Updating tests.

Author: AdvancedImagingUTSW

src/navigate/controller/sub_controllers/channels_tab_controller.py

@@ -122,7 +122,7 @@ def __init__(self, view, parent_controller=None):
         self.filter_wheel_delay = None
 
         #: dict: The microscope state dictionary.
-        self.microscope_state_dict = None
+        self.microscope_state_dict = {}
 
         # laser/stack cycling event binds
         self.stack_acq_vals["cycling"].trace_add("write", self.update_cycling_setting)
@@ -193,10 +193,6 @@ def initialize(self):
     def populate_experiment_values(self):
         """Distribute initial MicroscopeState values to this and sub-controllers and
         associated views.
-
-        Examples
-        --------
-        >>> self.populate_experiment_values()
         """
         self.in_initialization = True
         self.microscope_state_dict = self.parent_controller.configuration["experiment"][
@@ -313,11 +309,9 @@ def set_mode(self, mode):
         ----------
         mode : str
             acquisition mode
-
-        Examples
-        --------
-        >>> self.set_mode(mode)
         """
+
+        # TODO: Why do we have mode and image_mode?
         image_mode = self.microscope_state_dict["image_mode"]
         self.mode = mode
         self.channel_setting_controller.set_mode(mode)
@@ -375,10 +369,6 @@ def update_z_steps(self, *args):
         args : dict
             Values is a dict as follows {'step_size':  'start_position': ,
                                          'end_position': ,'number_z_steps'}
-
-        Examples
-        --------
-        >>> self.update_z_steps()
         """
 
         # won't do any calculation when initialization
@@ -463,10 +453,6 @@ def update_start_position(self, *args):
         args : dict
             Values is a dict as follows {'start_position': , 'abs_z_start': ,
             'stack_z_origin': }
-
-        Examples
-        --------
-        >>> self.update_start_position()
         """
 
         # We have a new origin
@@ -497,9 +483,6 @@ def update_end_position(self, *args):
             Values is a dict as follows {'end_position': , 'abs_z_end': ,
             'stack_z_origin': }
 
-        Examples
-        --------
-        >>> self.update_end_position()
         """
         # Grab current values
         z_end = self.parent_controller.configuration["experiment"]["StageParameters"][
@@ -550,9 +533,6 @@ def update_cycling_setting(self, *args):
             Values is a dict as follows {'cycling_setting': , 'cycling_setting': ,
                                          'stack_z_origin': }
 
-        Examples
-        --------
-        >>> self.update_cycling_setting()
         """
         # won't do any calculation when initializing
         if self.in_initialization:
@@ -579,10 +559,6 @@ def update_save_setting(self, *args):
         args : dict
             Values is a dict as follows {'save_data': , 'save_data': ,
                                          'stack_z_origin': }
-
-        Examples
-        --------
-        >>> self.update_save_setting()
         """
 
         if self.in_initialization:
@@ -610,9 +586,6 @@ def update_timepoint_setting(self, call_parent=False):
         call_parent : bool
             Tell parent controller that time point setting has changed.
 
-        Examples
-        --------
-        >>> self.update_timepoint_setting()
         """
 
         if self.in_initialization:
@@ -736,10 +709,6 @@ def toggle_multiposition(self):
         """Toggle Multi-position Acquisition.
 
         Recalculates the experiment duration.
-
-        Examples
-        --------
-        >>> self.toggle_multiposition()
         """
         self.is_multiposition = self.is_multiposition_val.get()
         self.microscope_state_dict["is_multiposition"] = self.is_multiposition
@@ -767,10 +736,6 @@ def launch_tiling_wizard(self):
 
         Will only launch when button in GUI is pressed, and will not duplicate.
         Pressing button again brings popup to top
-
-        Examples
-        --------
-        >>> self.launch_tiling_wizard()
         """
 
         if hasattr(self, "tiling_wizard_controller"):
@@ -788,11 +753,6 @@ def set_info(self, vals, values):
             List of variables to set.
         values : list
             List of values to set to variables.
-
-        Examples
-        --------
-        >>> self.set_info([self.timepoint_vals['timepoint_interval'],
-                           self.timepoint_vals['stack_pause']], [1, 1])
         """
         for name in values.keys():
             if name in vals:
@@ -813,10 +773,6 @@ def execute(self, command, *args):
         -------
         command : object
             Returns parent_controller.execute(command) if command = 'get_stage_position'
-
-        Examples
-        --------
-        >>> self.execute('recalculate_timepoint')
         """
         if command == "recalculate_timepoint":
             # update selected channels num
@@ -880,7 +836,7 @@ def set_exposure_time(self, channel, exposure_time):
         channel : str
             Channel name, such as "channel_1", "channel_2",...
         exposure_time : float
-            Exposure time in miliseconds.
+            Exposure time in milliseconds.
         """
         idx = int(channel[channel.index("_") + 1 :]) - 1
         self.channel_setting_controller.in_initialization = True

test/config/test_config.py

@@ -78,7 +78,7 @@ def test_config_methods():
         "verify_waveform_constants",
         "verify_configuration",
         "yaml",
-        "build_ref_name"
+        "build_ref_name",
     ]
     for method in methods:
         assert method in desired_methods
@@ -101,8 +101,6 @@ def test_get_navigate_path_windows(monkeypatch):
     assert path_string.startswith("LOCALAPPDATA")
     assert path_string.endswith(".navigate")
 
-    
-
 
 def test_get_navigate_path_mac(monkeypatch):
     """Test that the Navigate path is a string."""
@@ -121,7 +119,7 @@ def test_get_configuration_paths():
     paths = config.get_configuration_paths()
     for path in paths:
         assert isinstance(path, pathlib.Path)
-    assert len(paths) == 5
+    assert len(paths) == 6
 
 
 def test_get_configuration_paths_create_dir(monkeypatch):
@@ -136,6 +134,7 @@ def test_get_configuration_paths_create_dir(monkeypatch):
     # delete generated folder
     delete_folder("TESTPATH")
 
