Merge pull request #241 from vivarium-collective/python-3.12

Drop Python 3.9 support in favor of 3.12 and 3.13

.pylintrc

@@ -16,6 +16,7 @@ disable=raw-checker-failed,
         missing-function-docstring,
         missing-module-docstring,
 # Rules we ignore that are not ignored by default
+        too-many-positional-arguments,
         too-many-instance-attributes,
         too-many-return-statements,
         too-many-arguments,

CHANGELOG.md

@@ -1,5 +1,11 @@
 # Changelog
 
+## v1.6.5
+* (#241) Drop Python 3.9 support in favor of 3.12 and 3.13,
+bump required networkx to 3.4, fix issue with plot_topology
+on networkx 3.4+, and change default multiprocessing
+start method to safer ``forkserver`` method on Linux
+
 ## v1.6.4
 * (#240) fix Pint Quantity import error by using more recent version.
 

doc/conf.py

@@ -71,7 +71,7 @@
 #
 html_theme = 'sphinx_rtd_theme'
 html_theme_options = {
-    'display_version': True,
+    'version_selector': True,
 }
 
 # Add any paths that contain custom static files (such as style sheets) here,

doc/getting_started.rst

@@ -46,7 +46,7 @@ installed.
 Python 3
 --------
 
-Vivarium Core requires Python 3.9, 3.10, or 3.11.
+Vivarium Core requires Python 3.10, 3.11, 3.12, or 3.13.
 
 *Check Installation*
 
@@ -55,7 +55,7 @@ Vivarium Core requires Python 3.9, 3.10, or 3.11.
     $ python --version
     Python <version>
 
-Make sure you see a version starting with 3.9, 3.10, or 3.11.
+Make sure you see a version starting with 3.10, 3.11, 3.12, or 3.13.
 
 *Install*
 

doc/getting_started_dev.rst

@@ -53,7 +53,7 @@ installed.
 Python 3
 --------
 
-Vivarium Core requires Python 3.9, 3.10, or 3.11.
+Vivarium Core requires Python 3.10, 3.11, 3.12, or 3.13.
 
 *Check Installation*
 
@@ -62,7 +62,7 @@ Vivarium Core requires Python 3.9, 3.10, or 3.11.
     $ python --version
     Python <version>
 
-Make sure you see a version beginning with 3.9, 3.10, or 3.11.
+Make sure you see a version beginning with 3.10, 3.11, 3.12, or 3.13.
 
