From ca1d7dead749447d6b05b1e73d5459b9e8dd55ef Mon Sep 17 00:00:00 2001
From: Joshua Hoskins <jrh4dy@gmail.com>
Date: Wed, 4 Oct 2023 10:18:00 -0400
Subject: [PATCH 1/6] Add docstring to tests for client, extract_holog and
 holog.

---
 tests/unit/test_client.py        | 22 +++++--
 tests/unit/test_extract_holog.py | 16 ++++++
 tests/unit/test_holog.py         | 98 +++++++++++++++++++++-----------
 3 files changed, 98 insertions(+), 38 deletions(-)

diff --git a/tests/unit/test_client.py b/tests/unit/test_client.py
index 2c6f30e7..6670046d 100644
--- a/tests/unit/test_client.py
+++ b/tests/unit/test_client.py
@@ -23,7 +23,10 @@ def teardown_method(self):
         pass
 
     def test_client_spawn(self):
-        """ Test client """
+        """
+            Run astrohack_local_client with N cores and with a memory_limit of M GB to create an instance of the
+            astrohack Dask client.
+        """
         import distributed
 
         from astrohack.client import astrohack_local_client
@@ -47,7 +50,10 @@ def test_client_spawn(self):
         client.shutdown()
 
     def test_client_dask_dir(self):
-        """ Test client """
+        """
+            Run astrohack_local_client with N cores and with a memory_limit of M GB to create an instance of the
+            astrohack Dask client. Check that temporary files are written to dask_local_dir.
+        """
         import distributed
 
         from astrohack.client import astrohack_local_client
@@ -56,7 +62,12 @@ def test_client_dask_dir(self):
 
         log_parms = {'log_level':'DEBUG'}
 
-        client = astrohack_local_client(cores=2, memory_limit='8GB', log_parms=log_parms, dask_local_dir='./dask_test_dir')
+        client = astrohack_local_client(
+            cores=2,
+            memory_limit='8GB',
+            log_parms=log_parms,
+            dask_local_dir='./dask_test_dir'
+        )
         
         try:
             if os.path.exists('./dask_test_dir') is False:
@@ -69,7 +80,10 @@ def test_client_dask_dir(self):
             client.shutdown()
 
     def test_client_logger(self):
-        """ Test client """
+        """
+            Run astrohack_local_client with N cores and with a memory_limit of M GB without any errors and the messages
+            will be logged in the terminal.
+        """
         import os
         import re
         import distributed
diff --git a/tests/unit/test_extract_holog.py b/tests/unit/test_extract_holog.py
index 77572daf..9cc7fb53 100644
--- a/tests/unit/test_extract_holog.py
+++ b/tests/unit/test_extract_holog.py
@@ -32,6 +32,9 @@ def teardown_method(self):
         pass
 
     def test_extract_holog_obs_dict(self):
+        '''
+           Specify a holography observations dictionary and check that the proper dictionary is created.
+        '''
 
         # Generate pointing file
         extract_pointing(
@@ -72,6 +75,9 @@ def test_extract_holog_obs_dict(self):
         assert holog_obs_test_dict == holog_obs_dict
 
     def test_extract_holog_ddi(self):
+        '''
+            Specify a ddi value to be process and check that it is the only one processed.
+        '''
 
         # Generate pointing file
         extract_pointing(
@@ -107,6 +113,9 @@ def test_extract_holog_ddi(self):
         assert list(holog_mds.keys()) == ['ddi_1']
 
     def test_extract_holog_overwrite(self):
+        '''
+            Specify that the output file should be overwritten if it exists; check that it is overwritten.
+        '''
 
         # Generate pointing file
         extract_pointing(
@@ -151,6 +160,10 @@ def test_extract_holog_overwrite(self):
         assert initial_time != final_time
 
     def test_extract_holog_baseline_average_distance(self):
+        '''
+            Run extract_holog using the baseline average distance as a filter; check that only the baselines with this
+            average distance are returned.
+        '''
 
         # extract pointing data
         pnt_mds = extract_pointing(
@@ -174,6 +187,9 @@ def test_extract_holog_baseline_average_distance(self):
         assert list(holog_mds['ddi_0']['map_0'].keys()) == ['ant_ea25']
 
     def test_extract_holog_baseline_average_nearest(self):
+        '''
+            Run extract_holog using the nearest baseline as a filter; check that only the nearest baselines are returned.
+        '''
 
         # extract pointing data
         pnt_mds = extract_pointing(
diff --git a/tests/unit/test_holog.py b/tests/unit/test_holog.py
index 97362170..cda4a978 100644
--- a/tests/unit/test_holog.py
+++ b/tests/unit/test_holog.py
@@ -11,8 +11,10 @@
 from astrohack.extract_holog import extract_holog
 from astrohack.extract_pointing import extract_pointing
 
+
 def relative_difference(result, expected):
-        return 2*np.abs(result - expected)/(abs(result) + abs(expected))
+    return 2 * np.abs(result - expected) / (abs(result) + abs(expected))
+
 
 class TestHolog():
     @classmethod
@@ -20,7 +22,7 @@ def setup_class(cls):
         """ setup any state specific to the execution of the given test class
         such as fetching test data """
         astrohack.data.datasets.download(file="ea25_cal_small_after_fixed.split.ms", folder="data/")
-        
+
         astrohack.data.datasets.download(file='extract_holog_verification.json')
         astrohack.data.datasets.download(file='holog_numerical_verification.json')
 
@@ -51,7 +53,7 @@ def setup_class(cls):
 
         holog(
             holog_name='data/ea25_cal_small_after_fixed.split.holog.zarr',
-            image_name='data/ea25_cal_small_after_fixed.split.image.zarr', 
+            image_name='data/ea25_cal_small_after_fixed.split.image.zarr',
             overwrite=True,
             parallel=False
         )
@@ -73,8 +75,11 @@ def teardown_method(self):
         """ teardown any state that was previously setup for all methods of the given class """
         pass
 
