December 2021 release
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:
### DEBUG STATS ###
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) - Equivalent class default setting changed from
all
toasserted only
(pull). 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. You have to actively switch it off by settingensure_owl2dl_profile
toFALSE
in your config file.
- 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
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.)