Lupus example

[pnrobinson]

added opens org.phenopackets.phenopackettools.command to info.picocli; to the module-info in phenopacket-tools-cli @ielis is this optimal?

Also cleaned up a bit and started SLE example.

[julesjacobsen]

Why did you remove the PhenopacketExamples class?

[pnrobinson]

PhenopacketExamples did not add any useful functionality or am I missing something?

[ielis]

@pnrobinson yes, adding opens is better than adding exports since opens allows the access only during runtime while exports allows access during both compile time and runtime. Adding the opens clause is enough for picocli.

[julesjacobsen]

PhenopacketExamples did not add any useful functionality or am I missing something?

It made for a terser and easily discoverable public API - e.g.

var phenopacket = PhenopacketExamples.bethlemMyopathy(); 
# instead of 
var otherPhenopacket = new BethlehamMyopathy().getPhenopacket();

[pnrobinson]

These examples are not intended to be library code -- they are just part of this application, and it was tedious to have to add everything to a separate class! :smile: