2.13.0
     # via
@@ -164,7 +164,7 @@ parso==0.8.5
     # via jedi
 pexpect==4.9.0
     # via ipython
-pillow==12.0.0
+pillow==12.1.0
     # via
     #   bokeh
     #   cairosvg
@@ -185,7 +185,7 @@ ptyprocess==0.7.0
     # via pexpect
 pure-eval==0.2.3
     # via stack-data
-pycparser==2.23
+pycparser==3.0
     # via cffi
 pydata-sphinx-theme==0.16.1
     # via pyopenms_viz (pyproject.toml)
@@ -200,7 +200,7 @@ pygments==2.19.2
     #   sphinx
 pymzml==2.6.0
     # via pyopenms_viz (pyproject.toml)
-pyparsing==3.3.1
+pyparsing==3.3.2
     # via matplotlib
 pytest==9.0.2
     # via
@@ -225,7 +225,7 @@ referencing==0.37.0
     # via
     #   jsonschema
     #   jsonschema-specifications
-regex==2025.11.3
+regex==2026.1.15
     # via pymzml
 requests==2.32.5
     # via sphinx
@@ -239,7 +239,7 @@ six==1.17.0
     # via python-dateutil
 snowballstemmer==3.0.1
     # via sphinx
-soupsieve==2.8.1
+soupsieve==2.8.3
     # via beautifulsoup4
 sphinx==9.0.4
     # via