@philwilkinson In your traceback I see the 'Pymakr' package folder with a capital, instead of lowercase. This is a known issue (happened after pymakr renamed in v1.2.5).
I just added this to the known issues with the solution in the readme file on the develop branch of the pymakr github. Read it here, at the bottom of the page: https://github.com/pycom/pymakr-atom/tree/develop#any-error-where-the-traceback-contains-atompackagespymakr-with-a-capital-p
Try the solutions listed there and let me know if that fixes your issue.