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aind-codeocean-api

License Code Style

Python wrapper around CodeOcean's REST API.

DEPRECATION WARNING

Code Ocean has published their own SDK:

https://github.com/codeocean/codeocean-sdk-python

We will be dropping support of this package in favor of the official SDK.

Installation

To install from PyPI, run:

pip install aind-codeocean-api

To install from a clone of the repository, in the root directory, run

pip install -e .

To install the development libraries of the code, run

pip install -e .[dev]

Usage

Example of getting data asset metadata:

from aind_codeocean_api.codeocean import CodeOceanClient

domain = "https://acmecorp.codeocean.com"
token = "AN_API_TOKEN" # Replace with your api token
data_asset_id = "37a93748-ce90-4980-913b-2de0908d5212"
co_client = CodeOceanClient(domain=domain, token=token)
response = co_client.get_data_asset(data_asset_id=data_asset_id)
metadata = response.json()

To store credentials locally, run:

python -m aind_codeocean_api.credentials

Contributing

Linters and testing

There are several libraries used to run linters, check documentation, and run tests.

  • Please test your changes using the coverage library, which will run the tests and log a coverage report:
coverage run -m unittest discover && coverage report
  • Use interrogate to check that modules, methods, etc. have been documented thoroughly:
interrogate .
  • Use flake8 to check that code is up to standards (no unused imports, etc.):
flake8 .
  • Use black to automatically format the code into PEP standards:
black .
  • Use isort to automatically sort import statements:
isort .

Pull requests

For internal members, please create a branch. For external members, please fork the repo and open a pull request from the fork. We'll primarily use Angular style for commit messages. Roughly, they should follow the pattern:

<type>(<scope>): <short summary>

where scope (optional) describes the packages affected by the code changes and type (mandatory) is one of:

  • build: Changes that affect the build system or external dependencies (example scopes: pyproject.toml, setup.py)
  • ci: Changes to our CI configuration files and scripts (examples: .github/workflows/ci.yml)
  • docs: Documentation only changes
  • feat: A new feature
  • fix: A bug fix
  • perf: A code change that improves performance
  • refactor: A code change that neither fixes a bug nor adds a feature
  • test: Adding missing tests or correcting existing tests

Documentation

To generate the rst files source files for documentation, run

sphinx-apidoc -o doc_template/source/ src

Then to create the documentation html files, run

sphinx-build -b html doc_template/source/ doc_template/build/html

More info on sphinx installation can be found here: https://www.sphinx-doc.org/en/master/usage/installation.html