Merge pull request spacetelescope#1490 from york-stsci/github_ci

Moved ON_GITHUB_ACTIONS and ON_READTHEDOCS to constants.py

jwql/database/database_interface.py

@@ -84,10 +84,9 @@
 from jwql.utils.constants import ANOMALIES_PER_INSTRUMENT
 from jwql.utils.constants import FILE_SUFFIX_TYPES
 from jwql.utils.constants import JWST_INSTRUMENT_NAMES
+from jwql.utils.constants import ON_GITHUB_ACTIONS
 from jwql.utils.utils import get_config
 
-ON_GITHUB_ACTIONS = '/home/runner' in os.path.expanduser('~') or '/Users/runner' in os.path.expanduser('~')
-
 
 # Monkey patch Query with data_frame method
 @property

jwql/edb/engineering_database.py

@@ -58,20 +58,20 @@
 from astroquery.mast import Mast
 from bokeh.embed import components
 from bokeh.layouts import column
-from bokeh.models import BoxAnnotation, ColumnDataSource, DatetimeTickFormatter, HoverTool, Range1d
+from bokeh.models import BoxAnnotation, ColumnDataSource, DatetimeTickFormatter, HoverTool
+from bokeh.models import Range1d
 from bokeh.plotting import figure, output_file, show, save
 import numpy as np
 
 from jwst.lib.engdb_tools import ENGDB_Service
 from jwql.utils.constants import MIRI_POS_RATIO_VALUES
+from jwql.utils.constants import ON_GITHUB_ACTIONS
 from jwql.utils.credentials import get_mast_base_url, get_mast_token
 from jwql.utils.utils import get_config
 
 MAST_EDB_MNEMONIC_SERVICE = 'Mast.JwstEdb.Mnemonics'
 MAST_EDB_DICTIONARY_SERVICE = 'Mast.JwstEdb.Dictionary'
 
-# Temporary until JWST operations: switch to test string for MAST request URL
-ON_GITHUB_ACTIONS = '/home/runner' in os.path.expanduser('~') or '/Users/runner' in os.path.expanduser('~')
 if not ON_GITHUB_ACTIONS:
     Mast._portal_api_connection.MAST_REQUEST_URL = get_config()['mast_request_url']
 
@@ -283,7 +283,7 @@ def __mul__(self, mnem):
                 before = np.where(common_dates == self.data['dates'][block])[0]
 
                 if len(before) > 0:
-                    new_blocks.append(before[0]) # + 1)
+                    new_blocks.append(before[0])  # + 1)
             except IndexError:
                 # The final block value is usually equal to the length of the array, and will
                 # therefore cause an Index Error in the lines above. Ignore that error here.
@@ -421,7 +421,7 @@ def block_stats(self, sigma=3, ignore_vals=[], ignore_edges=False, every_change=
             # calculated, remove those every change values and block values from the EdbMnemonic
             # instance.
             if every_change:
-                if len(remove_change_indexes)  > 0:
+                if len(remove_change_indexes) > 0:
                     self.every_change_values = np.delete(self.every_change_values, remove_change_indexes)
                     self.blocks = np.delete(self.blocks, remove_change_indexes)
 
@@ -439,7 +439,7 @@ def block_stats(self, sigma=3, ignore_vals=[], ignore_edges=False, every_change=
                     stdevs.append(stdevval)
                     maxs.append(meanval)
                     mins.append(meanval)
-                    #if hasattr(self, 'every_change_values'):
+                    # if hasattr(self, 'every_change_values'):
                     #        updated_every_change_vals.append(self.every_change_values[i + 1])
         self.mean = means
         self.median = medians
@@ -510,9 +510,9 @@ def block_stats_filter_positions(self, sigma=5):
                                                                                          self.data["euvalues"].data[index:self.blocks[i + 1]],
                                                                                          sigma=sigma)
                     if np.isfinite(meanval):
-                        #this is preventing the nans above from being added. not sure what to do here.
-                        #bokeh cannot deal with nans. but we need entries in order to have the blocks indexes
-                        #remain correct. but maybe we dont care about the block indexes after averaging
+                        # this is preventing the nans above from being added. not sure what to do here.
+                        # bokeh cannot deal with nans. but we need entries in order to have the blocks indexes
+                        # remain correct. but maybe we dont care about the block indexes after averaging
                         medtimes.append(calc_median_time(self.data["dates"].data[index:self.blocks[i + 1]][good]))
                         means.append(meanval)
                         medians.append(medianval)
@@ -523,7 +523,7 @@ def block_stats_filter_positions(self, sigma=5):
             # If there were blocks composed entirely of bad data, meaning no mean values were
             # calculated, remove those every change values and block values from the EdbMnemonic
             # instance.
-            if len(remove_change_indexes)  > 0:
+            if len(remove_change_indexes) > 0:
                 self.every_change_values = np.delete(self.every_change_values, remove_change_indexes)
                 self.blocks = np.delete(self.blocks, remove_change_indexes)
 
