Merge branch 'main' into add-oak

README.md

@@ -15,7 +15,7 @@ This is a toolkit that assists with:
 
 These can be composed together. For example, run `tsvs2linkml` followed by `annotate-enums`
 
-The toolkit is still experimental. It is intended as an aid to schema creation rather than act as a formal conversion
-tool
+The toolkit is still experimental. It is intended as an aid to schema creation rather than as a formal conversion
+tool.
 
-[Full Documentation](https://linkml.io/schema-automator/)
+[Full Documentation](https://linkml.io/schema-automator/)

pyproject.toml

@@ -51,6 +51,7 @@ build-backend = "poetry.core.masonry.api"
 [tool.poetry.scripts]
 schemauto = "schema_automator.cli:main"
 tsv2linkml = "schema_automator.importers.csv_import_engine:tsv2model"
+tsvs2linkml = "schema_automator.importers.csv_import_engine:tsvs2model"
 enum_annotator = "schema_automator.annotators.enum_annotator:enum_annotator"
 enums_to_curateable = "schema_automator.annotators.enums_to_curateable:enums_to_curateable"
 curated_to_enums = "schema_automator.annotators.curated_to_enums:curated_to_enums"

schema_automator/generalizers/csv_data_generalizer.py

@@ -675,7 +675,7 @@ def tsv2model(tsvfile, output, separator, class_name, schema_name, **kwargs):
 @click.argument('tsvfiles', nargs=-1)  # input TSV (must have column headers
 @click.option('--output', '-o', help='Output file')
 @click.option('--schema_name', '-n', default='example', help='Schema name')
-@click.option('--sep', '-s', default='\t', help='separator')
+@click.option('--file_separator', '-s', default='\t', help='separator')
 @click.option('--downcase-header/--no-downcase-header', default=False, help='if true make headers lowercase')
 @click.option('--infer-foreign-keys/--no-infer-foreign-keys', default=False, help='infer ranges/foreign keys')
 @click.option('--enum-columns', '-E', multiple=True, help='column(s) that is forced to be an enum')