-
     def test_holog_grid_cell_size(self):
+        """
+           Calculate the correct grid and cell size when compared to known values in the test file; known values are
+           provided by a test json file.
+        """
 
         tolerance = 2.e-5
 
@@ -83,28 +88,33 @@ def test_holog_grid_cell_size(self):
 
         with open('data/ea25_cal_small_after_fixed.split.image.zarr/.image_attr') as attr_file:
             image_attr = json.load(attr_file)
-    
+
         for i, _ in enumerate(image_attr['cell_size']):
             assert relative_difference(
-                image_attr['cell_size'][i], 
+                image_attr['cell_size'][i],
                 reference_dict["vla"]['cell_size'][i]
             ) < tolerance
 
             assert relative_difference(
-                image_attr['grid_size'][i], 
+                image_attr['grid_size'][i],
                 reference_dict["vla"]['grid_size'][i]
             ) < tolerance
 
-    
     def test_holog_image_name(self):
+        """
+            Test holog image name created correctly.
+        """
 
         assert os.path.exists('data/ea25_cal_small_after_fixed.split.image.zarr')
 
     def test_holog_ant_id(self):
+        """
+            Specify a single antenna to process; check that is the only antenna returned.
+        """
 
         image_mds = holog(
             holog_name='data/ea25_cal_small_after_fixed.split.holog.zarr',
-            image_name='data/ea25_cal_small_after_fixed.split.image.zarr',     
+            image_name='data/ea25_cal_small_after_fixed.split.image.zarr',
             ant_id=['ea25'],
             overwrite=True,
             parallel=False
@@ -113,10 +123,13 @@ def test_holog_ant_id(self):
         assert list(image_mds.keys()) == ['ant_ea25']
 
     def test_holog_ddi(self):
+        """
+            Specify a single ddi to process; check that is the only ddi returned.
+        """
 
         image_mds = holog(
             holog_name='data/ea25_cal_small_after_fixed.split.holog.zarr',
-            image_name='data/ea25_cal_small_after_fixed.split.image.zarr', 
+            image_name='data/ea25_cal_small_after_fixed.split.image.zarr',
             overwrite=True,
             ddi=[0],
             parallel=False
@@ -126,14 +139,15 @@ def test_holog_ddi(self):
             for ddi in image_mds[ant].keys():
                 assert ddi == "ddi_0"
 
-    
-
     def test_holog_padding_factor(self):
+        """
+            Specify a padding factor to use in the image creation; check that image size is created.
+        """
 
         image_mds = holog(
             holog_name='data/ea25_cal_small_after_fixed.split.holog.zarr',
-            image_name='data/ea25_cal_small_after_fixed.split.image.zarr', 
-            padding_factor=50, 
+            image_name='data/ea25_cal_small_after_fixed.split.image.zarr',
+            padding_factor=50,
             overwrite=True,
             parallel=False
         )
@@ -143,27 +157,33 @@ def test_holog_padding_factor(self):
                 assert image_mds[ant][ddi].APERTURE.shape == (1, 1, 4, 529, 529)
 
     def test_holog_chan_average(self):
+        """
+            Check that channel average flag was set holog is run.
+        """
         image_mds = holog(
             holog_name='data/ea25_cal_small_after_fixed.split.holog.zarr',
-            image_name='data/ea25_cal_small_after_fixed.split.image.zarr', 
+            image_name='data/ea25_cal_small_after_fixed.split.image.zarr',
             chan_average=True,
             overwrite=True,
             parallel=False
         )
 
         with open('data/ea25_cal_small_after_fixed.split.image.zarr/.image_attr') as json_attr:
-            json_file = json.load(json_attr)     
-        
+            json_file = json.load(json_attr)
+
         assert json_file['chan_average'] == True
 
     def test_holog_scan_average(self):
+        """
+            Check that scan average flag was set holog is run.
+        """
         image_mds = holog(
             holog_name='data/ea25_cal_small_after_fixed.split.holog.zarr',
-            image_name='data/ea25_cal_small_after_fixed.split.image.zarr', 
+            image_name='data/ea25_cal_small_after_fixed.split.image.zarr',
             scan_average=False,
             overwrite=True,
             parallel=False
-        )     
+        )
 
         with open('data/ea25_cal_small_after_fixed.split.image.zarr/.image_attr') as json_attr:
             json_file = json.load(json_attr)
@@ -171,55 +191,67 @@ def test_holog_scan_average(self):
         assert json_file['scan_average'] == False
 
     def test_holog_grid_interpolation(self):
+        """
+            Check that grid interpolation flag was set holog is run.
+        """
         image_mds = holog(
             holog_name='data/ea25_cal_small_after_fixed.split.holog.zarr',
-            image_name='data/ea25_cal_small_after_fixed.split.image.zarr', 
+            image_name='data/ea25_cal_small_after_fixed.split.image.zarr',
             grid_interpolation_mode='nearest',
             overwrite=True,
             parallel=False
         )
 
         with open('data/ea25_cal_small_after_fixed.split.image.zarr/.image_attr') as json_attr:
-            json_file = json.load(json_attr)        
+            json_file = json.load(json_attr)
 
         assert json_file['grid_interpolation_mode'] == 'nearest'
 
     def test_holog_chan_tolerance(self):
+        """
+            Check that channel tolerance ir propagated correctly.
+        """
         image_mds = holog(
             holog_name='data/ea25_cal_small_after_fixed.split.holog.zarr',
-            image_name='data/ea25_cal_small_after_fixed.split.image.zarr', 
+            image_name='data/ea25_cal_small_after_fixed.split.image.zarr',
             chan_tolerance_factor=0.0049,
             overwrite=True,
             parallel=False
         )
 
         with open('data/ea25_cal_small_after_fixed.split.image.zarr/.image_attr') as json_attr:
-            json_file = json.load(json_attr)     
+            json_file = json.load(json_attr)
 
