Fixes to e2e tests.

.github/workflows/e2e.yaml

@@ -45,7 +45,7 @@ jobs:
 
       - name: Test Master Bias Creation
         run: |
-          kubectl exec banzai-e2e-test -c banzai-listener -- pytest -o log_cli=true -s --pyargs banzai.tests --durations=0 --junitxml=/archive/engineering/pytest-master-bias.xml -m master_bias
+          kubectl exec banzai-e2e-test -c banzai-listener -- pytest -o log_cli=true -s --pyargs banzai --durations=0 --junitxml=/archive/engineering/pytest-master-bias.xml -m master_bias
       
       - name: Cleanup
         run: |

MANIFEST.in

@@ -13,3 +13,4 @@ prune docs/_build
 prune docs/api
 
 include pyproject.toml
+include pytest.ini

banzai/photometry.py

@@ -108,7 +108,7 @@ def do_stage(self, image):
                                                 npixels=self.min_area, nlevels=32,
                                                 contrast=0.005, progress_bar=False,
                                                 nproc=1, mode='sinh')
-            logger.info('Finished deblending. Estimat', image=image)
+            logger.info('Finished deblending. Saving catalog', image=image)
             # Convert the segmentation map to a source catalog
             catalog = SourceCatalog(data, deblended_seg_map, convolved_data=convolved_data, error=error,
                                     background=bkg.background)
@@ -141,7 +141,7 @@ def do_stage(self, image):
             # Flag = 4 for sources that have saturated pixels
             flag_sources(sources, catalog.labels, deblended_seg_map, image.mask, flag=4, mask_value=2)
             # Flag = 8 if kron aperture falls off the image
-            flag_edge_sources(image, sources, flag_pixel=8)
+            flag_edge_sources(image, sources, flag_value=8)
             # Flag = 16 if source has cosmic ray pixels
             flag_sources(sources, catalog.labels, deblended_seg_map, image.mask, flag=16, mask_value=8)
 

banzai/settings.py

@@ -80,7 +80,7 @@
                                   'elp': {'minute': 0, 'hour': 23},
                                   'ogg': {'minute': 0, 'hour': 3}}
 
-ASTROMETRY_SERVICE_URL = os.getenv('ASTROMETRY_SERVICE_URL', 'http://astrometry.lco.gtn/catalog/')
+ASTROMETRY_SERVICE_URL = os.getenv('ASTROMETRY_SERVICE_URL', ' ')
 
 CALIBRATION_FILENAME_FUNCTIONS = {'BIAS': ('banzai.utils.file_utils.config_to_filename',
                                            'banzai.utils.file_utils.ccdsum_to_filename'),

banzai/tests/test_end_to_end.py

@@ -124,7 +124,7 @@ def get_expected_number_of_calibrations(raw_filename_pattern, calibration_type):
             if site in frame['filename'] and instrument in frame['filename']
             and dayobs in frame['filename'] and raw_filename_pattern in frame['filename']
         ]
-        if 'calibration_type.lower()' == 'skyflat':
+        if calibration_type.lower() == 'skyflat':
             # Group by filter
             observed_filters = []
             for frame in raw_frames_for_this_dayobs:
@@ -244,7 +244,7 @@ def test_if_stacked_flat_frame_was_created(self):
 @pytest.mark.e2e
 @pytest.mark.science_files
 class TestScienceFileCreation:
-    @pytest.fixture(autouse=True)
+    @pytest.fixture(autouse=True, scope='class')
     @mock.patch('banzai.utils.observation_utils.requests.get', side_effect=observation_portal_side_effect)
     def reduce_science_frames(self, mock_observation_portal):
         run_reduce_individual_frames('e00.fits')
@@ -254,7 +254,7 @@ def test_if_science_frames_were_created(self):
         created_files = []
         for day_obs in DAYS_OBS:
             expected_files += [filename.replace('e00', 'e91')
-                               for filename in TEST_FRAMES['filename']]
+                               for filename in TEST_FRAMES['filename'] if 'e00.fits' in filename]
             created_files += [os.path.basename(filename) for filename in glob(os.path.join(DATA_ROOT, day_obs,
                                                                                            'processed', '*e91*'))]
         assert len(expected_files) > 0
@@ -266,6 +266,6 @@ def test_that_photometric_calibration_succeeded(self):
         for day_obs in DAYS_OBS:
             science_files += [filepath for filepath in glob(os.path.join(DATA_ROOT, day_obs,
                                                                          'processed', '*e91*'))]
-        zeropoints = [fits.open(file)['SCI'].header.get('L1ZP') for file in science_files]
+        zeropoints = [fits.open(filename)['SCI'].header.get('L1ZP') for filename in science_files]
         # check that at least one of our images contains a zeropoint
         assert zeropoints.count(None) != len(zeropoints)

pytest.ini

@@ -1,11 +1,11 @@
 [pytest]
-minversion = 3.5
-norecursedirs = build docs/_build
-doctest_plus = enabled
-addopts = -p no:warnings
+minversion = "3.5"
+norecursedirs = "build docs/_build"
+doctest_plus = "enabled"
+addopts = "-p no:warnings"
 log_cli = True
-log_level = info
-log_cli_level = info
+log_level = "info"
+log_cli_level = "info"
 markers =
     # E2E test markers
     e2e : End-to-end test suite