Add get_version_pins method to utils, remove final VERSION_PINS variable

src/pyobo/api/utils.py

@@ -3,18 +3,22 @@
 """Utilities for high-level API."""
 
 import json
+import logging
+import os
 from typing import Optional
 
 import bioversions
 
-from ..constants import VERSION_PINS
 from ..utils.path import prefix_directory_join
 
 __all__ = [
     "get_version",
+    "get_version_pins",
     "VersionError",
 ]
 
+logger = logging.getLogger(__name__)
+
 
 class VersionError(ValueError):
     """A catch-all for version getting failure."""
@@ -27,7 +31,7 @@ def get_version(prefix: str) -> Optional[str]:
     :return: The version if available else None
     """
     # Prioritize loaded environmental variable VERSION_PINS dictionary
-    version = VERSION_PINS.get(prefix)
+    version = get_version_pins().get(prefix)
     if version:
         return version
     try:
@@ -46,3 +50,40 @@ def get_version(prefix: str) -> Optional[str]:
         return data["version"]
 
     return None
+
+
+def get_version_pins():
+    """Retrieve the resource version pins."""
+    try:
+        version_pins_str = os.getenv("VERSION_PINS")
+        if not version_pins_str:
+            version_pins = {}
+        else:
+            version_pins = json.loads(version_pins_str)
+            invalid_prefixes = []
+            for prefix, version in version_pins.items():
+                if not isinstance(prefix, str) or not isinstance(version, str):
+                    logger.error(
+                        f"The prefix:{prefix} and version:{version} name must both be strings"
+                    )
+                    invalid_prefixes.append(prefix)
+            for prefix in invalid_prefixes:
+                version_pins.pop(prefix)
+    except ValueError as e:
+        logger.error(
+            "The value for the environment variable VERSION_PINS must be a valid JSON string: %s"
+            % e
+        )
+        version_pins = {}
+
+    if version_pins:
+        logger.debug(
+            f"These are the resource versions that are pinned.\n"
+            f"{version_pins}. "
+            f"\nPyobo will download the latest version of a resource if it's "
+            f"not pinned.\nIf you want to use a specific version of a "
+            f"resource, edit your VERSION_PINS environmental "
+            f"variable which is a JSON string to include a prefix and version "
+            f"name."
+        )
+    return version_pins

src/pyobo/constants.py

@@ -2,9 +2,7 @@
 
 """Constants for PyOBO."""
 
-import json
 import logging
-import os
 import re
 
 import pystow
@@ -13,8 +11,6 @@
     "RAW_DIRECTORY",
     "DATABASE_DIRECTORY",
     "SPECIES_REMAPPING",
-    "VERSION_PINS",
-    "get_version_pins",
 ]
 
 logger = logging.getLogger(__name__)
@@ -102,43 +98,3 @@
     "isbn",
     "issn",
 }
-
-
-def get_version_pins():
-    """Retrieve the resource version pins."""
-    try:
-        version_pins_str = os.getenv("VERSION_PINS")
-        if not version_pins_str:
-            version_pins = {}
-        else:
-            version_pins = json.loads(version_pins_str)
-            invalid_prefixes = []
-            for prefix, version in version_pins.items():
-                if not isinstance(prefix, str) or not isinstance(version, str):
-                    logger.error(
-                        f"The prefix:{prefix} and version:{version} name must both be strings"
-                    )
-                    invalid_prefixes.append(prefix)
-            for prefix in invalid_prefixes:
-                version_pins.pop(prefix)
-    except ValueError as e:
-        logger.error(
-            "The value for the environment variable VERSION_PINS must be a valid JSON string: %s"
-            % e
-        )
-        version_pins = {}
-
-    if version_pins:
-        logger.debug(
-            f"These are the resource versions that are pinned.\n"
-            f"{version_pins}. "
-            f"\nPyobo will download the latest version of a resource if it's "
-            f"not pinned.\nIf you want to use a specific version of a "
-            f"resource, edit your VERSION_PINS environmental "
-            f"variable which is a JSON string to include a prefix and version "
-            f"name."
-        )
-    return version_pins
-
-
-VERSION_PINS = get_version_pins()

tests/test_version_pins.py

@@ -5,10 +5,9 @@
 import unittest
 from unittest import mock
 
-from pyobo.api.utils import get_version
-from pyobo.constants import get_version_pins
+from pyobo.api.utils import get_version, get_version_pins
 
-MOCK_VERSION_PINS = '{"ncbitaxon": "2024-05-08", "vo":"2024-04-09", ' '"chebi":"235", "bfo":5}'
+MOCK_VERSION_PINS = '{"ncbitaxon": "2024-07-03", "vo":"2024-04-09", ' '"chebi":"235", "bfo":5}'
 
 
 @mock.patch.dict(os.environ, {"VERSION_PINS": MOCK_VERSION_PINS})