Update to Python 3.13 (#92)

* Add Python 3.13.0rc2 to GHA pytest workflow Added Python 3.13.0rc2 to the pytest-with-coverage workflow python-version matrix to test compatibility with the latest release candidate. Also added 'conda-forge/label/python_rc' channel to the test environment configuration to enable installation of the release candidate. * Change to Python 3.13 in GHA pytest workflow Changed from Python 3.13.0rc2 to 3.13 in the pytest-with-coverage workflow python-version matrix to test compatibility with the final release. Also dropped the 'conda-forge/label/python_rc' channel from the test environment configuration because it is no longer needed. * Update ReadTheDocs build config Upgraded the OS to Ubuntu 24.04 and updated the Python toolchain to mambaforge-23.11 in the .readthedocs.yaml file. This ensures compatibility with the latest environment settings. * Update to Python 3.13 in envs & GHA sphinx-linkcheck Upgraded Python from version 3.12 to 3.13 across various YAML files. This includes updates to development, RTD, and HPC environments, as well as GHA sphinx-linkcheck workflow. * Update Sphinx & optional dependencies version pins Updated Sphinx and optional dependencies packages pinned versions in `environment-dev.yaml`, `environment-test.yaml`, and `environment-rtd.yaml` to get functional Python 3.13 environment. * Update to Python 3.13 for development and use Upgraded the required Python version to 3.13 in `pyproject.toml` and updated related documentation and links to reflect this change. * Revert Python version requirement to >=3.11 Reverted the required Python version from 3.13 to 3.11 in pyproject.toml because I made a mistake. It has to be the oldest version that the package supports, and we're leaving that at 3.11 due to several group members' envs on graham.
SalishSeaCast · Oct 27, 2024 · 6434f0f · 6434f0f
1 parent 74c15bf
commit 6434f0f
Show file tree

Hide file tree

Showing 12 changed files with 234 additions and 230 deletions.
diff --git a/.github/workflows/pytest-with-coverage.yaml b/.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 }}

diff --git a/.github/workflows/sphinx-linkcheck.yaml b/.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: ['3.12']
+        python-version: ['3.13']
     uses: UBC-MOAD/gha-workflows/.github/workflows/sphinx-linkcheck.yaml@main
     with:
       python-version: ${{ matrix.python-version }}

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -1,9 +1,9 @@
 version: 2
 
 build:
-  os: ubuntu-22.04
+  os: ubuntu-24.04
   tools:
-    python: "mambaforge-22.9"
+    python: "mambaforge-23.11"
 
 conda:
   environment: envs/environment-rtd.yaml

diff --git a/README.rst b/README.rst
@@ -24,7 +24,7 @@ NEMO Command Processor
 |                            |     :target: https://github.com/SalishSeaCast/NEMO-Cmd/releases                                                                                                                                  |
 |                            |     :alt: Releases                                                                                                                                                                               |
 |                            | .. image:: https://img.shields.io/python/required-version-toml?tomlFilePath=https://raw.githubusercontent.com/SalishSeaCast/NEMO-Cmd/main/pyproject.toml&logo=Python&logoColor=gold&label=Python |
-|                            |      :target: https://docs.python.org/3.12/                                                                                                                                                      |
+|                            |      :target: https://docs.python.org/3.13/                                                                                                                                                      |
 |                            |      :alt: Python Version from PEP 621 TOML                                                                                                                                                      |
 |                            | .. image:: https://img.shields.io/github/issues/SalishSeaCast/NEMO-Cmd?logo=github                                                                                                               |
 |                            |     :target: https://github.com/SalishSeaCast/NEMO-Cmd/issues                                                                                                                                    |

diff --git a/docs/CHANGES.rst b/docs/CHANGES.rst
@@ -2,10 +2,10 @@
 Change Log
 **********
 
-v23.2.dev0 (unreleased)
+v24.1.dev0 (unreleased)
 =======================
 
-*
+* Change to Python 3.13 for package development.
 