@@ -690,37 +690,33 @@ def bokeh_plot(self, show_plot=False, savefig=False, out_dir='./', nominal_value
                 if plot_mean:
                     source_mean = ColumnDataSource(data={'mean_x': self.median_times, 'mean_y': self.mean})
                     mean_data = fig.scatter(x='mean_x', y='mean_y', line_width=1, line_color='orange', alpha=0.75, source=source_mean)
-                    mean_hover_tool = HoverTool(tooltips=[('Mean', '@mean_y'),
-                                                          ('Date', '@mean_x{%d %b %Y %H:%M:%S}')
-                                                         ], mode='mouse', renderers=[mean_data])
+                    mean_hover_tool = HoverTool(tooltips=[('Mean', '@mean_y'), ('Date', '@mean_x{%d %b %Y %H:%M:%S}')],
+                                                mode='mouse', renderers=[mean_data])
                     mean_hover_tool.formatters = {'@mean_x': 'datetime'}
                     fig.tools.append(mean_hover_tool)
 
                 if plot_median:
                     source_median = ColumnDataSource(data={'median_x': self.median_times, 'median_y': self.median})
                     median_data = fig.scatter(x='median_x', y='median_y', line_width=1, line_color='orangered', alpha=0.75, source=source_median)
-                    median_hover_tool = HoverTool(tooltips=[('Median', '@median_y'),
-                                                            ('Date', '@median_x{%d %b %Y %H:%M:%S}')
-                                                           ], mode='mouse', renderers=[median_data])
+                    median_hover_tool = HoverTool(tooltips=[('Median', '@median_y'), ('Date', '@median_x{%d %b %Y %H:%M:%S}')],
+                                                  mode='mouse', renderers=[median_data])
                     median_hover_tool.formatters = {'@median_x': 'datetime'}
                     fig.tools.append(median_hover_tool)
 
-                 # If the max and min arrays are to be plotted, create columndata sources for them as well
+                # If the max and min arrays are to be plotted, create columndata sources for them as well
                 if plot_max:
                     source_max = ColumnDataSource(data={'max_x': self.median_times, 'max_y': self.max})
                     max_data = fig.scatter(x='max_x', y='max_y', line_width=1, color='black', line_color='black', source=source_max)
-                    max_hover_tool = HoverTool(tooltips=[('Max', '@max_y'),
-                                                         ('Date', '@max_x{%d %b %Y %H:%M:%S}')
-                                                        ], mode='mouse', renderers=[max_data])
+                    max_hover_tool = HoverTool(tooltips=[('Max', '@max_y'), ('Date', '@max_x{%d %b %Y %H:%M:%S}')],
+                                               mode='mouse', renderers=[max_data])
                     max_hover_tool.formatters = {'@max_x': 'datetime'}
                     fig.tools.append(max_hover_tool)
 
                 if plot_min:
                     source_min = ColumnDataSource(data={'min_x': self.median_times, 'min_y': self.min})
                     min_data = fig.scatter(x='min_x', y='min_y', line_width=1, color='black', line_color='black', source=source_min)
-                    minn_hover_tool = HoverTool(tooltips=[('Min', '@min_y'),
-                                                          ('Date', '@min_x{%d %b %Y %H:%M:%S}')
-                                                         ], mode='mouse', renderers=[min_data])
+                    minn_hover_tool = HoverTool(tooltips=[('Min', '@min_y'), ('Date', '@min_x{%d %b %Y %H:%M:%S}')],
+                                                mode='mouse', renderers=[min_data])
                     min_hover_tool.formatters = {'@min_x': 'datetime'}
                     fig.tools.append(min_hover_tool)
 

