deeporiginbio / deeporigin-client

Deep Origin CLI and Python client

deeporigin

This repository contains the deeporigin CLI and Python client, which allows you to interact with Deep Origin from the command line and Python.

Warning

The deeporigin client is under active development. Features may change or be removed.

Installing

Caution

As a best practice, we recommend installing this package in a virtual environment.

To install this package, run the following:

pip install deeporigin

Configuration

If you are running deeporigin outside of a Deep Origin workstation (for example, on your own computer), you need to configure this. Run the following to configure your organization, replacing org-id with the ID of the organization you would like to work with.

deeporigin config set organization_id [org-id]

Developing

First, download the source code from GitHub:

git clone [email protected]:deeporiginbio/deeporigin-client.git
cd deeporigin-client

Second, run the code below to create a virtual environment and install this package into it. This requires make v4.4 or higher.

make install

Testing

Running the tests locally

To run the tests locally, execute the following:

make test

By default, the tests are run using mocked responses. To run the tests against the live Deep Origin API, execute the following:

make test client=default

Automated tests on GitHub Actions

The tests are automatically run on GitHub Actions on every commit to every pull request.

License

MIT

deeporigin-client's Issues

Rather than make a copy of the user's configuration file (if it exists), would it be better to have an "export" method that exports the current configuration value to a YAML file?

          Rather than make a copy of the user's configuration file (if it exists), would it be better to have an "export" method that exports the current configuration value to a YAML file?

Originally posted by @jonrkarr in #50 (comment)

I think we should generalize the description further -- "Command line tool and Python client for working ..."

          I think we should generalize the description further -- "Command line tool and Python client for working ..."

Originally posted by @jonrkarr in #1 (comment)

After CLI add "and Python client"

          After CLI add "and Python client"

Originally posted by @jonrkarr in #1 (comment)

Another small function that would be helpful to add is a function that prints out the path to the user configuration file.

Another small function that would be helpful to add is a function that prints out the path to the user configuration file.

Originally posted by @jonrkarr in #50 (comment)

Remove "CLI"

          Remove "CLI"

Originally posted by @jonrkarr in #1 (comment)

I believe these lines can be removed

          I believe these lines can be removed

Originally posted by @jonrkarr in #1 (comment)

I think we should generalize the description further -- "Command line tool and Python client for working ..."

          I think we should generalize the description further -- "Command line tool and Python client for working ..."

Originally posted by @jonrkarr in #1 (comment)