*Allotrope® is a registered trademark of the Allotrope Foundation; no affiliation with the Allotrope Foundation is claimed or implied.
Test Introduction
Welcome to allotropy -- a Python library by Benchling for converting instrument data into the Allotrope Simple Model (ASM).
View the list of instrument software currently supported in SUPPORTED_INSTRUMENT_SOFTWARE.
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.
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_dict = 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_dict = allotrope_from_io(f, Vendor.MOLDEV_SOFTMAX_PRO)
bytes_io = BytesIO(file_stream)
asm_dict = 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.
Tell git to use .githooks:
git config core.hooksPath .githooks
Dependencies
To add requirements used by the library, update dependencies in pyproject.toml:
- For project dependencies, update
dependenciesunder[project]. - For script dependencies, update
dependenciesunder[tool.hatch.envs.default]. - For lint dependencies, update
dependenciesunder[tool.hatch.envs.lint]. - For test dependencies, update
dependenciesunder[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 in the default python enviroment (currently: 3.11.9)
hatch run test
Run all tests against all supported python versions (currently 3.10-3.12) Note: this is checked against in CI - your change must pass this to merge.
hatch run test_all:test
Run against a specific python version (useful for debugging if a test is failing in one environment)
hatch run test_all.py3.12: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
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