Update NIRISS WFSS regtest with in-flight data (#7012)

* Update NIRISS WFSS regtest with in-flight data

* fix flake8

(cherry picked from commit 58491d6)

jwst/regtest/test_niriss_wfss.py

@@ -2,79 +2,86 @@
 import pytest
 from astropy.io.fits.diff import FITSDiff
 
-from jwst.regtest import regtestdata as rt
+from jwst.stpipe import Step
 
 
 @pytest.fixture(scope='module')
 def run_nis_wfss_spec2(jail, rtdata_module):
-    """Run the calwebb_spec2 pipeline"""
-    step_params = {
-        'input_path': 'niriss/wfss/nir_wfss_spec2_asn.json',
-        'step': 'calwebb_spec2',
-        'args': [
+    """Run the calwebb_spec2 pipeline on NIRISS WFSS exposures"""
+    rtdata = rtdata_module
+
+    # These are the 4 WFSS exposures we'll be processing
+    spec2_asns = [
+        "niriss/wfss/jw01324-o001_20220629t171902_spec2_001_asn.json",
+        "niriss/wfss/jw01324-o001_20220629t171902_spec2_002_asn.json",
+        "niriss/wfss/jw01324-o001_20220629t171902_spec2_005_asn.json",
+        "niriss/wfss/jw01324-o001_20220629t171902_spec2_007_asn.json",
+    ]
+
+    # Only the first exposure will be used to do comparisons
+    rtdata.get_asn(spec2_asns[0])
+    args = ["calwebb_spec2", rtdata.input,
             '--steps.assign_wcs.save_results=true',
             '--steps.bkg_subtract.save_results=true',
-            '--steps.imprint_subtract.save_results=true',
-            '--steps.msa_flagging.save_results=true',
             '--steps.flat_field.save_results=true',
             '--steps.extract_2d.save_results=true',
             '--steps.srctype.save_results=true',
-            '--steps.straylight.save_results=true',
-            '--steps.fringe.save_results=true',
             '--steps.pathloss.save_results=true',
-            '--steps.barshadow.save_results=true',
-            '--steps.wfss_contam.save_results=true',
             '--steps.photom.save_results=true',
-            '--steps.resample_spec.save_results=true',
-            '--steps.cube_build.save_results=true',
             '--steps.extract_1d.save_results=true',
             '--save_wfss_esec=true',
-        ]
-    }
+            '--steps.extract_2d.wfss_nbright=10']
+    Step.from_cmdline(args)
 
-    return rt.run_step_from_dict(rtdata_module, **step_params)
+    # Run the remaining exposures without doing comparisons, just so that
+    # fresh results are available for level-3 processing
+    for asn in spec2_asns[1:]:
+        rtdata.get_asn(asn)
+        args = ["calwebb_spec2", rtdata.input,
+                "--steps.extract_2d.wfss_nbright=10"]
+        Step.from_cmdline(args)
 
 
 @pytest.mark.bigdata
 @pytest.mark.parametrize(
     'suffix',
     ['assign_wcs', 'bsub', 'cal', 'esec', 'extract_2d', 'flat_field', 'photom', 'srctype', 'x1d']
 )
-def test_nis_wfss_spec2(run_nis_wfss_spec2, fitsdiff_default_kwargs, suffix):
+def test_nis_wfss_spec2(run_nis_wfss_spec2, rtdata_module, fitsdiff_default_kwargs, suffix):
     """Regression test for calwebb_spec2 applied to NIRISS WFSS data"""
-    rt.is_like_truth(
-        run_nis_wfss_spec2, fitsdiff_default_kwargs, suffix, 'truth/test_niriss_wfss'
-    )
+    rtdata = rtdata_module
+    rtdata.input = "jw01324001001_03101_00001_nis_rate.fits"
+    output = "jw01324001001_03101_00001_nis_" + suffix + ".fits"
+    rtdata.output = output
+    rtdata.get_truth(f"truth/test_niriss_wfss/{output}")
+
+    diff = FITSDiff(rtdata.output, rtdata.truth, **fitsdiff_default_kwargs)
+    assert diff.identical, diff.report()
 
 
 @pytest.fixture(scope='module')
-def run_nis_wfss_spec3(jail, rtdata_module):
+def run_nis_wfss_spec3(run_nis_wfss_spec2, rtdata_module, jail):
     """Run the calwebb_spec3 pipeline"""
-    step_params = {
-        'input_path': 'niriss/wfss/jw00625-o030_20191121t041727_spec3_001_asn.json',
-        'step': 'calwebb_spec3',
-        'args': [
-            '--steps.extract_1d.save_results=true',
-            '--steps.combine_1d.save_results=true',
-        ]
-    }
+    rtdata = rtdata_module
 
-    return rt.run_step_from_dict(rtdata_module, **step_params)
+    # Get the level3 association file and run the spec3 pipeline on it.
+    # We don't need to retrieve any of the cal members of the association,
+    # because they were all just created by the preceding spec2 test.
+    rtdata.get_data("niriss/wfss/jw01324-o001_20220629t171902_spec3_003_asn.json")
+    args = ["calwebb_spec3", rtdata.input]
+    Step.from_cmdline(args)
 
 
 @pytest.mark.bigdata
 @pytest.mark.parametrize('suffix', ['cal', 'x1d', 'c1d'])
-@pytest.mark.parametrize('source_id', ['s00001', 's00002'])
-def test_nis_wfss_spec3(run_nis_wfss_spec3, suffix, source_id, fitsdiff_default_kwargs):
+@pytest.mark.parametrize('source_id', ['s00015', 's00104'])
+def test_nis_wfss_spec3(run_nis_wfss_spec3, rtdata_module, suffix, source_id, fitsdiff_default_kwargs):
     """Regression test of the calwebb_spec3 pipeline applied to NIRISS WFSS data"""
-
-    # Run the pipeline
-    rtdata = run_nis_wfss_spec3
-
-    # Get outputs and truths
-    output = "jw00625-o030_" + source_id + "_niriss_f090w-gr150c-gr150r_" + suffix + ".fits"
+    rtdata = rtdata_module
+    rtdata.input = "jw01324-o001_20220629t171902_spec3_003_asn.json"
+    output = "jw01324-o001_" + source_id + "_niriss_f115w-gr150c-gr150r_" + suffix + ".fits"
     rtdata.output = output
-    rtdata.get_truth("truth/test_niriss_wfss/" + output)
+    rtdata.get_truth(f"truth/test_niriss_wfss/{output}")
 
     # Compare the results
     fitsdiff_default_kwargs['atol'] = 1e-5