divbase-cli 0.1.0a1__tar.gz → 0.1.0a3__tar.gz

{divbase_cli-0.1.0a1 → divbase_cli-0.1.0a3}/.gitignore

@@ -34,6 +34,12 @@ split_scaffold_files.txt
 scripts/benchmarking/*.yaml
 scripts/benchmarking/results
 
+# pytest-cov generate files
+.coverage
+.coverage.*
+htmlcov/
+docker/coverage-data/
+
 #MacOS artifacts
 .DS_Store
 
@@ -41,6 +47,7 @@ scripts/benchmarking/results
 .cache/
 # mkdocs auto generated files
 docs/cli/_auto_generated/*.md
+docs/releases/index.md
 
 # pypi 
 dist/

{divbase_cli-0.1.0a1 → divbase_cli-0.1.0a3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: divbase-cli
-Version: 0.1.0a1
+Version: 0.1.0a3
 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
@@ -18,7 +18,7 @@ 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==0.1.0a1
+Requires-Dist: divbase-lib==0.1.0a3
 Requires-Dist: keyring>=25.7.0
 Requires-Dist: typer==0.24.1
 Description-Content-Type: text/markdown

{divbase_cli-0.1.0a1 → divbase_cli-0.1.0a3}/pyproject.toml

@@ -10,7 +10,7 @@ requires-python = ">=3.12"
 dependencies = [
     "typer==0.24.1",
     "keyring>=25.7.0",
-    "divbase-lib==0.1.0a1",
+    "divbase-lib==0.1.0a3",
 ]
 dynamic = ["version"]
 

divbase_cli-0.1.0a3/src/divbase_cli/__init__.py

@@ -0,0 +1 @@
+__version__ = "0.1.0a3"

{divbase_cli-0.1.0a1 → divbase_cli-0.1.0a3}/src/divbase_cli/cli_commands/auth_cli.py

@@ -73,6 +73,8 @@ def login(
 def logout():
     """
     Log out of the DivBase server.
+
+    Removes your locally stored credentials and invalidates the server-side refresh token.
     """
     logout_of_divbase()
     print("Logged out successfully.")

{divbase_cli-0.1.0a1 → divbase_cli-0.1.0a3}/src/divbase_cli/cli_commands/dimensions_cli.py

@@ -32,7 +32,7 @@ dimensions_app = typer.Typer(
 def update_dimensions_index(
     project: str | None = PROJECT_NAME_OPTION,
 ) -> None:
-    """Calculate and add the dimensions of a VCF file to the dimensions index file in the project."""
+    """Calculate and add the dimensions of all VCF files in the project to the dimensions index in the project."""
 
     project_config = resolve_project(project_name=project)
 
@@ -279,7 +279,7 @@ def create_metadata_template_with_project_samples_names(
     project: str | None = PROJECT_NAME_OPTION,
 ) -> None:
     """
-    Create a template sample metadata file (TSV format) pre-filled with the sample names from the project's VCF files based on the information stored in the project's VCF dimensions cache. Tip: run 'divbase-cli dimensions update' first to ensure that the VCF dimensions areup-to-date.
+    Create a template sample metadata file (TSV format) pre-filled with the sample names from the project's VCF files based on the information stored in the project's VCF dimensions cache. Tip: run 'divbase-cli dimensions update' first to ensure that the VCF dimensions are up-to-date.
     """
     project_config = resolve_project(project_name=project)
     logged_in_url = ensure_logged_in(desired_url=project_config.divbase_url)

{divbase_cli-0.1.0a1 → divbase_cli-0.1.0a3}/src/divbase_cli/cli_commands/file_cli.py

@@ -48,7 +48,7 @@ DISABLE_VERIFY_CHECKSUMS_OPTION = typer.Option(
     "--disable-verify-checksums",
     "-nc",
     help="Turn off checksum verification which is on by default. "
-    "Checksum verification means all downloaded files are verified against their MD5 checksums."
+    "Checksum verification means all downloaded files are verified against their MD5 checksums. "
     "It is recommended to leave checksum verification enabled unless you have a specific reason to disable it.",
 )
 PROJECT_VERSION_OPTION = typer.Option(
@@ -89,7 +89,7 @@ def list_files(
     project: str | None = PROJECT_NAME_OPTION,
 ):
     """
-    list all currently available files in the project's DivBase store.
+    List all currently available files in the project's DivBase store.
 
