test cli print params

micrant/main_cli.py

@@ -75,13 +75,13 @@ def set(common_spreadsheet_file=None):
 @click.option("--print-params", "-pp", is_flag=True, help="Print parameters")
 def gui(params, print_params):
     mainapp = micrant_app.MicrAnt()
+    app_tools.set_parameters_by_path(mainapp.parameters, params)
     if print_params:
         import pprint
-
-        pprint.pprint(mainapp.parameters_to_dict())
+        pprint.pprint(app_tools.params_and_values(mainapp.parameters))
         exit()
-    for param in params:
-        mainapp.set_parameter(param[0], value=ast.literal_eval(param[1]))
+    # for param in params:
+    #     mainapp.set_parameter(param[0], value=ast.literal_eval(param[1]))
         # mainapp.parameters.param(*param[0].split(";")).setValue(ast.literal_eval(param[1]))
     mainapp.start_gui()
 

tests/cli_test.py

@@ -40,16 +40,6 @@ def test_cli_print_params():
     Add image data to common spreadsheet file.
     :return:
     """
-    # pth = io3d.datasets.join_path(
-    #     "medical", "orig", "sample_data", "SCP003", "SCP003.ndpi", get_root=True
-    # )
-    #
-    # logger.debug(f"pth={pth}, exists={Path(pth).exists()}")
-    # common_xlsx = Path("test_data.xlsx")
-    # logger.debug(f"expected_pth={common_xlsx}, exists: {common_xlsx.exists()}")
-    # if common_xlsx.exists():
-    #     logger.debug(f"Deleting file {common_xlsx} before tests")
-    #     os.remove(common_xlsx)
 
     runner = click.testing.CliRunner()
     # runner.invoke(anwa.main_click.nogui, ["-i", str(pth)])
@@ -58,3 +48,17 @@ def test_cli_print_params():
         ["nogui", "-pp", "-p", "Processing;Intensity Normalization", "True", "-p", "Annotation;Upper Threshold", "1.5"],
     )
     assert result.output.find(" 'Annotation;Upper Threshold': 1.5,") > 0
+
+def test_cli_print_params():
+    """
+    Add image data to common spreadsheet file.
+    :return:
+    """
+
+    runner = click.testing.CliRunner()
+    # runner.invoke(anwa.main_click.nogui, ["-i", str(pth)])
+    result = runner.invoke(
+        micrant.main_cli.run,
+        ["gui", "-pp", "-p", "Processing;Intensity Normalization", "True", "-p", "Annotation;Upper Threshold", "1.5"],
+    )
+    assert result.output.find(" 'Annotation;Upper Threshold': 1.5,") > 0