multiple changes (#3)

* Adding CLI to pyproject, see INCATools/kgcl-rdflib#24

* Added some typing, see INCATools/kgcl-rdflib#39

* Test refactoring.

Using subfolders to differentiate different kinds of tests.
Adding a test for grammar INCATools/kgcl-rdflib#41
Adding tests for string issue INCATools/kgcl-rdflib#36

* Using correct paths for imports, see INCATools/kgcl-rdflib#40

* Adding tests for grammar and rendering. Fixes INCATools/kgcl-rdflib#41

* Adding click tests.
Making CLI more clig-compliant - changing some arguments to options
Fixes INCATools/kgcl-rdflib#45

* Deprecating duplicative slots that store the type of the entity.
See INCATools/kgcl-rdflib#44

* Adding collection of test cases that can be reused for testing different subcomponents:
parsing, diffing, applyimg, rendering
INCATools/kgcl-rdflib#42
INCATools/kgcl-rdflib#41

* noting deprecation, see INCATools/kgcl-rdflib#46

* Adding test cases

* logging

* refactoring so that about_node_type is no longer necessary
See INCATools/kgcl-rdflib#44

* adding a CLI for parser. See INCATools/kgcl-rdflib#45

* fixing yaml/json/rdf generators and loaders

* regenerating products.
Adding pytest cache to ignore

* Adding CLI for parser. See INCATools/kgcl-rdflib#45

* Fixing grammar such that replacement in obsoletion can be a CURIE. Fixes INCATools/kgcl-rdflib#48
Changed pattern of regex for CURIE prefix to be more permissive and allow numbers and underscores

* regen

* Fixing owl URI for someValuesFrom. Fixes INCATools/kgcl-rdflib#49

* regenerate

* Do not check in derived files

* Annotating methods with typing, see INCATools/kgcl-rdflib#39
Using more idiomatic python for type checking, see INCATools/kgcl-rdflib#40

* Removing unused/redundant package. Fixes INCATools/kgcl-rdflib#47

* various minor changes

.gitignore

@@ -2,3 +2,6 @@ docs/*
 .vscode/*
 dist/*
 __pycache__
+.pytest_cache
+.idea
+tmp/

project.Makefile

@@ -1 +1,4 @@
 ## Add your own custom Makefile targets here
+
+test:
+	poetry run pytest

project/docs/about_node_representation.md

@@ -1,5 +1,5 @@
 
-# Slot: about node representation
+# Slot: ~~about node representation~~ _(deprecated)_
 
 
 The representation of a node (URI, CURIE, label)

project/docs/filler.md

@@ -1,5 +1,5 @@
 
-# Slot: filler
+# Slot: ~~filler~~ _(deprecated)_
 
 
 

project/docs/filler_type.md

@@ -1,5 +1,5 @@
 
-# Slot: filler type
+# Slot: ~~filler type~~ _(deprecated)_
 
 
 

project/docs/object_representation.md

@@ -1,5 +1,5 @@
 
-# Slot: object representation
+# Slot: ~~object representation~~ _(deprecated)_
 
 
 

project/docs/predicate_representation.md

@@ -1,5 +1,5 @@
 
-# Slot: predicate representation
+# Slot: ~~predicate representation~~ _(deprecated)_
 
 
 

project/docs/property_type.md

@@ -1,5 +1,5 @@
 
-# Slot: property type
+# Slot: ~~property type~~ _(deprecated)_
 
 
 

project/docs/subject_representation.md

@@ -1,5 +1,5 @@
 
-# Slot: subject representation
+# Slot: ~~subject representation~~ _(deprecated)_
 
 
 

project/jsonld/kgcl.context.jsonld

@@ -1,5 +1,5 @@
 {
-   "_comments": "Auto generated from kgcl.yaml by jsonldcontextgen.py version: 0.1.1\n    Generation date: 2022-06-30T14:43:29\n    Schema: kgcl\n    metamodel version: 1.7.0\n    model version: 0.0.1\n    \n    id: https://w3id.org/kgcl\n    description: A data model for describing change operations at a high level on an ontology or ontology-like artefact, such as a Knowledge Graph.\n\n* [Browse Schema](https://cmungall.github.io/knowledge-graph-change-language/)\n* [GitHub](https://github.com/cmungall/knowledge-graph-change-language)\n    license: https://creativecommons.org/publicdomain/zero/1.0/\n    ",
+   "_comments": "Auto generated from kgcl.yaml by jsonldcontextgen.py version: 0.1.1\n    Generation date: 2022-07-02T16:19:57\n    Schema: kgcl\n    metamodel version: 1.7.0\n    model version: 0.0.1\n    \n    id: https://w3id.org/kgcl\n    description: A data model for describing change operations at a high level on an ontology or ontology-like artefact, such as a Knowledge Graph.\n\n* [Browse Schema](https://cmungall.github.io/knowledge-graph-change-language/)\n* [GitHub](https://github.com/cmungall/knowledge-graph-change-language)\n    license: https://creativecommons.org/publicdomain/zero/1.0/\n    ",
    "@context": {
       "IAO": {
          "@id": "http://purl.obolibrary.org/obo/IAO_",

