refscan 0.1.1__tar.gz → 0.1.2__tar.gz

{refscan-0.1.1 → refscan-0.1.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: refscan
-Version: 0.1.1
+Version: 0.1.2
 Summary: Command-line program that scans the NMDC MongoDB database for referential integrity violations
 Home-page: https://github.com/microbiomedata/refscan
 Keywords: mongodb,mongo,relationships,reference,database,data,referential integrity,scan
@@ -240,7 +240,7 @@ That package will have a version identifier that matches the name of the Git tag
 
 The GitHub Actions workflow will automatically 
 
-### Testing the build process locally
+### Test the build process locally
 
 In case you want to test the build process locally, you can do so by running:
 

{refscan-0.1.1 → refscan-0.1.2}/README.md

@@ -221,7 +221,7 @@ That package will have a version identifier that matches the name of the Git tag
 
 The GitHub Actions workflow will automatically 
 
-### Testing the build process locally
+### Test the build process locally
 
 In case you want to test the build process locally, you can do so by running:
 

{refscan-0.1.1 → refscan-0.1.2}/pyproject.toml

@@ -2,7 +2,7 @@
 
 [tool.poetry]
 name = "refscan"
-version = "v0.1.1"
+version = "v0.1.2"
 description = "Command-line program that scans the NMDC MongoDB database for referential integrity violations"
 authors = []
 readme = "README.md"

refscan-0.1.2/refscan/__init__.py

@@ -0,0 +1,18 @@
+from importlib.metadata import metadata, PackageMetadata, PackageNotFoundError
+
+
+def get_package_metadata(key: str) -> str:
+    r"""
+    Returns metadata about the installed package.
+
+    References:
+    - https://docs.python.org/3/library/importlib.metadata.html#distribution-metadata
+    - https://github.com/python-poetry/poetry/issues/273#issuecomment-570999678
+    """
+    metadata_value = ""
+    try:
+        package_metadata: PackageMetadata = metadata("refscan")
+        metadata_value = package_metadata.get(key)
+    except PackageNotFoundError:
+        pass
+    return metadata_value

{refscan-0.1.1 → refscan-0.1.2}/refscan/refscan.py

@@ -26,10 +26,12 @@ app = typer.Typer(
     rich_markup_mode="markdown",  # enables use of Markdown in docstrings and CLI help
 )
 
+app_version = get_package_metadata("Version")
 
-def show_project_version_and_exit(is_active: bool = False) -> None:
+
+def display_app_version_and_exit(is_active: bool = False) -> None:
     r"""
-    Displays the version number of the installed package, then exists.
+    Displays the app's version number, then exists.
 
     Note: The `is_active` flag will be `True` if the program was
           invoked with the associated CLI option.
@@ -37,8 +39,7 @@ def show_project_version_and_exit(is_active: bool = False) -> None:
     Reference: https://typer.tiangolo.com/tutorial/options/version/
     """
     if is_active:
-        version = get_package_metadata("Version")
-        console.print(f"[white]{version}[/white]")
+        console.print(f"[white]{app_version}[/white]")
         raise typer.Exit()
 
 
@@ -90,7 +91,7 @@ def scan(
         )] = "violations.tsv",
         version: Annotated[Optional[bool], typer.Option(
             "--version",
-            callback=show_project_version_and_exit,
+            callback=display_app_version_and_exit,
             is_eager=True,  # tells Typer to process this option first
             help="Show version number and exit.",
         )] = None,
@@ -103,9 +104,11 @@ def scan(
         console.print(f"Schema YAML file: {schema_file_path}")
     schema_view = linkml_runtime.SchemaView(schema_file_path)
 
-    # Show high-level information about the schema and LinkML runtime.
-    console.print(f"Schema version:         {schema_view.schema.version}")
-    console.print(f"LinkML runtime version: {linkml_runtime.__version__}")
+    # Show high-level information about the application and schema.
+    console.print(f"refscan version: {app_version}")
+    console.print(f"Schema version: {schema_view.schema.version}")
+
+    console.rule("[bold]Identifying references")
 
     # Make a more self-documenting alias for the CLI option that can be specified multiple times.
     names_of_source_collections_to_skip: list[str] = [] if skip_source_collection is None else skip_source_collection
@@ -181,6 +184,8 @@ def scan(
     if verbose:
         console.print(references.as_table())
 
+    console.rule("[bold]Scanning for violations")
+
     # Get a dictionary that maps source class names to the names of their fields that can contain references.
     reference_field_names_by_source_class_name = references.get_reference_field_names_by_source_class_name()
 
@@ -314,6 +319,8 @@ def scan(
     # Close the connection to the MongoDB server.
     mongo_client.close()
 
+    console.rule("[bold]Results summary")
+
     # Create a violation report in TSV format — for all collections combined.
     all_violations = ViolationList()
     for collection_name, violations in sorted(source_collections_and_their_violations.items(), key=get_lowercase_key):

refscan-0.1.1/refscan/__init__.py

@@ -1,11 +0,0 @@
-import importlib.metadata
-
-
-def get_package_metadata(key: str) -> str:
-    r"""
-    Returns metadata about the installed package.
-
-    Reference: https://github.com/python-poetry/poetry/issues/273#issuecomment-570999678
-    """
-    package_metadata = importlib.metadata.metadata("refscan")
-    return package_metadata[key] if key in package_metadata else ""