diff --git a/.github/workflows/pytest-with-coverage.yaml b/.github/workflows/pytest-with-coverage.yaml index a4e1615..9ac2a00 100644 --- 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 index c6e3421..b53a08d 100644 --- 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 index 4707d46..e3c19a6 100644 --- 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 index 21ac903..879a2da 100644 --- 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 index 29ca828..300ea4d 100644 --- 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 index c2c2e98..f1f1e41 100644 --- a/docs/development.rst +++ b/docs/development.rst @@ -44,7 +44,7 @@ | | :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 | @@ -74,10 +74,10 @@ Python Versions =============== .. 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 -The :kbd:`NEMO-Cmd` package is developed using `Python`_ 3.12. +The :kbd:`NEMO-Cmd` package is developed using `Python`_ 3.13. The minimum supported Python version is 3.11. The :ref:`NEMO-CmdContinuousIntegration` workflow on GitHub ensures that the package is tested for all versions of Python>=3.11. @@ -118,7 +118,7 @@ all of the Python packages necessary for development, testing, and building the documentation with the commands below. -.. _Conda: https://conda.io/en/latest/ +.. _Conda: https://docs.conda.io/en/latest/ .. _Miniconda3: https://docs.conda.io/en/latest/miniconda.html .. code-block:: bash @@ -222,7 +222,7 @@ Building and Previewing the Documentation ----------------------------------------- Building the documentation is driven by the :file:`docs/Makefile`. -With your :kbd:`mohid-cmd` development environment activated, +With your :kbd:`nemo-cmd` development environment activated, use: .. code-block:: bash @@ -230,33 +230,47 @@ use: (nemo-cmd)$ (cd docs && make clean html) to do a clean build of the documentation. -The output looks something like:: - - Removing everything under '_build'... - Running Sphinx v3.3.0 - making output directory... done - loading intersphinx inventory from https://docs.python.org/3/objects.inv... - loading intersphinx inventory from https://salishseacmd.readthedocs.io/en/latest/objects.inv... - loading intersphinx inventory from https://salishsea-meopar-docs.readthedocs.io/en/latest/objects.inv... - building [mo]: targets for 0 po files that are out of date - building [html]: targets for 9 source files that are out of date - updating environment: [new config] 9 added, 0 changed, 0 removed - reading sources... [100%] subcommands - looking for now-outdated files... none found - pickling environment... done - checking consistency... done - preparing documents... done - writing output... [100%] subcommands - generating indices... genindex done - highlighting module code... [100%] nemo_cmd.prepare - writing additional pages... search done - copying static files... done - copying extra files... done - dumping search index in English (code: en)... done - dumping object inventory... done - build succeeded. - - The HTML pages are in _build/html. +The output looks something like: + +.. code-block:: text + + Removing everything under '_build'... + Running Sphinx v8.1.3 + loading translations [en]... done + making output directory... done + Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`. + loading intersphinx inventory 'python' from https://docs.python.org/3/objects.inv ... + loading intersphinx inventory 'salishseacmd' from https://salishseacmd.readthedocs.io/en/latest/objects.inv ... + loading intersphinx inventory 'salishseadocs' from https://salishsea-meopar-docs.readthedocs.io/en/latest/objects.inv ... + building [mo]: targets for 0 po files that are out of date + writing output... + building [html]: