terralab-cli 0.0.6

Command line interface for interacting with the Terra Scientific Pipelines Service, or Teaspoons.

Terralab CLI

Overview

The Terralab CLI provides a command-line interface with which to interact with the Terra Scientific Pipelines Service, or Teaspoons.

Currently, Terralab supports running Genotype Imputation (for public release in early 2025).

Note that in order to use Terralab and Teaspoons, you must have a Terra account.

User instructions coming soon.

Installation

You can install the Terralab CLI from PyPi using your favorite package management tool.

For example, run

pip install terralab-cli

Using the CLI

Once installed, to run the CLI, run the following command:

terralab COMMAND [ARGS]

For example, to list the pipelines you can run using Terralab, run the following command:

terralab pipelines list

(Internal) WIP documentation for the CLI.

Python CLI structure

The CLI code is structured as follows:

terra-scientific-pipelines-service-cli
├── terralab
│   └── commands
│   │   └── __init__.py
│   │   └── auth_commands.py
│   │   └── pipelines_commands.py
│   └── logic
│   │   └── __init__.py
│   │   └── auth_logic.py
│   │   └── pipelines_logic.py
│   └── __init__.py
│   └── auth_helper.py
│   └── cli.py
│   └── client.py
│   └── config.py
│   └── teaspoons
├── tests
│   └── commands
│   │   └── test_auth_commands.py
│   │   └── test_pipelines_commands.py
│   └── logic
│   │   └── test_auth_logic.py
│   │   └── test_pipelines_logic.py
│   └── __init__.py
│   └── auth_helper.py
│   └── cli.py
│   └── client.py
│   └── config.py
│   └── terralab
├── .gitignore
├── .terralab-cli-config
├── poetry.lock
├── pyproject.toml
├── README.md

In the terralab directory, we have the following files and subdirectories:

• auth_helper.py contains the code for authenticating with the Terra Scientific Pipelines Service (Terra, via b2c).
• cli.py is the entrypoint for the CLI. It configures logging and assembles the CLI sub-modules that are defined in commands/.
• client.py contains the code for wrapping API calls to the Terra Scientific Pipelines Service.
• config.py contains the code for managing the CLI configuration via environment variables.
• utils.py contains utility functions that are used across the CLI.
• The commands directory contains the CLI sub-modules. This is effectively the controller layer for the CLI.
• The logic directory contains the business logic for the CLI, including calling Terra Scientific Pipelines Service APIs via the thin teaspoons_client, which is autogenerated and published by the Terra Scientific Pipelines Service repository.

In the tests directory, we have test files that can be run with pytest.

Development

You'll need to have poetry installed to manage python dependencies. Instructions for installing poetry can be found here.

To install the CLI locally, run the following commands from the root project directory:

poetry lock      # only needed if you updated dependencies in pyproject.toml
poetry install

You do not need to re-run these commands each time you update code locally, unless you've added dependencies in pyproject.toml.

If you do update dependencies in pyproject.toml, run poetry lock and check in the resulting changes to poetry.lock along with the rest of your code changes.

To run the tests, execute the following command from the root project (terra-scientific-pipelines-service-cli) directory:

poetry run pytest

To run tests with a coverage report printed to the terminal:

poetry run pytest --cov-report term --cov=terralab

To run the formatter, execute the following command from the root project directory:

poetry run black .

To run the linter with fixes, execute the following command from the root project directory:

poetry run ruff check --fix

To run the linter as a check without fixes, omit the --fix flag.