 
 v23.1 (2023-11-20)

diff --git a/docs/development.rst b/docs/development.rst
diff --git a/docs/installation.rst b/docs/installation.rst
@@ -37,7 +37,7 @@ These instructions assume that:
   (`Miniforge`_ or `Miniconda3`_)
   installed
 
-  .. _Conda: https://conda.io/en/latest/
+  .. _Conda: https://docs.conda.io/en/latest/
   .. _Miniforge: https://github.com/conda-forge/miniforge
   .. _Miniconda3: https://docs.conda.io/en/latest/miniconda.html
 

diff --git a/envs/environment-dev.yaml b/envs/environment-dev.yaml
@@ -27,7 +27,7 @@ dependencies:
   - f90nml
   - gitpython
   - pip
-  - python=3.12
+  - python=3.13
   - pyyaml
 
   # For coding style, repo QA, and pkg management
@@ -41,9 +41,9 @@ dependencies:
   - pytest-randomly
 
   # For documentation
-  - sphinx=5.3.0
-  - sphinx-notfound-page=1.0.0
-  - sphinx-rtd-theme=1.3.0
+  - sphinx=8.1.3
+  - sphinx-notfound-page=1.0.4
+  - sphinx-rtd-theme=3.0.0
 
   - pip:
     - python-hglib

diff --git a/envs/environment-hpc.yaml b/envs/environment-hpc.yaml
@@ -19,7 +19,7 @@ dependencies:
   - f90nml
   - gitpython
   - pip
-  - python=3.12
+  - python=3.13
   - pyyaml
 
   - pip:

diff --git a/envs/environment-rtd.yaml b/envs/environment-rtd.yaml
@@ -8,12 +8,12 @@ channels:
 
 dependencies:
   - pip
-  - python=3.12
+  - python=3.13
 
 # Sphinx and extensions
-  - sphinx=5.3.0
-  - sphinx-notfound-page=1.0.0
-  - sphinx-rtd-theme=1.3.0
+  - sphinx=8.1.3
+  - sphinx-notfound-page=1.0.4
+  - sphinx-rtd-theme=3.0.0
 
   # readthedocs build system packages
   - mock

diff --git a/envs/environment-test.yaml b/envs/environment-test.yaml
@@ -25,9 +25,9 @@ dependencies:
   - pytest-randomly
 
   # For documentation links checking
-  - sphinx=5.3.0
-  - sphinx-notfound-page=1.0.0
-  - sphinx-rtd-theme=1.3.0
+  - sphinx=8.1.3
+  - sphinx-notfound-page=1.0.4
+  - sphinx-rtd-theme=3.0.0
 
   - pip:
     - python-hglib

diff --git a/envs/requirements.txt b/envs/requirements.txt
@@ -7,113 +7,112 @@
 # Create/update this file with:
 #   (nemo-cmd)$ python -m pip list --format=freeze >> envs/requirements.txt
 