         assert json_file['chan_tolerance_factor'] == 0.0049
 
     def test_holog_to_stokes(self):
+        """
+            Check that to_stokes flag was set holog is run.
+        """
         image_mds = holog(
             holog_name='data/ea25_cal_small_after_fixed.split.holog.zarr',
-            image_name='data/ea25_cal_small_after_fixed.split.image.zarr', 
+            image_name='data/ea25_cal_small_after_fixed.split.image.zarr',
             to_stokes=True,
             overwrite=True,
             parallel=False
         )
 
         with open('data/ea25_cal_small_after_fixed.split.image.zarr/.image_attr') as json_attr:
-            json_file = json.load(json_attr)     
+            json_file = json.load(json_attr)
 
         assert json_file['to_stokes'] == True
 
         assert (image_mds['ant_ea25']['ddi_0'].pol.values == np.array(['I', 'Q', 'U', 'V'])).all()
 
     def test_holog_overwrite(self):
+        """
+            Specify the output file should be overwritten; check that it WAS.
+        """
         initial_time = os.path.getctime('data/ea25_cal_small_after_fixed.split.image.zarr')
-        
+
         image_mds = holog(
             holog_name='data/ea25_cal_small_after_fixed.split.holog.zarr',
-            image_name='data/ea25_cal_small_after_fixed.split.image.zarr', 
+            image_name='data/ea25_cal_small_after_fixed.split.image.zarr',
             overwrite=True,
             parallel=False
         )
@@ -229,12 +261,15 @@ def test_holog_overwrite(self):
         assert initial_time != modified_time
 
     def test_holog_not_overwrite(self):
+        """
+           Specify the output file should be NOT be overwritten; check that it WAS NOT.
+        """
         initial_time = os.path.getctime('data/ea25_cal_small_after_fixed.split.image.zarr')
-        
+
         try:
             holog(
                 holog_name='data/ea25_cal_small_after_fixed.split.holog.zarr',
-                image_name='data/ea25_cal_small_after_fixed.split.image.zarr', 
+                image_name='data/ea25_cal_small_after_fixed.split.image.zarr',
                 overwrite=False,
                 parallel=False
             )
@@ -246,8 +281,3 @@ def test_holog_not_overwrite(self):
             modified_time = os.path.getctime('data/ea25_cal_small_after_fixed.split.image.zarr')
 
             assert initial_time == modified_time
-
-        
-
-
-    
\ No newline at end of file

From 34c71ad1583d674c5a42010eb60278c2d211ab53 Mon Sep 17 00:00:00 2001
From: Joshua Hoskins <jrh4dy@gmail.com>
Date: Wed, 4 Oct 2023 10:27:46 -0400
Subject: [PATCH 2/6] Add docstrings to panel tests.

---
 tests/unit/test_panel.py | 48 ++++++++++++++++++++++++++--------------
 1 file changed, 32 insertions(+), 16 deletions(-)

diff --git a/tests/unit/test_panel.py b/tests/unit/test_panel.py
index fcaa58fc..9122b15e 100644
--- a/tests/unit/test_panel.py
+++ b/tests/unit/test_panel.py
@@ -12,8 +12,10 @@
 from astrohack.extract_holog import extract_holog
 from astrohack.extract_pointing import extract_pointing
 
+
 def relative_difference(result, expected):
-        return 2*np.abs(result - expected)/(abs(result) + abs(expected))
+    return 2 * np.abs(result - expected) / (abs(result) + abs(expected))
+
 
 class TestPanel():
     @classmethod
@@ -21,10 +23,10 @@ def setup_class(cls):
         """ setup any state specific to the execution of the given test class
         such as fetching test data """
         astrohack.data.datasets.download(file="ea25_cal_small_after_fixed.split.ms", folder="data/")
-        
+
         astrohack.data.datasets.download(file='extract_holog_verification.json')
         astrohack.data.datasets.download(file='holog_numerical_verification.json')
-        
+
         astrohack.data.datasets.download(file='panel_cutoff_mask')
 
         extract_pointing(
@@ -54,7 +56,7 @@ def setup_class(cls):
 
         holog(
             holog_name='data/ea25_cal_small_after_fixed.split.holog.zarr',
-            image_name='data/ea25_cal_small_after_fixed.split.image.zarr', 
+            image_name='data/ea25_cal_small_after_fixed.split.image.zarr',
             overwrite=True,
             parallel=False
         )
@@ -86,12 +88,17 @@ def teardown_method(self):
         """ teardown any state that was previously setup for all methods of the given class """
         pass
 
-    
     def test_panel_name(self):
+        """
+            Check that the panel output name was created correctly.
+        """
 
         assert os.path.exists('data/ea25_cal_small_after_fixed.split.panel.zarr')
 
     def test_panel_ant_id(self):
+        """
+           Specify a single antenna to process; check that only that antenna was processed.
+        """
 
         panel_mds = panel(
             image_name='data/ea25_cal_small_after_fixed.split.image.zarr',
@@ -108,6 +115,9 @@ def test_panel_ant_id(self):
         assert list(panel_mds.keys()) == ['ant_ea25']
 
     def test_panel_ddi(self):
+        """
+            Specify a single ddi to process; check that only that ddi was processed.
+        """
 
         panel_mds = panel(
             image_name='data/ea25_cal_small_after_fixed.split.image.zarr',
@@ -125,8 +135,11 @@ def test_panel_ddi(self):
                 assert ddi == "ddi_0"
 
     def test_panel_overwrite(self):
+        """
+            Specify the output file should be overwritten; check that it WAS.
+        """
         initial_time = os.path.getctime('data/ea25_cal_small_after_fixed.split.image.zarr')
-        
+
         panel_mds = panel(
             image_name='data/ea25_cal_small_after_fixed.split.image.zarr',
             panel_name='data/ea25_cal_small_after_fixed.split.panel.zarr',
@@ -142,8 +155,11 @@ def test_panel_overwrite(self):
         assert initial_time != modified_time
 
