Ontology Development Kit

Attention: breaking changes below!

• Updated to ROBOT 1.8.2
• Updated to DOSDP tools 0.18
• Adding use_base_merging to config files, which enables the BASE file pipeline, a completely different way to handle imports. This feature is not ready for primetime, but if you are interested in testing this, get in touch. For more details read (pull).
• Adding back ssh/scp
• Migrated to Java 11 as the base Java in ODK (pull)
• Adding make_base feature that allows to autogenerate base files from ontologies where they do not exist (pull)
• Adding new command sh run.sh make no-mirror-refresh-imports which refreshes imports without refreshing mirrors. Can be used for individual ontologies as well.
• Making owltools where necessary configurable with a bespoke memory parameter (pull)
• Fixing the GitHub action to auto-deploy the documentation (pr).
• Fixed a bug where the DOSDP pages in ODK where generated in the wrong part of the mkdocs documentation.
• New command sh run.sh make explain_unsat which generates a nicely formatted set of explanations for your unsatisfiable classes (pull)
• Adding method to measure the memory consumption of your builds. For example, you can now run IMAGE=odklite ODK_DEBUG=yes ./run.sh make prepare_release to run your release on the (much lighter) odklite container of ODK, and get a nice benchmark summary at the end: ```

Elapsed time: 7:49.24 Peak memory: 6517356 kb

- _Breaking changes_:
  - Imported modules are no longer generated in OBO format automatically (only OWL). This reflects the fact that in most ontologies, even those where the editors file is in OBO format, imported ontologies are usually in OWL format. You can use the `export_obo` option to add them back  ([pull](https://github.com/INCATools/ontology-development-kit/pull/496/files))
  - Equivalent class default setting changed from `all` to `asserted only` ([pull](https://github.com/INCATools/ontology-development-kit/pull/497)). This means that from now on, if you dont change the setting deliberately, your pipeline will fail if their are equivalent classes that are not deliberately asserted.
  - OWL 2 DL profile checking is now `true` by [default](https://github.com/INCATools/ontology-development-kit/pull/481). You have to actively switch it off by setting `ensure_owl2dl_profile` to `FALSE` in your config file. 

To update to the latest version of ODK:

docker pull obolibrary/odkfull

To mirgate your repository to the latest version of ODK:

cd myont/src/ontology sh run.sh make update_repo sh run.sh make update_repo #(needs to be run twice since the update process also updates the update process.) ```