[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

romancal/assign_wcs/assign_wcs_step.py

@@ -39,12 +39,14 @@ def process(self, input):
                     result = input_model
                     result.meta.cal_step.assign_wcs = "SKIPPED"
                     return result
-                
+
                 reference_file_names[reftype] = reffile if reffile else ""
             log.info("Using reference files: %s for assign_wcs", reference_file_names)
-            #result = load_wcs(input_model, reference_file_names)
-                # Frames
-            detector = cf.Frame2D(name="detector", axes_order=(0, 1), unit=(u.pix, u.pix))
+            # result = load_wcs(input_model, reference_file_names)
+            # Frames
+            detector = cf.Frame2D(
+                name="detector", axes_order=(0, 1), unit=(u.pix, u.pix)
+            )
             v2v3 = cf.Frame2D(
                 name="v2v3",
                 axes_order=(0, 1),
@@ -74,7 +76,6 @@ def process(self, input):
 
         output_model.meta.cal_step["assign_wcs"] = "COMPLETE"
 
-
         if self.save_results:
             try:
                 self.suffix = "assignwcs"

romancal/assign_wcs/tests/test_wcs.py

@@ -1,5 +1,3 @@
-import os
-
 import numpy as np
 import pytest
 from gwcs.wcstools import grid_from_bounding_box
@@ -95,7 +93,6 @@ def test_wcs(tmpdir, distortion, step):
 @pytest.mark.parametrize("step", create_step())
 def test_crds_getbestref(step):
     l2im = create_image()
-    l2_wcs = AssignWcsStep.call(l2im, override_distortion='N/A')
+    l2_wcs = AssignWcsStep.call(l2im, override_distortion="N/A")
 
-    assert l2_wcs.meta.cal_step.assign_wcs == 'SKIPPED'
-
+    assert l2_wcs.meta.cal_step.assign_wcs == "SKIPPED"

romancal/dark_current/dark_current_step.py

@@ -25,11 +25,11 @@ def process(self, input):
             # Get the name of the dark reference file to use
             self.dark_name = self.get_reference_file(input_model, "dark")
             # Check for a valid reference file
-            if self.dark_name == 'N/A':
-                self.log.warning('No DARK reference file found')
-                self.log.warning('Dark current step will be skipped')
+            if self.dark_name == "N/A":
+                self.log.warning("No DARK reference file found")
+                self.log.warning("Dark current step will be skipped")
                 result = input_model
-                result.meta.cal_step.dark = 'SKIPPED'
+                result.meta.cal_step.dark = "SKIPPED"
                 return result
 
             self.log.info("Using DARK reference file: %s", self.dark_name)

romancal/dark_current/tests/test_dark.py

@@ -2,7 +2,6 @@
 Unit tests for dark current correction
 """
 
-import os
 
 import numpy as np
 import pytest
@@ -107,6 +106,7 @@ def test_dark_step_output_dark_file(tmpdir, instrument, exptype):
     assert dark_out_file_model.data.shape == shape
     assert dark_out_file_model.dq.shape == shape[1:]
 
+
 @pytest.mark.parametrize(
     "instrument, exptype",
     [
@@ -124,9 +124,8 @@ def test_dark_step_getbestrefs(tmpdir, instrument, exptype):
     ramp_model, darkref_model = create_ramp_and_dark(shape, instrument, exptype)
 
     # Perform Dark Current subtraction step with override = N/A
-    result = DarkCurrentStep.call(ramp_model, override_dark='N/A')
-    assert result.meta.cal_step.dark == 'SKIPPED'
-
+    result = DarkCurrentStep.call(ramp_model, override_dark="N/A")
+    assert result.meta.cal_step.dark == "SKIPPED"
 
     # Perform Dark Current subtraction step
     DarkCurrentStep.call(ramp_model, override_dark=darkref_model, dark_output=path)

romancal/dq_init/dq_init_step.py

@@ -80,7 +80,7 @@ def process(self, input):
         reference_file_name = self.get_reference_file(output_model, "mask")
 
