grz-cli 1.1.1__tar.gz → 1.1.2__tar.gz

{grz_cli-1.1.1 → grz_cli-1.1.2}/CHANGELOG.md

@@ -1,5 +1,12 @@
 # Changelog
 
+## [1.1.2](https://github.com/BfArM-MVH/grz-tools/compare/grz-cli-v1.1.1...grz-cli-v1.1.2) (2025-08-05)
+
+
+### Bug Fixes
+
+* **grz-cli,grz-common,grzctl:** fix logging and migrate to grz-common ([#319](https://github.com/BfArM-MVH/grz-tools/issues/319)) ([51ada07](https://github.com/BfArM-MVH/grz-tools/commit/51ada073a2af93ba1a1c48f069b4546ce9bd2975))
+
 ## [1.1.1](https://github.com/BfArM-MVH/grz-tools/compare/grz-cli-v1.1.0...grz-cli-v1.1.1) (2025-07-23)
 
 

{grz_cli-1.1.1 → grz_cli-1.1.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: grz-cli
-Version: 1.1.1
+Version: 1.1.2
 Summary: Tool for validation, encryption and upload of MV submissions to GDCs.
 Project-URL: Homepage, https://github.com/BfArM-MVH/grz-tools
 Project-URL: Repository, https://github.com/BfArM-MVH/grz-tools
@@ -16,7 +16,7 @@ Requires-Python: >=3.12
 Requires-Dist: boto3<2,>=1.36
 Requires-Dist: click<9,>=8.2
 Requires-Dist: crypt4gh<2,>=1.7
-Requires-Dist: grz-common<2,>=1.1.1
+Requires-Dist: grz-common<2,>=1.2.1
 Requires-Dist: grz-pydantic-models<3,>=2.1.2
 Requires-Dist: jsonschema<5,>=4.23.0
 Requires-Dist: platformdirs<5,>=4.3.6
@@ -220,7 +220,16 @@ Alternatively, install `uv` and `tox` and run `uv run tox`.
 
 ## Contributing
 
-<!-- Add details about how others can contribute to the project -->
+### Running unreleased/development versions
+
+First, install `uv`.
+We recommend using Conda or [Pixi](https://pixi.sh/latest).
+
+After cloning the desired branch of the `grz-tools` repo locally, you can run `grz-cli` directly from the repo using:
+
+```
+uv run --project path/to/cloned/grz-tools grz-cli --help
+```
 
 ## License
 

{grz_cli-1.1.1 → grz_cli-1.1.2}/README.md

@@ -189,7 +189,16 @@ Alternatively, install `uv` and `tox` and run `uv run tox`.
 
 ## Contributing
 
-<!-- Add details about how others can contribute to the project -->
+### Running unreleased/development versions
+
+First, install `uv`.
+We recommend using Conda or [Pixi](https://pixi.sh/latest).
+
+After cloning the desired branch of the `grz-tools` repo locally, you can run `grz-cli` directly from the repo using:
+
+```
+uv run --project path/to/cloned/grz-tools grz-cli --help
+```
 
 ## License
 

{grz_cli-1.1.1 → grz_cli-1.1.2}/pyproject.toml

@@ -26,7 +26,7 @@ dependencies = [
     "pysam ==0.23.*",
     "rich ==13.*",
     "requests >=2.32.3,<3",
-    "grz-common >=1.1.1,<2",
+    "grz-common >=1.2.1,<2",
 ]
 classifiers = [
     "Programming Language :: Python :: 3",

grz_cli-1.1.2/src/grz_cli/__init__.py

@@ -0,0 +1 @@
+__version__ = "1.1.2"

{grz_cli-1.1.1 → grz_cli-1.1.2}/src/grz_cli/cli.py

@@ -8,15 +8,14 @@ from importlib.metadata import version
 
 import click
 import grz_pydantic_models.submission.metadata
+from grz_common.logging import setup_cli_logging
 
 from .commands.encrypt import encrypt
 from .commands.submit import submit
 from .commands.upload import upload
 from .commands.validate import validate
-from .constants import PACKAGE_ROOT
-from .logging_setup import add_filelogger
 
