NEMO-Cmd Package Development

Continuous Integration

 Pytest with Coverage Status Codecov Testing Coverage Report CodeQL analysis

Documentation

 Documentation Status Sphinx linkcheck

Package

 Releases Python Version from PEP 621 TOML Issue Tracker

Meta

 Licensed under the Apache License, Version 2.0 Git on GitHub Pixi pre-commit The uncompromising Python code formatter Hatch project

Python Versions

Python Version from PEP 621 TOML

The NEMO-Cmd package is developed using Python 3.14. The minimum supported Python version is 3.12. The Continuous Integration workflow on GitHub ensures that the package is tested for all versions of Python>=3.12. An old version of the package running under Python 3.5 is deployed on the Westgrid orcinus HPC platform. That version is tagged in the repository as orcinus-python-3.5.

Getting the Code

Git on GitHub

Clone the code and documentation repository from GitHub with:

$ git clone git@github.com:SalishSeaCast/NEMO-Cmd.git

Development Environment

Pixi

NEMO-Cmd uses Pixi to manage dependencies and operating environments. If you don’t already have Pixi installed, please follow its installation instructions to do so.

Most commands are executed using pixi run in the MEMO-Cmd/ directory (or a sub-directory). Dependencies will be downloaded and linked in to environments when you use pixi run for the first time.

  • The default environment has the packages installed that are required to run the NEMO-Cmd command-line interface; e.g. pixi run nemo help

  • Other environments use by commands in the sections below have addition packages for running the test suite, building and link checking the documentation, etc.

  • If you are using an integrated development environment like VSCode or PyCharm where you need a Python interpreter to support coding assistance features, run development tasks, etc., use the interpreter in the dev environment. You can get its full path with pixi run -e dev which python

To get detailed information about the environments, the packages installed in them, pixi tasks that are defined for them, etc., :use command:pixi info.

NEMO-Cmd is installed in editable install mode in all of the environments that Pixi creates. That means that changes you make to the code are immediately reflected in the environments.

Coding Style

pre-commit The uncompromising Python code formatter

The NEMO-Cmd package uses Git pre-commit hooks managed by pre-commit to maintain consistent code style and and other aspects of code, docs, and repo QA.

To install the pre-commit hooks in a newly cloned repo, run pre-commit install:

$ cd NEMO-Cmd
$ pixi run -e dev pre-commit install

Note

You only need to install the hooks once immediately after you make a new clone of the NEMO-Cmd repository

Building the Documentation

Documentation Status

The documentation for the NEMO-Cmd package is written in reStructuredText and converted to HTML using Sphinx.

If you have write access to the repository on GitHub, whenever you push changes to GitHub the documentation is automatically re-built and rendered at https://nemo-cmd.readthedocs.io/en/latest/.

Additions, improvements, and corrections to these docs are always welcome.

The quickest way to fix typos, etc. on existing pages is to use the Edit on GitHub link in the upper right corner of the page to get to the online editor for the page on GitHub.

For more substantial work, and to add new pages, follow the instructions in the Development Environment section above. In the development environment you can build the docs locally instead of having to push commits to GitHub to trigger a build on readthedocs.org and wait for it to complete. Below are instructions that explain how to:

  • build the docs with your changes, and preview them in Firefox

  • check the docs for broken links

Building and Previewing the Documentation

Building the documentation is driven by the docs/Makefile. To do a clean build of the documentation use:

$ cd NEMO-Cmd/
$ pixi run docs

The output looks something like:

 ✨ Pixi task (docs in docs): make clean html
 Removing everything under '_build'...
 Running Sphinx v8.1.3
 loading translations [en]... done
 making output directory... done
 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
 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.

 The HTML pages are in _build/html.

The HTML rendering of the docs ends up in NEMO-Cmd/docs/_build/html/. You can open the 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.

Whenever you push changes to the NEMO-Cmd repository on GitHub the documentation is automatically re-built and rendered at https://nemo-cmd.readthedocs.io/en/latest/.

Running the Unit Tests

The test suite for the NEMO-Cmd package is in NEMO-Cmd/tests/. The pytest tool is used for test fixtures and as the test runner for the suite.

