June 2022 Release

Official Changelog:

• Update to ROBOT 1.9.0, see ROBOT release notes. One major change concerning ODK: the OBOGraphs JSON serialiser has been updated significantly, which means obographs json files may look a bit different. Most important change: empty elements (xrefs) are no longer serialised.
• Added shortcut make commands for recreating components: recreate-components and recreate-% (pull).
• Added new shortcut command for fast releases: make prepare_release_fast.
• New tools:
  • Ontology Access Kit, a python library for interacting with ontologies, the the ODK (pull).
  • gh: GitHub CLI for running releases, createing pull requests and more
  • j2cli: Jinja template client
  • rdftab: RDF Tables with Rust
  • gizmos: Python utilities for ontology development
  • Other: obographviz, node.js, graphviz, npm
• The ontology diff GitHub action, a tool that allows you to create diffs for you ontology pull requests, is now automatically synced with your ODK setup (pull).
• Added workflows option to ODK config. This allows users to choose which workflows (at the moment GitHub actions-based) should be automatically synchronised.
• Custom ROBOT SPARQL reports now consider the imports by default (pull)
• Base IRIs can now be configured for ROBOT report, similar to what OBO Dashboard does
• Technical
  • Run internal make and $(MAKE) to ensure that parameters are propagated correctly (issue).
  • Mirror goal is only run when mirrors have been downloaded (pull)
  • src/ontology/run.sh can now be configured with a ODK_JAVA_OPTS parameter at runtime, rather than just with a robot_java_args option in the projects ODK config file. This allows to more easily run releases across environments with different levels of memory. Example: ODK_JAVA_OPTS=-Xmx4G ODK_DEBUG=yes ./run.sh make odkversion
  • src/ontology/run.sh warns the user in certain cases to update their local ODK image.
  • Better linebreaks in Makefile to make lines more.
• Documentation
  • Added improved CONTRIBUTING.md to ODK repo template
  • Removed history.md page from ODK documentation
  • Some improved settings to default mkdocs documentation pages, such as better search, edit buttons and more.
  • Some improved documentation on components (pull)
  • All ODK-related general docs now moved to https://oboacademy.github.io/obook.
  • DOSDP documentation pages are now only created when dosdp is configured.
• Bugs
  • The automatic docs workflow now correctly uses: mhausenblas/mkdocs-deploy-gh-pages@master.
  • In ODK 1.3.0 prepare_release depended on all, which caused some cyclicity for some customised setups. This is now changed to a separate all_odk goal.
  • Simple ontology release artefacts now correctly depend on the simple seed.
  • Similar to subset declarations, ODK now injects synonymtype declarations when extracting a module.
  • diff.yaml no longer added by default, has to be configured.

For changes on previous versions see complete CHANGELOG

Automated GitHub Changelog:

• Make sure diff.yml action is automatically copied during update by @shawntanzk in #564
• Update dosdp-tools to 0.19.2 by @balhoff in #575
• added components doc by @shawntanzk in #577
• Removed files that are repeated in obook by @shawntanzk in #578
• Add oaklib by @gouttegd in #586
• First fixes 131: components, $(MAKE) and reports by @matentzn in #570
• Build rdftab from source. by @gouttegd in #593
• Improving run.sh.jinja2 by @matentzn in #594
• Adding missing ontology annotations on imports by @matentzn in #597
• Update dosdp-tools version by @balhoff in #596
• issue 589 by @cmungall in #590
• Add ontodev-gizmos, psycopg2, pyspellchecker. by @gouttegd in #602
• Fix argument passing in the Windows run.bat script. by @gouttegd in #603
• ont.is_large only makes sense with module type slme by @matentzn in #607
• Upgrade base system by @gouttegd in #604
• Add ability to set base IRIs for report in ODK by @matentzn in #609
• [WIP] Update contribution guidelines by @cthoyt in #598
• Add Robot 1.9.0 to Dockerfile by @matentzn in #621
• Removing History page and add nice default config for mkdocs by @matentzn in #611
• New contribution guide by @matentzn in #620
• Add break lines to makefile by @anitacaron in #612

New Contributors

• @cthoyt made their first contribution in #598

Full Changelog: v1.3.0...v1.3.1