fix: Standardize package imports and configure explicit exports

__init__.py

@@ -14,3 +14,20 @@ from .doi2dataset import (
     sanitize_filename,
     validate_email_address,
 )
+
+# Explicit exports for package API
+__all__ = [
+    "AbstractProcessor",
+    "APIClient",
+    "CitationBuilder",
+    "Config",
+    "License",
+    "LicenseProcessor",
+    "MetadataProcessor",
+    "NameProcessor",
+    "Person",
+    "PIFinder",
+    "SubjectMapper",
+    "sanitize_filename",
+    "validate_email_address",
+]

doi2dataset.py

@@ -65,11 +65,12 @@ except ImportError:
 # TODO: Remove once the warning is stripped from idutils
 warnings.filterwarnings("ignore", category=DeprecationWarning)
 
-from idutils.normalizers import normalize_doi, normalize_orcid, normalize_pmid
+from idutils.normalizers import (  # noqa: E402
-from idutils.validators import is_doi
+    normalize_doi,
-
+    normalize_orcid,
-# Script version
+    normalize_pmid,
-VERSION = "1.0"
+)
+from idutils.validators import is_doi  # noqa: E402
 
 # Icon definitions for console output
 ICONS = {
@@ -558,7 +559,7 @@ class APIClient:
     Attributes:
         session (requests.Session): The underlying requests session.
     """
-    def __init__(self, contact_mail: str | None = None, user_agent: str = f"UDE-Doi2Dataset/{VERSION}", token: str | None = None) -> None:
+    def __init__(self, contact_mail: str | None = None, user_agent: str = f"UDE-Doi2Dataset/{__version__}", token: str | None = None) -> None:
         """
         Initialize the API client with optional contact mail, user agent, and token.
 

tests/conftest.py

@@ -5,4 +5,4 @@ import sys
 parent_dir = os.path.abspath(os.path.join(os.path.dirname(__file__), ".."))
 
 # Add the parent directory to sys.path
-sys.path.insert(0, parent_dir)
+sys.path.insert(0, parent_dir)

tests/test_citation_builder.py

@@ -10,7 +10,7 @@ from doi2dataset import CitationBuilder, Person, PIFinder
 def openalex_data():
     """Load the saved JSON response from the file 'srep45389.json'"""
     json_path = os.path.join(os.path.dirname(__file__), "srep45389.json")
-    with open(json_path, "r", encoding="utf-8") as f:
+    with open(json_path, encoding="utf-8") as f:
         data = json.load(f)
     return data
 

tests/test_fetch_doi_mock.py

@@ -46,7 +46,7 @@ def fake_openalex_response():
     located in the same directory as this test file.
     """
     json_path = os.path.join(os.path.dirname(__file__), "srep45389.json")
-    with open(json_path, "r", encoding="utf-8") as f:
+    with open(json_path, encoding="utf-8") as f:
         data = json.load(f)
     return data
 

tests/test_license_processor.py

@@ -1,5 +1,5 @@
-import pytest
+from doi2dataset import License, LicenseProcessor
-from doi2dataset import LicenseProcessor, License
+
 
 def test_license_processor_cc_by():
     """Test processing a CC BY license"""
@@ -59,4 +59,4 @@ def test_license_processor_no_primary_location():
     assert isinstance(license_obj, License)
     assert license_obj.short == "unknown"
     assert license_obj.name == ""
-    assert license_obj.uri == ""
+    assert license_obj.uri == ""

tests/test_metadata_processor.py

@@ -11,7 +11,7 @@ from doi2dataset import MetadataProcessor
 def openalex_data():
     """Load the saved JSON response from the file 'srep45389.json'"""
     json_path = os.path.join(os.path.dirname(__file__), "srep45389.json")
-    with open(json_path, "r", encoding="utf-8") as f:
+    with open(json_path, encoding="utf-8") as f:
         data = json.load(f)
     return data
 

tests/test_publication_utils.py

@@ -1,10 +1,10 @@
-import json
-import os
-import pytest
 from unittest.mock import MagicMock
 
+import pytest
+
 from doi2dataset import MetadataProcessor
 
+
 @pytest.fixture
 def metadata_processor():
     """Create a MetadataProcessor instance with mocked dependencies"""
@@ -54,4 +54,4 @@ def test_get_publication_year_with_invalid_data(metadata_processor):
         "publication_date": "invalid-date"
     }
     year = metadata_processor._get_publication_year(data)
-    assert year == "not-a-year"
+    assert year == "not-a-year"