Merge pull request #147 from Roestlab/4c2bdependabot/pip/sphinx-rtd-t…

…heme-3.0.1

deps: bump sphinx-rtd-theme from 2.0.0 to 3.0.1

pyproject.toml

@@ -41,7 +41,7 @@ dependencies = [
 [project.optional-dependencies]
 
 conformer= [ 'onnxruntime' ]
-docs = [ 'nbsphinx', 'sphinx-copybutton', 'sphinx-rtd-theme', 'sphinx==5.3.0', 'ipykernel' ]
+docs = [ 'nbsphinx', 'sphinx-copybutton', 'sphinx-rtd-theme', 'sphinx', 'ipykernel' ]
 gui = [ 'streamlit>=1.30.0', 'streamlit-javascript', 'tk', 'pyautogui' ] 
 testing = ["pytest", "syrupy", "tables" ]
 

requirements.txt

@@ -1,10 +1,10 @@
 #
-# This file is autogenerated by pip-compile with Python 3.11
+# This file is autogenerated by pip-compile with Python 3.10
 # by the following command:
 #
 #    pip-compile --all-extras --output-file=requirements.txt
 #
-alabaster==0.7.16
+alabaster==1.0.0
     # via sphinx
 altair==5.4.1
     # via streamlit
@@ -18,7 +18,7 @@ babel==2.16.0
     # via sphinx
 beautifulsoup4==4.12.3
     # via nbconvert
-bleach==6.1.0
+bleach==6.2.0
     # via nbconvert
 blinker==1.8.2
     # via streamlit
@@ -50,11 +50,15 @@ decorator==5.1.1
     # via ipython
 defusedxml==0.7.1
     # via nbconvert
-docutils==0.19
+docutils==0.21.2
     # via
     #   nbsphinx
     #   sphinx
     #   sphinx-rtd-theme
+exceptiongroup==1.2.2
+    # via
+    #   ipython
+    #   pytest
 executing==2.1.0
     # via stack-data
 fastjsonschema==2.20.0
@@ -77,7 +81,7 @@ iniconfig==2.0.0
     # via pytest
 ipykernel==6.29.5
     # via massdash (pyproject.toml)
-ipython==8.28.0
+ipython==8.29.0
     # via ipykernel
 jedi==0.19.1
     # via ipython
@@ -114,7 +118,7 @@ kiwisolver==1.4.7
     # via matplotlib
 markdown-it-py==3.0.0
     # via rich
-markupsafe==3.0.0
+markupsafe==3.0.2
     # via
     #   jinja2
     #   nbconvert
@@ -137,7 +141,7 @@ mpmath==1.3.0
     # via sympy
 msgpack==1.1.0
     # via blosc2
-narwhals==1.9.1
+narwhals==1.13.2
     # via altair
 nbclient==0.10.0
     # via nbconvert
@@ -168,13 +172,12 @@ numpy==1.26.4
     #   numexpr
     #   onnxruntime
     #   pandas
-    #   pyarrow
     #   pydeck
     #   pyopenms
     #   scipy
     #   streamlit
     #   tables
-onnxruntime==1.19.2
+onnxruntime==1.20.0
     # via massdash (pyproject.toml)
 packaging==24.1
     # via
@@ -201,7 +204,7 @@ parso==0.8.4
     # via jedi
 pexpect==4.9.0
     # via ipython
-pillow==10.4.0
+pillow==11.0.0
     # via
     #   bokeh
     #   matplotlib
@@ -215,11 +218,11 @@ pluggy==1.5.0
     # via pytest
 prompt-toolkit==3.0.48
     # via ipython
-protobuf==5.28.2
+protobuf==5.28.3
     # via
     #   onnxruntime
     #   streamlit
-psutil==6.0.0
+psutil==6.1.0
     # via
     #   ipykernel
     #   massdash (pyproject.toml)
@@ -231,7 +234,7 @@ py-cpuinfo==9.0.0
     # via
     #   blosc2
     #   tables
-pyarrow==17.0.0
+pyarrow==18.0.0
     # via streamlit
 pyautogui==0.9.54
     # via massdash (pyproject.toml)
@@ -289,9 +292,9 @@ requests==2.32.3
     #   massdash (pyproject.toml)
     #   sphinx
     #   streamlit
-rich==13.9.2
+rich==13.9.4
     # via streamlit
-rpds-py==0.20.0
+rpds-py==0.21.0
     # via
     #   jsonschema
     #   referencing
@@ -300,15 +303,14 @@ scipy==1.14.1
 six==1.16.0
     # via
     #   asttokens
-    #   bleach
     #   python-dateutil
 smmap==5.0.1
     # via gitdb
 snowballstemmer==2.2.0
     # via sphinx
 soupsieve==2.6
     # via beautifulsoup4
-sphinx==5.3.0
+sphinx==8.1.3
     # via
     #   massdash (pyproject.toml)
     #   nbsphinx
@@ -317,7 +319,7 @@ sphinx==5.3.0
     #   sphinxcontrib-jquery
 sphinx-copybutton==0.5.2
     # via massdash (pyproject.toml)
-sphinx-rtd-theme==2.0.0
+sphinx-rtd-theme==3.0.1
     # via massdash (pyproject.toml)
 sphinxcontrib-applehelp==2.0.0
     # via sphinx
@@ -335,7 +337,7 @@ sphinxcontrib-serializinghtml==2.0.0
     # via sphinx
 stack-data==0.6.3
     # via ipython
-streamlit==1.39.0
+streamlit==1.40.0
     # via
     #   massdash (pyproject.toml)
     #   streamlit-javascript
@@ -351,19 +353,23 @@ tenacity==9.0.0
     # via
     #   plotly
     #   streamlit
-tinycss2==1.3.0
+tinycss2==1.4.0
     # via nbconvert
 tk==0.1.0
     # via massdash (pyproject.toml)
 toml==0.10.2
     # via streamlit
+tomli==2.0.2
+    # via
+    #   pytest
+    #   sphinx
 tornado==6.4.1
     # via
     #   bokeh
     #   ipykernel
     #   jupyter-client
     #   streamlit
-tqdm==4.66.5
+tqdm==4.67.0
     # via massdash (pyproject.toml)
 traitlets==5.14.3
     # via
@@ -382,6 +388,7 @@ typing-extensions==4.12.2
     #   altair
     #   bokeh
     #   ipython
+    #   rich
     #   streamlit
     #   tables
 tzdata==2024.2