project/jsonld/kgcl.jsonld

@@ -441,6 +441,7 @@
       "name": "about_node_representation",
       "definition_uri": "http://w3id.org/kgcl/about_node_representation",
       "description": "The representation of a node (URI, CURIE, label) ",
+      "deprecated": "no longer required",
       "from_schema": "https://w3id.org/kgcl",
       "slot_uri": "http://w3id.org/kgcl/about_node_representation",
       "owner": "NodeChange",
@@ -1009,6 +1010,7 @@
     {
       "name": "filler",
       "definition_uri": "http://w3id.org/kgcl/om/filler",
+      "deprecated": "no longer required",
       "from_schema": "https://w3id.org/kgcl/ontology",
       "slot_uri": "http://w3id.org/kgcl/om/filler",
       "owner": "Annotation",
@@ -1022,6 +1024,7 @@
     {
       "name": "property_type",
       "definition_uri": "http://w3id.org/kgcl/om/property_type",
+      "deprecated": "no longer required",
       "from_schema": "https://w3id.org/kgcl/ontology",
       "slot_uri": "http://w3id.org/kgcl/om/property_type",
       "owner": "Annotation",
@@ -1034,6 +1037,7 @@
     {
       "name": "filler_type",
       "definition_uri": "http://w3id.org/kgcl/om/filler_type",
+      "deprecated": "no longer required",
       "from_schema": "https://w3id.org/kgcl/ontology",
       "slot_uri": "http://w3id.org/kgcl/om/filler_type",
       "owner": "Annotation",
@@ -1046,6 +1050,7 @@
     {
       "name": "subject_representation",
       "definition_uri": "http://w3id.org/kgcl/om/subject_representation",
+      "deprecated": "no longer required",
       "from_schema": "https://w3id.org/kgcl/ontology",
       "slot_uri": "http://w3id.org/kgcl/om/subject_representation",
       "owner": "Edge",
@@ -1058,6 +1063,7 @@
     {
       "name": "predicate_representation",
       "definition_uri": "http://w3id.org/kgcl/om/predicate_representation",
+      "deprecated": "no longer required",
       "from_schema": "https://w3id.org/kgcl/ontology",
       "slot_uri": "http://w3id.org/kgcl/om/predicate_representation",
       "owner": "Edge",
@@ -1070,6 +1076,7 @@
     {
       "name": "object_representation",
       "definition_uri": "http://w3id.org/kgcl/om/object_representation",
+      "deprecated": "no longer required",
       "from_schema": "https://w3id.org/kgcl/ontology",
       "slot_uri": "http://w3id.org/kgcl/om/object_representation",
       "owner": "Edge",
@@ -2208,7 +2215,7 @@
       ],
       "from_schema": "https://w3id.org/kgcl",
       "is_a": "node_move_change_description",
-      "string_serialization": "shallowed {about} from {old value} to {new value}",
+      "string_serialization": "shallowed {about node} from {old value} to {new value}",
       "domain": "NodeShallowing",
       "slot_uri": "http://w3id.org/kgcl/change_description",
       "alias": "change description",
@@ -2334,7 +2341,7 @@
       ],
       "from_schema": "https://w3id.org/kgcl",
       "is_a": "change_description",
-      "string_serialization": "rename {about} from {old value} to {new value}",
+      "string_serialization": "rename {about node} from {old value} to {new value}",
       "domain": "NodeRename",
       "slot_uri": "http://w3id.org/kgcl/change_description",
       "alias": "change description",
@@ -2379,7 +2386,7 @@
       ],
       "from_schema": "https://w3id.org/kgcl",
       "is_a": "change_description",
-      "string_serialization": "changed {about} name language from {old value} to {new value}",
+      "string_serialization": "changed {about node} name language from {old value} to {new value}",
       "domain": "SetLanguageForName",
       "slot_uri": "http://w3id.org/kgcl/change_description",
       "alias": "change description",
@@ -2457,7 +2464,7 @@
       ],
       "from_schema": "https://w3id.org/kgcl",
       "is_a": "change_description",
-      "string_serialization": "synonym {synonym} becomes new name of {about}, and name {name} becomes a synonym",
