transcriptic/marshmallow_dataclass

Automatic generation of marshmallow schemas from dataclasses.

Transcriptic Python Library

The Transcriptic Python Library (TxPy) provides a Python interface for managing Transcriptic organizations, projects, runs, datasets and more. One can either interface with our library through the bundled command line interface (CLI) or through a Jupyter notebook using a Python client.

We recommend using the Jupyter interface as it provides a nice rendering and presentation of the objects, as well as provide additional analysis and properties functions specific to the Transcriptic objects.

Transcriptic is the robotic cloud laboratory for the life sciences. https://www.transcriptic.com

Setup

Organization

TxPy is separated into three main components: 1) Core. The core modules provide a barebones client for making calls to the Transcriptic webapp to create and obtain data. This can be done via the api object or via the command-line using the CLI. 2) Jupyter. This module provides a Jupyter-centric means for interacting with objects returned from the Transcriptic webapp such as Run, Project and Dataset. 3) Analysis. This module provides some basic analysis wrappers around datasets returned from the webapp using standard Python scientific libraries.

Installation

For a barebones CLI install, you’ll do:

pip install transcriptic

We recommend installing the jupyter module for Jupyter-centric navigation:

pip install transcriptic[jupyter]

Lastly, we recommend installing the analysis module for a full-fledged experience:

pip install transcriptic[analysis]

Alternatively, if you’re interested in contributing or living at the edge:

git clone https://github.com/strateos/transcriptic.git
cd transcriptic
pip install .[jupyter,analysis]

to upgrade to the latest version using pip or check whether you’re already up to date:

pip install transcriptic --upgrade

Then, login to your Transcriptic account:

$ transcriptic login
Email: [email protected]
Password:
Logged in as [email protected] (example-lab)

Tab Completion

To enable auto-completion for the Transcriptic CLI, you’ll need to download an appropriate auto-complete file and add it your shell configuration.

Here’s an example script for installing it on a bash shell in your ~/.config directory.

export INSTALL_DIR=~/.config && mkdir -p $INSTALL_DIR
curl -L https://raw.githubusercontent.com/strateos/transcriptic/master/autocomplete/bash.sh > $INSTALL_DIR/tx_complete.sh && chmod +x $INSTALL_DIR/tx_complete.sh
echo ". $INSTALL_DIR/tx_complete.sh" >> ~/.bash_profile

• Ubuntu and Fedora note: Modify your ~/.bashrc instead of ~/.bash_profile
• Zsh note: Use autocomplete/zsh.sh instead of bash.sh. Modify your ~/.zshrc instead of ~/.bash_profile
• Fish note: Use autocomplete/fish.sh instead of bash.sh. Change $INSTALL_DIR to ~/.config/fish/completions and rename tx-complete.sh to tx-complete.fish. Skip the last step.

Documentation

CLI

See the Transcriptic Developer Documentation for detailed information about how to use this package, including learning about how to package protocols and build releases.

Jupyter

Click on the icon to open an interactive notebook environment for using the library.

Developer

View Developer Specific Documentation

Permissions

Note that direct analysis and submission of Autoprotocol is currently restricted. Please contact [email protected] if you would like to do so.

Contributing

Read Contributing for more information on contributing to TxPy.