Biolinkml

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* 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

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* 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

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* 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

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* 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

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* 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

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* 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