Add Python 3.13 support (#124)

* Add Python 3.13 to GHA pytest-with-coverage matrix

Include Python 3.13 in the GitHub Actions workflow for pytest with coverage.
This ensures compatibility and testing for the latest Python version.

* Change to Python 3.13 for development

Update Python version to 3.13 in development and documentation environments, and
revise documentation to reflect Python 3.11 as the minimum supported version.
Bump various package versions across requirements and configuration files to
their latest stable releases.

* Update breaking changes doc for version 25.1

Document the incompatibility of version 25.1 with earlier versions, in
particular, the new minimum Python version requirement (3.11) and the use of
Python 3.13 for development.

.github/workflows/pytest-with-coverage.yaml

@@ -15,7 +15,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [ '3.11', '3.12' ]
+        python-version: [ '3.11', '3.12', '3.13' ]
     uses: UBC-MOAD/gha-workflows/.github/workflows/pytest-with-coverage.yaml@main
     with:
       python-version: ${{ matrix.python-version }}

SalishSeaTools/docs/pkg_development.rst

@@ -16,26 +16,25 @@
 
 .. _SalishSeaToolsPackageDevelopment:
 
-*****************************************
-:kbd:`SalishSeaTools` Package Development
-*****************************************
+********************************************
+:py:obj:`SalishSeaTools` Package Development
+********************************************
 
 .. _SalishSeaToolsPythonVersions:
 
 Python Versions
 ===============
 
-The :kbd:`SalishSeaTools` package is developed and tested using `Python`_ 3.9.
-The package uses some Python language features that are not available in versions prior to 3.6,
-in particular:
+.. image:: https://img.shields.io/python/required-version-toml?tomlFilePath=https://raw.githubusercontent.com/SalishSeaCast/SalishSeaCmd/main/pyproject.toml&logo=Python&logoColor=gold&label=Python
+    :target: https://docs.python.org/3
+    :alt: Python Version from PEP 621 TOML
 
-* `formatted string literals`_
-  (aka *f-strings*)
-* the `file system path protocol`_
+The :py:obj:`SalishSeaTools` package is developed using `Python`_ 3.13.
+The minimum supported Python version is 3.11.
+The :ref:`SalishSeaToolsContinuousIntegration` workflow on GitHub ensures that the package
+is tested for all versions of Python>=3.11.
 
 .. _Python: https://www.python.org/
-.. _formatted string literals: https://docs.python.org/3/reference/lexical_analysis.html#f-strings
-.. _file system path protocol: https://docs.python.org/3/whatsnew/3.6.html#whatsnew36-pep519
 
 
 .. _SalishSeaToolsGettingTheCode:

SalishSeaTools/envs/environment-dev.yaml

@@ -36,7 +36,7 @@ dependencies:
   - openpyxl
   - pandas
   - pip
-  - python=3.12
+  - python=3.13
   - pytz
   - python-dateutil
   - pyyaml

SalishSeaTools/envs/requirements.txt

@@ -9,7 +9,7 @@
 
 alabaster==1.0.0
 angles==2.0
-anyio==4.7.0
+anyio==4.8.0
 argon2-cffi==23.1.0
 argon2-cffi-bindings==21.2.0
 arrow==1.3.0
@@ -29,7 +29,7 @@ certifi==2024.12.14
 cffi==1.17.1
 cfgv==3.3.1
 cftime==1.6.4
-charset-normalizer==3.4.0
+charset-normalizer==3.4.1
 click==8.1.8
 cliff==4.8.0
 cmd2==2.5.8
@@ -68,11 +68,11 @@ httpcore==1.0.7
 httpx==0.28.1
 hyperframe==6.0.1
 hyperlink==21.0.0
-identify==2.6.4
+identify==2.6.5
 idna==3.10
 imagesize==1.4.1
 importlib_metadata==8.5.0
-importlib_resources==6.4.5
+importlib_resources==6.5.2
 iniconfig==2.0.0
 ipdb==0.13.13
 ipykernel==6.29.5
@@ -92,7 +92,7 @@ jupyter_client==8.6.3
 jupyter_core==5.7.2
 jupyter-events==0.11.0
 jupyter-lsp==2.2.5
-jupyter_server==2.14.2
+jupyter_server==2.15.0
 jupyter_server_terminals==0.5.3
 jupyterlab==4.3.4
 jupyterlab_pygments==0.3.0
@@ -105,12 +105,12 @@ MarkupSafe==3.0.2
 matplotlib==3.10.0
 matplotlib-inline==0.1.7
 mdurl==0.1.2
-mistune==3.0.2
+mistune==3.1.0
 more-itertools==10.5.0
 munkres==1.1.4
 mypy_extensions==1.0.0
-nbclient==0.10.1
-nbconvert==7.16.4
+nbclient==0.10.2
+nbconvert==7.16.5
 nbformat==5.10.4
 nbsphinx==0.9.5
 nest_asyncio==1.6.0
@@ -128,7 +128,7 @@ pathspec==0.12.1
 pbr==6.1.0
 pexpect==4.9.0
 pickleshare==0.7.5
-pillow==11.0.0
+pillow==11.1.0
 pip==24.3.1
 pkgutil_resolve_name==1.3.10
 platformdirs==4.3.6
@@ -137,12 +137,12 @@ pre_commit==4.0.1
 prettytable==3.12.0
 prometheus_client==0.21.1
 prompt_toolkit==3.0.48
-psutil==6.1.0
+psutil==6.1.1
 ptyprocess==0.7.0
 pure_eval==0.2.3
 pycparser==2.22
-Pygments==2.18.0
-pyparsing==3.2.0
+Pygments==2.19.1
+pyparsing==3.2.1
 pyperclip==1.9.0
 PySide6==6.8.1
 PySocks==1.7.1
@@ -161,7 +161,7 @@ rfc3339_validator==0.1.4
 rfc3986-validator==0.1.1
 rich==13.9.4
 rpds-py==0.22.3
-SalishSeaTools==24.1.dev0
+SalishSeaTools==25.1.dev0
 scipy==1.15.0
 SecretStorage==3.3.3
 Send2Trash==1.8.3
@@ -198,16 +198,14 @@ typing_extensions==4.12.2
 typing_utils==0.1.0
 tzdata==2024.2
 ukkonen==1.0.1
-unicodedata2==15.1.0
 uri-template==1.3.0
-urllib3==2.2.3
+urllib3==2.3.0
 userpath==1.9.2
 virtualenv==20.28.1
 wcwidth==0.2.13
 webcolors==24.11.1
 webencodings==0.5.1
 websocket-client==1.8.0
-wheel==0.45.1
-xarray==2025.1.0
+xarray==2025.1.1
 zipp==3.21.0
 zstandard==0.23.0

docs/breaking_changes.rst

@@ -22,6 +22,18 @@
 Changes That Break Backward Compatibility
 *****************************************
 
+.. _BreakingChangesVersion25.1:
+
+Version 25.1 (unreleased)
+=========================
+
+The following changes that were introduced in version 25.1 of the ``tools`` repository
+are incompatible with earlier versions:
+
+* The minimum supported version of Python is 3.11.
+  Development of the :py:obj:`SalishSeaTools` package is done using Python 3.13.
+
+
 .. _BreakingChangesVersion24.1:
 
 Version 24.1 (2025-01-09)

environment-rtd.yaml

@@ -12,7 +12,7 @@ dependencies:
   - jupyter
   - matplotlib
   - pip
-  - python=3.12
+  - python=3.13
 
   # Sphinx and extensions we use
   - nbsphinx==0.9.5