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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

Exporting designs with helix groups to cadnano v2 #132

Closed tcosmo closed 4 years ago

tcosmo commented 4 years ago

Designs with helix groups sharing the same grid should be exportable to cadnano v2.

tcosmo commented 4 years ago

@dave-doty : the file "scadnano-python-package/tests_inputs/cadnano_v2_export/test_6_helix_bundle_honeycomb.sc" was explicitely being ignored in .gitignored whereas the unittest TestExportCadnanoV2.test_6_helix_bundle_honeycomb explicitely requires the file. Indeed, the test is lazy and does not code the design in scadnano but directly load the .sc file which is one of the examples featured in scadnano.org.

Either you are fine with this execption (i.e. it is the only .sc file not ignored in scadnano-python-package/tests_inputs/cadnano_v2_export/) either I can copy paster the design generation from the corresponding examply py file.

dave-doty commented 4 years ago

I'm not sure exactly how this file was being used.

Mostly I just don't want files in the repo to change just because we run the unit tests. I don't care which files we ignore and which we track, but I prefer if anything we track doesn't change just as a result of running unit tests. (So we can stop ignoring this one if that's the case here.)

tcosmo commented 4 years ago

Yeah this file is only being read by the test but not changed by the run.

tcosmo commented 4 years ago

@dave-doty oligo names are not stored under cadnano v2 file format, only comes with cadnano v2.5