Update to Python 3.12 (#49)

* Add Python 3.12 to GHA pytest-with-coverage workflow

This lets us use the workflow to test whether all the packages NEMO-Cmd depends
on have been updated to support Python 3.12.

* Add workflow_dispatch trigger to GHA CI workflow

Enables workflow to be triggered from GitHub CLI, browser, or via API.

This is primarily to allow the workflow to be run via
    gh workflow run pytest-with-coverage --ref py312
during the conda-forge Python 3.12 migration to test if the environment is
solvable yet.

* Update pkgs & versions used in recent dev env

* pre-commit autoupdate

* Change dev, hpc & rtd envs to Python 3.12

* Drop TROVE classifiers

They are now just outdated maintenance overhead.

* Change sphinx-linkcheck workflow to Python 3.12

The Python version used in the 'sphinx-linkcheck.yaml' GitHub actions
workflow has been updated from '3.11' to '3.12'. This change aligns with the
recent migration to Python 3.12 for development.

* Change to Python 3.12 for development

* Drop support for Python 3.10

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

@@ -3,6 +3,9 @@ name: pytest-with-coverage
 on:
   push:
     branches: [ '*' ]
+  # Enable workflow to be triggered from GitHub CLI, browser, or via API
+  # primarily for testing conda env solution for new Python versions
+  workflow_dispatch:
 
 jobs:
   pytest-with-coverage:
@@ -12,7 +15,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [ '3.10', '3.11' ]
+        python-version: [ '3.11', '3.12' ]
     uses: UBC-MOAD/gha-workflows/.github/workflows/pytest-with-coverage.yaml@main
     with:
       python-version: ${{ matrix.python-version }}

.github/workflows/sphinx-linkcheck.yaml

@@ -15,7 +15,7 @@ jobs:
       matrix:
         # Need to specify Python version here because we use test env which gets its
         # Python version via matrix
-        python-version: [ '3.11' ]
+        python-version: [ '3.12' ]
     uses: UBC-MOAD/gha-workflows/.github/workflows/sphinx-linkcheck.yaml@main
     with:
       python-version: ${{ matrix.python-version }}

.pre-commit-config.yaml

@@ -16,6 +16,6 @@ repos:
       - id: check-added-large-files
   # Code formatting with black
   - repo: https://github.com/psf/black
-    rev: 23.10.1
+    rev: 23.11.0
     hooks:
       - id: black

README.rst

@@ -5,8 +5,8 @@ SalishSeaCast NEMO Command Processor
 .. image:: https://img.shields.io/badge/license-Apache%202-cb2533.svg
     :target: https://www.apache.org/licenses/LICENSE-2.0
     :alt: Licensed under the Apache License, Version 2.0
-.. image:: https://img.shields.io/badge/Python-3.10%20%7C%203.11-blue?logo=python&label=Python&logoColor=gold
-    :target: https://docs.python.org/3.11/
+.. image:: https://img.shields.io/badge/Python-3.11%20%7C%203.12-blue?logo=python&label=Python&logoColor=gold
+    :target: https://docs.python.org/3.12/
     :alt: Python Version
 .. image:: https://img.shields.io/badge/version%20control-git-blue.svg?logo=github
     :target: https://github.com/SalishSeaCast/SalishSeaCmd

docs/breaking_changes.rst

@@ -22,6 +22,18 @@
 ``SalishSeaCmd`` Changes That Break Backward Compatibility
 *************************************************************
 
+.. _BreakingChangesVersion23.1:
+
+Version 23.1
+============
+
+The following change that was introduced in version 23.1 of the ``SalishSeaCmd``
+package is incompatible with earlier versions:
+
+* Drop support for Python 3.10.
+  Minimum supported Python version is now 3.11.
+
+
 .. _BreakingChangesVersion22.3:
 
 Version 22.3

docs/development.rst

@@ -25,8 +25,8 @@
 .. image:: https://img.shields.io/badge/license-Apache%202-cb2533.svg
     :target: https://www.apache.org/licenses/LICENSE-2.0
     :alt: Licensed under the Apache License, Version 2.0
-.. image:: https://img.shields.io/badge/Python-3.10%20%7C%203.11-blue?logo=python&label=Python&logoColor=gold
-    :target: https://docs.python.org/3.11/
+.. image:: https://img.shields.io/badge/Python-3.11%20%7C%203.12-blue?logo=python&label=Python&logoColor=gold
+    :target: https://docs.python.org/3.12/
     :alt: Python Version
 .. image:: https://img.shields.io/badge/version%20control-git-blue.svg?logo=github
     :target: https://github.com/SalishSeaCast/SalishSeaCmd
@@ -65,14 +65,14 @@
 Python Versions
 ===============
 
