ChangeLog

CHANGES
=======

* Automated update to docs with GitHub Actions
* Automated adding outputs from tests
* Fix for issue #326
* Automated adding outputs from tests
* Add Decimal type as import to metamodelcore.py
* Automated update to docs with GitHub Actions
* Automated adding outputs from tests
* Automatically generated requirements.txt and requirements-dev.txt
* Remove notebook tests temporarily
* Remove 3.9 from tests - doesn't seem to exist yet
* Update generate notebooks code
* Include debug elements in pipenv
* Remove pyc files
* First cut at Enumerations
* Checkpoint
* Automated adding outputs from tests
* Sync w/ master branch
* Tweaks to jupyter notebook
* Checkpoint -- all tests pass and code generation is complete

v1.6.1
------

* Automated adding outputs from tests
* Automatically generated requirements.txt and requiremetns-dev.txt
* Reversed the order of Annotation and Annotatable in annotations.yaml
* Checkpoint Refactored code generation, ready to start adding the code set hooks once we kick the tires a bit
* Quick patch to try fixing domain/range error for mixins (not  sure  what  else  needs to be changed)
* Remove all mixin  \`abstract: true\`  tags  (superfluous now?)
* issue\_38.yaml clinical profile conflicts with latest Biolink Model
* Use 'Exposures  & Outcomes' Biolink Model YAML file as  test input
* Automated adding outputs from tests
* delete \_\_pycache\_\_  artifacts
* adding new check
* docs
* wrapper
* Adding SPARQL queries and checks that can be used to query and validate both schemas and instances. See #229
* ttl target
* Automated adding outputs from tests
* more rdf examples
* Automated adding outputs from tests
* Adding more docs about generating RDF and JSON-LD contexts
* Temporarily adding the first prototype for the OBO --> TCCM filter and its application to HPO
* Add decimal to types.yaml
* Add an automated update of the notebooks directory
* Checkpoint -- all tests pass and code generation is complete
* Temporary copy of alternative.py output until we get a full merge done
* Python for all test cases generating
* Automated adding outputs from tests
* Automatically generated requirements.txt and requiremetns-dev.txt
* Enumerations are now a core part of the model.py
* Automated adding outputs from tests
* clarify prefix registration
* Automated adding outputs from tests
* tiny typo
* Checkpoint before moving enumerations to includes
* Add enums to typreferences
* Automated update to docs with GitHub Actions
* Automated adding outputs from tests
* incremental documentation improvements
* First successful python generation for basic enumeration type
* Automated adding outputs from tests
* Elaborate  inheritance  metadata
* Automated adding outputs from tests
* Elaborated inheritance mechanisms
* Automated adding outputs from tests
* Clarify 'class' usage
* Automated adding outputs from tests
* Add link to SPECIFICATION.md
* further refinement on string\_serialization
* Add example of string\_serialization for basic discussion
* Checkpoint.   First cut at python code generation for enumeration
* Initial model for enumerations
* Correct an issue where classes with multiple identifiers aren't detected
* Add \`parse\` to the Pipfile
* Proposed changes for issue #159
* Automated adding outputs from tests
* Update to latest version of biolink-model for testing

v1.6.0
------

* Automated adding outputs from tests
* Add the context generator back to the unit test
* Add proposed case insensitivity to prefix handling
* Automated update to docs with GitHub Actions
* Automated adding outputs from tests
* Update the Python comparator to correctly test the generated code
* Automated update to docs with GitHub Actions
* Automated adding outputs from tests
* Update resolver3.json
* Update of the documentation
* Major update to the generated Python
* Sync with the latest biolink model for testing
* Automated adding outputs from tests
* Fixed #290
* made test case for #290, fails as expected for now
* added test for #290

v1.5.10
-------

* Automated adding outputs from tests
* Fixes for issues #281 and #282
* Automated adding outputs from tests
* Accidentally picked up some WIP from another branch.  Pared down to just this issue
* Fixed issue #276.  Tightened up the YAML importer to fail on empty list elements
* Automated adding outputs from tests
* Checkpoint on pattern branch