     def test_panel_not_overwrite(self):
+        """
+           Specify the output file should be NOT be overwritten; check that it WAS NOT.
+        """
         initial_time = os.path.getctime('data/ea25_cal_small_after_fixed.split.panel.zarr')
-        
+
         try:
             panel_mds = panel(
                 image_name='data/ea25_cal_small_after_fixed.split.image.zarr',
@@ -164,7 +180,10 @@ def test_panel_not_overwrite(self):
             assert initial_time == modified_time
 
     def test_panel_mode(self):
-        panel_list=['3-4', '5-27', '5-37', '5-38']
+        """
+           Specify panel computation mode and check that the data rms responded as expected.
+        """
+        panel_list = ['3-4', '5-27', '5-37', '5-38']
 
         panel_mds = panel(
             image_name='data/ea25_cal_small_after_fixed.split.image.zarr',
@@ -183,23 +202,20 @@ def test_panel_mode(self):
 
         mean_rms = panel_mds["ant_ea25"]["ddi_0"].sel(labels=panel_list).apply(np.std).PANEL_SCREWS.values
 
-        assert mean_rms < default_rms    
+        assert mean_rms < default_rms
 
     def test_panel_cutoff(self):
+        """
+           Set cutoff=0 and compare results to known truth value array.
+        """
         with open("panel_cutoff_mask.npy", "rb") as array:
             reference_array = np.load(array)
 
         panel_mds = panel(
-            image_name='data/ea25_cal_small_after_fixed.split.image.zarr', 
+            image_name='data/ea25_cal_small_after_fixed.split.image.zarr',
             cutoff=0.0,
             parallel=False,
             overwrite=True
         )
 
         assert np.all(panel_mds["ant_ea25"]["ddi_0"].MASK.values == reference_array)
-    
-
-        
-
-
-    
\ No newline at end of file

From 6e3392d9beff43d9f633f72a2059941aad47c583 Mon Sep 17 00:00:00 2001
From: Joshua Hoskins <jrh4dy@gmail.com>
Date: Wed, 4 Oct 2023 10:53:16 -0400
Subject: [PATCH 3/6] fix current extract_locit tests and add docstings more
 tests.

---
 tests/unit/test_extract_locit.py | 108 +++++++++++++++++++++----------
 1 file changed, 75 insertions(+), 33 deletions(-)

diff --git a/tests/unit/test_extract_locit.py b/tests/unit/test_extract_locit.py
index 3c503108..5218999c 100644
--- a/tests/unit/test_extract_locit.py
+++ b/tests/unit/test_extract_locit.py
@@ -1,9 +1,11 @@
+import os
 import pytest
 import shutil
 import astrohack
 
 from astrohack.extract_locit import extract_locit
 
+
 class TestExtractLocit():
     cal_table = './data/locit-input-pha.cal'
     locit_name = './data/locit-input-pha.locit.zarr'
@@ -13,58 +15,98 @@ def setup_class(cls):
         """ setup any state specific to the execution of the given test class
         such as fetching test data """
         astrohack.data.datasets.download(file="locit-input-pha.cal", folder="data")
-        
+
     @classmethod
     def teardown_class(cls):
         """ teardown any state that was previously setup with a call to setup_class
         such as deleting test data """
         shutil.rmtree("data")
-        
+
     def teardown_method(self):
         shutil.rmtree(self.locit_name)
 
-    def test_extract_locit_simple(self):
-    
+    def test_extract_locit_creation(self):
+        """
+           Create locit file with a cal-table and check it is created correctly.
+        """
+
         # Create locit_mds and check the dictionary structure
         locit_mds = extract_locit(self.cal_table, locit_name=self.locit_name)
-        
-        expected_keys = ['obs_info', 'ant_info', 'ant_ea01', 'ant_ea02', 'ant_ea04', 'ant_ea05', 'ant_ea06', 'ant_ea07', 'ant_ea08', 'ant_ea09', 'ant_ea10', 'ant_ea11', 'ant_ea12', 'ant_ea13', 'ant_ea15', 'ant_ea16', 'ant_ea17', 'ant_ea18', 'ant_ea19', 'ant_ea20', 'ant_ea21', 'ant_ea22', 'ant_ea23', 'ant_ea24', 'ant_ea25', 'ant_ea26', 'ant_ea27', 'ant_ea28']
-        
+
+        expected_keys = ['obs_info', 'ant_info', 'ant_ea01', 'ant_ea02', 'ant_ea04', 'ant_ea05', 'ant_ea06', 'ant_ea07',
+                         'ant_ea08', 'ant_ea09', 'ant_ea10', 'ant_ea11', 'ant_ea12', 'ant_ea13', 'ant_ea15', 'ant_ea16',
+                         'ant_ea17', 'ant_ea18', 'ant_ea19', 'ant_ea20', 'ant_ea21', 'ant_ea22', 'ant_ea23', 'ant_ea24',
+                         'ant_ea25', 'ant_ea26', 'ant_ea27', 'ant_ea28']
+
         for key in locit_mds.keys():
             assert key in expected_keys
-        
+
+        assert os.path.exists(self.locit_name)
+
     def test_extract_locit_antenna_select(self):
-    
-        locit_mds = extract_locit(self.cal_table, locit_name=self.locit_name, ant_id='ea17')
-        
+        """
+           Check that only specified antenna is processed.
+        """
+
+        locit_mds = extract_locit(
+            self.cal_table,
+            locit_name=self.locit_name,
+            ant_id='ea17'
+        )
+
         # There should only be 1 antenna in the dict named ea17
         assert len(locit_mds.keys()) == 3
-        assert 'ant_ea17' in locit_mds.keys()
-    
+
+        # Check that only the specific antenna is in the keys.
+        assert list(locit_mds.keys()) == ['ant_ea17']
+
     def test_extract_locit_ddi(self):
-    
+        """
+           Check that only specified ddi is processed.
+        """
+
         locit_mds = extract_locit(self.cal_table, locit_name=self.locit_name, ddi=0)
-        
-        # Usually each antenna has a ddi_0 and ddi_1 with all selected. This should just give ddi_0
+
+        # Check that only the specific ddi is in the keys.
         assert len(locit_mds['ant_ea01'].keys()) == 1
-        assert 'ddi_0' in locit_mds['ant_ea01'].keys()
-        
+        assert list(locit_mds['ant_ea01'].keys()) == ["ddi_0"]
+
     def test_extract_locit_overwrite(self):
-    
-        locit_mds = extract_locit(self.cal_table, locit_name=self.locit_name)
-        
-        # an exception shouldn't be raised with overwrite set to True
-        try:
-            locit_mds = extract_locit(self.cal_table, locit_name=self.locit_name, overwrite=True)
-        except:
-            assert False, "Failed to overwrite"
-            
+        """
+           Specify the output file should be overwritten; check that it WAS.
+        """
+
+        # To check this properly we need to not only know an exception was not thrown but that the file is ACTUALLY
+        # overwritten. We do this by checking the modification time.
+        initial_time = os.path.getctime(self.locit_name)
+
+        extract_locit(
+            self.cal_table,
+            locit_name=self.locit_name,
+            overwrite=True
+        )
+
+        modified_time = os.path.getctime(self.locit_name)
+
+        assert initial_time != modified_time
+
     def test_extract_locit_no_overwrite(self):
-    
-        locit_mds = extract_locit(self.cal_table, locit_name=self.locit_name, overwrite=False)
-        
-        # with overwrite set to False an exception should be raised
+        """
+            Specify the output file should be NOT be overwritten; check that it WAS NOT.
+        """
+        initial_time = os.path.getctime(self.locit_name)
+
         try:
-            locit_mds = extract_locit(self.cal_table, locit_name=self.locit_name, overwrite=False)
-        except:
+            extract_locit(
+                self.cal_table,
+                locit_name=self.locit_name,
+                overwrite=False
+            )
+
+        except FileExistsError:
             pass
+
+        finally:
+            modified_time = os.path.getctime(self.locit_name)
+
+            assert initial_time == modified_time

