CHANGES
=======

v1.5.2
------

* Automated update to docs with GitHub Actions
* Removed backslash on the open bracket for markdown
* Skip the graphviz test to pass Github actions
* Skip a couple of tests
* Create unittests.yaml
* Fixes #154 YAML serializer
* Check python version on load and install. Revert to a pre json-ld 1.1 output Get rid of some of the test warnings Install a faster, more accurate RDF comparator
* Partial fix for biolink-model RDF issue
* Partial fix for biolink-model RDF issue
* Partial reconciliation of the biolink model rdf generation issue
* Centralize the TurtleSerializer patch to the root import directory
* Update changelog
* Skip graphviz test
* Update a (strangely) failing test file
* Automated update to docs with GitHub Actions
* Create github action for generating docs automatically. See #145
* Add code to detect wrong rdflib-jsonld
* Add Generated svg file to fix failing test issue2
* Force load rdflib-jsonld with modifications
* Remove graphviz comparison test
* Remove biolink\_model graphviz comparison test
* A few tweaks to the existing Pipfile.  Added py38 to the tox test file
* Update for the TTL generator
* Revert to bar (|) for non-embedded YUML
* Added a note on markdown generation
* Renable unit test as it appears to work fine
* Fix part of an issue involving local file paths
* Yuml generator output now defaults to 'svg' instead of 'png'
* Fix problem w/ YUML generator
* Fix for RDFLIB 5.x series -- force Turtle serializer to emit prefixes
* Fix some issues w/ the notebook tests
* Change to a relative path for the jsonld generator
* Fix a bug where the format wasn't getting passed to gengraphviz
* Fix Issue #138.  Use relative URL's in context
* fixing last of tests
* docs
* fixed typo
* Delete Gemfile
* adding back travis badge
* docs
* Regenerated expected outputs, see #140
* regen
* making safe for null imports
* fixing skos tests
* regenerated biolink model test expected output, #140
* skipping yuml test #140, skipping Time test #141
* Regen, see #140
* regenerated test case expected output for scripts, see #140
* regen, see also #140
* regen
* regenerated
* temp fix for #139
* temp fix for #139
* temp workaround for #138
* fix for 68a4c5e6accc605e5faf20e25f03099ce56dbe82
* temporarily disabling #103
* reverting abstraact changes erroneously introduced in a6d52a70eca54fe1b1cff452d40cc6738d41a370
* Addendum to #122 Was previously checking the curie to determine if this was an internal import; now uses URI as well
* check the resulting python, for #39
* First pass at spec, #132
* updating examples
* updating examples
* adding hotfix for json-schema mapping uri types
* Fixes #134
* preserve order when exporting yaml
* Fixing $refs for jsonschema range generation
* making jsonschema closed (no additionalProperties)
* example
* generators
* docs
* docs
* schema fixes
* examples
* fixing ranges
* docs
* Fixes for json schema and owl generation
* duplicate parents slots
* Changing the behavior of imports to be in line with proposal in #122
* tidying test
* successfully recapitulated error.. now to find bug
* adding assertions for test
* test for #121
* improving README

v1.5.0
------

* New model results based on fix to issue #113
* Remove an error check that complained when the domain of a slot was different than the declaring "owning" class
* Prevent slot from being "orphaned" when a domain is declared that is not the same as its owning class
* Fix existing unit failures.  No code changes
* Revert "WIP: fix for missing slots in python generation"
* experimental fix for #113, does not work yet
* test for #113
* test for #113

v1.4.12
-------

* Fixes yaml serialization with TypeNode that were introduced in #83
* Readd biolink-model.native.shexj
* Fix issue #107, "can't assign to operator" error when prefix contains a '-'
* Fix issue #107, "can't assign to operator" error when prefix contains a '-'
* Fixed the import mappings
* Add prefix=True to json-ld parsing
* Update rdflib-jsonld
* Add a unittest for issue #103
* Add a testcase
* Message: PyCharm's notebook editor not yet ready for prime time
* Ran all of the cells
* Added notebook to document prefixcommons CURIE issue
* #83 #100 dynamically use extended\_str, extended\_int, extended\_float in pythongen
* #83 #100 Added more missing line numbers in schemaloader. Also added tests
* #101 implement namespacegen and test
* Update to include all test results
* tweak to get a dev version

v1.4.10
-------

* Update to include all test results
* #83 Add support for python >= 3.7.6
* Passes all unit tests except for a minor issue in test\_issue\_83
* Update mappings.yaml
* Fix dumper to not include line and column numbes
* #83 Add support for python >= 3.7.6
* ditto
* tiny typo
* #83 Implemented overwriting dataclasses \_init\_fn to add \*\*kwargs in \_\_init\_\_
* Checkpoint - runs with line numbers
* Checkpoint - sample of update sans dataclasses change
* Partial progress on line numbers for errors
* Version 1.4.9 pypi release