jwql/instrument_monitors/common_monitors/bad_pixel_monitor.py

@@ -105,19 +105,13 @@
 from jwql.shared_tasks.shared_tasks import only_one, run_pipeline, run_parallel_pipeline
 from jwql.utils import crds_tools, instrument_properties, monitor_utils
 from jwql.utils.constants import DARKS_BAD_PIXEL_TYPES, DARK_EXP_TYPES, FLATS_BAD_PIXEL_TYPES, FLAT_EXP_TYPES
-from jwql.utils.constants import JWST_INSTRUMENT_NAMES, JWST_INSTRUMENT_NAMES_MIXEDCASE
+from jwql.utils.constants import JWST_INSTRUMENT_NAMES, JWST_INSTRUMENT_NAMES_MIXEDCASE, ON_GITHUB_ACTIONS
+from jwql.utils.constants import ON_READTHEDOCS
 from jwql.utils.logging_functions import log_info, log_fail
 from jwql.utils.mast_utils import mast_query
 from jwql.utils.permissions import set_permissions
 from jwql.utils.utils import copy_files, create_png_from_fits, ensure_dir_exists, get_config, filesystem_path
 
-# Determine if the code is being run by Github Actions
-ON_GITHUB_ACTIONS = '/home/runner' in os.path.expanduser('~') or '/Users/runner' in os.path.expanduser('~')
-
-# Determine if the code is being run as part of a Readthedocs build
-ON_READTHEDOCS = False
-if 'READTHEDOCS' in os.environ:  # pragma: no cover
-    ON_READTHEDOCS = os.environ['READTHEDOCS']
 
 if not ON_GITHUB_ACTIONS and not ON_READTHEDOCS:
     from jwql.website.apps.jwql.monitor_pages.monitor_bad_pixel_bokeh import BadPixelPlots

jwql/instrument_monitors/common_monitors/readnoise_monitor.py

@@ -44,18 +44,19 @@
 import crds
 import matplotlib
 matplotlib.use('Agg')
-import matplotlib.pyplot as plt  # noqa: E348 (comparison to true)
-import numpy as np  # noqa: E348 (comparison to true)
-from pysiaf import Siaf  # noqa: E348 (comparison to true)
-
-# astroquery.mast import that depends on value of auth_mast
-# this import has to be made before any other import of astroquery.mast
-ON_GITHUB_ACTIONS = '/home/runner' in os.path.expanduser('~') or '/Users/runner' in os.path.expanduser('~')
-
-# Determine if the code is being run as part of a Readthedocs build
-ON_READTHEDOCS = False
-if 'READTHEDOCS' in os.environ:  # pragma: no cover
-    ON_READTHEDOCS = os.environ['READTHEDOCS']
+import matplotlib.pyplot as plt  # noqa: E402 (module level import not at top of file)
+import numpy as np  # noqa: E402 (module level import not at top of file)
+from pysiaf import Siaf  # noqa: E402 (module level import not at top of file)
+
+from jwql.shared_tasks.shared_tasks import only_one, run_pipeline, run_parallel_pipeline  # noqa: E402 (module level import not at top of file)
+from jwql.instrument_monitors import pipeline_tools  # noqa: E402 (module level import not at top of file)
+from jwql.utils import instrument_properties, monitor_utils  # noqa: E402 (module level import not at top of file)
+from jwql.utils.constants import JWST_INSTRUMENT_NAMES, JWST_INSTRUMENT_NAMES_MIXEDCASE  # noqa: E402 (module level import not at top of file)
+from jwql.utils.constants import ON_GITHUB_ACTIONS, ON_READTHEDOCS  # noqa: E402 (module level import not at top of file)
+from jwql.utils.logging_functions import log_info, log_fail  # noqa: E402 (module level import not at top of file)
+from jwql.utils.monitor_utils import update_monitor_table  # noqa: E402 (module level import not at top of file)
+from jwql.utils.permissions import set_permissions  # noqa: E402 (module level import not at top of file)
+from jwql.utils.utils import ensure_dir_exists, filesystem_path, get_config, copy_files  # noqa: E402 (module level import not at top of file)
 
 if not ON_GITHUB_ACTIONS and not ON_READTHEDOCS:
     # Need to set up django apps before we can access the models
@@ -67,15 +68,6 @@
     # for this monitor
     from jwql.website.apps.jwql.monitor_models.readnoise import *  # noqa: E402 (module level import not at top of file)
 
