@@ -129,7 +129,7 @@ def generalize_tsv(tsvfile, output, class_name, schema_name, pandera: bool, anno
129129
130130 Example:
131131
132- schemauto generalize-tsv --class-name Person --schema-name PersonInfo my/data/persons.tsv
132+ `` schemauto generalize-tsv --class-name Person --schema-name PersonInfo my/data/persons.tsv``
133133 """
134134 kwargs = {k :v for k , v in kwargs .items () if v is not None }
135135 if pandera :
@@ -161,11 +161,11 @@ def generalize_tsvs(tsvfiles, output, schema_name, **kwargs):
161161
162162 See :ref:`generalizers` for more on the generalization framework
163163
164- This uses :ref:` CsvDataGeneralizer.convert_multiple`
164+ This uses CsvDataGeneralizer.convert_multiple
165165
166166 Example:
167167
168- schemauto generalize-tsvs --class-name Person --schema-name PersonInfo my/data/*.tsv
168+ `` schemauto generalize-tsvs --class-name Person --schema-name PersonInfo my/data/*.tsv``
169169 """
170170 ie = CsvDataGeneralizer (** kwargs )
171171 schema = ie .convert_multiple (tsvfiles , schema_name = schema_name )
@@ -229,7 +229,7 @@ def import_dosdps(dpfiles, output, **args):
229229
230230 Example:
231231
232- schemauto import-dosdps --range-as-enums patterns/*yaml -o my-schema.yaml
232+ `` schemauto import-dosdps --range-as-enums patterns/*. yaml -o my-schema.yaml``
233233 """
234234 ie = DOSDPImportEngine ()
235235 schema = ie .convert (dpfiles , ** args )
@@ -309,7 +309,7 @@ def generalize_json(input, output, schema_name, depluralize: bool, format, omit_
309309
310310 Example:
311311
312- schemauto generalize-json my/data/persons.json -o my.yaml
312+ `` schemauto generalize-json my/data/persons.json -o my.yaml``
313313 """
314314 ie = JsonDataGeneralizer (omit_null = omit_null , depluralize_class_names = depluralize )
315315 if inlined_map :
@@ -336,7 +336,7 @@ def generalize_toml(input, output, schema_name, omit_null, **kwargs):
336336
337337 Example:
338338
339- schemauto generalize-toml my/data/conf.toml -o my.yaml
339+ `` schemauto generalize-toml my/data/conf.toml -o my.yaml``
340340 """
341341 ie = JsonDataGeneralizer (omit_null = omit_null )
342342 schema = ie .convert (input , format = 'toml' , ** kwargs )
@@ -365,7 +365,7 @@ def import_json_schema(input, output, import_project: bool, schema_name, format,
365365
366366 Example:
367367
368- schemauto import-json-schema my/schema/personinfo.schema.json
368+ `` schemauto import-json-schema my/schema/personinfo.schema.json``
369369 """
370370 ie = JsonSchemaImportEngine (** kwargs )
371371 if not import_project :
@@ -390,7 +390,7 @@ def import_kwalify(input, output, schema_name, **kwargs):
390390
391391 Example:
392392
393- schemauto import-kwalify my/schema/personinfo.kwalify.yaml
393+ `` schemauto import-kwalify my/schema/personinfo.kwalify.yaml``
394394 """
395395 ie = KwalifyImportEngine (** kwargs )
396396 schema = ie .convert (input , output , name = schema_name , format = format )
@@ -409,7 +409,7 @@ def import_frictionless(input, output, schema_name, schema_id, **kwargs):
409409
410410 Example:
411411
412- schemauto import-frictionless cfde.package.json
412+ `` schemauto import-frictionless cfde.package.json``
413413 """
414414 ie = FrictionlessImportEngine (** kwargs )
415415 schema = ie .convert (input , name = schema_name , id = schema_id )
@@ -429,7 +429,7 @@ def import_cadsr(input, output, schema_name, schema_id, **kwargs):
429429
430430 Example:
431431
432- schemauto import-cadsr "cdes/*.json"
432+ `` schemauto import-cadsr "cdes/*.json"``
433433 """
434434 ie = CADSRImportEngine ()
435435 paths = [str (gf .absolute ()) for gf in Path ().glob (input ) if gf .is_file ()]
@@ -460,7 +460,7 @@ def import_owl(owlfile, output, **args):
460460
461461 Example:
462462
463- schemauto import-owl prov.ofn -o my.yaml
463+ `` schemauto import-owl prov.ofn -o my.yaml``
464464 """
465465 sie = OwlImportEngine ()
466466 schema = sie .convert (owlfile , ** args )
@@ -509,7 +509,7 @@ def generalize_rdf(rdffile, dir, output, **args):
509509
510510 Example:
511511
512- schemauto generalize-rdf my/data/persons.ttl
512+ `` schemauto generalize-rdf my/data/persons.ttl``
513513 """
514514 sie = RdfDataGeneralizer ()
515515 if not os .path .exists (dir ):
@@ -539,13 +539,13 @@ def annotate_schema(schema: str, input: str, output: str, **kwargs):
539539
540540 Example:
541541
542- schemauto annotate-schema -i bioportal: my-schema.yaml -o annotated.yaml
542+ `` schemauto annotate-schema -i bioportal: my-schema.yaml -o annotated.yaml``
543543
544544 This will require you setting the API key via OAK - see OAK docs.
545545
546546 You can specify a specific ontology
547547
548- schemauto annotate-schema -i bioportal:ncbitaxon my-schema.yaml -o annotated.yaml
548+ `` schemauto annotate-schema -i bioportal:ncbitaxon my-schema.yaml -o annotated.yaml``
549549
550550 In future OAK will support a much wider variety of annotators including:
551551
@@ -594,13 +594,13 @@ def enrich_using_ontology(schema: str, input: str, output: str, annotate: bool,
594594
595595 Example:
596596
597- schemauto enrich-using-ontology -i bioportal: my-schema.yaml -o my-enriched.yaml
597+ `` schemauto enrich-using-ontology -i bioportal: my-schema.yaml -o my-enriched.yaml``
598598
599599 If your schema has no mappings you can use --annotate to add them
600600
601601 Example:
602602
603- schemauto enrich-using-ontology -i so.obo --annotate my-schema.yaml -o my-enriched.yaml --annotate
603+ `` schemauto enrich-using-ontology -i so.obo --annotate my-schema.yaml -o my-enriched.yaml --annotate``
604604 """
605605 impl = get_implementation_from_shorthand (input )
606606 annr = SchemaAnnotator (impl )
@@ -630,7 +630,7 @@ def enrich_using_llm(schema: str, model: str, output: str, **args):
630630
631631 Example:
632632
633- pip install schema-automator[llm]
633+ `` pip install schema-automator[llm]``
634634
635635 """
636636 logging .info (f"Enriching: { schema } )
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