moad_tools Package Development

Licensed under the Apache License, Version 2.0 Python Version Git on GitHub The uncompromising Python code formatter Documentation Status Sphinx linkcheck Issue Tracker

The UBC EOAS MOAD Group Tools package (moad_tools) is a collection of Python modules that facilitate code reuse for the UBC EOAS MOAD Group.

Python Versions

Python Version

The moad_tools package is developed using Python 3.9. It is tested for Python versions >=3.8. The package uses some Python language features that are not available in versions prior to 3.8, in particular:

Getting the Code

Git on GitHub

Clone the code and documentation repository from GitHub with:

$ git clone git@github.com:UBC-MOAD/moad_tools.git

Development Environment

Setting up an isolated development environment using Conda is recommended. Assuming that you have the Anaconda Python Distribution or Miniconda3 installed, you can create and activate an environment called moad-tools that will have all of the Python packages necessary for development, testing, and building the documentation with the commands below:

$ cd moad_tools
$ conda env create -f envs/environment-dev.yaml
$ conda activate moad-tools
(moad-tools)$ python3 -m pip install --editable .

The --editable option in the pip install command above installs the moad_tools package via a symlink so that the installed package will be automatically updated as the repo evolves.

To deactivate the environment use:

(moad-tools)$ conda deactivate

Coding Style

The uncompromising Python code formatter

The moad_tools package uses the black code formatting tool to maintain a coding style that is very close to PEP 8.

black is installed as part of the Development Environment setup.

To run black on the entire code-base use:

$ cd moad_tools
$ conda activate moad-tools
(moad-tools)$ black ./

in the repository root directory. The output looks something like:

reformatted /media/doug/warehouse/MOAD/moad_tools/docs/conf.py
reformatted /media/doug/warehouse/MOAD/moad_tools/moad_tools/observations.py
All done! ✨ 🍰 ✨
2 files reformatted, 5 files left unchanged.

Documentation

Documentation Status

The :moad_tools documentation 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://ubc-moad-tools.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. With your moad-tools environment activated, use:

(moad-tools)$ cd moad_tools/docs/
(moad-tools) docs$ make clean html

to do a clean build of the documentation. The output looks something like:

Removing everything under '_build'...
Running Sphinx v3.1.1
making output directory... done
loading intersphinx inventory from https://mohid-cmd.readthedocs.io/en/latest/objects.inv...
loading intersphinx inventory from https://numpy.org/doc/1.18/objects.inv...
loading intersphinx inventory from https://pandas.pydata.org/docs/objects.inv...
loading intersphinx inventory from https://docs.python.org/3/objects.inv...
loading intersphinx inventory from https://rasterio.readthedocs.io/en/latest/objects.inv...
loading intersphinx inventory from https://xarray.pydata.org/en/stable/objects.inv...
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 3 source files that are out of date
updating environment: [new config] 3 added, 0 changed, 0 removed
reading sources... [100%] pkg_development
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
writing output... [100%] pkg_development
generating indices...  genindex py-modindexdone
highlighting module code... [100%] moad_tools.observations
writing additional pages...  searchdone
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 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. To preview in Firefox from the command-line you can do:

(moad-tools) docs$ firefox _build/html/index.html

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://ubc-moad-tools.readthedocs.io/en/latest/.

Running the Unit Tests

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

With your moad-tools development environment activated, use:

(mohid-cmd)$ cd moad_tools/
(mohid-cmd)$ pytest

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

============================ test session starts ============================
platform linux -- Python 3.8.3, pytest-5.4.3, py-1.9.0, pluggy-0.13.1
rootdir: /media/doug/warehouse/MOAD/moad_tools
collected 11 items
tests/test_observations.py ..                                          [ 18%]
tests/test_random_oil_spills.py .........                              [100%]

============================ 11 passed in 1.98s =============================

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

(mohid-cmd)$ cd moad_tools/
(mohid-cmd)$ pytest --cov=./

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

Alternatively, you can use

(mohid-cmd)$ pytest --cov=./ --cov-report html

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

Continuous Integration

GitHub Workflow Status Codecov Testing Coverage Report

The moad_tools 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 moad_tools package code and documentation source files are available in the moad_tools Git repository at https://github.com/UBC-MOAD/moad_tools.

Issue Tracker

Issue Tracker

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

License

Licensed under the Apache License, Version 2.0

The UBC EOAS MOAD Group moad_tools Python package code and documentation are copyright 2018-2021 by the UBC EOAS MOAD Group and The University of British Columbia.

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