v1.5.9
------

* Automated adding outputs from tests
* Changed the type of subproperty\_of to SlotDefinition
* Add a more informative error message when you feed the loader an empty file. Change the syntax of the yaml error message so that JetBrains IDE's can find the file and line
* Correct a couple of errors on generating the new slot
* Attributes introduced to metamodel
* Automated adding outputs from tests
* Add new output directory
* Add the test case input
* Fix for issue #260
* Automated adding outputs from tests
* adding users
* Automated adding outputs from tests

v1.5.8
------

* Partial fix for issue #258.  Set model version to 1.5.8, next PyPi addition
* Automated update to docs with GitHub Actions
* Automated adding outputs from tests
* Final fix for issue #168
* Automated update to docs with GitHub Actions
* Fix issue #213
* Add test for issue #213 (fixed elsewhere)
* Automated adding outputs from tests
* Multiple fixes -- will add issue numbers to pull request
* Centralize header metadata function.  Note: This should eliminate the need for a lot of the test filters. Add a list of known generators to \_\_init\_\_.py to allow iteration Add a "directory\_output" to generators that emit directories (dotgen, golrgen, markdowngen) Change default output type of context generator from "json" to "context" to prevent clashes with jsonldcontextgen.py Couple of small tweaks in the test\_environment to keep output of multi-test Add minimal model test to tccm\_issues tests and a batch generator to make sure that the minimal model works in all generators
* Automated adding outputs from tests
* Import any identifier / key slots that are defined in another module
* Fixes issue in merge where mappings aren't always correctly inherited
* Automated adding outputs from tests
* Update yamlgen.py
* Update README.md
* Added gen-yaml command line tool for validating and emitting complete YAML
* Added gen-yaml command line tool for validating and emitting complete YAML
* Tighten up URI and CURIE instance testing
* Automated update to docs with GitHub Actions
* Automated adding outputs from tests
* Update test\_gen\_jsonld.py
* Automated adding outputs from tests

v1.5.7
------

* Automated adding outputs from tests
* Fix problem where slot\_usage slots used as inline definitions don't emit actual slots
* Add a tccm test case for addressing issues found in tccm development
* Comment out an integrity test that is failing under certain conditions
* Change the default default\_range message to a logger info to clean up the output
* Correct typo in API
* Add an command line/runtime option to control import merges
* Update to reflect the latest greatest biolink model
* Fix issue #222
* #223 remove temp and \_\_pycache\_\_ directories in tests
* Automated adding outputs from tests
* #223 fix the issue that git add --force added too many files in tests
* Update README.md
* Automated adding outputs from tests
* Fix an annoying issue where the genrdf test\_scripts output keeps getting replaced
* Fix an annoying issue w/ the examples.txt output where it keeps getting updated
* Additional input for issue #101
* link to pipenv (for neophytes)
* Automated adding outputs from tests
* tiny typo
* adding more mappings slots to parallel skos

v1.5.4
------

* Automated adding outputs from tests
* Fix for Issue #102
* Automated update to docs with GitHub Actions
* Automated adding outputs from tests
* Update to the w3id rewrite rules to include extensions and annotations
* Reset to use the master import map
* Automated adding outputs from tests
* Temporarily set the local import map to True to get pushed to master
* First cut at fixing issue #167 and #126
* First cut at fixing issue #167 and #126
* Add OIO to prefixes that need emitting
* Fix an issue where aliases were incorrectly reported as errors
* Add annotations as a specialization of extension
* Process inline range classes as wither a list of dictionaries or, if two attributes, a key/value tuple
* Fix a couple of issues with slot specialization (slot\_usage)
* Stop using is\_usage\_slot (it is deprecated and will be removed) and switch to usage\_slot\_name
* Don't assume that subproperty\_of references a slot
* First cut at adding extensible to all elements
* Clean up an unresolved TODO in the import generator
* Automated adding outputs from tests
* Add --force to git add tests
* Automated adding outputs from tests
* Delete mappings.py
* Delete mappings.jsonld
* Delete mappings.context.jsonld
* Automated adding outputs from tests
* Fix Issue #106  --- whatever the issue was, it seems to have gone away..
* Automated adding outputs from tests
* Fix issue #141.  (no idea when it got resolved but it works now...)
* Automated adding outputs from tests
* Fix problem where python issues were getting updated in output file
* Automated adding outputs from tests
* Fix Issue #202 -- re-enanabled the test against the web version
* Automated update to docs with GitHub Actions
* Automated adding outputs from tests
* Further output updates
* Issue 58 wasn't final
* Automated update to docs with GitHub Actions
* Automated adding outputs from tests
* Get the importmap integrated into all of the tooling
* Get the importmap integrated into all of the tooling
* Update on the directory compare function
* Fix Issue #201, #188 and #58
* Basic fix for issue #58 -- get the correct URI into the markdowngen.py
* Automated adding outputs from tests
* Issue #194. Use a local config file for test settings
* Automated adding outputs from tests
* Fix doc generation