-from jwql.shared_tasks.shared_tasks import only_one, run_pipeline, run_parallel_pipeline  # noqa: E348 (comparison to true)
-from jwql.instrument_monitors import pipeline_tools  # noqa: E348 (comparison to true)
-from jwql.utils import instrument_properties, monitor_utils  # noqa: E348 (comparison to true)
-from jwql.utils.constants import JWST_INSTRUMENT_NAMES, JWST_INSTRUMENT_NAMES_MIXEDCASE  # noqa: E348 (comparison to true)
-from jwql.utils.logging_functions import log_info, log_fail  # noqa: E348 (comparison to true)
-from jwql.utils.monitor_utils import update_monitor_table  # noqa: E348 (comparison to true)
-from jwql.utils.permissions import set_permissions  # noqa: E348 (comparison to true)
-from jwql.utils.utils import ensure_dir_exists, filesystem_path, get_config, copy_files  # noqa: E348 (comparison to true)
-
 
 class Readnoise():
     """Class for executing the readnoise monitor.

jwql/tests/test_api_views.py

@@ -29,9 +29,8 @@
 
 from jwql.utils.utils import get_base_url
 from jwql.utils.constants import JWST_INSTRUMENT_NAMES
+from jwql.utils.constants import ON_GITHUB_ACTIONS
 
-# Determine if tests are being run on Github Actions
-ON_GITHUB_ACTIONS = '/home/runner' in os.path.expanduser('~') or '/Users/runner' in os.path.expanduser('~')
 
 urls = []
 

jwql/tests/test_bad_pixel_monitor.py

@@ -32,9 +32,7 @@
 from jwql.database.database_interface import FGSBadPixelQueryHistory, FGSBadPixelStats
 from jwql.instrument_monitors.common_monitors import bad_pixel_monitor
 from jwql.tests.resources import has_test_db
-
-# Determine if tests are being run on Github Actions
-ON_GITHUB_ACTIONS = '/home/runner' in os.path.expanduser('~') or '/Users/runner' in os.path.expanduser('~')
+from jwql.utils.constants import ON_GITHUB_ACTIONS
 
 
 def test_bad_map_to_list():

jwql/tests/test_bias_monitor.py

@@ -28,8 +28,7 @@
 from jwql.instrument_monitors.common_monitors import bias_monitor
 from jwql.tests.resources import has_test_db
 from jwql.utils.utils import get_config
-
-ON_GITHUB_ACTIONS = '/home/runner' in os.path.expanduser('~') or '/Users/runner' in os.path.expanduser('~')
+from jwql.utils.constants import ON_GITHUB_ACTIONS
 
 
 def test_collapse_image():

jwql/tests/test_cosmic_ray_monitor.py

@@ -26,8 +26,7 @@
 from jwql.instrument_monitors.common_monitors.cosmic_ray_monitor import CosmicRay
 from jwql.database.database_interface import MIRICosmicRayQueryHistory
 from jwql.utils.utils import get_config
-
-ON_GITHUB_ACTIONS = '/home/runner' in os.path.expanduser('~') or '/Users/runner' in os.path.expanduser('~')
+from jwql.utils.constants import ON_GITHUB_ACTIONS
 
 
 def define_test_data(nints):

jwql/tests/test_dark_monitor.py

@@ -29,8 +29,7 @@
 from jwql.tests.resources import has_test_db
 from jwql.utils.monitor_utils import mast_query_darks
 from jwql.utils.utils import get_config
-
-ON_GITHUB_ACTIONS = '/home/runner' in os.path.expanduser('~') or '/Users/runner' in os.path.expanduser('~')
+from jwql.utils.constants import ON_GITHUB_ACTIONS
 
 
 def test_find_hot_dead_pixels():

jwql/tests/test_data_containers.py

@@ -31,18 +31,18 @@
 import pandas as pd
 import pytest
 
+from jwql.utils.constants import ON_GITHUB_ACTIONS
+
 os.environ.setdefault("DJANGO_SETTINGS_MODULE", "jwql.website.jwql_proj.settings")
 
 # Skip testing this module if on Github Actions
-ON_GITHUB_ACTIONS = '/home/runner' in os.path.expanduser('~') or '/Users/runner' in os.path.expanduser('~')
-from jwql.website.apps.jwql import data_containers
-from jwql.tests.resources import (
-    MockSessionFileAnomaly, MockSessionGroupAnomaly,
-    MockGetRequest, MockPostRequest)
-from jwql.utils import constants
+from jwql.website.apps.jwql import data_containers  # noqa: E402 (module level import not at top of file)
+from jwql.tests.resources import MockSessionFileAnomaly, MockSessionGroupAnomaly  # noqa: E402 (module level import not at top of file)
+from jwql.tests.resources import MockGetRequest, MockPostRequest  # noqa: E402 (module level import not at top of file)
+from jwql.utils import constants  # noqa: E402 (module level import not at top of file)
 
 if not ON_GITHUB_ACTIONS:
-    from jwql.utils.utils import get_config
+    from jwql.utils.utils import get_config  # noqa: E402 (module level import not at top of file)
 
