additional flake8 updates

jwql/instrument_monitors/common_monitors/bad_pixel_monitor.py

@@ -91,8 +91,8 @@
 from jwql.database.database_interface import FGSBadPixelQueryHistory, FGSBadPixelStats
 from jwql.instrument_monitors import pipeline_tools
 from jwql.utils import crds_tools, instrument_properties
-from jwql.utils.constants import JWST_INSTRUMENT_NAMES, JWST_INSTRUMENT_NAMES_MIXEDCASE, \
-                                 FLAT_EXP_TYPES, DARK_EXP_TYPES
+from jwql.utils.constants import JWST_INSTRUMENT_NAMES, JWST_INSTRUMENT_NAMES_MIXEDCASE
+from jwql.utils.constants import FLAT_EXP_TYPES, DARK_EXP_TYPES
 from jwql.utils.logging_functions import log_info, log_fail
 from jwql.utils.mast_utils import mast_query
 from jwql.utils.monitor_utils import initialize_instrument_monitor, update_monitor_table
@@ -685,8 +685,8 @@ def most_recent_search(self, file_type='dark'):
         elif file_type.lower() == 'flat':
             run_field = self.query_table.run_bpix_from_flats
 
-        query = session.query(self.query_table).filter(self.query_table.aperture==self.aperture). \
-                                                filter(run_field==True)
+        query = session.query(self.query_table).filter(self.query_table.aperture == self.aperture). \
+                              filter(run_field == True)
 
         dates = np.zeros(0)
         if file_type.lower() == 'dark':
@@ -888,7 +888,7 @@ def process(self, illuminated_raw_files, illuminated_slope_files, dark_raw_files
             logging.info('\tFound {} new {} pixels'.format(len(bad_location_list[0]), bad_type))
 
             if bad_type in badpix_types_from_flats:
-                self.add_bad_pix(bad_location_list, bad_type, illuminated_slope_files, 
+                self.add_bad_pix(bad_location_list, bad_type, illuminated_slope_files,
                                  min_illum_time, mid_illum_time, max_illum_time, baseline_file)
             elif bad_type in badpix_types_from_darks:
                 self.add_bad_pix(bad_location_list, bad_type, dark_slope_files,
@@ -958,7 +958,7 @@ def run(self):
                     lamp = 'LINE2'
 
                 # What lamp is most appropriate for FGS?
-                #if self.instrument == 'fgs':
+                # if self.instrument == 'fgs':
                 #    lamp = 'G2LAMP1'
 
                 logging.info('')

jwql/instrument_monitors/common_monitors/bias_monitor.py

@@ -416,7 +416,7 @@ def run(self):
 
             # Get a list of all possible full-frame apertures for this instrument
             siaf = Siaf(self.instrument)
-            possible_apertures = [aperture for aperture in siaf.apertures if siaf[aperture].AperType=='FULLSCA']
+            possible_apertures = [aperture for aperture in siaf.apertures if siaf[aperture].AperType == 'FULLSCA']
 
             for aperture in possible_apertures:
 

jwql/instrument_monitors/common_monitors/dark_monitor.py

@@ -441,8 +441,8 @@ def most_recent_search(self):
             Date (in MJD) of the ending range of the previous MAST query
             where the dark monitor was run.
         """
-        query = session.query(self.query_table).filter(self.query_table.aperture==self.aperture). \
-                                                filter(self.query_table.run_monitor==True)
+        query = session.query(self.query_table).filter(self.query_table.aperture == self.aperture). \
+                              filter(self.query_table.run_monitor == True)
 
         dates = np.zeros(0)
         for instance in query:
@@ -993,8 +993,7 @@ def stats_by_amp(self, image, amps):
             degrees_of_freedom = len(hist) - 3.
             total_pix = np.sum(hist[positive])
             p_i = gauss_fit[positive] / total_pix
-            gaussian_chi_squared[key] = (np.sum((hist[positive] - (total_pix * p_i) ** 2) / (total_pix * p_i)) /
-                                         degrees_of_freedom)
+            gaussian_chi_squared[key] = (np.sum((hist[positive] - (total_pix * p_i) ** 2) / (total_pix * p_i)) / degrees_of_freedom)
 