From d872e17913abcb603c323ced37ce59c7c5620454 Mon Sep 17 00:00:00 2001
From: Joshua Hoskins <jrh4dy@gmail.com>
Date: Wed, 4 Oct 2023 11:02:33 -0400
Subject: [PATCH 4/6] Formatting changes.

---
 tests/unit/test_astrohack_import_template.py |  1 +
 tests/unit/test_client.py                    | 31 +++++++++---------
 tests/unit/test_dio.py                       | 22 ++++++-------
 tests/unit/test_extract_holog.py             | 34 ++++++++++----------
 4 files changed, 45 insertions(+), 43 deletions(-)

diff --git a/tests/unit/test_astrohack_import_template.py b/tests/unit/test_astrohack_import_template.py
index 8fa50a9d..c2d6b849 100644
--- a/tests/unit/test_astrohack_import_template.py
+++ b/tests/unit/test_astrohack_import_template.py
@@ -1,5 +1,6 @@
 import pytest
 
+
 class TestAstrohack():
     @classmethod
     def setup_class(cls):
diff --git a/tests/unit/test_client.py b/tests/unit/test_client.py
index 6670046d..30bb7511 100644
--- a/tests/unit/test_client.py
+++ b/tests/unit/test_client.py
@@ -1,6 +1,7 @@
 import os
 import pytest
 
+
 class TestAstrohack():
     @classmethod
     def setup_class(cls):
@@ -31,19 +32,19 @@ def test_client_spawn(self):
 
         from astrohack.client import astrohack_local_client
 
-        DEFAULT_DASK_ADDRESS="127.0.0.1:8786"
+        DEFAULT_DASK_ADDRESS = "127.0.0.1:8786"
 
-        log_parms = {'log_level':'DEBUG'}
+        log_parms = {'log_level': 'DEBUG'}
 
         client = astrohack_local_client(cores=2, memory_limit='8GB', log_parms=log_parms)
-        
+
         if not distributed.client._get_global_client():
             try:
                 distributed.Client(DEFAULT_DASK_ADDRESS, timeout=2)
 
             except OSError:
                 assert False
-            
+
             finally:
                 client.shutdown()
 
@@ -58,9 +59,9 @@ def test_client_dask_dir(self):
 
         from astrohack.client import astrohack_local_client
 
-        DEFAULT_DASK_ADDRESS="127.0.0.1:8786"
+        DEFAULT_DASK_ADDRESS = "127.0.0.1:8786"
 
-        log_parms = {'log_level':'DEBUG'}
+        log_parms = {'log_level': 'DEBUG'}
 
         client = astrohack_local_client(
             cores=2,
@@ -68,14 +69,14 @@ def test_client_dask_dir(self):
             log_parms=log_parms,
             dask_local_dir='./dask_test_dir'
         )
-        
+
         try:
             if os.path.exists('./dask_test_dir') is False:
                 raise FileNotFoundError
 
         except FileNotFoundError:
             assert False
-            
+
         finally:
             client.shutdown()
 
@@ -90,27 +91,27 @@ def test_client_logger(self):
 
         from astrohack.client import astrohack_local_client
 
-        DEFAULT_DASK_ADDRESS="127.0.0.1:8786"
+        DEFAULT_DASK_ADDRESS = "127.0.0.1:8786"
 
         log_parms = {
-            'log_level':'DEBUG',
-            'log_to_file':True,
+            'log_level': 'DEBUG',
+            'log_to_file': True,
             'log_file': 'astrohack_log_file'
         }
 
         client = astrohack_local_client(cores=2, memory_limit='8GB', log_parms=log_parms)
-        
+
         files = os.listdir(".")
 
         try:
             for file in files:
                 if re.match("^astrohack_log_file+[0-9].*log", file) is not None:
                     return
-                    
+
             raise FileNotFoundError
 
         except FileNotFoundError:
             assert False
-            
+
         finally:
-            client.shutdown()
\ No newline at end of file
+            client.shutdown()
diff --git a/tests/unit/test_dio.py b/tests/unit/test_dio.py
index d8225557..6f5d6bcb 100644
--- a/tests/unit/test_dio.py
+++ b/tests/unit/test_dio.py
@@ -13,6 +13,7 @@
 from astrohack.panel import panel
 from astrohack import holog
 