         # Test for reference file
-        if reference_file_name != 'N/A' and reference_file_name is not None:
+        if reference_file_name != "N/A" and reference_file_name is not None:
             # If there are mask files, perform dq step
             # Open the relevant reference files as datamodels
             reference_file_model = rdm.open(reference_file_name)

romancal/dq_init/tests/test_dq_init.py

@@ -1,5 +1,3 @@
-import os
-
 import numpy as np
 import pytest
 from astropy import units as u
@@ -240,7 +238,6 @@ def test_dqinit_step_interface(instrument, exptype):
         ("WFI", "WFI_IMAGE"),
     ],
 )
-
 def test_dqinit_refpix(instrument, exptype):
     """Test that the basic inferface works for data requiring a DQ reffile"""
 
@@ -292,7 +289,7 @@ def test_dqinit_refpix(instrument, exptype):
     [
         ("WFI", "WFI_IMAGE"),
     ],
-)    
+)
 def test_dqinit_getbestref(instrument, exptype):
     """Test that the step is skipped if the CRDS reffile is N/A"""
 
@@ -313,5 +310,5 @@ def test_dqinit_getbestref(instrument, exptype):
     wfi_sci_raw_model = ScienceRawModel(wfi_sci_raw)
 
     # Perform Data Quality application step
-    result = DQInitStep.call(wfi_sci_raw_model, override_mask='N/A')
-    assert result.meta.cal_step.dq_init == 'SKIPPED'
+    result = DQInitStep.call(wfi_sci_raw_model, override_mask="N/A")
+    assert result.meta.cal_step.dq_init == "SKIPPED"

romancal/flatfield/tests/test_flatfield.py

@@ -1,5 +1,3 @@
-import os
-
 import numpy as np
 import pytest
 from astropy import units as u
@@ -62,13 +60,12 @@ def test_flatfield_step_interface(instrument, exptype):
     assert result.var_flat.shape == shape
     assert result.meta.cal_step.flat_field == "COMPLETE"
 
-
     # test that the step is skipped if the reference file is N/A
-    result = FlatFieldStep.call(wfi_image_model, override_flat='N/A')
+    result = FlatFieldStep.call(wfi_image_model, override_flat="N/A")
+
+    assert result.meta.cal_step.flat_field == "SKIPPED"
 
-    assert result.meta.cal_step.flat_field == 'SKIPPED'
 
-
 @pytest.mark.parametrize(
     "instrument, exptype",
     [

romancal/jump/tests/test_jump_step.py

@@ -1,7 +1,6 @@
 """
  Unit tests for the Roman jump step code
 """
-import os
 from itertools import cycle
 
 import numpy as np

romancal/linearity/tests/test_linearity.py

@@ -7,10 +7,10 @@
 import pytest
 from astropy import units as u
 from roman_datamodels import maker_utils
-from roman_datamodels.datamodels import ScienceRawModel, LinearityRefModel
+from roman_datamodels.datamodels import LinearityRefModel, ScienceRawModel
 
-from romancal.lib import dqflags
 from romancal.dq_init import DQInitStep
+from romancal.lib import dqflags
 from romancal.linearity import LinearityStep
 
 
@@ -40,39 +40,36 @@ def test_linearity_coeff(instrument, exptype):
     wfi_sci_raw_model = ScienceRawModel(wfi_sci_raw)
 
     result = DQInitStep.call(wfi_sci_raw_model)
-    result = LinearityStep.call(result, override_linearity='N/A')
+    result = LinearityStep.call(result, override_linearity="N/A")
 
-    assert result.meta.cal_step.linearity == 'SKIPPED'
+    assert result.meta.cal_step.linearity == "SKIPPED"
 
     # Set coefficient values in reference file to check the algorithm
     # Equation is DNcorr = L0 + L1*DN(i) + L2*DN(i)^2 + L3*DN(i)^3 + L4*DN(i)^4
     # DN(i) = signal in pixel, Ln = coefficient from ref file
     # L0 = 0 for all pixels for CDP6
 
