*Allotrope® is a registered trademark of the Allotrope Foundation; no affiliation with the Allotrope Foundation is claimed or implied.
Welcome to allotropy
-- a Python library by Benchling for converting instrument data into the Allotrope Simple Model (ASM).
The objective of this library is to read text or Excel based instrument software output and return a JSON representation that conforms to the published ASM schema. The code in this library does not convert from proprietary/binary output formats and so has no need to interact with any of the specific vendor softwares.
If you aren't familiar with Allotrope, we suggest you start by reading the Allotrope Product Overview.
We have chosen to have this library output ASM since JSON is easy to read and consume in most modern systems and can be checked by humans without any special tools needed. All of the published open source ASMs can be found in the ASM Gitlab repository.
We currently have parser support for the following instruments:
- Agilent Gen5
- Applied Bio QuantStudio
- Applied Bio AbsoluteQ
- Beckman Vi-Cell BLU
- Beckman Vi-Cell XR
- ChemoMetec Nucleoview
- Luminex xPONENT
- MolDev SoftMax Pro
- NovaBio Flex2
- PerkinElmer Envision
- Roche Cedex BioHT
- Thermo Fisher NanoDrop Eight
- Unchained Labs Lunatic
This code is published under the permissive MIT license because we believe that standardized instrument data is a benefit for everyone in science.
We welcome community contributions to this library and we hope that together we can expand the coverage of ASM-ready data for everyone. If you are interested, please read our contribution guidelines.
Convert a file to an ASM dictionary:
from allotropy.parser_factory import Vendor
from allotropy.to_allotrope import allotrope_from_file
asm_schema = allotrope_from_file("filepath.txt", Vendor.MOLDEV_SOFTMAX_PRO)
or, convert any IO:
from allotropy.parser_factory import Vendor
from allotropy.to_allotrope import allotrope_from_io
with open("filename.txt") as f:
asm_schema = allotrope_from_io(f, Vendor.MOLDEV_SOFTMAX_PRO)
bytes_io = BytesIO(file_stream)
asm_schema = allotrope_from_io(bytes_io, Vendor.MOLDEV_SOFTMAX_PRO)
.gitignore
: used standard GitHub Python template and added their recommended JetBrains lines
Install Hatch: https://hatch.pypa.io/latest/
Install Python: https://www.python.org/downloads/
This library supports Python 3.9 or higher. Hatch will install a matching version of Python (defined in pyproject.toml
) when it sets up your environment.
Add pre-push checks to your repo:
hatch run scripts:setup-pre-push
To add requirements used by the library, update dependencies
in pyproject.toml
:
- For project dependencies, update
dependencies
under[project]
. - For script dependencies, update
dependencies
under[tool.hatch.envs.default]
. - For lint dependencies, update
dependencies
under[tool.hatch.envs.lint]
. - For test dependencies, update
dependencies
under[tool.hatch.envs.test]
.
List all environments:
hatch env show
Run all lint:
hatch run lint:all
Auto-fix all possible lint issues:
hatch run lint:fmt
Run all tests:
hatch run test:test
Run a specific test file (replace the filepath with your own):
hatch run test:test tests/allotrope/allotrope_test.py
Run all tests with coverage:
hatch run test:cov
Spawn a shell within an environment for development:
hatch shell
To publish a new version, update the version in src/allotropy/__about__.py
and run:
hatch build
hatch publish