             # Double Gaussian fit only for full frame data (and only for
             # NIRISS, NIRCam at the moment.)
@@ -1018,10 +1017,10 @@ def stats_by_amp(self, image, amps):
 
         logging.info('\tMean dark rate by amplifier: {}'.format(amp_means))
         logging.info('\tStandard deviation of dark rate by amplifier: {}'.format(amp_means))
-        logging.info('\tBest-fit Gaussian parameters [amplitude, peak, width]'.format(gaussian_params))
+        logging.info('\tBest-fit Gaussian parameters [amplitude, peak, width]: {}'.format(gaussian_params))
         logging.info('\tReduced chi-squared associated with Gaussian fit: {}'.format(gaussian_chi_squared))
         logging.info('\tBest-fit double Gaussian parameters [amplitude1, peak1, width1, amplitude2, peak2, '
-                     'width2]'.format(double_gaussian_params))
+                     'width2]: {}'.format(double_gaussian_params))
         logging.info('\tReduced chi-squared associated with double Gaussian fit: {}'
                      .format(double_gaussian_chi_squared))
 

jwql/jwql_monitors/generate_preview_images.py

@@ -611,7 +611,7 @@ def group_filenames(filenames):
                         subgroup.append(file_to_match)
 
             else:
-                # filename_dict['filename_type'] may be 'guider' or 'time_series', for instance. Treat individually.  
+                # filename_dict['filename_type'] may be 'guider' or 'time_series', for instance. Treat individually. 
                 matched_names.append(filename)
                 subgroup.append(filename)
 

jwql/tests/test_calculations.py

@@ -58,8 +58,8 @@ def test_gaussian1d_fit():
 
     assert np.isclose(peak[0], mean_value, atol=0.0035, rtol=0.)
     assert np.isclose(width[0], sigma_value, atol=0.0035, rtol=0.)
-    assert ((mean_value <= peak[0]+7*peak[1]) & (mean_value >= peak[0]-7*peak[1]))
-    assert ((sigma_value <= width[0]+7*width[1]) & (sigma_value >= width[0]-7*width[1]))
+    assert ((mean_value <= peak[0] + 7 * peak[1]) & (mean_value >= peak[0] - 7 * peak[1]))
+    assert ((sigma_value <= width[0] + 7 * width[1]) & (sigma_value >= width[0] - 7 * width[1]))
 
 
 def test_mean_image():

jwql/tests/test_dark_monitor.py

@@ -98,7 +98,7 @@ def test_mast_query_darks():
                        'jw82600016001_02102_00001_nrca1_dark.fits']
 
     assert len(query) == 14
-    assert apernames == [aperture]*len(query)
+    assert apernames == [aperture] * len(query)
     assert filenames == truth_filenames
 
 

jwql/tests/test_database_interface.py

@@ -76,8 +76,8 @@ def test_anomaly_records():
     """Test to see that new records can be entered"""
 
     # Add some data
-    random_rootname = ''.join(random.SystemRandom().choice(string.ascii_lowercase + \
-                                                           string.ascii_uppercase + \
+    random_rootname = ''.join(random.SystemRandom().choice(string.ascii_lowercase +
+                                                           string.ascii_uppercase +
                                                            string.digits) for _ in range(10))
     di.session.add(di.FGSAnomaly(rootname=random_rootname,
                                  flag_date=datetime.datetime.today(),

jwql/tests/test_permissions.py

@@ -121,7 +121,7 @@ def test_file_group(test_file):
     # attempt to retrieve a group name different from default
     group_index = 0
     test_group = grp.getgrgid(os.getgroups()[group_index]).gr_name
-    test_group_2 = grp.getgrgid(os.getgroups()[group_index+1]).gr_name
+    test_group_2 = grp.getgrgid(os.getgroups()[group_index + 1]).gr_name
 
     # Change the file group
     set_permissions(test_file, group=test_group, owner=owner)

jwql/utils/permissions.py

@@ -82,7 +82,7 @@
 DEFAULT_GROUP = 'jwql_dev'
 
 # set the default mode for DEFAULT_OWNER
-DEFAULT_MODE = stat.S_IRWXU | stat.S_IRGRP | stat.S_IXGRP # equivalent to '?rwxr-x---'
+DEFAULT_MODE = stat.S_IRWXU | stat.S_IRGRP | stat.S_IXGRP  # equivalent to '?rwxr-x---'
 
 
 def get_group_string(pathname):

jwql/website/apps/jwql/bokeh_dashboard.py

@@ -172,18 +172,18 @@ def dashboard_files_per_day(self):
         tab2 = Panel(child=p2, title='Storage')
 