targets for 9 source files that are out of date + updating environment: [new config] 9 added, 0 changed, 0 removed + reading sources... [100%] subcommands + /media/doug/warehouse/MEOPAR/NEMO-Cmd/docs/development.rst:236: WARNING: Literal block expected; none found. [docutils] + looking for now-outdated files... none found + pickling environment... done + checking consistency... done + preparing documents... done + copying assets... + copying static files... + Writing evaluated template result to /media/doug/warehouse/MEOPAR/NEMO-Cmd/docs/_build/html/_static/language_data.js + Writing evaluated template result to /media/doug/warehouse/MEOPAR/NEMO-Cmd/docs/_build/html/_static/documentation_options.js + Writing evaluated template result to /media/doug/warehouse/MEOPAR/NEMO-Cmd/docs/_build/html/_static/basic.css + Writing evaluated template result to /media/doug/warehouse/MEOPAR/NEMO-Cmd/docs/_build/html/_static/js/versions.js + copying static files: done + copying extra files... + copying extra files: done + copying assets: done + writing output... [100%] subcommands + generating indices... genindex done + highlighting module code... [100%] nemo_cmd.prepare + writing additional pages... search done + dumping search index in English (code: en)... done + dumping object inventory... done + build succeeded, 1 warning. + + The HTML pages are in _build/html. The HTML rendering of the docs ends up in :file:`NEMO-Cmd/docs/_build/html/`. You can open the :file:`index.html` file in that directory tree in your browser to preview the results of the build before committing and pushing your changes to GitHub. @@ -282,127 +296,118 @@ use: (mohid-cmd)$ cd NEMO-Cmd/docs/ (mohid-cmd) docs$ make linkcheck -The output looks something like:: - - Running Sphinx v3.3.0 - making output directory... done - loading intersphinx inventory from https://docs.python.org/3/objects.inv... - loading intersphinx inventory from https://salishseacmd.readthedocs.io/en/latest/objects.inv... - loading intersphinx inventory from https://salishsea-meopar-docs.readthedocs.io/en/latest/objects.inv... - building [mo]: targets for 0 po files that are out of date - building [linkcheck]: targets for 9 source files that are out of date - updating environment: [new config] 9 added, 0 changed, 0 removed - reading sources... [100%] subcommands - looking for now-outdated files... none found - pickling environment... done - checking consistency... done - preparing documents... done - writing output... [ 11%] CHANGES - (line 23) ok https://f90nml.readthedocs.io/en/latest/ - (line 20) ok https://nemo-cmd.readthedocs.io/en/latest/run_description_file/3.6_yaml_file.html#vcs-revisions-section - (line 27) ok https://ubc-moad-docs.readthedocs.io/en/latest/python_packaging/pkg_structure.html - (line 42) ok https://black.readthedocs.io/en/stable/ - (line 9) ok https://app.codecov.io/gh/SalishSeaCast/NEMO-Cmd - (line 115) ok https://slurm.schedmd.com/ - (line 46) ok https://calver.org/ - (line 127) ok http://agrif.imag.fr/ - (line 107) ok https://bugs.launchpad.net/python-cliff/+bug/1719465 - (line 157) ok https://nemo-cmd.readthedocs.io/en/latest/run_description_file/3.6_yaml_file.html#restart-section - (line 9) ok https://github.com/SalishSeaCast/NEMO-Cmd/actions - (line 181) ok https://nemo-cmd.readthedocs.io/en/latest/run_description_file/3.6_yaml_file.html#pbs-resources-section - (line 13) ok https://github.com/SalishSeaCast/NEMO-Cmd - (line 187) ok https://nemo-cmd.readthedocs.io/en/latest/run_description_file/3.6_yaml_file.html#modules-to-load-section - (line 177) ok https://github.com/SalishSeaCast/NEMO-Cmd/issues/16 - (line 193) ok https://nemo-cmd.readthedocs.io/en/latest/run_description_file/3.6_yaml_file.html#grid-section - (line 149) ok https://github.com/SalishSeaCast/NEMO-Cmd/issues/19 - (line 198) ok https://nemo-cmd.readthedocs.io/en/latest/api.html#functions-for-working-with-file-system-paths - (line 239) ok https://tox.wiki/en/latest/ - (line 154) ok https://github.com/SalishSeaCast/NEMO-Cmd/issues/20 - (line 187) ok https://github.com/SalishSeaCast/NEMO-Cmd/issues/11 - (line 181) ok https://github.com/SalishSeaCast/NEMO-Cmd/issues/10 - (line 193) ok https://github.com/SalishSeaCast/NEMO-Cmd/issues/5 - writing output... [ 22%] api - (line 21) ok https://docs.python.org/3/library/pathlib.html#pathlib.Path - (line 21) ok https://docs.python.org/3/library/pathlib.html#pathlib.Path - (line 21) ok https://docs.python.org/3/library/pathlib.html#pathlib.Path - (line 21) ok https://docs.python.org/3/library/functions.html#int - (line 21) ok https://docs.python.org/3/library/stdtypes.html#str - (line 21) ok https://docs.python.org/3/library/stdtypes.html#str - (line 21) ok https://docs.python.org/3/library/stdtypes.html#str - (line 21) ok https://docs.python.org/3/library/stdtypes.html#str - (line 21) ok https://docs.python.org/3/library/stdtypes.html#str - (line 21) ok https://docs.python.org/3/library/constants.html#None - (line 21) ok https://docs.python.org/3/library/constants.html#None - (line 21) ok https://docs.python.org/3/library/constants.html#None - (line 45) ok https://salishseacmd.readthedocs.io/en/latest/index.html#salishseacmdprocessor - (line 21) ok https://docs.python.org/3/library/stdtypes.html#dict - (line 21) ok https://docs.python.org/3/library/stdtypes.html#dict - (line 20) ok https://docs.python.org/3/library/exceptions.html#SystemExit - (line 21) ok https://docs.python.org/3/library/stdtypes.html#dict - (line 21) ok https://docs.python.org/3/library/stdtypes.html#dict - (line 11) ok https://docs.python.org/3/library/exceptions.html#SystemExit - (line 96) ok https://docs.python.org/3/library/constants.html#True - (line 43) ok https://docs.python.org/3/library/stdtypes.html#dict - (line 96) ok https://docs.python.org/3/library/constants.html#True - (line 43) ok https://docs.python.org/3/library/stdtypes.html#list - (line 29) ok https://docs.python.org/3/library/exceptions.html#KeyError - (line 96) ok https://docs.python.org/3/library/exceptions.html#KeyError - (line 6) ok https://github.com/SalishSeaCast/NEMO-Cmd/issues/18 - writing output... [ 33%] development - (line 21) ok https://docs.python.org/3.12/ - (line 21) ok https://nemo-cmd.readthedocs.io/en/latest/ - (line 61) ok https://www.python.org/ - (line 95) ok https://conda.io/en/latest/ - (line 21) ok https://github.com/SalishSeaCast/NEMO-Cmd/issues - (line 21) ok https://www.apache.org/licenses/LICENSE-2.0 - (line 95) ok https://docs.conda.io/en/latest/miniconda.html - (line 131) ok https://peps.python.org/pep-0008/ - (line 21) ok https://github.com/SalishSeaCast/NEMO-Cmd/actions?query=workflow%3ACI - (line 168) ok https://www.sphinx-doc.org/en/master/ - (line 168) ok https://www.sphinx-doc.org/en/master/usage/restructuredtext/index.html - (line 21) ok https://github.com/SalishSeaCast/NEMO-Cmd/actions?query=workflow%3A - (line 392) ok https://docs.pytest.org/en/latest/ - (line 425) ok https://coverage.readthedocs.io/en/latest/ - (line 425) ok https://pytest-cov.readthedocs.io/en/latest/ - (line 184) ok https://readthedocs.org/projects/nemo-cmd/builds/ - (line 470) ok https://docs.github.com/en/actions - (line 249) ok https://github.com/SalishSeaCast/NEMO-Cmd/actions?query=workflow%3A - (line 484) ok https://git-scm.com/ - (line 21) ok https://img.shields.io/badge/license-Apache%202-cb2533.svg - (line 21) ok https://img.shields.io/badge/python-3.8+-blue.svg - (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 382) ok https://github.com/SalishSeaCast/NEMO-Cmd/actions?query=workflow:sphinx-linkcheck - (line 21) ok https://github.com/SalishSeaCast/NEMO-Cmd/workflows/sphinx-linkcheck/badge.svg - (line 21) ok https://readthedocs.org/projects/nemo-cmd/badge/?version=latest - (line 510) ok https://github.com/SalishSeaCast/docs/blob/main/CONTRIBUTORS.rst - (line 21) ok https://github.com/SalishSeaCast/NEMO-Cmd/workflows/CI/badge.svg - (line 21) ok https://app.codecov.io/gh/SalishSeaCast/NEMO-Cmd/branch/main/graph/badge.svg - (line 450) ok https://app.codecov.io/gh/SalishSeaCast/NEMO-Cmd/branch/main/graph/badge.svg - (line 459) ok https://github.com/SalishSeaCast/NEMO-Cmd/commits/main - (line 450) ok https://github.com/SalishSeaCast/NEMO-Cmd/workflows/CI/badge.svg - (line 21) ok https://img.shields.io/github/issues/SalishSeaCast/NEMO-Cmd?logo=github - (line 492) ok https://img.shields.io/github/issues/SalishSeaCast/NEMO-Cmd?logo=github - writing output... [ 44%] index - (line 58) ok https://www.apache.org/licenses/LICENSE-2.0 - (line 23) ok https://www.nemo-ocean.eu/ - writing output... [ 55%] installation - (line 67) ok https://en.wikipedia.org/wiki/Command-line_completion - writing output... [ 66%] run_description_file/3.6_agrif_yaml_file - writing output... [ 77%] run_description_file/3.6_yaml_file - (line 195) ok https://docs.python.org/3/library/constants.html#False - (line 458) ok https://docs.python.org/3/library/constants.html#False - (line 195) ok https://salishsea-meopar-docs.readthedocs.io/en/latest/code-notes/salishsea-nemo/land-processor-elimination/index.html#landprocessorelimination - (line 188) ok https://salishsea-meopar-docs.readthedocs.io/en/latest/code-notes/salishsea-nemo/land-processor-elimination/index.html#landprocessorelimination - (line 641) ok http://modules.sourceforge.net/ - writing output... [ 88%] run_description_file/index - (line 23) ok https://pyyaml.org/wiki/PyYAMLDocumentation - writing output... [100%] subcommands - (line 232) ok https://en.wikipedia.org/wiki/Universally_unique_identifier - - build succeeded. - - Look for any errors in the above output or in _build/linkcheck/output.txt +The output looks something like: + +.. code-block:: text + + (/media/doug/warehouse/conda_envs/nemo-cmd) /media/doug/warehouse/MEOPAR/NEMO-Cmd/docs git:[py313] + make clean linkcheck + Removing everything under '_build'... + Running Sphinx v8.1.3 + loading translations [en]... done + making output directory... done + Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`. + loading intersphinx inventory 'python' from https://docs.python.org/3/objects.inv ... + loading intersphinx inventory 'salishseacmd' from https://salishseacmd.readthedocs.io/en/latest/objects.inv ... + loading intersphinx inventory 'salishseadocs' from https://salishsea-meopar-docs.readthedocs.io/en/latest/objects.inv ... + building [mo]: targets for 0 po files that are out of date + writing output... + building [linkcheck]: targets for 9 source files that are out of date + updating environment: [new config] 9 added, 0 changed, 0 removed + reading sources... [100%] subcommands + looking for now-outdated files... none found + pickling environment... done + checking consistency... done + preparing documents... done + copying assets... + copying assets: done + writing output... [100%] subcommands + + ( CHANGES: line 102) ok https://black.readthedocs.io/en/stable/ + ( CHANGES: line 69) ok https://app.codecov.io/gh/SalishSeaCast/NEMO-Cmd + ( development: line 29) ok https://codecov.io/gh/SalishSeaCast/NEMO-Cmd/graph/badge.svg?token=ZDCF36TYDQ + ( development: line 347) ok https://coverage.readthedocs.io/en/latest/ + ( development: line 114) ok https://docs.conda.io/en/latest/ + ( development: line 392) ok https://docs.github.com/en/actions + ( CHANGES: line 106) ok https://calver.org/ + ( development: line 23) ok https://docs.python.org/3.13/ + (run_description_file/3.6_yaml_file: line 197) ok https://docs.python.org/3/library/constants.html#False + ( api: line 23) ok https://docs.python.org/3/library/constants.html#None + ( api: line 98) ok https://docs.python.org/3/library/constants.html#True + ( development: line 314) ok https://docs.pytest.org/en/latest/ + ( api: line 98) ok https://docs.python.org/3/library/exceptions.html#KeyError + ( api: line 20) ok https://docs.python.org/3/library/exceptions.html#SystemExit + ( development: line 114) ok https://docs.conda.io/en/latest/miniconda.html + ( CHANGES: line 167) ok https://bugs.launchpad.net/python-cliff/+bug/1719465 + (run_description_file/3.6_agrif_yaml_file: line 25) ok https://agrif.imag.fr/ + ( api: line 23) ok https://docs.python.org/3/library/functions.html#int + ( api: line 23) ok https://docs.python.org/3/library/pathlib.html#pathlib.Path + ( CHANGES: line 83) ok https://f90nml.readthedocs.io/en/latest/ + ( subcommands: line 234) ok https://en.wikipedia.org/wiki/Universally_unique_identifier + ( api: line 45) ok https://docs.python.org/3/library/stdtypes.html#list + ( api: line 23) ok https://docs.python.org/3/library/stdtypes.html#str + ( development: line 407) ok https://git-scm.com/ + ( api: line 23) ok https://docs.python.org/3/library/stdtypes.html#dict + ( development: line 32) ok https://github.com/SalishSeaCast/NEMO-Cmd/actions/workflows/codeql-analysis.yaml/badge.svg + ( development: line 26) ok https://github.com/SalishSeaCast/NEMO-Cmd/actions/workflows/pytest-with-coverage.yaml/badge.svg + ( CHANGES: line 73) ok https://github.com/SalishSeaCast/NEMO-Cmd + ( CHANGES: line 187) ok https://forge.ipsl.fr/nemo/wiki/Users/ModelInterfacing/AGRIF + ( development: line 39) ok https://github.com/SalishSeaCast/NEMO-Cmd/actions/workflows/sphinx-linkcheck.yaml/badge.svg + ( CHANGES: line 69) ok https://github.com/SalishSeaCast/NEMO-Cmd/actions + ( development: line 23) ok https://github.com/SalishSeaCast/NEMO-Cmd/actions?query=workflow:CodeQL + ( development: line 23) ok https://github.com/SalishSeaCast/NEMO-Cmd/issues + ( development: line 381) ok https://github.com/SalishSeaCast/NEMO-Cmd/commits/main + ( CHANGES: line 241) ok https://github.com/SalishSeaCast/NEMO-Cmd/issues/10 + ( development: line 23) ok https://github.com/SalishSeaCast/NEMO-Cmd/actions?query=workflow:pytest-with-coverage + ( CHANGES: line 247) ok https://github.com/SalishSeaCast/NEMO-Cmd/issues/11 + ( development: line 23) ok https://github.com/SalishSeaCast/NEMO-Cmd/actions?query=workflow:sphinx-linkcheck + ( CHANGES: line 237) ok https://github.com/SalishSeaCast/NEMO-Cmd/issues/16 + ( api: line 6) ok https://github.com/SalishSeaCast/NEMO-Cmd/issues/18 + ( CHANGES: line 209) ok https://github.com/SalishSeaCast/NEMO-Cmd/issues/19 + ( CHANGES: line 253) ok https://github.com/SalishSeaCast/NEMO-Cmd/issues/5 + ( CHANGES: line 214) ok https://github.com/SalishSeaCast/NEMO-Cmd/issues/20 + ( development: line 23) ok https://github.com/SalishSeaCast/NEMO-Cmd/releases + ( CHANGES: line 29) ok https://hatch.pypa.io/ + ( development: line 65) ok https://img.shields.io/badge/%F0%9F%A5%9A-Hatch-4051b5.svg + ( development: line 62) ok https://img.shields.io/badge/code%20style-black-000000.svg + ( development: line 53) ok https://img.shields.io/badge/license-Apache%202-cb2533.svg + ( development: line 59) ok https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white + ( development: line 56) ok