AtlantisCmd 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

The AtlantisCmd package (atlantis_cmd) is a command-line tool for doing various operations associated with the Salish Sea Atlantis project version of the CSIRO Atlantis ecosystem model. AtlantisCmd is based on, and provides Atlantis-specific extensions for https://github.com/SalishSeaCast/NEMO-Cmd.

Python Versions

Python Version

The atlantis_cmd package is developed and tested using Python 3.14. The Continuous Integration workflow on GitHub ensures that the package is tested whenever changes in the repository are pushed or merged.

Getting the Code

Git on GitHub

Clone the code and documentation repository from GitHub with:

$ git clone git@github.com:SS-Atlantis/AtlantisCmd.git

or copy the URI (the stuff after git clone above) from the Code button on the repository page.

Note

The git clone command above assumes that your are connecting to GitHub using SSH. If it fails, please follow the instructions in our Secure Remote Access docs to set up your SSH keys and Copy Your Public ssh Key to GitHub.

Development Environment

Pixi

AtlantisCmd uses Pixi for package and environment management. 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 AtlantisCmd/ 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 AtlantisCmd command-line interface; e.g. pixi run atlantis help

  • Other environments used 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.

AtlantisCmd 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 AtlantisCmd package uses the 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 AtlantisCmd
$ 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 AtlantisCmd repository.

Building the Documentation

Documentation Status

The documentation for the AtlantisCmd package is written in reStructuredText and converted to HTML using Sphinx. Building the documentation is driven by the docs/Makefile. To do a clean build of the documentation use:

$ cd AtlantisCmd
$ 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 'moaddocs' from https://ubc-moad-docs.readthedocs.io/en/latest/objects.inv ...
loading intersphinx inventory 'nemocmd' from https://nemo-cmd.readthedocs.io/en/latest/objects.inv ...
building [mo]: targets for 0 po files that are out of date
writing output...
building [html]: targets for 7 source files that are out of date
updating environment: [new config] 7 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/Atlantis/AtlantisCmd/docs/_build/html/_static/language_data.js
Writing evaluated template result to /media/doug/warehouse/Atlantis/AtlantisCmd/docs/_build/html/_static/documentation_options.js
Writing evaluated template result to /media/doug/warehouse/Atlantis/AtlantisCmd/docs/_build/html/_static/basic.css
Writing evaluated template result to /media/doug/warehouse/Atlantis/AtlantisCmd/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
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 docs/_build/html/. You can open the index.html file in that directory tree in your browser to preview the results of the build.

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://atlantiscmd.readthedocs.io/en/latest/.

Running the Unit Tests

The test suite for the AtlantisCmd package is in AtlantisCmd/tests/. The pytest tool is used for test parametrization and as the test runner for the suite.

Use:

$ cd AtlantisCmd/
$ pixi run pytest

to run the test suite. The output looks something like:

================================ test session starts =================================
platform linux -- Python 3.14.3, pytest-9.0.2, pluggy-1.6.0
Using --randomly-seed=2919284692
rootdir: /media/doug/warehouse/Atlantis/AtlantisCmd
configfile: pyproject.toml
plugins: randomly-3.15.0, cov-7.1.0
collected 49 items

tests/test_run.py .........................................                         [ 83%]
tests/test_post_gen_project.py ........                                             [100%]

================================= 49 passed in 0.84s =================================

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

$ cd AtlantisCmd/
$ pixi run pytest-cov

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

Alternatively, you can use

$ pixi run pytest-cov-html

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

Continuous Integration

Pytest with Coverage Status Codecov Testing Coverage Report

The AtlantisCmd 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 AtlantisCmd package code and documentation source files are available as a Git repository at https://github.com/SS-Atlantis/AtlantisCmd.

Issue Tracker

Issue Tracker

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

License

Licensed under the Apache License, Version 2.0

The code and documentation of the Atlantis Command Processor project are copyright 2021 – present by the Salish Sea Atlantis project contributors, The University of British Columbia, and CSIRO.

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. Use pixi update ensure that the new version is reflected in the Pixi lock file

  3. Commit the version bump

  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. v25.1

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

    • Set the Description to something like v25.1 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. Use pixi update ensure that the new version is reflected in the Pixi lock file

  13. Commit the version bump

  14. Push the version bump commit to GitHub