To run the test suite in the most recent supported version of Python use:

$ cd NEMO-Cmd/
$ pixi run -e test pytest

The output looks something like:

 ================================== test session starts ===============================
 platform linux -- Python 3.14.2, pytest-9.0.2, pluggy-1.6.0
 Using --randomly-seed=894334699
 rootdir: /media/doug/warehouse/MEOPAR/NEMO-Cmd
 configfile: pyproject.toml
 plugins: cov-7.0.0, randomly-3.15.0
 collected 192 items

 tests/test_deflate.py ........                                                  [  4%]
 tests/test_run.py .....................................................         [ 31%]
 tests/test_gather.py .....                                                      [ 34%]
 tests/test_combine.py ............                                              [ 40%]
 tests/test_api.py ........                                                      [ 44%]
 tests/test_prepare.py ................................................................
 ..........................................                                      [100%]

   ===============================  192 passed in 3.16s ===============================

You can monitor what lines of code the test suite exercises using the coverage.py and pytest-cov tools with the command:

$ cd NEMO-Cmd/
$ pixi run -e test pytest-cov

The test coverage report will be displayed below the test suite run output.

Alternatively, you can use

$ cd NEMO-Cmd/
$ pixi run -e test pytest-cov-html

to produce an HTML report that you can view in your browser by opening NEMO-Cmd/htmlcov/index.html.

Continuous Integration

Pytest with Coverage Status Codecov Testing Coverage Report

The NEMO-Cmd package unit test suite is run and a coverage report is generated whenever changes are pushed to GitHub. The results are visible on the repo actions page, from the green checkmarks beside commits on the repo commits page, or from the green checkmark to the left of the “Latest commit” message on the repo code overview page . The testing coverage report is uploaded to codecov.io

The GitHub Actions workflow configuration that defines the continuous integration tasks is in the .github/workflows/pytest-coverage.yaml file.

Version Control Repository

Git on GitHub

The NEMO-Cmd package code and documentation source files are available from the Git repository at https://github.com/SalishSeaCast/NEMO-Cmd.

Issue Tracker

Issue Tracker

Development tasks, bug reports, and enhancement ideas are recorded and managed in the issue tracker at https://github.com/SalishSeaCast/NEMO-Cmd/issues.

License

Licensed under the Apache License, Version 2.0

The NEMO command processor and documentation are copyright 2013 – present by the SalishSeaCast Project Contributors and The University of British Columbia.

They are licensed under the Apache License, Version 2.0. https://www.apache.org/licenses/LICENSE-2.0 Please see the LICENSE file for details of the license.

Release Process

Releases Hatch project

Releases are done at Doug’s discretion when significant pieces of development work have been completed.

The release process steps are:

  1. Use pixi run -e dev hatch version release to bump the version from .devn to the next release version identifier

  2. Edit docs/CHANGES.rst to update the version identifier and replace unreleased with the release date

  3. Commit the version bump and change log update

  4. Create and annotated tag for the release with Git -> New Tag… in PyCharm or git tag -e -a vyy.n

  5. Push the version bump commit and tag to GitHub

  6. Use the GitHub web interface to create a release, editing the auto-generated release notes into sections:

    • Features

    • Bug Fixes

    • Documentation

    • Maintenance

    • Dependency Updates

  7. Use the GitHub Issues -> Milestones web interface to edit the release milestone:

    • Change the Due date to the release date

    • Delete the “when it’s ready” comment in the Description

  8. Use the GitHub Issues -> Milestones web interface to create a milestone for the next release:

    • Set the Title to the next release version, prepended with a v; e.g. v23.1

    • Set the Due date to the end of the year of the next release

    • Set the Description to something like v23.1 release - when it's ready :-)

    • Create the next release milestone

  9. Review the open issues, especially any that are associated with the milestone for the just released version, and update their milestone.

  10. Close the milestone for the just released version.

  11. Use pixi run -e dev hatch version minor,dev to bump the version for the next development cycle, or use pixi run -e dev hatch version major,minor,dev for a year rollover version bump

  12. Edit docs/CHANGES.rst to add a new section for the unreleased dev version

  13. Commit the version bump and change log update

  14. Push the version bump commit to GitHub