-.. image:: https://img.shields.io/badge/Python-3.10%20%7C%203.11-blue?logo=python&label=Python&logoColor=gold
-    :target: https://docs.python.org/3.11/
+.. image:: https://img.shields.io/badge/Python-3.11%20%7C%203.12-blue?logo=python&label=Python&logoColor=gold
+    :target: https://docs.python.org/3.12/
     :alt: Python Version
 
-The :kbd:`SalishSeaCmd` package is developed using `Python`_ 3.11.
-The minimum supported Python version is 3.10.
+The :kbd:`SalishSeaCmd` package is developed using `Python`_ 3.12.
+The minimum supported Python version is 3.11.
 The :ref:`SalishSeaCmdContinuousIntegration` workflow on GitHub ensures that the package
-is tested for all versions of Python>=3.10.
+is tested for all versions of Python>=3.11.
 An old version of the package running under Python 3.5 is depoloyed on the
 Westgrid :kbd:`orcinus` HPC platform.
 That version is tagged in the repository as ``orcinus-python-3.5``.
@@ -349,7 +349,7 @@ The output looks something like::
   (line  497) ok        https://github.com/SalishSeaCast/SalishSeaCmd/issues
   (line  491) ok        https://github.com/SalishSeaCast/SalishSeaCmd/issues
   (line   21) ok        https://img.shields.io/badge/license-Apache%202-cb2533.svg
-  (line   21) ok        https://img.shields.io/badge/Python-3.10%20%7C%203.11-blue?logo=python&label=Python&logoColor=gold
+  (line   21) ok        https://img.shields.io/badge/Python-3.11%20%7C%203.12-blue?logo=python&label=Python&logoColor=gold
   (line   21) ok        https://img.shields.io/badge/version%20control-git-blue.svg?logo=github
   (line   21) ok        https://img.shields.io/badge/code%20style-black-000000.svg
   (line   21) ok        https://codecov.io/gh/SalishSeaCast/SalishSeaCmd/branch/main/graph/badge.svg

envs/environment-dev.yaml

@@ -5,8 +5,8 @@
 #
 #   $ conda env create -f SalishSeaCmd/envs/environment-dev.yaml
 #   $ conda activate salishsea-cmd
-#   (salishsea-cmd)$ python3 -m pip install --editable NEMO-Cmd/
-#   (salishsea-cmd)$ python3 -m pip install --editable SalishSeaCmd/
+#   (salishsea-cmd)$ python -m pip install --editable NEMO-Cmd/
+#   (salishsea-cmd)$ python -m pip install --editable SalishSeaCmd/
 #
 # The environment includes all the tools used to develop,
 # test, and document the SalishSeaCmd package.
@@ -27,7 +27,7 @@ dependencies:
   - f90nml
   - gitpython
   - pip
-  - python=3.11
+  - python=3.12
   - pyyaml
 
   # For coding style, repo QA, and pkg management

envs/environment-hpc.yaml

@@ -4,8 +4,8 @@
 #
 #   $ conda env create -f SalishSeaCmd/envs/environment-hpc.yaml
 #   $ conda activate salishsea-cmd
-#   (salishsea-cmd)$ python3 -m pip install --user --editable NEMO-Cmd/
-#   (salishsea-cmd)$ python3 -m pip install --user --editable SalishSeaCmd/
+#   (salishsea-cmd)$ python -m pip install --user --editable NEMO-Cmd/
+#   (salishsea-cmd)$ python -m pip install --user --editable SalishSeaCmd/
 
 name: salishsea-cmd
 
@@ -19,7 +19,7 @@ dependencies:
   - f90nml
   - gitpython
   - pip
-  - python=3.11
+  - python=3.12
   - pyyaml
 
   - pip:

envs/environment-rtd.yaml

@@ -12,7 +12,7 @@ channels:
 
 dependencies:
   - pip
-  - python=3.11
+  - python=3.12
 
   # readthedocs packages
   - mock

envs/requirements.txt

@@ -5,53 +5,52 @@
 # to create an isolated development environment.
 #
 # Create/update this file with:
-#   (salishsea-cmd)$ python3 -m pip list --format=freeze >> envs/requirements.txt
+#   (salishsea-cmd)$ python -m pip list --format=freeze >> envs/requirements.txt
 
