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 (except for documentation) 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 (PRs), but replace references to the main branch with the dev development branch. See this description of the gitflow workflow. This diagram depicts the complete workflow we use in the source GitHub repository:

graph LR classDef patch fill:#f2ece4 main --> stable main --> dev p1([doc patch]):::patch -.-> stable p2([code patch]):::patch -.-> dev stable --> |docs merge| rel[release/0.x.y] dev --> |dev merge| rel rel --> main

doc patch: Updates to the documentation that refer to the current echopype release can be pushed out immediately to the echopype documentation site by contibuting patches (PRs) to the stable branch. See Documentation development below for more details.
code patch: Code development is carried out as patches (PRs) to the dev branch; changes in the documentation corresponding to changes in the code can be carried out in this branch as well.
New releases are prepared in a new release branch that merges changes in dev and stable.

To maintain a clean and readable commit history, use “Merge pull request > Squash and merge” when merging an individual PR to dev or a documentation-only PR to stable. This will highlight the specific feature(s) contributed by the PR. When merging an echopype release PR to main, use “Merge pull request > Create a merge commit” in order to retain all the squashed PR commits in the commit history.

Installation for echopype development¶

To access and test the latest, unreleased development version of echopype, clone the main 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=3.9 --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.

Tests and test infrastructure¶

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/main/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 found 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). Then:

# Install and/or deploy the echopype docker containers for testing.
# Test data files will be downloaded
python .ci_helpers/docker/setup-services.py --deploy

# Run all the tests. But first make sure the
# echopype development conda environment is activated
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.

.ci_helpers/run-test.py

will execute all tests. The entire test suite can be a bit slow, taking up to 40 minutes or more. If your changes impact only some of the subpackages (convert, calibrate, preprocess, etc), you can run run-test.py with only a subset of tests by passing as an argument a comma-separated list of the modules that have changed. For example:

python .ci_helpers/run-test.py --local --pytest-args="-vv" echopype/calibrate/calibrate_ek.py,echopype/preprocess/noise_est.py

will run only tests associated with the calibrate and preprocess subpackages.

For run-test.py usage information, use the -h argument: python .ci_helpers/run-test.py -h

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 (PR) triggers the CI. See echopype/.github/workflows, especially pr.yaml.

The entire test suite can be a bit slow, taking up to 40 minutes or more. To mitigate this, the CI default is to run tests only for subpackages that were modified in the PR; this is done via .ci_helpers/run-test.py (see the Running the tests section). To have the CI execute the entire test suite, add the GitHub label Needs Complete Testing to the PR before submitting it.

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¶

Function and object doc strings¶

For inline strings documenting functions and objects (“doc strings”), we use the numpydoc style (Numpy docstring format).

Sphinx ReadTheDocs documentation¶

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.

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 main 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.

Contributing to echopype

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