Reshapr 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 pre-commit The uncompromising Python code formatter Hatch project

The Reshapr package (Reshapr) is Command-line tool based on Xarray and Dask for extraction of model variable time series from model products like SalishSeaCast, HRDPS & CANESM2/CGCM4.

Python Versions

Python Version from PEP 621 TOML

The Reshapr package is developed and tested using Python 3.12. The package uses some Python language features that are not available in various earlier versions, in particular:

Getting the Code

Git on GitHub

Clone the code and documentation repository from GitHub with:

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

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

$ cd Reshapr
$ conda env create -f envs/environment-dev.yaml
$ conda activate reshapr-dev

Reshapr is installed in editable install mode as part of the conda environment creation process. That means that the package is installed from the cloned repo via symlinks so that it will be automatically updated as the repo evolves.

To deactivate the environment use:

(reshapr-dev)$ conda deactivate

Coding Style

pre-commit The uncompromising Python code formatter

The Reshapr 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, activate the conda development environment, and run pre-commit install:

$ cd Reshapr
$ conda activate reshapr-dev
(reshapr-dev)$ pre-commit install

Note

You only need to install the hooks once immediately after you make a new clone of the Reshapr repository and build your Development Environment.

Building the Documentation

Documentation Status

The documentation for the Reshapr package is written in reStructuredText and converted to HTML using Sphinx. Creating a Development Environment as described above includes the installation of Sphinx. Building the documentation is driven by the docs/Makefile. With your reshapr-dev development environment activated, use:

(reshapr-dev)$ (cd docs && make clean html)

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

Removing everything under '_build'...
Running Sphinx v5.3.0
making output directory... done
loading intersphinx inventory from https://arrow.readthedocs.io/en/latest/objects.inv...
loading intersphinx inventory from https://docs.dask.org/en/stable/objects.inv...
loading intersphinx inventory from https://ubc-moad-docs.readthedocs.io/en/latest/objects.inv...
loading intersphinx inventory from https://docs.python.org/objects.inv...
loading intersphinx inventory from https://docs.xarray.dev/en/stable/objects.inv...
loading intersphinx inventory from https://docs.python.org/3/objects.inv...
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 19 source files that are out of date
updating environment: [new config] 19 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 done
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 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 use Firefox, you can probably accomplish that with:

(reshapr-dev)$ firefox docs/_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://reshapr.readthedocs.io/en/latest/.

Running the Unit Tests

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

With your reshapr-dev development environment activated, use:

(reshapr-dev)$ cd Reshapr/
(reshapr-dev)$ pytest

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

================================ test session starts =================================
platform linux -- Python 3.12.0, pytest-7.4.3, pluggy-1.3.0
Using --randomly-seed=3126613157
rootdir: /media/doug/warehouse/MOAD/Reshapr
plugins: randomly-3.15.0, cov-4.1.0
collected 246 items

tests/test_model_profiles.py .............................................................
.........                                                                           [ 28%]
tests/api/v1/test_extract_api_v1.py .......                                         [ 31%]
tests/core/test_extract.py ...............................................................
...........................................................                         [ 80%]
tests/test_cluster_configs.py .....                                                 [ 82%]
tests/cli/test_cli.py ..                                                            [ 83%]
tests/core/test_dask_cluster.py .........                                           [ 87%]
tests/core/test_info.py ..........................                                  [ 97%]
tests/utils/test_date_formatters.py .....                                           [100%]

================================== 246 passed in 4.32s ===============================

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

(reshapr-dev)$ cd Reshapr/
(reshapr-dev)$ pytest --cov=./

and generate a test coverage report with:

(reshapr-dev)$ coverage report

to produce a plain text report, or

(reshapr-dev)$ coverage html

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

Continuous Integration

Pytest with Coverage Status Codecov Testing Coverage Report

The Reshapr 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 Reshapr package code and documentation source files are available as a Git repository at https://github.com/UBC-MOAD/Reshapr.

Issue Tracker

Issue Tracker

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

License

Licensed under the Apache License, Version 2.0

The code and documentation of the Reshapr project are copyright 2022 – present by the UBC EOAS MOAD Group 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 hatch version release to bump the version from .devn to the next release version identifier; e.g. 23.1.dev0 to 23.1

  2. Commit the version bump

  3. Create an annotated tag for the release with Git -> New Tag… in PyCharm or git tag -e -a vyy.n; git tag -e -a v23.1

  4. Push the version bump commit and tag to GitHub

  5. Use the GitHub web interface to create a release, editing the auto-generated release notes as necessary

  6. 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

  7. 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. v23.2

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

    • Set the Description to something like v23.2 release - when it's ready :-)

    • Create the next release milestone

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

  9. Close the milestone for the just released version.

  10. Use hatch version minor,dev to bump the version for the next development cycle, or use hatch version major,minor,dev for a year rollover version bump

  11. Commit the version bump

  12. Push the version bump commit to GitHub