Add setup_logger in main entrypoint

Author: tintinrevient

pyproject.toml

@@ -1,6 +1,5 @@
 [project]
 name = "pg2-benchmark"
-version = "0.1.0"
 description = "Add your description here"
 readme = "README.md"
 authors = [
@@ -10,6 +9,7 @@ authors = [
     { name = "Henning Redestig", email = "Henning.Redestig@iff.com" },
     { name = "Karel van der Weg", email = "karel.weg@iff.com" },
 ]
+dynamic = ["version"]  # Dynamically set hatch version using git tags
 requires-python = ">=3.12"
 dependencies = [
     "typer>=0.15.2",
@@ -28,18 +28,21 @@ pg2-benchmark = "pg2_benchmark.__main__:app"
 requires = ["hatchling"]
 build-backend = "hatchling.build"
 
+[tool.hatch.version]
+path = "src/pg2_benchmark/__about__.py"
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/pg2_benchmark"]
+
 [tool.uv.sources]
 pg2-dataset = { git = "https://github.com/ProteinGym2/pg2-dataset.git", rev = "58c327e13bade1effe1312eb2b8d5445016a5a8f" }
 
 [tool.ruff]
 line-length = 88
 
-[tool.click]
-logging_level = "INFO"
-logging_format = "%(asctime)s - %(name)s - %(levelname)s - %(message)s"
-
 [dependency-groups]
 dev = [
+    "hatch>=1.14.1",
     "isort>=6.0.1",
     "pre-commit>=4.2.0",
     "pytest>=8.4.1",

src/pg2_benchmark/__about__.py

@@ -0,0 +1,9 @@
+"""Metadata file to store version used by hatch.
+
+> BE CAREFUL WITH MANUALLY CHANGING THIS FILE!
+
+References:
+    https://hatch.pypa.io/latest/version/
+"""
+
+__version__ = "0.1.0b1"

src/pg2_benchmark/__main__.py

@@ -4,10 +4,10 @@
 
 import typer
 
+from pg2_benchmark.__about__ import __version__
 from pg2_benchmark.cli.dataset import dataset_app
 from pg2_benchmark.cli.metric import metric_app
 from pg2_benchmark.cli.sagemaker import sagemaker_app
-from pg2_benchmark.logger import setup_logger
 from pg2_benchmark.model_card import ModelCard
 
 app = typer.Typer(
@@ -20,9 +20,6 @@
 app.add_typer(metric_app, name="metric", help="Metric operations")
 app.add_typer(sagemaker_app, name="sagemaker", help="SageMaker operations")
 
-setup_logger()
-logger = logging.getLogger("pg2_benchmark")
-
 
 class ModelPath:
     """Configuration class for model-related file paths.
@@ -35,28 +32,75 @@ class ModelPath:
     """Default location for model card files relative to model root directory."""
 
 
+def setup_logger(*, level: int = logging.CRITICAL) -> None:
+    """Set up the logger for the application.
+
+    Args:
+        log_level (int): The logging level to set. Defaults to `logging.CRITICAL`.
+    """
+    logger = logging.getLogger("pg2_benchmark")
+    logger.setLevel(level)
+
+    stream_handler = logging.StreamHandler()
+    stream_handler.setLevel(level)
+
+    formatter = logging.Formatter(
+        "%(asctime)s - %(name)s - %(levelname)s - %(message)s"
+    )
+    stream_handler.setFormatter(formatter)
+    logger.addHandler(stream_handler)
+
+
+@app.callback(invoke_without_command=True)
+def main(
+    ctx: typer.Context,
+    verbose: Annotated[int, typer.Option("--verbose", "-v", count=True)] = 3,
+    version: Annotated[
+        bool, typer.Option("--version", help="Show version and exit")
+    ] = False,
+) -> None:
+    """Main entry point for the CLI.
+
+    Args:
+        ctx (typer.Context): The context for the CLI.
+        verbose (int): The verbosity level. Use `-v` or `--verbose` to increase
+            verbosity. Each `-v` increases the verbosity level:
+            0: CRITICAL, 1: ERROR, 2: WARNING, 3: INFO, 4: DEBUG.
+            Defaults to 3 (INFO).
+        version (bool): If `True`, show the package version. Defaults to `False`.
+
+    Raises:
+        typer.Exit: If version is `True`, exits after showing the version.
+    """
+    setup_logger(level=logging.CRITICAL - verbose * 10)
+
+    if version:
+        typer.echo(f"v{__version__}")
+        raise typer.Exit()
+
+    if not ctx.invoked_subcommand:
+        typer.echo("Welcome to the PG2 Dataset CLI!")
+        typer.echo("Use --help to see available commands.")
+
+
 @app.command()
 def validate(
-    model_name: Annotated[
-        str, typer.Argument(help="Model name defined in the model card")
-    ],
     model_path: Annotated[
         Path,
         typer.Argument(
             help="Root path containting the model source code and model card",
             exists=True,
             dir_okay=True,
-            file_okay=False,
+            file_okay=True,
         ),
     ],
 ):
-    model_card_path = model_path / ModelPath.MODEL_CARD_PATH
+    logger = logging.getLogger("pg2_benchmark")
 
