Vedran Kasalica

Hi @HelenParr, thank you for bringing this to our attention. Unfortunately, as it is not a direct dependency, it is not trivial for us to identify the problem. Could you...

Bug is in the pipeline, but the reason might be the graphviz-java library used to print the graphs in the process.

If I understood correctly, this happened when the configuration uses `"strict_tool_annotations": "true"`. APE trims the ontology to include only data types and formats that can be processed by the annotated...

> I fully agree, and would suggest to also reduce the issue template; in particular, the checkbox to check for existing issues can be removed, because it adds an unnecessary...

The comment was fine, no worries! :) ## Issue Templates About the Issue template, I am not sure if a checkbox is better than a simple text that the user...

@mr-c thank you for the update, I will work on the project and test it next week and let you know!

> Hi @vedran-kasalica, what is the plan for this PR? Hi @eladrion, this was my effort to disentangle the encodings of the `domain annotations` and the `run configuration`, as it...

> Hi @vedran-kasalica. Okay, get that. I will discuss that internally at UP and this PR will then stay open for now thanks! I opened an issue as well https://github.com/sanctuuary/APE/issues/128

Is there some symbolism in the issue number? :) On a more serious note, I do like the current name, it's self-explanatory.

I looked into the issue and the PDF can be generated locally without issues not as a GitHUb action with `docsify-pdf-converter` (we looked into alternatives and `docker-docsify-pdf` looked promising). It...