search

PHI-base / phipo

Pathogen-Host Interaction Phenotype Ontology
Other
5 stars 5 forks source link

Full release with ODK v1.4.1 #396

Closed jseager7 closed 1 year ago

jseager7 commented 1 year ago

@matentzn Currently the full release is not working due to timeout issues with ChEBI.

Previous discussion is here: https://github.com/INCATools/ontology-development-kit/issues/884

jseager7 commented 1 year ago

@matentzn I've updated the Makefile with update_repo and prepared a release with the slim version of ChEBI on this branch. I didn't see any errors reported in the console so I'm assuming everything went okay.

If everything looks okay to you, I'll merge this PR and tag the release. If you don't get a chance to respond today then I'll remake the release later.

jseager7 commented 1 year ago

Whoops, didn't notice the merge conflicts. That's due to a partial release I did earlier so we could use the latest PHIPO terms with another tool. I'll fix that.

jseager7 commented 1 year ago

I'm a bit concerned about the size of the commit: 734,712 insertions and 1,307,936 deletions! Are there files that aren't being ignored that should be? Or is this just because we haven't updated the import files in a long time?

matentzn commented 1 year ago

There was a major update to our serialisers in version 1.4 Just spot check some changes in see if they are mostly related to xsd :string

jseager7 commented 1 year ago

Just spot check some changes in see if they are mostly related to xsd :string

I think that explains the changes in the PHIPO release files, thanks. The import files also seem to have changed from RDF/XML syntax to Functional Syntax, which accounts for the really massive diff on some files.

matentzn commented 1 year ago

Yes thats right! A one time large diff is expected. I would recommend doing that release today, and make another one soon, and double check then that the diff looks sane.

jseager7 commented 1 year ago

Thanks for your help. I'll make the release on GitHub now and sometime this week I'll prepare another release to check the diff of the files.

jseager7 commented 1 year ago

@matentzn One more question: I've merged these changes with a merge commit (6c8720bf4d37e792c5571318175b7b5d887a8231), should I tag the merge commit for the release, or should I tag the final commit of the PR? (06efae3ac231fe8efe541d3afd19ea707ded2c2f)

I'm just wondering whether the OBO guidelines would prefer the most recent commit to be tagged, or whether it doesn't matter as long as the files are the same.

matentzn commented 1 year ago

This is not in any OBO guidelines, but you must tag the commit that contains all the changes. If you did a merge commit, the other commits will have been removed, so you have to tag the merge commit!

jseager7 commented 1 year ago

If you did a merge commit, the other commits will have been removed, so you have to tag the merge commit!

Sorry, I didn't mean a squash commit. I didn't squash the PR commits into one commit, I just chose the option that adds a separate commit for the whole merge in addition to the commits contained in the merge.

I tagged the merge commit anyway since it was easier to tag the latest commit automatically than to manually create the tag on a previous commit. The release is published now.