2020-08-06 (1.2.23) ODK Release

Changes:

• New ROBOT (v 1.7.0)
• New owltools (v. 2020-04-06)
• Added SWI Prolog and C. Mungall's sparqlprog tools
• Release artefacts are now annotated with owl:versionInfo
• run.sh now got the JAVA_OPTS parameter which is necessary to set the maximum memory allowed for owltools
• Bug fixes:
  • base-modules are now correctly annotated with resource references rather than strings (issue)
  • The ODK_VERSION variable in the Makefile was misnamed, which causes a circularity with updating it correctly when the Makefile is updated with a new ODK. This is fixed, but for the fix to kick in, you have to run sh run.sh make update_repo twice this time!

Please get the latest ODK from dockerhub.

2020-08-06 (1.2.23) ODK Release (UPDATED)

Changes:

Original changes:

• New ROBOT (v 1.7.0)
• New owltools (v. 2020-04-06)
• Added SWI Prolog and C. Mungall's sparqlprog tools
• Release artefacts are now annotated with owl:versionInfo
• run.sh now got the JAVA_OPTS parameter which is necessary to set the maximum memory allowed for owltools
• Bug fixes:
  • base-modules are now correctly annotated with resource references rather than strings (issue)
  • The ODK_VERSION variable in the Makefile was misnamed, which causes a circularity with updating it correctly when the Makefile is updated with a new ODK. This is fixed, but for the fix to kick in, you have to run sh run.sh make update_repo twice this time!

Please get the latest ODK from dockerhub.

Updated version:

• Added new version of fastobo (v0.3.0)
• Added rdflib to Python environment
• Added xlsx2csv command line tool

2020-03-06 (1.2.22) ODK Release

• New ROBOT (v. 1.6.0)
• Bugfixes:
  • Small fixes to update_repo method
  • the sparql query for extracting labeled subsets is now fixed
  • Some unneeded files (ontologyterms.txt) are removed from the default template.
  • a few more files are added to the .gitignore file
  • The catalog file is restructured to preclude Protege from changing it in unwanted ways.
  • the license in the ontology metadata is now required to be an IRI rather than a string.
  • The odk.py should now be executable in a non-docker context
  • JSON versions of imports are not anymore generated. OBO versions are only generated if OBO is used as the edit file serialisation.
  • PAT=false now skips pattern download
• Fixes to DOSDP pipeline
  • DOSDP tools is updated to version 0.14. This version comes with some great changes, including:
    • a mode in which multiple patterns can be compiled at once (batch mode)
    • we finally have have optional columns and column values!
  • external.txt can now be empty
  • instead of abnormalAnatomicalEntity, an example.yaml is added to the default pattern directory
• Infrastructure (only relevant to ODK developers):
  • The test framework for ODK is now more dynamic:
    1. Travis now correctly builds the ODK from scratch and runs the tests against the new build version
    2. Instead of adding new tests to the Makefile, you can simply now drop a new YAML file into the tests/ directory.
  • ODK Dockerfile has been optimised a bit for size (avoiding superfluous chmod calls)
  • the yaml loader in the ODK is now replaced by a safe loader

2020-01-23 Release (v. 1.2.21)

https://hub.docker.com/r/obolibrary/odkfull/tags?page=1&ordering=last_updated

• Changed base image of docker file
• added Ammonite to ODK

1.1.4 release

Added a .bat wrapper for windows users

1.1.3 release

Changes

• fixing bug in which running seed-via-docker did not enter interactive mode when no arguments provided
• added convenience wrapper scripts

Migration guide

• New .sh scripts in src/ontology can be directly copied across

1.1.2 release

Changes

• added interactive mode
• added DOSDP support

Docker

• odkfull v1.1.2 includes robot 1.1.0

Migration guide

This release adds a new template in the src/patterns folder. These can be copied across to an existing repo.

1.1.1 release

Changes

Name of repo has changed to ontology-developer-kit

• changing name of docker image to odk
• Upgrade dosdp-tools to release 0.9.
• Make docker commands workable on windows
• Dockerize travis
• Imports automatically generated
• Added python dosdp checker to docker, fixes #55
• use robot not owltools in all places

Migration guide

If you built your repo from a previous version of ODK, here is a rough guide to migrating:

• Update your .travis.yml, in order to use Docker (optional but recommended)
• change the name of the docker image to odkfull in your run.sh

1.1.0 release

This release adds a run.sh in the template for Docker

1.0.2 release

v1.0.2

Merge branch 'fix-build'