v1.5.3
------

* Add python 3.8 in the classifier
* #196 Integrate test output generation and commit
* Add hide\_test\_changes.sh and show\_test\_changes.sh to mask or show the changes in the output directories
* Automated update to docs with GitHub Actions
* Sync output files
* Sync output files
* Removed warning on slot namespace from owlgen
* Switch test to use slash instead of hash
* Issue 177: Implement tree\_root
* Remove redirect\_to\_file param in generate\_single\_file. Add return statement
* Update mergeutils.py
* Automated update to docs with GitHub Actions
* Documentation update
* Add yaml filter, fix a couple of test paths
* Fix issue #188
* Add output files to the mix.  Turn of RDF compare
* Fix for issue #18
* Add new test output files
* Change docs generation to add image directory
* Issue 117: add tree\_root slot
* Fix for issue #63
* Fix issue #183 - explicitly include mixins in the python
* Added test for issue #180 to test\_issue\_14.py
* Test for issue #120
* Update biolink-model to latest master
* Add alias issue test
* Another fix in testing
* Another fix in testing
* Turn of RDF compare for online testing
* merge with master
* Automated update to docs with GitHub Actions
* Reset \_\_init\_\_.py to default state
* Fix issue #179.  More testing cleanups
* Fix issue #179.  More testing cleanups
* Add domain\_of to SlotDefinition slots
* Get examples.txt resynced.  Start of revised model changes document
* Add domain\_of property, allowing multi domain, deprecate owner property
* Fixes bug where owlgen placed all classes, properties into meta namespace. The fix incvolves changing how definition\_uri is populated while schema loading. Fixes #163
* Fix issue #14
* Add a couple more tweaks
* Always remember -- run the complete test suite before committing
* Change line number error message so Python IDE can click through
* Double check that issue #113 is fully fixed
* Automated update to docs with GitHub Actions
* Get all test output in
* Fix issue #112
* Add dependency on test to pushing requirements.txt (#174)
* Fix the main action. only commit requirements.txt once (#172)
* Automatically generated requirements.txt and requiremetns-dev.txt
* Timing issue where temp directory not created..
* Turn off Graphviz tests
* Remove extraneous txt file
* Add initial output files pending actions commits
* Getting closer to passing everything
* Remove several issues w/ reproducibility
* Fix one of the remaining failures
* Switch to default report action (vs fail)
* All tests moved over to new idiom
* test\_utils updated to new testing environment
* Further refactoring on the test\_scripts tests
* Update readme to add documentation on pypi release (#166)
* script test updates
* Add pypi-publishing github action (#165)
* Automated update to docs with GitHub Actions
* Add docs if they were deleted (#162)
* Automated update to docs with GitHub Actions
* Add docs back (#161)
* Delete .travis.yml
* Attempt to get travis to run w/ a decent python
* Put back language to travis config
* Re-introduce Gemfile to make Travis work
* Update GH actions workflow. Add badge to README (#160)
* Update .travis.yml
* Update .travis.yml
* Re-enable the biolink RDF tests
* Meta model update to version 1.4.4
* Use log file for warnings test
* pypi release 1.5.2

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'
* proposed new metaslot for string serialization, #128
* proposed new metaslots
* 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