feat: add analysis results creation #8
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chore: cleanup a bit chore: nicer output
chore: it has been a while since I wrote code fix: fix zipfile method that was resaving the zipfile chore: no idea how this passed linting chore: use shutil.make_archive chore: rename as the file gets moved chore: this is getting annoying chore: ugh chore: needs to be an absolute path chore: an absolute path
chore: remove prints and fix imports
chore: Don't check in generated files chore: remove OUTPUT_TYPE env var chore: rename uploaded files chore: sort inputs
y3rsh
approved these changes
Nov 28, 2023
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Description
This change adds the creation of:
protocols_and_analyses.zip- This file contains all the protocols and their respective analysis results zipped togethersummary.md- This file provides a summary of what is in the zip file.summary.mdcontains the following information:Changes
There aren't many large changes to the existing functionality. The main change to existing functionality is the added
ProtocolPathsdataclass.Each protocol becomes an instance of this dataclass, and contains the following:
The way this changed the functionality was to, generate the expected analysis paths after the protocol paths were generated. This logic was pulled out of the
analyzefunction and instead added inside of themainfunction. This was done to make the pairing of the protocol and its respective analysis file easier. This pairing is utilized when generating the markdown file to group each result by protocol name.The other functionality is mainly additions that don't directly interact with the main functionality of analyzing a protocol.
Testing
I modified the existing tests to use the
ProtocolPathsdataclass.Besides that I didn't add any testing, didn't think it was worth it to ensure the markdown was created correctly at this point.
I could unzip one of the created zipfiles. But all I am doing is using
shutil.make_archiveto create the entire thing. There is basically no logic at all for this.