+
 class TestAstrohackDio():
     datafolder = 'dioData'
     holog_mds = dict()
@@ -21,16 +22,15 @@ class TestAstrohackDio():
 
     @classmethod
     def setup_class(cls):
-        
         astrohack.data.datasets.download(file="ea25_cal_small_after_fixed.split.ms", folder=cls.datafolder)
-        
+
         extract_pointing(
             ms_name=cls.datafolder + '/ea25_cal_small_after_fixed.split.ms',
             point_name=cls.datafolder + '/ea25_cal_small_after_fixed.split.point.zarr',
             parallel=True,
             overwrite=True
         )
-        
+
         cls.holog_mds = extract_holog(
             ms_name=cls.datafolder + '/ea25_cal_small_after_fixed.split.ms',
             point_name=cls.datafolder + '/ea25_cal_small_after_fixed.split.point.zarr',
@@ -58,32 +58,32 @@ def setup_class(cls):
     @classmethod
     def teardown_class(cls):
         shutil.rmtree(cls.datafolder)
-        
+
     def test_open_holog(self):
         '''Open a holog file and return a holog data object'''
         holog_data = open_holog(self.datafolder + '/ea25_cal_small_after_fixed.split.holog.zarr')
 
         assert holog_data == self.holog_mds
-        
+
     def test_open_image(self):
         '''Open an image file and return an image data object'''
         image_data = open_image(self.datafolder + '/ea25_cal_small_after_fixed.split.image.zarr')
-        
+
         assert image_data == self.image_mds
-        
+
     def test_open_panel(self):
         '''Open a panel file and return a panel data object'''
         panel_data = open_panel(self.datafolder + '/ea25_cal_small_after_fixed.split.panel.zarr')
-        
+
         assert panel_data == self.panel_mds
-        
+
     def test_open_pointing(self):
         '''Open a pointing file and return a pointing data object'''
         pointing_data = open_pointing(self.datafolder + '/ea25_cal_small_after_fixed.split.point.zarr')
         # check if keys match expected?
         # How to check xarray content...
-        
+
         expected_keys = ['point_meta_ds', 'ant_ea25', 'ant_ea04', 'ant_ea06']
-        
+
         for key in pointing_data.keys():
             assert key in expected_keys
diff --git a/tests/unit/test_extract_holog.py b/tests/unit/test_extract_holog.py
index 9cc7fb53..c344473e 100644
--- a/tests/unit/test_extract_holog.py
+++ b/tests/unit/test_extract_holog.py
@@ -9,6 +9,7 @@
 from astrohack.extract_pointing import extract_pointing
 from astrohack.extract_holog import generate_holog_obs_dict
 
+
 class TestExtractHolog():
     @classmethod
     def setup_class(cls):
@@ -24,7 +25,7 @@ def teardown_class(cls):
 
     def setup_method(self):
         """ setup any state specific to all methods of the given class """
-                
+
         pass
 
     def teardown_method(self):
@@ -32,9 +33,9 @@ def teardown_method(self):
         pass
 
     def test_extract_holog_obs_dict(self):
-        '''
+        """
            Specify a holography observations dictionary and check that the proper dictionary is created.
-        '''
+        """
 
         # Generate pointing file
         extract_pointing(
@@ -68,16 +69,16 @@ def test_extract_holog_obs_dict(self):
         # Get holog_obs_dict created by extract_holog
         with open(".holog_obs_dict.json") as holog_dict_file:
             holog_obs_test_dict = json.load(holog_dict_file)
-            
+
         holog_obs_test_dict = json.loads(holog_obs_test_dict)
 
         # Check that the holog_obs_dict used in extract_holog matches the input holog_obs_dict
         assert holog_obs_test_dict == holog_obs_dict
 
     def test_extract_holog_ddi(self):
-        '''
+        """
             Specify a ddi value to be process and check that it is the only one processed.
-        '''
+        """
 
         # Generate pointing file
         extract_pointing(
@@ -107,15 +108,14 @@ def test_extract_holog_ddi(self):
             parallel=False,
             overwrite=True
         )
-        
 
         # Check that the holog_obs_dict used in extract_holog matches the input holog_obs_dict
         assert list(holog_mds.keys()) == ['ddi_1']
 
     def test_extract_holog_overwrite(self):
-        '''
+        """
             Specify that the output file should be overwritten if it exists; check that it is overwritten.
-        '''
+        """
 
         # Generate pointing file
         extract_pointing(
@@ -142,7 +142,7 @@ def test_extract_holog_overwrite(self):
             parallel=False,
             overwrite=True
         )
-        
+
         initial_time = os.path.getctime('data/ea25_cal_small_after_fixed.split.holog.zarr')
 
         # Extract holography data
@@ -160,10 +160,10 @@ def test_extract_holog_overwrite(self):
         assert initial_time != final_time
 
     def test_extract_holog_baseline_average_distance(self):
-        '''
+        """
             Run extract_holog using the baseline average distance as a filter; check that only the baselines with this
             average distance are returned.
-        '''
+        """
 
         # extract pointing data
         pnt_mds = extract_pointing(
@@ -182,14 +182,14 @@ def test_extract_holog_baseline_average_distance(self):
             parallel=False,
             overwrite=True
         )
-        
+
         # Check that the expected antenna is present.
         assert list(holog_mds['ddi_0']['map_0'].keys()) == ['ant_ea25']
 
     def test_extract_holog_baseline_average_nearest(self):
-        '''
+        """
             Run extract_holog using the nearest baseline as a filter; check that only the nearest baselines are returned.
-        '''
+        """
 
         # extract pointing data
         pnt_mds = extract_pointing(
@@ -208,6 +208,6 @@ def test_extract_holog_baseline_average_nearest(self):
             parallel=False,
             overwrite=True
         )
-        
+
         # Check that the expected antenna is present.
-        assert list(holog_mds['ddi_0']['map_0'].keys()).sort() == ['ant_ea25', 'ant_ea06'].sort()
\ No newline at end of file
+        assert list(holog_mds['ddi_0']['map_0'].keys()).sort() == ['ant_ea25', 'ant_ea06'].sort()

From 12f6d61f9ca5d5266d440c2d37d8e853500565c4 Mon Sep 17 00:00:00 2001
From: Joshua Hoskins <jrh4dy@gmail.com>
Date: Wed, 4 Oct 2023 11:41:33 -0400
Subject: [PATCH 5/6] Fix download error.