 *Install*
 

doc/requirements.txt

@@ -1,87 +1,105 @@
-alabaster==0.7.13
-asttokens==2.2.1
-attrs==23.1.0
-Babel==2.12.1
+alabaster==1.0.0
+astroid==3.3.5
+asttokens==3.0.0
+attrs==24.2.0
+babel==2.16.0
 backcall==0.2.0
-beautifulsoup4==4.12.2
-bleach==6.0.0
-certifi==2023.5.7
-charset-normalizer==3.1.0
-contourpy==1.1.0
-cycler==0.11.0
+beautifulsoup4==4.12.3
+bleach==6.2.0
+certifi==2024.8.30
+charset-normalizer==3.4.0
+contourpy==1.3.1
+coverage==7.6.8
+cycler==0.12.1
 decorator==5.1.1
 defusedxml==0.7.1
-dnspython==2.3.0
-docutils==0.18.1
-exceptiongroup==1.1.1
-executing==1.2.0
-fastjsonschema==2.17.1
-fonttools==4.40.0
-idna==3.4
+dill==0.3.9
+dnspython==2.7.0
+docutils==0.21.2
+executing==2.1.0
+fastjsonschema==2.21.0
+flexcache==0.3
+flexparser==0.4
+fonttools==4.55.0
+idna==3.10
 imagesize==1.4.1
-importlib-metadata==6.7.0
+importlib_metadata==8.5.0
 iniconfig==2.0.0
-ipython==8.14.0
-jedi==0.18.2
-Jinja2==3.1.2
-jsonschema==4.17.3
-jupyter_client==8.3.0
-jupyter_core==5.3.1
-jupyterlab-pygments==0.2.2
-kiwisolver==1.4.4
-MarkupSafe==2.1.3
-matplotlib==3.7.1
-matplotlib-inline==0.1.6
-mistune==3.0.1
-nbclient==0.8.0
-nbconvert==7.6.0
-nbformat==5.9.0
-nbsphinx==0.9.2
-networkx==3.1
-numpy==1.25.0
-orjson==3.9.1
-packaging==23.1
-pandocfilters==1.5.0
-parso==0.8.3
-pexpect==4.8.0
+ipython==8.30.0
+isort==5.13.2
+jedi==0.19.2
+Jinja2==3.1.4
+jsonschema==4.23.0
+jsonschema-specifications==2024.10.1
+jupyter_client==8.6.3
+jupyter_core==5.7.2
+jupyterlab_pygments==0.3.0
+kiwisolver==1.4.7
+lazy-object-proxy==1.10.0
+MarkupSafe==3.0.2
+matplotlib==3.9.3
+matplotlib-inline==0.1.7
+mccabe==0.7.0
+mistune==3.0.2
+mypy==1.13.0
+mypy-extensions==1.0.0
+nbclient==0.10.1
+nbconvert==7.16.4
+nbformat==5.10.4
+nbsphinx==0.9.5
+networkx==3.4.2
+numpy==2.1.3
+orjson==3.10.12
+packaging==24.2
+pandocfilters==1.5.1
+parso==0.8.4
+pexpect==4.9.0
 pickleshare==0.7.5
-Pillow==9.5.0
-Pint==0.22
-platformdirs==3.8.0
-pluggy==1.2.0
-prompt-toolkit==3.0.38
+pillow==11.0.0
+Pint==0.24.4
+platformdirs==4.3.6
+pluggy==1.5.0
+prompt_toolkit==3.0.48
 ptyprocess==0.7.0
-pure-eval==0.2.2
+pure_eval==0.2.3
 py==1.11.0
-Pygments==2.15.1
-pymongo==4.4.0
-pyparsing==3.1.0
-pyrsistent==0.19.3
-pytest==7.4.0
-python-dateutil==2.8.2
-pytz==2023.3
-pyzmq==25.1.0
-requests==2.31.0
-scipy==1.11.0
+Pygments==2.18.0
+pylint==3.3.2
+pymongo==4.10.1
+pyparsing==3.2.0
+pyrsistent==0.20.0
+pytest==8.3.4
+pytest-cov==6.0.0
+python-dateutil==2.9.0.post0
+pytz==2024.2
+pyzmq==26.2.0
+referencing==0.35.1
+requests==2.32.3
+rpds-py==0.21.0
+scipy==1.14.1
+setuptools==73.0.1
 six==1.16.0
 snowballstemmer==2.2.0
-soupsieve==2.4.1
-Sphinx==6.2.1
-sphinx-rtd-theme==1.2.2
-sphinxcontrib-applehelp==1.0.4
-sphinxcontrib-devhelp==1.0.2
-sphinxcontrib-htmlhelp==2.0.1
+soupsieve==2.6
+Sphinx==8.1.3
+sphinx-rtd-theme==3.0.2
+sphinxcontrib-applehelp==2.0.0
+sphinxcontrib-devhelp==2.0.0
+sphinxcontrib-htmlhelp==2.1.0
 sphinxcontrib-jquery==4.1
 sphinxcontrib-jsmath==1.0.1
-sphinxcontrib-qthelp==1.0.3
-sphinxcontrib-serializinghtml==1.1.5
-stack-data==0.6.2
-tinycss2==1.2.1
+sphinxcontrib-qthelp==2.0.0
+sphinxcontrib-serializinghtml==2.0.0
+stack-data==0.6.3
+tinycss2==1.4.0
 toml==0.10.2
-tornado==6.3.2
-traitlets==5.9.0
-typing_extensions==4.6.3
-urllib3==2.0.3
-wcwidth==0.2.6
+tomli==2.2.1
+tomlkit==0.13.2
+tornado==6.4.2
+traitlets==5.14.3
+typing_extensions==4.12.2
+urllib3==2.2.3
+wcwidth==0.2.13
 webencodings==0.5.1
-zipp==3.15.0
+wrapt==1.17.0
+zipp==3.21.0

doc/vale/styles/Vocab/All/vocab.txt

@@ -40,3 +40,6 @@ Skalnik
 Bioinformatics
 parallelization
 deserialized
+py
+func
+api