-    if not model_card_path.exists():
-        logger.error(
-            f"❌ Model {model_name} does not have a model card at {str(model_card_path)}"
-        )
-        raise typer.Exit(1)
+    if model_path.is_dir():
+        model_card_path = model_path / ModelPath.MODEL_CARD_PATH
+    else:
+        model_card_path = model_path
 
     try:
         model_card = ModelCard.from_path(model_card_path)

src/pg2_benchmark/cli/metric.py

@@ -5,11 +5,6 @@
 from pycm import ConfusionMatrix
 from scipy.stats import spearmanr
 
-from pg2_benchmark.logger import setup_logger
-
-setup_logger()
-logger = logging.getLogger("pg2_benchmark")
-
 metric_app = typer.Typer()
 
 
@@ -18,6 +13,7 @@ def calc(
     output_path: str = typer.Option(help="Path to the model output file"),
     metric_path: str = typer.Option(help="Path to the metric output file"),
 ):
+    logger = logging.getLogger("pg2_benchmark")
     logger.info("Calculating metrics...")
 
     df = pd.read_csv(output_path)

src/pg2_benchmark/logger.py

@@ -49,23 +49,22 @@ def test_model_card_validation_success(
     model_card_file = model_dir / ModelPath.MODEL_CARD_PATH
     model_card_file.write_text(valid_model_card_content)
 
-    result = runner.invoke(app, ["validate", model_name, str(model_dir)])
+    result = runner.invoke(app, ["validate", str(model_dir)])
 
     assert result.exit_code == 0
     assert "✅ Loaded test_model" in caplog.text
     assert "learning_rate" in caplog.text and "batch_size" in caplog.text
 
 
-def test_model_card_validation_missing_file(tmp_path: Path, runner: CliRunner, caplog):
+def test_model_card_validation_missing_file(runner: CliRunner):
     """Test validation when model card file doesn't exist."""
     model_name = "nonexistent_model"
-    model_dir = tmp_path / "models" / model_name
-    model_dir.mkdir(parents=True)
 
-    result = runner.invoke(app, ["validate", model_name, str(model_dir)])
+    result = runner.invoke(app, ["validate", str(model_name)])
 
-    assert result.exit_code == 1
-    assert "❌ Model nonexistent_model does not have a model card" in caplog.text
+    # Typer returns exit code 2 for parameter validation errors
+    assert result.exit_code == 2
+    assert "does not exist" in result.output
 
 
 def test_model_card_validation_invalid_content(
@@ -79,7 +78,7 @@ def test_model_card_validation_invalid_content(
     model_card_file = model_dir / ModelPath.MODEL_CARD_PATH
     model_card_file.write_text(invalid_model_card_content)
 
-    result = runner.invoke(app, ["validate", model_name, str(model_dir)])
+    result = runner.invoke(app, ["validate", str(model_dir)])
 
     assert result.exit_code == 1
     assert "❌ Error loading model card" in caplog.text
@@ -94,7 +93,7 @@ def test_model_card_validation_empty_file(tmp_path: Path, runner: CliRunner, cap
     model_card_file = model_dir / ModelPath.MODEL_CARD_PATH
     model_card_file.write_text("")
 
-    result = runner.invoke(app, ["validate", model_name, str(model_dir)])
+    result = runner.invoke(app, ["validate", str(model_dir)])
 
     assert result.exit_code == 1
     assert "❌ Error loading model card" in caplog.text