---
 src/astrohack/data/_dropbox.py   | 169 ++++++++++++++++---------------
 tests/unit/test_extract_locit.py |  19 +++-
 tests/unit/test_panel.py         |   6 +-
 3 files changed, 103 insertions(+), 91 deletions(-)

diff --git a/src/astrohack/data/_dropbox.py b/src/astrohack/data/_dropbox.py
index 83eb695d..427dfa9d 100644
--- a/src/astrohack/data/_dropbox.py
+++ b/src/astrohack/data/_dropbox.py
@@ -7,90 +7,91 @@
 from astrohack._utils._logger._astrohack_logger import _get_astrohack_logger
 
 FILE_ID = {
-  'ea25_cal_small_before_fixed.split.ms':
-  {
-    'file':'ea25_cal_small_before_fixed.split.ms.zip',
-    'id':'m2qnd2w6g9fhdxyzi6h7f',
-    'rlkey':'d4dgztykxpnnqrei7jhb1cu7m'
-  },
-  'ea25_cal_small_after_fixed.split.ms':
-  {
-    'file':'ea25_cal_small_after_fixed.split.ms.zip',
-    'id':'o3tl05e3qa440s4rk5owf',
-    'rlkey':'hoxte3zzeqgkju2ywnif2t7ko'
-  },
-  'J1924-2914.ms.calibrated.split.SPW3':
-  {
-    'file':'J1924-2914.ms.calibrated.split.SPW3.zip',
-    'id':'kyrwc5y6u7lxbmqw7fveh',
-    'rlkey':'r23qakcm24bid2x2cojsd96gs'
-  },
-  'extract_holog_verification.json':
-  {
-    'file': 'extract_holog_verification.json',
-    'id':'6pzucjd48a4n0eb74wys9',
-    'rlkey':'azuynw358zxvse9i225sbl59s'
-  },
-  'holog_numerical_verification.json':
-  {
-    'file':'holog_numerical_verification.json',
-    'id':'x69700pznt7uktwprdqpk',
-    'rlkey':'bxn9me7dgnxrtzvvay7xgicmi'
-  },
-  'locit-input-pha.cal':
-  {
-    'file':'locit-input-pha.cal.zip',
-    'id':'8fftz5my9h8ca2xdlupym',
-    'rlkey':'fxfid92953ycorh5wrhfgh78b'
-  },
-  'panel_cutoff_mask':
-  {
-    'file':'panel_cutoff_mask.npy',
-    'id':'8ta02t72vwcv4ketv8rfw',
-    'rlkey':'qsmos4hx2duz8upb83hghi6q8'
-  }
-  
-        
+    'ea25_cal_small_before_fixed.split.ms':
+        {
+            'file': 'ea25_cal_small_before_fixed.split.ms.zip',
+            'id': 'm2qnd2w6g9fhdxyzi6h7f',
+            'rlkey': 'd4dgztykxpnnqrei7jhb1cu7m'
+        },
+    'ea25_cal_small_after_fixed.split.ms':
+        {
+            'file': 'ea25_cal_small_after_fixed.split.ms.zip',
+            'id': 'o3tl05e3qa440s4rk5owf',
+            'rlkey': 'hoxte3zzeqgkju2ywnif2t7ko'
+        },
+    'J1924-2914.ms.calibrated.split.SPW3':
+        {
+            'file': 'J1924-2914.ms.calibrated.split.SPW3.zip',
+            'id': 'kyrwc5y6u7lxbmqw7fveh',
+            'rlkey': 'r23qakcm24bid2x2cojsd96gs'
+        },
+    'extract_holog_verification.json':
+        {
+            'file': 'extract_holog_verification.json',
+            'id': '6pzucjd48a4n0eb74wys9',
+            'rlkey': 'azuynw358zxvse9i225sbl59s'
+        },
+    'holog_numerical_verification.json':
+        {
+            'file': 'holog_numerical_verification.json',
+            'id': 'x69700pznt7uktwprdqpk',
+            'rlkey': 'bxn9me7dgnxrtzvvay7xgicmi'
+        },
+    'locit-input-pha.cal':
+        {
+            'file': 'locit-input-pha.cal.zip',
+            'id': '8fftz5my9h8ca2xdlupym',
+            'rlkey': 'fxfid92953ycorh5wrhfgh78b'
+        },
+    'panel_cutoff_mask':
+        {
+            'file': 'panel_cutoff_mask.npy',
+            'id': '8ta02t72vwcv4ketv8rfw',
+            'rlkey': 'qsmos4hx2duz8upb83hghi6q8'
+        }
+
 }
 
