allotropy 0.1.47.post2

Converts to ASM (Allotrope Simple Model) from various file formats.

*Allotrope® is a registered trademark of the Allotrope Foundation; no affiliation with the Allotrope Foundation is claimed or implied.

Introduction

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. Note that some schemas do not yet match the published ASM schema, in these cases the CHANGE_NOTES.md file included alongside the schema details the differences and proposed changes to ASM or the library 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:

Recommended

• Agilent Gen5
• Agilent Gen5 Image
• Agilent TapeStation Analysis
• AppBio AbsoluteQ
• AppBio QuantStudio Design & Analysis
• AppBio QuantStudio RT-PCR
• Beckman PharmSpec
• Beckman Vi-Cell BLU
• Beckman Vi-Cell XR
• Bio-Rad Bio-Plex Manager
• CTL ImmunoSpot
• ChemoMetec Nucleoview
• Luminex xPONENT
• Mabtech Apex
• Methodical Mind
• Molecular Devices SoftMax Pro
• NovaBio Flex2
• PerkinElmer Envision
• Qiacuity dPCR
• Revvity Kaleido
• Roche Cedex BioHT
• Roche Cedex HiRes
• Thermo Fisher NanoDrop Eight
• Thermo Fisher Qubit 4
• Thermo Fisher Qubit Flex
• Unchained Labs Lunatic

Candidate Release

Working Draft

• BMG MARS

The parsers follow maturation levels of: Recommended, Candidate Release, Working Draft - see release_state.py for additional details.

This code is published under the permissive MIT license because we believe that standardized instrument data is a benefit for everyone in science.

Contributing

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.

Usage

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)

Specific setup and build instructions

.gitignore: used standard GitHub Python template and added their recommended JetBrains lines

Setup

Install Hatch: https://hatch.pypa.io/latest/ Install Python: https://www.python.org/downloads/ This library supports Python 3.10 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

Dependencies

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].

Useful Hatch commands

List all environments:

hatch env show

Run all lint:

hatch run lint:all

Auto-fix all possible lint issues:

hatch run fix

Run all tests:

hatch run test

Run a specific test file (replace the filepath with your own):

hatch run 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

Publish

NOTE: only package admins can publish allotropy.

To publish a new version:

hatch run scripts:update-version

Merge the resulting PR, and then run on main:

hatch build
hatch publish