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rename IDTFields to VendorFields #279

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dave-doty opened this issue Aug 29, 2023 · 1 comment
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rename IDTFields to VendorFields #279

dave-doty opened this issue Aug 29, 2023 · 1 comment
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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 dave-doty added the invalid This doesn't seem right label Aug 29, 2023
@dave-doty dave-doty self-assigned this Aug 29, 2023
dave-doty added a commit that referenced this issue Aug 30, 2023
…idtfields-to-vendorfields

closes #279: rename IDTFields to VendorFields
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dave-doty commented Aug 30, 2023

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:

  • class IDTFields --> VendorFields
  • field Modification.idt_text --> Modification.vendor_code
  • field Strand.idt --> Strand.vendor_fields

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.

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