         p1.xaxis.formatter = DatetimeTickFormatter(
-                hours=["%d %B %Y"],
-                days=["%d %B %Y"],
-                months=["%d %B %Y"],
-                years=["%d %B %Y"],
+            hours=["%d %B %Y"],
+            days=["%d %B %Y"],
+            months=["%d %B %Y"],
+            years=["%d %B %Y"],
             )
         p1.xaxis.major_label_orientation = pi / 4
 
         p2.xaxis.formatter = DatetimeTickFormatter(
-                hours=["%d %B %Y"],
-                days=["%d %B %Y"],
-                months=["%d %B %Y"],
-                years=["%d %B %Y"],
+            hours=["%d %B %Y"],
+            days=["%d %B %Y"],
+            months=["%d %B %Y"],
+            years=["%d %B %Y"],
             )
         p2.xaxis.major_label_orientation = pi / 4
 

jwql/website/apps/jwql/monitor_pages/monitor_bad_pixel_bokeh.py

@@ -85,7 +85,7 @@ def bad_pixel_history(self, bad_pixel_type):
 
         # Sum the number of bad pixels found from the earliest entry up to
         # each new entry
-        num_bad_pixels = [np.sum(num[0:i]) for i in range(1, len(num)+1)]
+        num_bad_pixels = [np.sum(num[0:i]) for i in range(1, len(num) + 1)]
 
         return num_bad_pixels, dates
 
@@ -287,7 +287,7 @@ def load_dummy_data(self):
             hover_values = np.array([datetime.datetime.strftime(t, "%d-%b-%Y") for t in times])
 
             self.bad_history[bad_pixel_type] = (times, num, hover_values)
-            self.bad_latest[bad_pixel_type] = (datetime.datetime(1999, 12, 31), [500+delta, 501+delta, 502+delta], [4, 4, 4])
+            self.bad_latest[bad_pixel_type] = (datetime.datetime(1999, 12, 31), [500 + delta, 501 + delta, 502 + delta], [4, 4, 4])
 
     def most_recent_data(self):
         """Get the bad pixel type and coordinates associated with the most

jwql/website/apps/jwql/monitor_pages/monitor_filesystem_bokeh.py

@@ -149,7 +149,7 @@ def update_plots(self, full=False):
             if new_sizes:
                 stype_dict = {'dates': new_sizes['timestamp'].datetime64}
                 stype_dict.update({x: new_sizes[y].data / (1024.**3)
-                    for x, y in zip(self.types_y, self.allowed_types)})
+                                  for x, y in zip(self.types_y, self.allowed_types)})
                 self.refs['source_sizes'].data = stype_dict
 
         if not self.statistics:

jwql/website/apps/jwql/oauth.py

@@ -115,11 +115,11 @@ def authorize(request):
     token = JWQL_OAUTH.mast_auth.authorize_access_token(request)
 
     # Determine domain
-    base_url = get_base_url()
-    if '127' in base_url:
-        domain = '127.0.0.1'
-    else:
-        domain = base_url.split('//')[-1]
+    # base_url = get_base_url()
+    # if '127' in base_url:
+    #     domain = '127.0.0.1'
+    # else:
+    #     domain = base_url.split('//')[-1]
 
     # Set secure cookie parameters
     cookie_args = {}

style_guide/typing_demo/typing_demo_1.py

@@ -18,7 +18,7 @@
 a_string: str = "jwql"
 a_list: List[int] = [1]
 a_set: Set[int] = {1, 2, 3}
-a_dict: Dict[str, bool] = {'jwql':True}  # Have to specify both keys and values
+a_dict: Dict[str, bool] = {'jwql': True}  # Have to specify both keys and values
 
 # For python versions prior to 3.6, the variable annotation syntax uses comments:
 #    annotated_variable = 1 # type: int

style_guide/typing_demo/typing_demo_2.py

@@ -27,6 +27,7 @@ def do_mutate(mut_dict: MutableMapping[Any, Any]) -> Set[Any]:
     mut_dict['jwql'] = True
     return set(mut_dict.keys())
 
+
 # Variables can be annotated without initializing
 stream: IO[str]
 print(__annotations__['stream'])

style_guide/typing_demo/typing_demo_3.py

@@ -26,6 +26,7 @@ def ive_got_your_number(num: int) -> bool:
     else:
         return "Jenny don't change your number"
 
+
 ive_got_your_number("jenny")  # no runtime error
 ive_got_your_number(555_1212)  # no runtime error
 

style_guide/typing_demo/typing_demo_4.py

@@ -15,4 +15,4 @@ def get_favorite_number():
 
 
 num = get_favorite_number()
-print("Twice your favorite number is", num*2)
+print("Twice your favorite number is", num * 2)