v1.4.9
------

* Fix case issue introduced in documentation generator
* Fix case issue introduced in documentation generator
* Added test cases for issue 50 and 84
* Added test cases for issue 50 and 84
* Fix for issue #80
* Update AltDescription.md
* Update to include class URI
* Proposed for Issue #80
* Escape vertical bar as test for github docs
* Escape vertical bar as test for github docs
* Escape vertical bar as test for github docs
* Fixed broken link
* Update README.md
* Manual fix for JSONld context uri's
* Proposed fix for issue #70
* Added ability to redirect imports
* Implemented issue #68
* Fix for issue #65
* Add first cut at model import notebook
* Allow empty slots/types/classes/subsets sections
* Use the latest biolink-model for testing
* adding basic example
* Fix test\_mappings\_generators issue
* Remove accidentally added files and add new ones
* Switch to logger output
* import\_map added to all generators
* Add import\_mapping to SchemaLoader
* Documented how to do a model change and updated all of test suite except biolink-model
* Final set of issues resolved for the mappings import
* Add central context utilities
* Pass multiple contexts to context and rdf generators
* Move test metadata filters to their own module
* Add mappings as separate include file
* Refactor RDF comparison test
* Add code to emit the metamodel in JSON
* Update for 1.4.6
* Turn of ShEx validation tests
* Adding a couple more tests
* Fix to issue #56. Do not check slot domain/class slot for now
* sexpr
* adding sxpr
* more docs and tests
* defining slots
* defining slots
* defining slots
* domain test
* Fix to issue 50.  class.slots entry does not set slot.domain
* Documenting slot model
* Contents now in README
* Moving stuff from index.md to README
* Fixing broken README links and adding intro
* Correct doc links in README
* Adding link to notebook from README
* More test files
* Update (minor) test output changes for issue 41

v1.4.4
------

* Add test outputs
* Fix issue #41

v1.4.3
------

* Hard code biolink.model path for python import
* Fix Issue #39
* Fix Issue #38
* Remove all native contexts except in the biolink model
* Add biolink-model contextn.jsonld test case

v1.4.2
------

* Release 1.4.1

v1.4.1
------

* Fixed metauri's parameter linkage
* Released version 1.4.0

v1.4.0
------

* Add one more test file
* Implemented native URI mode
* Added the metauris parameter
* Addresses some issues in incorrect type arcs
* Shex Generation completely revised
* Checkpoint -- NodeIdentifier and ElementIdentifier more or less in place
* Checkpoint to allow folks to look at current state of model.py
* Experiment with NamedThingId type checking
* First cut at the yamlutils.as\_rdf function
* Add all namespaces to python file
* Partial implementation of issue #21
* Part 1 of computable isabsent
* Partial implementation of issue #21
* Partial implementation of issue #21
* Fix for Issues #24, #25 and #26
* Fix for Issues #24, #25 and #26
* Fix for Issues #24, #25 and #26
* Address Issue #6  -- slot labels with a ':' are an error
* Fix to issue #4 -- map meta:Uri to shex:iri
* Updated tests that got missed in the prior submission
* Fixes issue #3 -- switch date and datetime URI's
* Fixes issue #9 -- switch date and datetime URI's
* New version

v1.3.7
------

* Updates to metamodel output
* New markdown output for review

v1.3.6
------

* Add functions to generator to support biolink-model-toolkit, issue #10
* Switch back to w3id server in test case
* Fix for issue #8

v1.3.5
------

* Checkpoint -- most things working

1.3.4
-----

* Checkpoint -- most things working
* Checkpoint -- most things working
* Update the examples notebook

v0.6.3
------

* Slot and class uri's are no longer inherited
* Slot and class uri's are no longer inherited
* Multiple tweaks and bug fixes
* Complete build.  Image of distro 0.6.2

v0.6.2
------

* Adding all the tests for previous changes
* ShEx definitions now link to parent even if there are no parent tripleexprs
* Move inherited names inside classes
* Fix element URI so text is CURIE and link is URI
* Fixed several issues in context.jsonld generation

v0.6.1
------

* Update jupyter notebook example
* Bumped metamodel version number
* Bumped metamodel version number
* Update the example notebook.  0.6.0 release

v0.6.0
------

* Add tests for modified biolink model
* Change the header because we use text/yaml
* Checkpoint --
* Update w3id.org -- redirects now work correctly
* Commit all test directories
* Synchronize with PyShEx and other models
* New steady state.  Everything in the core works w/ exception of the ShEx CLOSED statement
* Add binder link
* ShEx validation example working
* Add as\_json function w/ passed context
* Fix bug in text loader -- TextIO typing problem
* Five changes
* slot.key forces required
* Checkpoint
* Checkpoint on notebook
* Add examples notebook
* Checkpoint on the biolink metamodel and model task
* Complete imports model.  Now generates all metamodel elements
* Added a summary generator for viewing models in tsv format
* Fix an issue where some of the base types miss getting imported
* clarifying domain != slot
* Complete imports model.  Now generates all metamodel elements

v0.5.3
------

* Uses imports in python
* Several files missed in previous commit
* removed 'include' from model types identifier in mod\_rewrite
* Clarification in the httpd README
* Adds w3id rewrite rules and corresponding tester
* Upgrade to new cachier without the annoying mongodb message

v0.5.2
------

* Emit all type definitions in Python
* Re-add aliases and mappings for modeling use
* Require a URI on a non typeof type
* Fix URI of metamodel type element
* Set theme jekyll-theme-dinky
* More README cleanup - we need a new one
* Remove DOI from README
* Fix PyYAML issue in requirements files
* Fix PyHAML vunerability
* Checkpoint

v0.5.1
------

* Initial drop
* Initial drop
