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UC-Davis-molecular-computing / scadnano-python-package

Python scripting library for generating designs readable by scadnano.
https://scadnano.org
MIT License
13 stars 7 forks source link

rename `IDTFields` to `VendorFields` #279

Closed dave-doty closed 11 months ago

dave-doty commented 12 months ago

The concept is more general than IDT, so VendorFields is a better name. Also change the names of JSON keys associated with these, and field names such as Strand.idt to Strand.vendor_fields and Modification.idt_text to Modification.vendor_code.

dave-doty commented 12 months ago

Release notes

BREAKING CHANGE: Renamed IDT-specific fields

Some names related to the DNA synthesis company IDT have been renamed to be more general. You will have to rename these in your own code for it to run:

Additionally, some keys in the JSON format for .sc files have changed as well. Scadnano (both the web interface and the Python package) should be able to read files with the old keys and convert them to the new keys upon saving. However, if you are manually editing the .sc file then use the new keys.

Some IDT-specific methods remain, such as Design.write_idt_plate_excel_file. These use the values in Strand.vendor_fields and Modification.vendor_code, but since the file format actually is specific to IDT, the method name is unchanged.

Although currently there are no methods for exporting to file formats recognized by other synthesis companies, in the meantime it should be straightforward to use the values in VendorFields to write custom code for such exports.