cherry picked changes from kgcl repo #50
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This was referenced Jul 6, 2022
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This was an attempt to cherry pick all the changes from INCATools/kgcl#3
apologies for the confusion re repos - we split the repos too soon
commit messages copied over:
Adding click tests.
Making CLI more clig-compliant - changing some arguments to options
Fixes CLI: make more clig-compliant, add click tests #45
Deprecating duplicative slots that store the type of the entity.
See Remove about_node_representation #44
Adding collection of test cases that can be reused for testing different subcomponents:
parsing, diffing, applyimg, rendering
Add tests for ontology diff #42
Add tests for grammar #41
noting deprecation, see retire kgcl_2_rdf.py #46
Adding test cases
logging
refactoring so that about_node_type is no longer necessary
See Remove about_node_representation #44
adding a CLI for parser. See CLI: make more clig-compliant, add click tests #45
fixing yaml/json/rdf generators and loaders
regenerating products.
Adding pytest cache to ignore
Adding CLI for parser. See CLI: make more clig-compliant, add click tests #45
Fixing grammar such that replacement in obsoletion can be a CURIE. Fixes parser fails on obsolete with replacement when replacement is a CURIE #48
Changed pattern of regex for CURIE prefix to be more permissive and allow numbers and underscores
regen
Fixing owl URI for someValuesFrom. Fixes diff fails on existential restrictions #49
regenerate
Do not check in derived files
Annotating methods with typing, see Annotate method inputs and outputs using typing #39
Using more idiomatic python for type checking, see Use modern python idioms #40
Removing unused/redundant package. Fixes retire render_kgcl.py #47
various minor changes