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 contributing 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

Below shows the steps to create a conda environment for echopype development (replace the Python version with your preferred version).

Attention

We recommend using the libmamba solver instead of the classic solver, since the conda create and conda install step could take very long or fail. See instructions here for installation and usage.

# create a conda environment using the supplied requirements files
# note the last one docs/requirements.txt is only required for building docs
conda create -c conda-forge -n echopype --yes python=3.9 --file requirements.txt --file requirements-dev.txt --file docs/requirements.txt

# switch to the newly built environment
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

# install echopype in editable mode (setuptools "develop mode")
# plot is an extra set of requirements that can be used for plotting.
# the command will install all the dependencies along with plotting dependencies.
pip install -e ".[plot]"

See the Installation and Examples page to simply install the latest echopype release from conda or PyPI.

Tests and test infrastructure

Test data files

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 or also run only particular test files by passing a comma-separated list of test files that you want to run. 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.

python .ci_helpers/run-test.py --local --pytest-args="-vv"  echopype/tests/convert/test_convert_azfp.py,echopype/tests/clean/test_noise.py

will run only the tests in the test_convert_azfp.py and test_noise.py files. 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 string “[all tests ci]” to the PR title. 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 adding the string “[skip ci]” to the PR title.

Documentation development

Function and object doc strings

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

Jupter Book ReadTheDocs documentation

Echopype documentation (https://echopype.readthedocs.io) is based on Jupyter Book which are rendered under the hood with Sphinx. The documentation is hosted at Read The Docs. The documentation package dependencies are found in the docs/requirements.txt file, and the source documentation files are in the docs/source directory. The echopype development conda environment will install all required dependencies.

Our documentation are currently a mixture of the following file formats:

• CommonMark and MySt Markdown

• Jupyter Notebook

• reStructuredText

To run Jupyter Book locally:

jupyter-book build docs/source --path-output docs

To view the HTML files generated by Jupyter Book, open the docs/_build/html/index.html in your browser.

Jupyter Book configurations can be found in the docs/source/_config.yml file. The table of contents arrangements for the sidebar can be found in docs/source/_toc.yml file.

When ready to commit your changes, please pull request your changes to the stable branch. Once the PR is submitted, the pre-commit CI will run for basic spelling and formatting check (See the pre-commit hooks section for more details). Any changes from the pre-commit check have to be pulled to your branch (via git pull) before your push further commits. You will also be able to view the newly built doc in the PR via the “docs/readthedocs.org:echopype” entry shown below.

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 dev branch and therefore it reflects the bleeding edge development code (which may occasionally break the documentation build). Finally, each new echopype release is built as a new release version on ReadTheDocs. Merging pull requests into stable or dev 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. This version is used to test one-off, major breaking changes.