aind-codeocean-utils 1.0.0
Generated from aind-library-template
License: MIT
Requires Python: >=3.9

# aind-codeocean-utils

[![License](https://img.shields.io/badge/license-MIT-brightgreen)](LICENSE)
![Code Style](https://img.shields.io/badge/code%20style-black-black)
[![semantic-release: angular](https://img.shields.io/badge/semantic--release-angular-e10079?logo=semantic-release)](https://github.com/semantic-release/semantic-release)
![Interrogate](https://img.shields.io/badge/interrogate-100.0%25-brightgreen)
![Coverage](https://img.shields.io/badge/coverage-100%25-brightgreen?logo=codecov)
![Python](https://img.shields.io/badge/python->=3.7-blue?logo=python)

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

## Installation

To use the package, you can install it from `pypi`:
```bash
pip install aind-codeocean-utils
```


To install the package from source, in the root directory, run
```bash
pip install -e .
```

To develop the code, run
```bash
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


```python
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:

```bash
coverage run -m unittest discover && coverage report
```

- Use **interrogate** to check that modules, methods, etc. have been documented thoroughly:

```bash
interrogate .
```

- Use **flake8** to check that code is up to standards (no unused imports, etc.):
```bash
flake8 .
```

- Use **black** to automatically format the code into PEP standards:
```bash
black .
```

- Use **isort** to automatically sort import statements:
```bash
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](https://github.com/angular/angular/blob/main/CONTRIBUTING.md#commit) style for commit messages. Roughly, they should follow the pattern:
```text
<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](https://github.com/semantic-release/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`<br><br>`BREAKING CHANGE: The graphiteWidth option has been removed.`<br>`The default graphite width of 10mm is always used for performance reasons.` | ~~Major~~ Breaking Release <br /> (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
```bash
sphinx-apidoc -o doc_template/source/ src 
```
Then to create the documentation HTML files, run
```bash
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).