-alabaster==0.7.16
-anyio==4.3.0
+alabaster==1.0.0
+anyio==4.6.2.post1
 arrow==1.3.0
-attrs==23.2.0
+attrs==24.2.0
 autopage==0.5.2
 Babel==2.14.0
 backports.tarfile==1.0.0
-black==24.4.2
+black==24.10.0
 Brotli==1.1.0
-certifi==2024.7.4
-cffi==1.16.0
+certifi==2024.8.30
+cffi==1.17.1
 cfgv==3.3.1
-charset-normalizer==3.3.2
+charset-normalizer==3.4.0
 click==8.1.7
-cliff==4.6.0
+cliff==4.7.0
 cmd2==2.4.3
 colorama==0.4.6
-coverage==7.5.1
+coverage==7.6.3
 cryptography==43.0.1
-distlib==0.3.8
-docutils==0.17.1
+distlib==0.3.9
+docutils==0.21.2
 editables==0.5
-exceptiongroup==1.2.0
+exceptiongroup==1.2.2
 f90nml==1.4.4
-filelock==3.14.0
+filelock==3.16.1
 gitdb==4.0.11
 GitPython==3.1.43
 h11==0.14.0
 h2==4.1.0
-hatch==1.10.0
-hatchling==1.24.2
+hatch==1.13.0
+hatchling==1.25.0
 hpack==4.0.0
-httpcore==1.0.5
-httpx==0.27.0
+httpcore==1.0.6
+httpx==0.27.2
 hyperframe==6.0.1
 hyperlink==21.0.0
-identify==2.5.36
-idna==3.7
+identify==2.6.1
+idna==3.10
 imagesize==1.4.1
-importlib_metadata==7.1.0
-importlib_resources==6.4.0
+importlib_metadata==8.5.0
+importlib_resources==6.4.5
 iniconfig==2.0.0
 jaraco.classes==3.4.0
 jaraco.context==5.3.0
 jaraco.functools==4.0.0
 jeepney==0.8.0
 Jinja2==3.1.4
-keyring==25.2.0
+keyring==25.4.1
 markdown-it-py==3.0.0
-MarkupSafe==2.1.5
+MarkupSafe==3.0.1
 mdurl==0.1.2
-more-itertools==10.2.0
+more-itertools==10.5.0
 mypy-extensions==1.0.0
-nodeenv==1.8.0
-packaging==24.0
+nodeenv==1.9.1
+packaging==24.1
 pathspec==0.12.1
-pbr==6.0.0
+pbr==6.1.0
 pexpect==4.9.0
-pip==24.0
-platformdirs==4.2.1
+pip==24.2
+platformdirs==4.3.6
 pluggy==1.5.0
-pre_commit==3.7.0
-prettytable==3.10.0
+pre_commit==4.0.1
+prettytable==3.11.0
 ptyprocess==0.7.0
 pycparser==2.22
 Pygments==2.18.0
-pyperclip==1.8.2
+pyperclip==1.9.0
 PySocks==1.7.1
-pytest==8.2.0
+pytest==8.3.3
 pytest-cov==5.0.0
 pytest-randomly==3.15.0
 python-dateutil==2.9.0
 python-hglib==2.6.2
-pytz==2024.1
-PyYAML==6.0.1
-requests==2.32.0
-rich==13.7.1
+pytz==2024.2
+PyYAML==6.0.2
+requests==2.32.3
+rich==13.9.2
 SecretStorage==3.3.3
-setuptools==70.0.0
+setuptools==75.1.0
 shellingham==1.5.4
 six==1.16.0
 smmap==5.0.0
 sniffio==1.3.1
 snowballstemmer==2.2.0
-Sphinx==5.3.0
-sphinx-notfound-page==1.0.0
-sphinx-rtd-theme==1.3.0
-sphinxcontrib-applehelp==1.0.8
-sphinxcontrib-devhelp==1.0.6
-sphinxcontrib-htmlhelp==2.0.5
+Sphinx==8.1.3
+sphinx-notfound-page==1.0.4
+sphinx_rtd_theme==3.0.0
+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==1.0.7
+sphinxcontrib-qthelp==2.0.0
 sphinxcontrib-serializinghtml==1.1.10
-stevedore==5.2.0
+stevedore==5.3.0
 toml==0.10.2
-tomli==2.0.1
-tomli_w==1.0.0
-tomlkit==0.12.4
-trove-classifiers==2024.4.10
-types-python-dateutil==2.9.0.20240316
-typing_extensions==4.11.0
+tomli==2.0.2
+tomli_w==1.1.0
+tomlkit==0.13.2
+trove-classifiers==2024.10.16
+types-python-dateutil==2.9.0.20241003
+typing_extensions==4.12.2
 ukkonen==1.0.1
-urllib3==2.2.2
+urllib3==2.2.3
 userpath==1.7.0
-virtualenv==20.26.1
+virtualenv==20.27.0
 wcwidth==0.2.13
-wheel==0.43.0
-zipp==3.19.1
-zstandard==0.22.0
+zipp==3.20.2
+zstandard==0.23.0
-Original file line number
+Diff line change
@@ Expand Up / @@ -19,7 +19,7 @@ dependencies: @@
       - f90nml
       - gitpython
       - pip
-      - python=3.12
+      - python=3.13
       - pyyaml
       - pip:
@@ Expand Down @@