+
 # test that the system is exited if no file is provided to load_yaml_config
 def test_load_yaml_config_no_file():
     """Test that the system exits if no file is provided."""
@@ -362,9 +361,7 @@ def setUp(self):
             "waveform_template": "Default",
         }
 
-        multipositions_sample = [
-            [10.0, 10.0, 10.0, 10.0, 10.0]
-        ]
+        multipositions_sample = [[10.0, 10.0, 10.0, 10.0, 10.0]]
 
         self.experiment_sample = {
             "Saving": saving_dict_sample,
@@ -669,8 +666,8 @@ def test_load_experiment_file_with_wrong_parameter_values(self):
                 "defocus": 0.0,
             }
         ]
-        # number_of_filter_wheels = 
-                
+        # number_of_filter_wheels =
+
         config.verify_experiment_config(self.manager, configuration)
         assert type(experiment["MicroscopeState"]["channels"]) is DictProxy
         assert len(list(experiment["MicroscopeState"]["channels"].keys())) == 0

test/controller/sub_controllers/test_acquire_bar_controller.py

@@ -45,26 +45,7 @@
 
 
 class TestAcquireBarController:
-    """Tests for the AcquireBarController class
-
-    Attributes
-    ----------
-    acqbarController : AcquireBarController
-        Instance of the AcquireBarController class
-
-    Methods
-    -------
-    test_init()
-        Tests the initialization of the AcquireBarController class
-    test_attr()
-        Tests the attributes of the AcquireBarController class
-    test_set_save()
-        Tests the set_save_option method of the AcquireBarController class
-    test_stop_acquire()
-        Tests the stop_acquire method of the AcquireBarController class
-    test_populate_experiment_values()
-        Tests the populate_experiment_values method of the AcquireBarController class
-    """
+    """Tests for the AcquireBarController class"""
 
     @pytest.fixture(autouse=True)
     def setup_class(self, dummy_controller):
@@ -78,17 +59,12 @@ def setup_class(self, dummy_controller):
         c = dummy_controller
         v = dummy_controller.view
 
-        self.acquire_bar_controller = AcquireBarController(
-            v.acqbar, c
-        )
+        self.acquire_bar_controller = AcquireBarController(v.acqbar, c)
         self.acquire_bar_controller.populate_experiment_values()
 
     def test_init(self):
         """Tests the initialization of the AcquireBarController class
 
-
-
-
         Raises
         ------
         AssertionError
@@ -99,9 +75,6 @@ def test_init(self):
     def test_attr(self):
         """Tests the attributes of the AcquireBarController class
 
-
-
-
         Raises
         ------
         AssertionError
@@ -237,8 +210,12 @@ def test_get_set_mode(self, mode):
         test = self.acquire_bar_controller.get_mode()
         assert test == mode, "Mode not set correctly"
         # assert imaging mode is updated in the experiment
-        assert self.acquire_bar_controller.parent_controller.configuration[
-                "experiment"]["MicroscopeState"]["image_mode"] == mode
+        assert (
+            self.acquire_bar_controller.parent_controller.configuration["experiment"][
+                "MicroscopeState"
+            ]["image_mode"]
+            == mode
+        )
 
     def test_set_save(self):
         """Tests the set_save method of the AcquireBarController class
@@ -313,8 +290,12 @@ def test_update_microscope_mode(self, user_mode, expected_mode):
 
         # Checking that new mode gets set by function
         assert self.acquire_bar_controller.mode == expected_mode
-        assert self.acquire_bar_controller.parent_controller.configuration[
-                "experiment"]["MicroscopeState"]["image_mode"] == expected_mode
+        assert (
+            self.acquire_bar_controller.parent_controller.configuration["experiment"][
+                "MicroscopeState"
+            ]["image_mode"]
+            == expected_mode
+        )
 
         # Resetting to live
         self.acquire_bar_controller.view.pull_down.set("Continuous Scan")

test/controller/sub_controllers/test_autofocus_popup_controller.py

@@ -45,11 +45,6 @@
 class TestAutofocusPopupController:
     """Class for testing autofocus popup controller
 
-    Attributes
-    ----------
-    af_controller : AutofocusPopupController
-        Controller for autofocus popup
-
     Methods
     -------
     test_init()
@@ -84,9 +79,6 @@ def setup_class(self, dummy_controller):
     def test_init(self):
         """Tests that the controller is initialized correctly
 
-
-
-
         Raises
         ------
         AssertionError
@@ -98,9 +90,6 @@ def test_init(self):
     def test_attr(self):
         """Tests that the attributes are initialized correctly
 
-
-
-
         Raises
         ------
         AssertionError
@@ -121,9 +110,6 @@ def test_attr(self):
     def test_populate_experiment_values(self):
         """Tests that the values are populated correctly
 
-
-
-
         Raises
         ------
         AssertionError
@@ -144,9 +130,6 @@ def test_populate_experiment_values(self):
     def test_update_experiment_values(self):
         """Tests that the values are updated correctly
 
-
-
-
         Raises
         ------
         AssertionError
@@ -183,9 +166,6 @@ def test_update_experiment_values(self):
     def test_start_autofocus(self):
         """Tests that the start autofocus function works correctly
 
-
-
-
         Raises
         ------
         AssertionError
@@ -207,9 +187,6 @@ def test_display_plot(self):
         Todo: Retrieve data from axessubplot instance and
         check that it is correct
 
-
-
-
         Raises
         ------
         AssertionError