Contributing to echopype¶
We welcome your contributions, large or small!
Contributing with Git and GitHub¶
Please submit questions or report problems via GitHub issues. If you’re new to GitHub, see these tips for submitting issues: “Creating issues on GitHub”.
For echopype development we use the gitflow workflow with forking. All development
changes are merged into the dev development branch. First create your own fork of the
source GitHub repository
https://github.com/OSOceanAcoustics/echopype/
(upstream), then clone your fork; your fork will be the origin remote. See
this excellent tutorial for
guidance on forking and opening pull requests, but replace references to the master
branch with the dev development branch. See
this description of the gitflow workflow.
The complete workflow we use is depicted in the diagram below, which includes
components involving documentation updates (see Documentation development below)
and preparation of releases.
Installation for echopype development¶
To access and test the latest, unreleased development version of echopype, clone the master branch from the source repository:
git clone https://github.com/OSOceanAcoustics/echopype.git
To set up your local environment to contribute to echopype,
please follow the git forking workflow as described above.
After forking the source repository, clone your fork,
then set the source repository as the upstream git remote:
git clone https://github.com/myusername/echopype.git
cd echopype
git remote add upstream https://github.com/OSOceanAcoustics/echopype.git
Create a conda environment for echopype development (replace the Python version with your preferred version):
conda create -c conda-forge -n echopype --yes python=3.8 --file requirements.txt --file requirements-dev.txt
conda activate echopype
# ipykernel is recommended, in order to use with JupyterLab and IPython
# to aid with development. We recommend you install JupyterLab separately
conda install -c conda-forge ipykernel
pip install -e .
See the Installation page to simply install the latest echopype release from conda or PyPI.
Test data files¶
Attention
Echopype previously used Git LFS for managing and accessing large test data files. We have deprecated its use starting with echopype version 0.5.0. The files in https://github.com/OSOceanAcoustics/echopype/tree/master/echopype/test_data are also being deprecated.
Test echosounder data files are managed in a private Google Drive folder and made available via the cormorack/http Docker image on Docker hub; the image is rebuilt daily when new test data are added on Google Drive. See the Running the tests section below for details.
Running the tests¶
To run the echopype unit tests in echopype/tests,
Docker
will need to be installed if not already present
(docker-compose is also used, but it’s installed
in the conda environment for echopype development). To run the tests:
# Install and/or deploy the echopype docker containers for testing
python .ci_helpers/docker/setup-services.py --deploy
# Run the tests
python .ci_helpers/run-test.py --local --pytest-args="-vv"
# When done, "tear down" the docker containers
python .ci_helpers/docker/setup-services.py --tear-down
The tests include reading and writing from locally set up (via docker) http and S3 object-storage sources, the latter via minio.
pre-commit hooks¶
The echopype development conda environment includes pre-commit,
and useful pre-commit “hooks” have been configured in the
.pre-commit-config.yaml file.
Current hooks include file formatting (linting) checks (trailing spaces, trailing lines,
JSON and YAML format checks, etc) and Python style autoformatters (PEP8 / flake8, black and isort).
To run pre-commit hooks locally, run pre-commit install before running the
docker setup-service deploy statement described above. The hooks will run automatically
during git commit and will give you options as needed before committing your changes.
You can also run pre-commit before actually doing git commit, as you edit the code, by running pre-commit run --all-files. See the pre-commit usage documentation for details.
Continuous integration GitHub Actions¶
echopype makes extensive use of GitHub Actions for continuous integration (CI) of unit tests and other code quality controls. Every pull request triggers the CI. See echopype/.github/workflows.
The CI tests can be a bit slow, taking up to 20-30 minutes. Under special circumstances, when the submitted changes have a very limited scope (such as contributions to the documentation) or you know exactly what you’re doing (you’re a seasoned echopype contributor), the CI can be skipped. This is done by including the string “[skip ci]” in your last commit’s message.
Documentation development¶
Echopype documentation (https://echopype.readthedocs.io) is based on
Sphinx and is hosted at
Read The Docs. The sphinx files are found
in the docs directory, and the source documentation files, written in
reStructuredText
(.rst) format, are in the docs/source directory. The echopype development
conda environment will install all required Sphinx dependencies.
To run Sphinx locally:
cd docs
sphinx-build -b html -d _build/doctrees source _build/html
To view the generated HTML files generated by Sphinx, open the
docs/_build/html/index.html in your browser.
Updates to the documentation that are based on the current echopype release (that is,
not involving echopype API changes) should be merged into the GitHub stable branch.
These updates will then become available immediately on the default ReadTheDocs version.
Examples of such updates include fixing spelling mistakes, expanding an explanation, and adding a new section that documents a previously undocumented feature.
Function and object doc strings¶
For inline strings documenting functions and objects (“doc strings”), we use the numpydoc style (Numpy docstring format).
Documentation versions¶
https://echopype.readthedocs.io redirects to the documentation stable version,
https://echopype.readthedocs.io/en/stable/, which is built from the stable branch
on the echopype GitHub repository. In addition, the latest version
(https://echopype.readthedocs.io/en/latest/) is built from the master branch,
while the hidden dev version (https://echopype.readthedocs.io/en/dev/) is built
from the dev branch. Finally, each new echopype release is built as a new release version
on ReadTheDocs. Merging pull requests into any of these three branches or issuing a
new tagged release will automatically result in a new ReadTheDocs build for the
corresponding version.
We also maintain a test version of the documentation at https://doc-test-echopype.readthedocs.io/ for viewing and debugging larger, more experimental changes, typically from a separate fork.