Merge pull request #46 from linkml/remove_noisy_warning

remove warning, change to log.info

Makefile

@@ -8,3 +8,9 @@ test:
 etl:
 	$(RUN) slurp-prefixmaps -d $(DATA)
 
+lint-fix:
+	$(RUN) tox -e lint-fix
+	$(RUN) tox -e flake8
+
+
+format: lint-fix

src/prefixmaps/datamodel/context.py

@@ -1,7 +1,7 @@
 """Classes for managing individual Contexts."""
 
+import logging
 import re
-import warnings
 from collections import defaultdict
 from dataclasses import dataclass, field
 from enum import Enum
@@ -25,6 +25,9 @@
 PREFIX_RE = re.compile(r"^[\w\.]+$")
 NAMESPACE_RE = re.compile(r"http[s]?://[\w\.\-\/]+[#/_:]$")
 
+logger = logging.getLogger()
+logger.setLevel(logging.INFO)
+
 
 class StatusType(Enum):
     """
@@ -304,8 +307,12 @@ def as_extended_prefix_map(self) -> List[curies.Record]:
                 expansion.status == StatusType.namespace_alias
                 and expansion.namespace not in reverse_prefix_map
             ):
-                warnings.warn(
-                    f"Namespace {expansion.namespace} has no canonical prefix", stacklevel=2
+                # this is too noisy, we need a logger here instead
+                # warnings.warn(
+                #    f"namespace alias {expansion.namespace} => {expansion.prefix} is not a canonical namespace"
+                # )
+                logger.info(
+                    f"namespace alias {expansion.namespace} => {expansion.prefix} is not a canonical namespace"
                 )
 
         return [

src/prefixmaps/ingest/ingest_go.py

@@ -30,7 +30,7 @@ def parse_go_xrefs(input: Union[str, TextIO]) -> Context:
     for p in prefixes:
         if "rdf_uri_prefix" in p:
             ns = p["rdf_uri_prefix"]
-            if not ns[-1] in ["/", "#", "_"]:
+            if ns[-1] not in ["/", "#", "_"]:
                 ns += "/"
             context.add_prefix(p["database"], ns)
     return context

tox.ini

@@ -19,6 +19,16 @@ commands =
     isort .
 description = Run linters.
 
+[testenv:lint-fix]
+deps =
+    black
+    ruff
+skip_install = true
+commands =
+    black src/ tests/
+    ruff --fix src/ tests/
+description = Run linters.
+
 [testenv:flake8]
 skip_install = true
 deps =