divbase-cli 0.1.0a14__tar.gz → 0.1.0a16__tar.gz

{divbase_cli-0.1.0a14 → divbase_cli-0.1.0a16}/.gitignore

@@ -50,9 +50,10 @@ docker/logs/*
 #MacOS artifacts
 .DS_Store
 
-# mkdocs build cache
+# mkdocs/zensical build cache
 .cache/
-# mkdocs auto generated files
+site/
+# documentation site's auto generated files
 docs/cli/_auto_generated/*.md
 docs/releases/index.md
 

{divbase_cli-0.1.0a14 → divbase_cli-0.1.0a16}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.4
+Metadata-Version: 2.5
 Name: divbase-cli
-Version: 0.1.0a14
+Version: 0.1.0a16
 Summary: Command Line Interface for Divbase
 Project-URL: Homepage, https://divbase.scilifelab-2-prod.sys.kth.se
 Project-URL: Documentation, https://scilifelabdatacentre.github.io/divbase
@@ -18,9 +18,9 @@ Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
 Classifier: Programming Language :: Python :: 3.14
 Requires-Python: >=3.12
-Requires-Dist: divbase-lib==0.1.0a14
+Requires-Dist: divbase-lib==0.1.0a16
 Requires-Dist: keyring==25.7.0
-Requires-Dist: typer==0.26.8
+Requires-Dist: typer==0.27.2
 Description-Content-Type: text/markdown
 
 # divbase-cli

{divbase_cli-0.1.0a14 → divbase_cli-0.1.0a16}/pyproject.toml

@@ -8,9 +8,9 @@ authors = [
 ]
 requires-python = ">=3.12"
 dependencies = [
-    "typer==0.26.8",
+    "typer==0.27.2",
     "keyring==25.7.0",
-    "divbase-lib==0.1.0a14",
+    "divbase-lib==0.1.0a16",
 ]
 dynamic = ["version"]
 

divbase_cli-0.1.0a16/src/divbase_cli/__init__.py

@@ -0,0 +1 @@
+__version__ = "0.1.0a16"

{divbase_cli-0.1.0a14 → divbase_cli-0.1.0a16}/src/divbase_cli/cli_commands/dimensions_cli.py

@@ -34,7 +34,7 @@ dimensions_app = typer.Typer(
 def update_dimensions_index(
     project: str | None = PROJECT_NAME_OPTION,
 ) -> None:
-    """Calculate and add the dimensions of all VCF files in the project to the dimensions index in the project."""
+    """Calculate and add the dimensions of all VCF files in the project to the dimensions cache in the project."""
     project_config = resolve_and_authenticate_project(project_name=project)
     response = make_authenticated_request(
         method="PUT",
@@ -96,7 +96,7 @@ def show_dimensions_index(
     project: str | None = PROJECT_NAME_OPTION,
 ) -> None:
     """
-    Show the dimensions index file for a project.
+    Show the dimensions cache file for a project.
     When running --unique-scaffolds, the sorting separates between numeric and non-numeric scaffold names.
     """
     if sample_names_output and sample_names_stdout:
@@ -290,7 +290,7 @@ def create_metadata_template_with_project_samples_names(
     )
 
     if sample_count == 0:
-        # Fallback in case there are no samples in the dimensions index. If no dimensions entry for the project
+        # Fallback in case there are no samples in the dimensions cache. If no dimensions entry for the project
         # VCFDimensionsEntryMissingError will be returned. But for some reason, there are no samples in the VCF, this will catch that.
         print("No samples found for this project. No file written.")
         return
@@ -337,7 +337,7 @@ def validate_metadata_template_versus_dimensions_and_formatting_constraints(
     """
     # Client-side validation of a sidecar metadata TSV file, intended to be run before upload to DivBase.
     # Uses the SharedMetadataValidator (that is also used on the server-side) which checks for formatting errors and also validates that the sample names
-    # in the TSV file match the sample names in the dimensions index for the project
+    # in the TSV file match the sample names in the dimensions cache for the project
     project_config = resolve_and_authenticate_project(project_name=project)
     print(f"Validating local metadata file: {input_path}")
     print(f"Project: {project_config.name}\n")

{divbase_cli-0.1.0a14 → divbase_cli-0.1.0a16}/src/divbase_cli/display_task_history.py

@@ -155,7 +155,7 @@ class TaskHistoryDisplayManager:
 
         elif isinstance(task.result, DimensionUpdateTaskResult):
             result_message = (
-                f"VCF file dimensions index added or updated:\n  {task.result.VCF_files_added}\n"
+                f"VCF file dimensions cache added or updated:\n  {task.result.VCF_files_added}\n"
                 f"VCF files skipped by this job (previous DivBase-generated result VCFs):\n  {task.result.VCF_files_skipped}\n"
                 f"VCF files that have been deleted from the project and now are dropped from the index:\n  {task.result.VCF_files_deleted}"
             )

divbase_cli-0.1.0a14/src/divbase_cli/__init__.py

@@ -1 +0,0 @@
-__version__ = "0.1.0a14"