aind-codeocean-utils

Library to contain useful utility methods to interface with Code Ocean.

Installation

To use the package, you can install it from pypi:

pip install aind-codeocean-utils

To install the package from source, in the root directory, run

pip install -e .

To develop the code, run

pip install -e .[dev]

Usage

The package includes helper functions to interact with Code Ocean:

APIHandler

This class enables one to:

1. Update asset tags in Code Ocean
2. Find external data assets that do not exist in S3
3. Find external data assets

import os

from codeocean.client import CodeOcean
from aind_codeocean_utils.api_handler import APIHandler

# Get token and domain parameters for CodeOcean client
CO_TOKEN = os.environ["CO_TOKEN"]
CO_DOMAIN = os.environ["CO_DOMAIN"]

co_client = CodeOcean(domain=CO_DOMAIN, token=CO_TOKEN)

api_handler = APIHandler(co_client)

data_assets = [
  co_client.data_assets.get_data_asset(data_asset_id="abc"),
  co_client.data_assets.get_data_asset(data_asset_id="def")
]

api_handler.update_tags(
  tags_to_remove=["test"],
  tags_to_add=["new_tag"],
  data_assets=data_assets,
)

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 repository 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 build tools 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 bugfix
• 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

Semantic Release

The table below, from semantic release, shows which commit message gets you which release type when semantic-release runs (using the default configuration):

Commit message	Release type
fix(pencil): stop graphite breaking when too much pressure applied	Patch Fix Release, Default release
feat(pencil): add 'graphiteWidth' option	Minor Feature Release
perf(pencil): remove graphiteWidth option BREAKING CHANGE: The graphiteWidth option has been removed. The default graphite width of 10mm is always used for performance reasons.	Major Breaking Release (Note that the BREAKING CHANGE: token must be in the footer of the commit)

Note: The automatic version bump workflow does not work for manual version changes. As shown above, use the appropriate scope and commit message that reflects changes included in a PR.

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.