https://img.shields.io/badge/version%20control-git-blue.svg?logo=github + ( development: line 49) ok https://img.shields.io/github/issues/SalishSeaCast/NEMO-Cmd?logo=github + ( development: line 43) ok https://img.shields.io/github/v/release/SalishSeaCast/NEMO-Cmd?logo=github + ( development: line 435) ok https://github.com/SalishSeaCast/docs/blob/main/CONTRIBUTORS.rst + ( development: line 46) ok 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 + ( CHANGES: line 35) ok https://github.com/UBC-MOAD/gha-workflows + ( development: line 23) ok https://nemo-cmd.readthedocs.io/en/latest/ + ( development: line 23) ok https://github.com/pypa/hatch + ( CHANGES: line 258) ok https://nemo-cmd.readthedocs.io/en/latest/api.html#functions-for-working-with-file-system-paths + ( CHANGES: line 253) ok https://nemo-cmd.readthedocs.io/en/latest/run_description_file/3.6_yaml_file.html#grid-section + ( CHANGES: line 247) ok https://nemo-cmd.readthedocs.io/en/latest/run_description_file/3.6_yaml_file.html#modules-to-load-section + (run_description_file/3.6_yaml_file: line 640) ok https://modules.sourceforge.net/ + ( installation: line 36) ok https://github.com/conda-forge/miniforge + ( CHANGES: line 241) ok https://nemo-cmd.readthedocs.io/en/latest/run_description_file/3.6_yaml_file.html#pbs-resources-section + ( CHANGES: line 217) ok https://nemo-cmd.readthedocs.io/en/latest/run_description_file/3.6_yaml_file.html#restart-section + ( CHANGES: line 80) ok https://nemo-cmd.readthedocs.io/en/latest/run_description_file/3.6_yaml_file.html#vcs-revisions-section + ( development: line 130) ok https://pip.pypa.io/en/stable/topics/local-project-installs/#editable-installs + (run_description_file/index: line 25) ok https://pyyaml.org/wiki/PyYAMLDocumentation + ( development: line 347) ok https://pytest-cov.readthedocs.io/en/latest/ + (run_description_file/3.6_yaml_file: line 190) ok https://salishsea-meopar-docs.readthedocs.io/en/latest/code-notes/salishsea-nemo/land-processor-elimination/index.html#landprocessorelimination + ( api: line 47) ok https://salishseacmd.readthedocs.io/en/latest/index.html#salishseacmdprocessor + ( development: line 23) ok https://pre-commit.com + ( development: line 156) ok https://pre-commit.com/ + ( CHANGES: line 175) ok https://slurm.schedmd.com/ + ( CHANGES: line 299) ok https://tox.wiki/en/latest/ + ( development: line 23) ok https://www.apache.org/licenses/LICENSE-2.0 + ( development: line 80) ok https://www.python.org/ + ( CHANGES: line 87) ok https://ubc-moad-docs.readthedocs.io/en/latest/python_packaging/pkg_structure.html + ( development: line 36) ok https://readthedocs.org/projects/nemo-cmd/badge/?version=latest + ( development: line 189) ok https://www.sphinx-doc.org/en/master/usage/restructuredtext/index.html + ( development: line 189) ok https://www.sphinx-doc.org/en/master/ + ( development: line 205) ok https://readthedocs.org/projects/nemo-cmd/builds/ + ( index: line 25) ok https://www.nemo-ocean.eu/ + build succeeded. + + Look for any errors in the above output or in _build/linkcheck/output.txt :command:`make linkcheck` is run monthly via a `scheduled GitHub Actions workflow`_ diff --git a/docs/installation.rst b/docs/installation.rst index 537ee9b..4836f80 100644 --- 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 index 11d64e5..9a612fd 100644 --- 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 index 3ad8084..8694d77 100644 --- 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 index b9dc344..6d9b556 100644 --- 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 index 7221d69..6a85e15 100644 --- 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 index 33587b6..9fa5434 100644 --- 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