=============================
Autoprotocol Python Library
=============================
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Autoprotocol_ is the standard way to express experiments in life science. This repository contains a python library for generating Autoprotocol.
Installation
------------
To work from the latest stable release:
.. code-block:: bash
pip install autoprotocol
check the the releases_ for more information about the changes that will be downloaded.
Alternatively to get more up-to-date features:
.. code-block:: bash
git clone https://github.com/autoprotocol/autoprotocol-python
cd autoprotocol-python
python setup.py install
check the changelog_ for information about features included on `master` but not yet released.
Building a Protocol
-------------------
A basic protocol is written by declaring :code:`Protocol.ref` objects and acting on them with :code:`Protocol.instruction` methods.
.. code-block:: python
import json
from autoprotocol.protocol import Protocol
# instantiate a protocol object
p = Protocol()
# generate a ref
# specify where it comes from and how it should be handled when the Protocol is done
plate = p.ref("test pcr plate", id=None, cont_type="96-pcr", discard=True)
# generate seal and spin instructions that act on the ref
# some parameters are explicitly specified and others are left to vendor defaults
p.seal(
ref=plate,
type="foil",
mode="thermal",
temperature="165:celsius",
duration="1.5:seconds"
)
p.spin(
ref=plate,
acceleration="1000:g",
duration="1:minute"
)
# serialize the protocol as Autoprotocol JSON
print(json.dumps(p.as_dict(), indent=2))
which prints
.. code-block:: json
{
"instructions": [
{
"op": "seal",
"object": "test pcr plate",
"type": "foil",
"mode": "thermal",
"mode_params": {
"temperature": "165:celsius",
"duration": "1.5:second"
}
},
{
"op": "spin",
"object": "test pcr plate",
"acceleration": "1000:g",
"duration": "1:minute"
}
],
"refs": {
"test pcr plate": {
"new": "96-pcr",
"discard": true
}
}
}
Extras
------
Select SublimeText snippets are included with this repository.
To use them copy the :code:`autoprotocol-python SublimeText Snippet` folder to your local Sublime :code:`/Packages/User` directory.
Documentation
-------------
For more information, see the documentation_.
Contributing
------------
For more information, see CONTRIBUTING_.
.. _Autoprotocol: http://www.autoprotocol.org
.. _releases: http://github.com/autoprotocol/autoprotocol-python/releases
.. _changelog: http://autoprotocol-python.readthedocs.io/en/latest/changelog.html
.. _CONTRIBUTING: http://autoprotocol-python.readthedocs.io/en/latest/CONTRIBUTING.html
.. _documentation: http://autoprotocol-python.readthedocs.org/en/latest/