-log = logging.getLogger(PACKAGE_ROOT + ".cli")
+log = logging.getLogger(__name__)
 
 
 class OrderedGroup(click.Group):
@@ -58,21 +57,7 @@ def build_cli():
         :param log_level: Log level for the logger. It should be one of the following:
                            DEBUG, INFO, WARNING, ERROR, CRITICAL.
         """
-        if log_file:
-            add_filelogger(
-                log_file,
-                log_level.upper(),
-            )  # Add file logger
-
-        # show only time and log level in STDOUT
-        logging.basicConfig(
-            format="%(asctime)s - %(levelname)s - %(message)s",
-        )
-
-        # set the log level for this package
-        logging.getLogger(PACKAGE_ROOT).setLevel(log_level.upper())
-
-        log.debug("Logging setup complete.")
+        setup_cli_logging(log_file, log_level)
 
     cli.add_command(validate)
     cli.add_command(encrypt)

grz_cli-1.1.1/src/grz_cli/__init__.py

@@ -1 +0,0 @@
-__version__ = "1.1.1"

grz_cli-1.1.1/src/grz_cli/constants.py

@@ -1,38 +0,0 @@
-"""Constants for logging configuration, JSON schema validation, and other settings."""
-
-PACKAGE_ROOT = "grz_cli"
-
-LOGGING_FORMAT = "%(asctime)s [%(levelname)s] %(name)s: %(message)s"
-LOGGING_DATEFMT = "%Y-%m-%d %I:%M %p"
-LOGGING_CONFIG = {
-    "version": 1,
-    "disable_existing_loggers": True,
-    "formatters": {
-        "standard": {
-            "format": LOGGING_FORMAT,
-            "datefmt": LOGGING_DATEFMT,
-        },
-    },
-    "handlers": {
-        "default": {
-            "level": "INFO",
-            "formatter": "standard",
-            "class": "logging.StreamHandler",
-        },
-    },
-    "loggers": {
-        "": {  # root logger
-            "handlers": ["default"],
-            "level": "WARNING",
-            "propagate": False,
-        },
-        PACKAGE_ROOT: {"handlers": ["default"], "level": "INFO", "propagate": False},
-        "__main__": {  # if __name__ == '__main__'
-            "handlers": ["default"],
-            "level": "DEBUG",
-            "propagate": False,
-        },
-    },
-}
-
-TQDM_SMOOTHING: float = 0.0001

grz_cli-1.1.1/src/grz_cli/logging_setup.py

@@ -1,59 +0,0 @@
-"""
-Module: logging_setup
-
-This module provides functions for setting up logging configuration.
-"""
-
-from __future__ import annotations
-
-import logging
-from os import PathLike
-from pathlib import Path
-
-from .constants import LOGGING_DATEFMT, LOGGING_FORMAT, PACKAGE_ROOT
-
-log = logging.getLogger(__name__)
-
-
-def add_filelogger(
-    file_path: str | PathLike | None = None,
-    level: str = "INFO",
-    logger_name: str = PACKAGE_ROOT,
-) -> None:
-    """
-    Add file logging for the specified package.
-
-    This function configures a file logger to capture log messages
-    for the package specified by _PACKAGE_ROOT. If no file path
-    is provided, a default log file will be created in the user's
-    home directory.
-
-    :param file_path: Optional; the path to the log file. If None,
-                      a default path will be used.
-    :param level: Optional; the logging level. Default is 'INFO'.
-                  Must be a valid logging level name (e.g., 'DEBUG', 'INFO').
-    :param logger_name:
-    """
-    logger = logging.getLogger(logger_name)
-
-    if file_path is None:
-        default_log_dir = Path.home() / "logs"
-        default_log_dir.mkdir(parents=True, exist_ok=True)
-        file_path = default_log_dir / f"{PACKAGE_ROOT}.log"
-        log.warning("No log file path provided, using default: %s", file_path)
-    else:
-        file_path = Path(file_path)
-
-    try:
-        fh = logging.FileHandler(file_path)
-        fh.setLevel(level.upper())
-        fh.setFormatter(logging.Formatter(LOGGING_FORMAT, LOGGING_DATEFMT))
-        logger.addHandler(fh)
-        log.info(
-            "File logger added for %s at %s with level %s.",
-            logger.name,
-            file_path,
-            level.upper(),
-        )
-    except Exception as e:
-        log.error("Failed to add file logger: %s", e)