add registration tests

mantis/analysis/settings/example_register_settings.yml

@@ -0,0 +1 @@
+TODO 

mantis/tests/conftest.py

@@ -33,6 +33,14 @@ def example_deskew_settings():
     yield settings_path, settings
 
 
+@pytest.fixture(scope="function")
+def example_register_settings():
+    settings_path = "./mantis/analysis/settings/example_register_settings.yml"
+    with open(settings_path) as file:
+        settings = yaml.safe_load(file)
+    yield settings_path, settings
+
+
 @pytest.fixture(scope="function")
 def example_plate(tmp_path):
     plate_path = tmp_path / "plate.zarr"

mantis/tests/test_cli/test_estimate_registration_cli copy.py

@@ -0,0 +1,25 @@
+from click.testing import CliRunner
+
+from mantis.cli.main import cli
+
+
+def test_estimate_registration_cli(tmp_path, example_plate):
+    plate_path, _ = example_plate
+    output_path = tmp_path / "config.yaml"
+
+    runner = CliRunner()
+    result = runner.invoke(
+        cli,
+        [
+            "estimate-registration",
+            "-lf",
+            str(plate_path) + "/A/1/0",
+            "-ls",
+            str(plate_path) + "/B/1/0",  # test could be improved with different stores
+            "-o",
+            str(output_path),
+        ],
+    )
+
+    # Weak test
+    assert "Enter phase_channel index to process" in result.output

mantis/tests/test_cli/test_register_cli.py

@@ -0,0 +1,28 @@
+from click.testing import CliRunner
+
+from mantis.cli.main import cli
+
+
+def test_regiser_cli(tmp_path, example_plate, examples_register_settings):
+    plate_path, _ = example_plate
+    config_path, _ = examples_register_settings
+    output_path = tmp_path / "config.yaml"
+
+    runner = CliRunner()
+    result = runner.invoke(
+        cli,
+        [
+            "register",
+            "-lf",
+            str(plate_path) + "/A/1/0",
+            "-ls",
+            str(plate_path) + "/B/1/0",  # test could be improved with different stores
+            "-c",
+            str(config_path),
+            "-o",
+            str(output_path),
+        ],
+    )
+
+    assert output_path.exists()
+    assert result.exit_code == 0