Update documentation

[hrshdhgd]

• Test if documentation auto deployment still works
• add the following to the workflow:
  • mvn clean package
  • java -jar phenopacket-tools-cli/target/phenopacket-tools-cli-0.4.6-SNAPSHOT.jar examples

[ielis]

Hi, all mvn invocations should be replaced by ./mvnw. This will use Maven wrapper instead of an arbitrary Maven version that is installed on wherever the build is being run.

I also wonder if we should coordinate CI runs. Based on your proposed changes, the pages.yml workflow includes Maven build. However, there is already another workflow main.yml that includes the build. We should make sure we test the build on one step only, right?

[hrshdhgd]

Hi @ielis ,

Thanks for the suggestion. Clearly I'm not a Java developer so any advice would be appreciated!

I actually just need the following directories generated by mvn clean package:

• families
• cohorts
• phenopackets

If there was a way wherein these directories were possibly generated by main.yaml and were accessible to the script when pages.yml is running (not aware of how to do this), that would be ideal. For right now I'm just testing it out in this workflow to see I could get the documentation on these files displayed.

[ielis]

The examples command should generate the examples, basically using the syntax that you included above. Of course, you first must build the JAR file before running the command, and that's where ./mvnw comes in. So, in principle something like the following should work if you put it into the Github workflow:

./mvnw -Prelease package
java -jar phenopacket-tools-cli/target/phenopacket-tools-cli-0.4.6-SNAPSHOT.jar examples

I am a bit worried about the version - it is a part of the JAR name, but it changes and it is not a good idea to just replace it with *. That may trick java to run Javadoc JAR - also a JAR file and in the folder.

Anyway, to generate the example folders, you do not likely need to run the CI in a matrix. It should be sufficient to run the build and example generation just once, right? E.g. on Ubuntu.

[hrshdhgd]

to generate the example folders, you do not likely need to run the CI in a matrix. It should be sufficient to run the build and example generation just once, right?

Do you mean generate the examples and push it to GitHub?

[hrshdhgd]

This PR is still a work in progress. Sorry @pnrobinson , I should have just left it as a draft

[pnrobinson]

Sorry, my fault, I was just worried about things getting out of synch!