 alabaster==0.7.13
-anyio==4.0.0
+anyio==4.1.0
 arrow==1.3.0
 attrs==23.1.0
 autopage==0.5.2
 Babel==2.13.1
-backports.functools-lru-cache==1.6.5
 black==23.10.1
 Brotli==1.1.0
-certifi==2023.7.22
+certifi==2023.11.17
 cffi==1.16.0
 cfgv==3.3.1
-charset-normalizer==3.3.1
+charset-normalizer==3.3.2
 click==8.1.7
-cliff==4.2.0
+cliff==4.4.0
 cmd2==2.4.3
 colorama==0.4.6
 coverage==7.3.2
-cryptography==41.0.6
+cryptography==41.0.7
 distlib==0.3.7
-docutils==0.17.1
+docutils==0.20.1
 editables==0.3
-exceptiongroup==1.1.3
+exceptiongroup==1.2.0
 f90nml==1.4.4
-filelock==3.12.4
+filelock==3.13.1
 gitdb==4.0.11
 GitPython==3.1.40
 h11==0.14.0
 h2==4.1.0
 hatch==1.7.0
 hatchling==1.18.0
 hpack==4.0.0
-httpcore==0.18.0
-httpx==0.25.0
+httpcore==1.0.2
+httpx==0.25.2
 hyperframe==6.0.1
 hyperlink==21.0.0
-identify==2.5.30
-idna==3.4
+identify==2.5.32
+idna==3.6
 imagesize==1.4.1
 importlib-metadata==6.8.0
 iniconfig==2.0.0
 jaraco.classes==3.3.0
 jeepney==0.8.0
 Jinja2==3.1.2
-keyring==24.2.0
+keyring==24.3.0
 markdown-it-py==3.0.0
 MarkupSafe==2.1.3
 mdurl==0.1.0
@@ -60,16 +59,16 @@ mypy-extensions==1.0.0
 nodeenv==1.8.0
 packaging==23.2
 pathspec==0.11.2
-pbr==5.11.1
+pbr==6.0.0
 pexpect==4.8.0
 pip==23.3.1
-platformdirs==3.11.0
+platformdirs==4.0.0
 pluggy==1.3.0
 pre-commit==3.5.0
 prettytable==3.9.0
 ptyprocess==0.7.0
 pycparser==2.21
-Pygments==2.16.1
+Pygments==2.17.2
 pyperclip==1.8.2
 PySocks==1.7.1
 pytest==7.4.3
@@ -80,17 +79,17 @@ python-hglib==2.6.2
 pytz==2023.3.post1
 PyYAML==6.0.1
 requests==2.31.0
-rich==13.6.0
+rich==13.7.0
 SecretStorage==3.3.3
 setuptools==68.2.2
 shellingham==1.5.4
 six==1.16.0
 smmap==5.0.0
 sniffio==1.3.0
 snowballstemmer==2.2.0
-Sphinx==5.3.0
+Sphinx==7.2.6
 sphinx-notfound-page==1.0.0
-sphinx-rtd-theme==1.3.0
+sphinx-rtd-theme==2.0.0
 sphinxcontrib-applehelp==1.0.7
 sphinxcontrib-devhelp==1.0.5
 sphinxcontrib-htmlhelp==2.0.4
@@ -102,14 +101,14 @@ stevedore==5.1.0
 toml==0.10.2
 tomli==2.0.1
 tomli_w==1.0.0
-tomlkit==0.12.1
-trove-classifiers==2023.10.18
+tomlkit==0.12.3
+trove-classifiers==2023.11.29
 types-python-dateutil==2.8.19.14
 typing_extensions==4.8.0
 ukkonen==1.0.1
-urllib3==2.0.7
+urllib3==2.1.0
 userpath==1.7.0
-virtualenv==20.24.6
-wcwidth==0.2.8
-wheel==0.41.2
+virtualenv==20.24.7
+wcwidth==0.2.12
+wheel==0.42.0
 zipp==3.17.0

pyproject.toml

@@ -28,7 +28,7 @@ name = "SalishSeaCmd"
 dynamic = [ "version" ]
 description = "SalishSeaCast NEMO Command Processor"
 readme = "README.rst"
-requires-python = ">=3.10"
+requires-python = ">=3.11"
 license = { file = "LICENSE" }
 authors = [
     { name = "Doug Latornell", email = "[email protected]" },
@@ -37,20 +37,6 @@ keywords = [
     "automation", "oceanography", "ocean modelling",
     "UBC-MOAD", "Salish Sea", "SalishSeaCast",
 ]
-classifiers = [
-    "Development Status :: 5 - Production/Stable",
-    "License :: OSI Approved :: Apache Software License",
-    "Programming Language :: Python :: Implementation :: CPython",
-    "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.10",
-    "Programming Language :: Python :: 3.11",
-    "Operating System :: POSIX :: Linux",
-    "Operating System :: Unix",
-    "Environment :: Console",
-    "Intended Audience :: Science/Research",
-    "Intended Audience :: Education",
-    "Intended Audience :: Developers",
-]
 dependencies = [
     # see envs/environment-dev.yaml for conda environment dev installation
     # see envs/requirements.txt for versions most recently used in development