+      "string_serialization": "synonym {synonym} becomes new name of {about node}, and name {name} becomes a synonym",
       "domain": "NameBecomesSynonym",
       "slot_uri": "http://w3id.org/kgcl/change_description",
       "alias": "change description",
@@ -2502,7 +2509,7 @@
       ],
       "from_schema": "https://w3id.org/kgcl",
       "is_a": "change_description",
-      "string_serialization": "removing {about} from {subset}",
+      "string_serialization": "removing {about node} from {subset}",
       "domain": "RemovedNodeFromSubset",
       "slot_uri": "http://w3id.org/kgcl/change_description",
       "alias": "change description",
@@ -2582,7 +2589,7 @@
       ],
       "from_schema": "https://w3id.org/kgcl",
       "is_a": "change_description",
-      "string_serialization": "obsoleting {about}",
+      "string_serialization": "obsoleting {about node}",
       "domain": "NodeObsoletion",
       "slot_uri": "http://w3id.org/kgcl/change_description",
       "alias": "change description",
@@ -2647,7 +2654,7 @@
       ],
       "from_schema": "https://w3id.org/kgcl",
       "is_a": "change_description",
-      "string_serialization": "unobsoleting {about}",
+      "string_serialization": "unobsoleting {about node}",
       "domain": "NodeUnobsoletion",
       "slot_uri": "http://w3id.org/kgcl/change_description",
       "alias": "change description",
@@ -2769,7 +2776,7 @@
       ],
       "from_schema": "https://w3id.org/kgcl",
       "is_a": "node_creation_change_description",
-      "string_serialization": "creating {about}",
+      "string_serialization": "creating {about node}",
       "domain": "ClassCreation",
       "slot_uri": "http://w3id.org/kgcl/change_description",
       "alias": "change description",
@@ -2814,7 +2821,7 @@
       ],
       "from_schema": "https://w3id.org/kgcl",
       "is_a": "change_description",
-      "string_serialization": "deleting {about}",
+      "string_serialization": "deleting {about node}",
       "domain": "NodeDeletion",
       "slot_uri": "http://w3id.org/kgcl/change_description",
       "alias": "change description",
@@ -2905,7 +2912,7 @@
       ],
       "from_schema": "https://w3id.org/kgcl",
       "is_a": "node_obsoletion_change_description",
-      "string_serialization": "obsoleting {about} and merging into {has direct replacement}",
+      "string_serialization": "obsoleting {about node} and merging into {has direct replacement}",
       "domain": "NodeDirectMerge",
       "slot_uri": "http://w3id.org/kgcl/change_description",
       "alias": "change description",
@@ -2976,7 +2983,7 @@
       ],
       "from_schema": "https://w3id.org/kgcl",
       "is_a": "node_obsoletion_change_description",
-      "string_serialization": "obsoleting {about} and replacing with {has direct replacement}",
+      "string_serialization": "obsoleting {about node} and replacing with {has direct replacement}",
       "domain": "NodeObsoletionWithDirectReplacement",
       "slot_uri": "http://w3id.org/kgcl/change_description",
       "alias": "change description",
@@ -3048,7 +3055,7 @@
       ],
       "from_schema": "https://w3id.org/kgcl",
       "is_a": "node_obsoletion_change_description",
-      "string_serialization": "obsoleting {about} considering {has nondirect replacement}",
+      "string_serialization": "obsoleting {about node} considering {has nondirect replacement}",
       "domain": "NodeObsoletionWithNoDirectReplacement",
       "slot_uri": "http://w3id.org/kgcl/change_description",
       "alias": "change description",
@@ -5143,9 +5150,9 @@
   ],
   "metamodel_version": "1.7.0",
   "source_file": "kgcl.yaml",
-  "source_file_date": "2022-06-30T14:40:21",
-  "source_file_size": 29496,
-  "generation_date": "2022-06-30T14:43:30",
+  "source_file_date": "2022-07-02T16:17:59",
+  "source_file_size": 29591,
+  "generation_date": "2022-07-02T16:19:58",
   "@type": "SchemaDefinition",
   "@context": [
     "project/jsonld/kgcl.context.jsonld",