+
 def download(file, folder='.'):
-  logger = _get_astrohack_logger()
-    
-  if os.path.exists('/'.join((folder, file))):
-    logger.info("File exists.")
-    return
-    
-  if file not in FILE_ID.keys():
-    logger.info("Requested file not found")
-    
-    return 
-  
-  fullname=FILE_ID[file]['file']
-  id=FILE_ID[file]['id']
-  rlkey=FILE_ID[file]['rlkey']
-    
-  url = 'https://www.dropbox.com/scl/fi/{id}/{file}?rlkey={rlkey}'.format(id=id, file=fullname, rlkey=rlkey)
-    
-  headers = {'user-agent': 'Wget/1.16 (linux-gnu)'}
-
-  r = requests.get(url, stream=True, headers=headers)
-  total = int(r.headers.get('content-length', 0))
-
-  fullname = '/'.join((folder, fullname))
-
-  with open(fullname, 'wb') as fd, tqdm(
-    desc=fullname,
-    total=total,
-    unit='iB',
-    unit_scale=True,
-    unit_divisor=1024) as bar:
-      for chunk in r.iter_content(chunk_size=1024):
-        if chunk:
-          size=fd.write(chunk)
-          bar.update(size)
-                
-  if zipfile.is_zipfile(fullname):                
-    shutil.unpack_archive(filename=fullname, extract_dir=folder)
-    
-    # Let's clean up after ourselves
-    os.remove(fullname)
\ No newline at end of file
+    logger = _get_astrohack_logger()
+
+    if os.path.exists('/'.join((folder, file))):
+        logger.info("File exists.")
+        return
+
+    if file not in FILE_ID.keys():
+        logger.info("Requested file not found")
+        logger.info(FILE_ID.keys())
+
+        return
+
+    fullname = FILE_ID[file]['file']
+    id = FILE_ID[file]['id']
+    rlkey = FILE_ID[file]['rlkey']
+
+    url = 'https://www.dropbox.com/scl/fi/{id}/{file}?rlkey={rlkey}'.format(id=id, file=fullname, rlkey=rlkey)
+
+    headers = {'user-agent': 'Wget/1.16 (linux-gnu)'}
+
+    r = requests.get(url, stream=True, headers=headers)
+    total = int(r.headers.get('content-length', 0))
+
+    fullname = '/'.join((folder, fullname))
+
+    with open(fullname, 'wb') as fd, tqdm(
+            desc=fullname,
+            total=total,
+            unit='iB',
+            unit_scale=True,
+            unit_divisor=1024) as bar:
+        for chunk in r.iter_content(chunk_size=1024):
+            if chunk:
+                size = fd.write(chunk)
+                bar.update(size)
+
+    if zipfile.is_zipfile(fullname):
+        shutil.unpack_archive(filename=fullname, extract_dir=folder)
+
+        # Let's clean up after ourselves
+        os.remove(fullname)
diff --git a/tests/unit/test_extract_locit.py b/tests/unit/test_extract_locit.py
index 5218999c..38224988 100644
--- a/tests/unit/test_extract_locit.py
+++ b/tests/unit/test_extract_locit.py
@@ -12,8 +12,11 @@ class TestExtractLocit():
 
     @classmethod
     def setup_class(cls):
-        """ setup any state specific to the execution of the given test class
-        such as fetching test data """
+        """
+            Setup any state specific to the execution of the given test class
+            such as fetching test data
+        """
+
         astrohack.data.datasets.download(file="locit-input-pha.cal", folder="data")
 
     @classmethod
@@ -58,7 +61,7 @@ def test_extract_locit_antenna_select(self):
         assert len(locit_mds.keys()) == 3
 
         # Check that only the specific antenna is in the keys.
-        assert list(locit_mds.keys()) == ['ant_ea17']
+        assert list(locit_mds.keys()) == ['obs_info', 'ant_info', 'ant_ea17']
 
     def test_extract_locit_ddi(self):
         """
@@ -76,6 +79,11 @@ def test_extract_locit_overwrite(self):
            Specify the output file should be overwritten; check that it WAS.
         """
 
+        extract_locit(
+            self.cal_table,
+            locit_name=self.locit_name
+        )
+
         # To check this properly we need to not only know an exception was not thrown but that the file is ACTUALLY
         # overwritten. We do this by checking the modification time.
         initial_time = os.path.getctime(self.locit_name)
@@ -94,6 +102,11 @@ def test_extract_locit_no_overwrite(self):
         """
             Specify the output file should be NOT be overwritten; check that it WAS NOT.
         """
+        extract_locit(
+            self.cal_table,
+            locit_name=self.locit_name
+        )
+
         initial_time = os.path.getctime(self.locit_name)
 
         try:
diff --git a/tests/unit/test_panel.py b/tests/unit/test_panel.py
index 9122b15e..6653e971 100644
--- a/tests/unit/test_panel.py
+++ b/tests/unit/test_panel.py
@@ -1,5 +1,3 @@
-import pytest
-
 import os
 import json
 import shutil
@@ -27,8 +25,6 @@ def setup_class(cls):
         astrohack.data.datasets.download(file='extract_holog_verification.json')
         astrohack.data.datasets.download(file='holog_numerical_verification.json')
 
-        astrohack.data.datasets.download(file='panel_cutoff_mask')
-
         extract_pointing(
             ms_name="data/ea25_cal_small_after_fixed.split.ms",
             point_name="data/ea25_cal_small_after_fixed.split.point.zarr",
@@ -208,6 +204,8 @@ def test_panel_cutoff(self):
         """
            Set cutoff=0 and compare results to known truth value array.
         """
+        astrohack.data.datasets.download(file='panel_cutoff_mask')
+
         with open("panel_cutoff_mask.npy", "rb") as array:
             reference_array = np.load(array)
 

From 7ffc79537ab491b1a13d16ab29b4664b28d9c213 Mon Sep 17 00:00:00 2001
From: Joshua Hoskins <jrh4dy@gmail.com>
Date: Wed, 4 Oct 2023 12:21:30 -0400
Subject: [PATCH 6/6] Update test_holog.py

Fix typo mentioned by Sandra
---
 tests/unit/test_holog.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/unit/test_holog.py b/tests/unit/test_holog.py
index cda4a978..72ef8764 100644
--- a/tests/unit/test_holog.py
+++ b/tests/unit/test_holog.py
@@ -209,7 +209,7 @@ def test_holog_grid_interpolation(self):
 
     def test_holog_chan_tolerance(self):
         """
-            Check that channel tolerance ir propagated correctly.
+            Check that channel tolerance is propagated correctly.
         """
         image_mds = holog(
             holog_name='data/ea25_cal_small_after_fixed.split.holog.zarr',