     You can optionally filter the listed files by providing a prefix.
     By default, DivBase query results files are hidden from the listing. Use the --include-results-files option to include them.
@@ -219,7 +219,7 @@ def download_files(
     files: list[str] = typer.Argument(
         None, help="Space separated list of files/objects to download from the project's store on DivBase."
     ),
-    file_list: Path | None = typer.Option(None, "--file-list", help="Text file with list of files to upload."),
+    file_list: Path | None = typer.Option(None, "--file-list", help="Text file with list of files to download."),
     download_dir: str = DOWNLOAD_DIR_OPTION,
     dry_run: bool = DRY_RUN_OPTION,
     disable_verify_checksums: bool = DISABLE_VERIFY_CHECKSUMS_OPTION,
@@ -235,7 +235,7 @@ def download_files(
 
     To download the latest version of a file, just provide its name. "file1" "file2" etc.
     To download a specific/older version of a file, use the format: "file_name:version_id"
-    You can get a file's version id using the 'divbase-cli file info [FILE_NAME]' command.
+    You can get a file's version id using the 'divbase-cli files info [FILE_NAME]' command.
     You can mix and match latest and specific versions in the same command.
     E.g. to download the latest version of file1 and version "3xcdsdsdiw829x"
     of file2: 'divbase-cli files download file1 file2:3xcdsdsdiw829x'
@@ -385,7 +385,7 @@ def stream_file(
         default=None,
         help="Specify this if you want to look at an older/specific version of the file. "
         "If not provided, the latest version of the file is used. "
-        "To get a file's version ids, use the 'divbase-cli file info [FILE_NAME]' command.",
+        "To get a file's version ids, use the 'divbase-cli files info [FILE_NAME]' command.",
     ),
     project: str | None = PROJECT_NAME_OPTION,
 ):
@@ -483,7 +483,7 @@ def upload_files(
 @file_app.command("rm")
 def remove_files(
     files: list[str] | None = typer.Argument(
-        None, help="Space seperated list of files/objects in the project's store on DivBase to delete."
+        None, help="Space separated list of files/objects in the project's store on DivBase to delete."
     ),
     file_list: Path | None = typer.Option(None, "--file-list", help="Text file with list of files to delete."),
     dry_run: bool = typer.Option(
@@ -528,7 +528,7 @@ def remove_files(
 @file_app.command("restore")
 def restore_soft_deleted_files(
     files: list[str] | None = typer.Argument(
-        None, help="Space seperated list of files/objects in the project's store on DivBase to restore."
+        None, help="Space separated list of files/objects in the project's store on DivBase to restore."
     ),
     file_list: Path | None = typer.Option(None, "--file-list", help="Text file with list of files to restore."),
     project: str | None = PROJECT_NAME_OPTION,

{divbase_cli-0.1.0a1 → divbase_cli-0.1.0a3}/src/divbase_cli/cli_commands/user_config_cli.py

@@ -66,9 +66,13 @@ def remove_project_command(
 
 @config_app.command("set-default")
 def set_default_project_command(
-    name: str = typer.Argument(..., help="Name of the project to add to the user configuration file."),
+    name: str = typer.Argument(..., help="Name of the project to set as the default."),
 ):
-    """Set your default project to use in all divbase-cli commands."""
+    """
+    Set the default project to use in all divbase-cli commands.
+
+    The project must already be added to your config file using the 'add' command.
+    """
     config = load_user_config()
     default_project_name = config.set_default_project(name=name)
     print(f"Default project is now set to '{default_project_name}'.")
@@ -89,13 +93,16 @@ def show_default_project_command() -> None:
 def set_default_dload_dir_command(
     download_dir: str = typer.Argument(
         ...,
-        help="""Set the default directory to download files to. 
-        By default files are downloaded to the current working directory.
-        You can specify an absolute path. 
-        You can use '.' to refer to the directory you run the command from.""",
+        help="Set the default directory to download files to. "
+        "By default files are downloaded to the current working directory. "
+        "Do not use a relative path. To use the current working directory (where each command is run from), use '.' as the argument.",
     ),
 ):
-    """Set the default download dir"""
+    """
+    Set the default download directory in your user configuration file.
+
+    This is by default unset, meaning files will be downloaded to the current working directory.
+    """
     config = load_user_config()
     dload_dir = config.set_default_download_dir(download_dir=download_dir)
     if dload_dir == ".":

{divbase_cli-0.1.0a1 → divbase_cli-0.1.0a3}/src/divbase_cli/user_auth.py

@@ -21,7 +21,7 @@ import httpx
 import keyring
 import stamina
 import yaml
-from keyring.errors import KeyringError, NoKeyringError, PasswordDeleteError
+from keyring.errors import KeyringError
 from pydantic import SecretStr
 
 from divbase_cli import __version__ as cli_version
@@ -85,7 +85,7 @@ class TokenData:
 
 def _delete_stored_jwts(token_path: Path) -> None:
     """Attempt to delete user JWTs from both the keyring and the fallback file."""
-    with contextlib.suppress(NoKeyringError, PasswordDeleteError):
+    with contextlib.suppress(KeyringError):
         keyring.delete_password(service_name=cli_settings.KEYRING_SERVICE, username=cli_settings.KEYRING_USERNAME)
     token_path.unlink(missing_ok=True)
 

divbase_cli-0.1.0a1/src/divbase_cli/__init__.py

@@ -1 +0,0 @@
-__version__ = "0.1.0a1"