Replace Click with Typer for CLI tools (#978)

* Replace Click with Typer

* Fix entry points

setup.cfg

@@ -38,13 +38,13 @@ project_urls =
 install_requires =
     Deprecated
     SimpleITK!=2.0.*,!=2.1.1.1
-    click
     humanize
     nibabel
     numpy>=1.15
     scipy
     torch>=1.1
     tqdm
+    typer[all]
 python_requires = >=3.7
 include_package_data = True
 zip_safe = False
@@ -54,9 +54,9 @@ where = src
 
 [options.entry_points]
 console_scripts =
-    tiohd=torchio.cli.print_info:main
-    tiotr=torchio.cli.apply_transform:main
-    torchio-transform=torchio.cli.apply_transform:main
+    tiohd=torchio.cli.print_info:app
+    tiotr=torchio.cli.apply_transform:app
+    torchio-transform=torchio.cli.apply_transform:app
 
 [options.extras_require]
 all =

src/torchio/cli/apply_transform.py

@@ -1,50 +1,63 @@
 # pylint: disable=import-outside-toplevel
-"""Console script for torchio."""
-import sys
 
-import click
+from pathlib import Path
 
+import typer
+from rich.progress import Progress, SpinnerColumn, TextColumn
 
-@click.command()
-@click.argument('input-path', type=click.Path(exists=True))
-@click.argument('transform-name', type=str)
-@click.argument('output-path', type=click.Path())
-@click.option(
-    '--kwargs', '-k',
-    type=str,
-    help='String of kwargs, e.g. "degrees=(-5,15) num_transforms=3".',
-)
-@click.option(
-    '--imclass', '-c',
-    type=str,
-    default='ScalarImage',
-    help='Subclass of torchio.Image used to instantiate the image.',
-)
-@click.option(
-    '--seed', '-s',
-    type=int,
-    help='Seed for PyTorch random number generator.',
-)
-@click.option(
-    '--verbose/--no-verbose', '-v',
-    type=bool,
-    default=False,
-    help='Print random transform parameters.',
-)
+
+app = typer.Typer()
+
+
+@app.command()
 def main(
-        input_path,
-        transform_name,
-        output_path,
-        kwargs,
-        imclass,
-        seed,
-        verbose,
+    input_path: Path = typer.Argument(  # noqa: B008
+        ...,
+        exists=True,
+        file_okay=True,
+        dir_okay=True,
+        readable=True,
+    ),
+    transform_name: str = typer.Argument(...),  # noqa: B008
+    output_path: Path = typer.Argument(  # noqa: B008
+        ...,
+        file_okay=True,
+        dir_okay=False,
+        writable=True,
+    ),
+    kwargs: str = typer.Option(  # noqa: B008
+        None,
+        '--kwargs', '-k',
+        help='String of kwargs, e.g. "degrees=(-5,15) num_transforms=3".',
+    ),
+    imclass: str = typer.Option(  # noqa: B008
+        'ScalarImage',
+        '--imclass', '-c',
+        help=(
+            'Name of the subclass of torchio.Image'
+            ' that will be used to instantiate the image.'
+        ),
+    ),
+    seed: int = typer.Option(  # noqa: B008
+        None,
+        '--seed', '-s',
+        help='Seed for PyTorch random number generator.',
+    ),
+    verbose: bool = typer.Option(  # noqa: B008
+        False,
+        help='Print random transform parameters.',
+    ),
+    show_progress: bool = typer.Option(  # noqa: B008
+        True,
+        '--show-progress/--hide-progress',
+        '-p/-P',
+        help='Show animations indicating progress.',
+    ),
 ):
     """Apply transform to an image.
 
-    \b
     Example:
-    $ torchio-transform -k "degrees=(-5,15) num_transforms=3" input.nrrd RandomMotion output.nii
+    $ tiotr input.nrrd RandomMotion output.nii "degrees=(-5,15) num_transforms=3" -v
     """  # noqa: E501
     # Imports are placed here so that the tool loads faster if not being run
     import torch
@@ -61,14 +74,20 @@ def main(
     transform = transform_class(**params_dict)
     if seed is not None:
         torch.manual_seed(seed)
-    apply_transform_to_file(
-        input_path,
-        transform,
-        output_path,
-        verbose=verbose,
-        class_=imclass,
-    )
-    return 0
+    with Progress(
+        SpinnerColumn(),
+        TextColumn('[progress.description]{task.description}'),  # noqa: FS003
+        transient=True,
+        disable=not show_progress,
+    ) as progress:
+        progress.add_task('Applying transform', total=1)
+        apply_transform_to_file(
+            input_path,
+            transform,
+            output_path,
+            verbose=verbose,
+            class_=imclass,
+        )
 