 
 @pytest.mark.skipif(ON_GITHUB_ACTIONS, reason='Requires access to django models.')
@@ -142,17 +142,10 @@ def test_get_all_proposals():
                            (['uncal', 'rate', 'bad'], {'bad'})),
                           (False, ['rate', 'uncal', 'bad'],
                            ['uncal', 'rate', 'bad']),
-                          (True,
-                           ['rate', 'uncal', 'bad',
-                           'o006_crfints', 'o001_crf'],
-                           (['uncal', 'rate', 'o001_crf',
-                             'o006_crfints', 'bad'], {'bad'})),
-                          (False,
-                           ['rate', 'uncal', 'bad',
-                           'o006_crfints', 'o001_crf'],
-                           ['uncal', 'rate', 'o001_crf',
-                            'o006_crfints', 'bad']),
-                          ])
+                          (True, ['rate', 'uncal', 'bad', 'o006_crfints', 'o001_crf'],
+                           (['uncal', 'rate', 'o001_crf', 'o006_crfints', 'bad'], {'bad'})),
+                          (False, ['rate', 'uncal', 'bad', 'o006_crfints', 'o001_crf'],
+                           ['uncal', 'rate', 'o001_crf', 'o006_crfints', 'bad'])])
 def test_get_available_suffixes(untracked, input_suffixes, expected):
     result = data_containers.get_available_suffixes(
         input_suffixes, return_untracked=untracked)
@@ -292,6 +285,7 @@ def test_get_anomaly_form_post_group(mocker):
     assert update_mock.call_count == 2
 """
 
+
 def test_get_dashboard_components():
     request = MockPostRequest()
 

jwql/tests/test_database_interface.py

@@ -29,9 +29,7 @@
 from jwql.database import database_interface as di
 from jwql.tests.resources import has_test_db
 from jwql.utils.utils import get_config
-
-# Determine if tests are being run on Github Actions
-ON_GITHUB_ACTIONS = '/home/runner' in os.path.expanduser('~') or '/Users/runner' in os.path.expanduser('~')
+from jwql.utils.constants import ON_GITHUB_ACTIONS
 
 
 @pytest.mark.skipif(ON_GITHUB_ACTIONS, reason='Requires access to development database server.')

jwql/tests/test_edb.py

@@ -28,9 +28,7 @@
 import pytest
 
 from jwql.edb import engineering_database as ed
-
-# Determine if tests are being run on Github Actions
-ON_GITHUB_ACTIONS = '/home/runner' in os.path.expanduser('~') or '/Users/runner' in os.path.expanduser('~')
+from jwql.utils.constants import ON_GITHUB_ACTIONS
 
 
 def test_add():
@@ -243,8 +241,8 @@ def test_multiplication():
     info['description'] = 'Voltage at some place'
     mnemonic1 = ed.EdbMnemonic('TEST_VOLTAGE', Time('2021-12-18T07:20:00'), Time('2021-12-18T07:30:00'), tab, {}, info, blocks=blocks1)
     mnemonic1.meta = {'Count': 1,
-                     'TlmMnemonics': [{'TlmMnemonic': 'TEST_VOLTAGE',
-                                       'AllPoints': 1}]}
+                      'TlmMnemonics': [{'TlmMnemonic': 'TEST_VOLTAGE',
+                                        'AllPoints': 1}]}
 
     dates2 = np.array([datetime(2021, 12, 18, 7, n, 10) for n in range(20, 30)])
     data2 = np.array([15, 15, 15, 19, 19, 19, 19, 19, 12, 12])
@@ -258,8 +256,8 @@ def test_multiplication():
     info['description'] = 'Current at some place'
     mnemonic2 = ed.EdbMnemonic('TEST_CURRENT', Time('2021-12-18T07:20:10'), Time('2021-12-18T07:30:10'), tab, {}, info, blocks=blocks2)
     mnemonic2.meta = {'Count': 1,
-                     'TlmMnemonics': [{'TlmMnemonic': 'TEST_CURRENT',
-                                       'AllPoints': 1}]}
+                      'TlmMnemonics': [{'TlmMnemonic': 'TEST_CURRENT',
+                                        'AllPoints': 1}]}
 
     prod = mnemonic1 * mnemonic2
     assert np.allclose(prod.data["euvalues"].data,