 
 def get_params_dict_from_kwargs(kwargs):
@@ -88,5 +107,4 @@ def get_params_dict_from_kwargs(kwargs):
 
 
 if __name__ == '__main__':
-    # pylint: disable=no-value-for-parameter
-    sys.exit(main())  # pragma: no cover
+    app()

src/torchio/cli/print_info.py

@@ -1,19 +1,39 @@
 # pylint: disable=import-outside-toplevel
-"""Console script for torchio."""
-import sys
+from pathlib import Path
 
-import click
+import typer
 
 
-@click.command()
-@click.argument('input-path', type=click.Path(exists=True))
-@click.option('--plot/--no-plot', '-p', default=False)
-@click.option('--show/--no-show', '-s', default=False)
-@click.option('--label/--scalar', '-l', default=False)
-def main(input_path, plot, show, label):
+app = typer.Typer()
+
+
+@app.command()
+def main(
+    input_path: Path = typer.Argument(  # noqa: B008
+        ...,
+        exists=True,
+        file_okay=True,
+        dir_okay=True,
+        readable=True,
+    ),
+    plot: bool = typer.Option(  # noqa: B008
+        False,
+        '--plot/--no-plot', '-p/-P',
+        help='Plot the image using Matplotlib or Pillow.',
+    ),
+    show: bool = typer.Option(  # noqa: B008
+        False,
+        '--show/--no-show', '-s/-S',
+        help='Show the image using specialized visualisation software.',
+    ),
+    label: bool = typer.Option(  # noqa: B008
+        False,
+        '--label/--scalar', '-l/-s',
+        help='Use torchio.LabelMap to instantiate the image.',
+    ),
+):
     """Print information about an image and, optionally, show it.
 
-    \b
     Example:
     $ tiohd input.nii.gz
     """
@@ -27,9 +47,7 @@ def main(input_path, plot, show, label):
         image.plot()
     if show:
         image.show()
-    return 0
 
 
 if __name__ == '__main__':
-    # pylint: disable=no-value-for-parameter
-    sys.exit(main())  # pragma: no cover
+    app()

tests/test_cli.py

@@ -1,47 +1,40 @@
 #!/usr/bin/env python
 """Tests for CLI tool package."""
-from click.testing import CliRunner
+from typer.testing import CliRunner
 from torchio.cli import apply_transform
 from torchio.cli import print_info
 
 from .utils import TorchioTestCase
 
 
+runner = CliRunner()
+
+
 class TestCLI(TorchioTestCase):
-    """Tests for CLI tool."""
-    def test_help(self):
-        """Test the CLI."""
-        runner = CliRunner()
-        help_result = runner.invoke(apply_transform.main, ['--help'])
-        assert help_result.exit_code == 0
-        assert 'Show this message and exit.' in help_result.output
 
     def test_cli_transform(self):
         image = str(self.get_image_path('cli'))
-        runner = CliRunner()
         args = [
             image,
             'RandomFlip',
             '--seed', '0',
             '--kwargs', 'axes=(0,1,2)',
+            '--hide-progress',
             image,
         ]
-        result = runner.invoke(apply_transform.main, args)
+        result = runner.invoke(apply_transform.app, args)
         assert result.exit_code == 0
-        assert result.output == ''
+        assert result.output.strip() == ''
 
     def test_bad_transform(self):
-        ValueError
         image = str(self.get_image_path('cli'))
-        runner = CliRunner()
         args = [image, 'RandomRandom', image]
-        result = runner.invoke(apply_transform.main, args)
+        result = runner.invoke(apply_transform.app, args)
         assert result.exit_code == 1
 
     def test_cli_hd(self):
         image = str(self.get_image_path('cli'))
-        runner = CliRunner()
         args = [image]
-        result = runner.invoke(print_info.main, args)
+        result = runner.invoke(print_info.app, args)
         assert result.exit_code == 0
         assert result.output == 'ScalarImage(shape: (1, 10, 20, 30); spacing: (1.00, 1.00, 1.00); orientation: RAS+; dtype: torch.DoubleTensor; memory: 46.9 KiB)\n'  # noqa: E501