     coeffs = np.zeros(shape, dtype=np.float32)
-    coeffs[1,:,:].fill(0.85)
-    coeffs[2,:,:].fill(4.62e-06)
-    coeffs[3,:,:].fill(-6.16e-11)
-    coeffs[4,:,:].fill(7.23e-16)
-    #coeffs = np.tile(coeffs,(5,20,4))
+    coeffs[1, :, :].fill(0.85)
+    coeffs[2, :, :].fill(4.62e-06)
+    coeffs[3, :, :].fill(-6.16e-11)
+    coeffs[4, :, :].fill(7.23e-16)
+    # coeffs = np.tile(coeffs,(5,20,4))
     # set one set of coeffs to 0 to check that the data values are not altered.
     # and that the DQ flag is set to NO_LIN_CORR
-    coeffs[0:,5,5] = 0.0
+    coeffs[0:, 5, 5] = 0.0
     # set one of the coeffs to NaN and check that the DQ flag is set to NO_LIN_CORR
-    coeffs[0:,6,5] = np.nan
+    coeffs[0:, 6, 5] = np.nan
     # save the pixel values to make sure they are not altered
-    pixels_55 = result.data[0:,5,5]
-    pixels_65 = result.data[0:,6,5]
-    linref = maker_utils.mk_linearity(shape=shape,coeffs=coeffs)
+    pixels_55 = result.data[0:, 5, 5]
+    pixels_65 = result.data[0:, 6, 5]
+    linref = maker_utils.mk_linearity(shape=shape, coeffs=coeffs)
     linref_model = LinearityRefModel(linref)
 
     LinearityStep.call(result, override_linearity=linref_model)
 
-    assert result.meta.cal_step.linearity == 'COMPLETE'
-    assert result.pixeldq[5,5] == dqflags.pixel["NO_LIN_CORR"]
-    assert result.pixeldq[6,5] == dqflags.pixel["NO_LIN_CORR"]
-    np.testing.assert_array_equal(result.data[0:,5,5],pixels_55)
-    np.testing.assert_array_equal(result.data[0:,6,5],pixels_65)
-
-
-
+    assert result.meta.cal_step.linearity == "COMPLETE"
+    assert result.pixeldq[5, 5] == dqflags.pixel["NO_LIN_CORR"]
+    assert result.pixeldq[6, 5] == dqflags.pixel["NO_LIN_CORR"]
+    np.testing.assert_array_equal(result.data[0:, 5, 5], pixels_55)
+    np.testing.assert_array_equal(result.data[0:, 6, 5], pixels_65)

romancal/outlier_detection/tests/test_outlier_detection.py

@@ -1,5 +1,3 @@
-import os
-
 import pytest
 from astropy import units as u
 from roman_datamodels import maker_utils

romancal/photom/photom_step.py

@@ -36,7 +36,7 @@ def process(self, input):
             reffile = self.get_reference_file(input_model, "photom")
 
             # Open the relevant photom reference file as a datamodel
-            if reffile is not None and reffile != 'N/A':
+            if reffile is not None and reffile != "N/A":
                 # If there is a reference file, perform photom application
                 photom_model = rdm.open(reffile)
                 self.log.debug(f"Using PHOTOM ref file: {reffile}")

romancal/photom/tests/test_photom.py

@@ -1,4 +1,3 @@
-import os
 import warnings
 
 import numpy as np
@@ -260,11 +259,12 @@ def test_photom_step_interface(instrument, exptype):
     else:
         assert result.meta.cal_step.photom == "SKIPPED"
 
-   # Run photom correction step with reffile as N/A
-    result = PhotomStep.call(wfi_image_model, override_photom='N/A')
+    # Run photom correction step with reffile as N/A
+    result = PhotomStep.call(wfi_image_model, override_photom="N/A")
+
+    assert result.meta.cal_step.photom == "SKIPPED"
+
 
-    assert result.meta.cal_step.photom == 'SKIPPED'
-
 @pytest.mark.parametrize(
     "instrument, exptype",
     [

romancal/ramp_fitting/tests/test_ramp_fit_cas22.py

@@ -1,5 +1,4 @@
 """Ramp Fitting tests involving MultiAccum Tables"""
-import os
 
 import numpy as np
 import pytest

romancal/ramp_fitting/tests/test_ramp_fit_ols.py

@@ -1,5 +1,3 @@
-import os
-
 import numpy as np
 import pytest
 from astropy import units as u

romancal/refpix/refpix_step.py

@@ -42,15 +42,14 @@ def process(self, input):
         # Get the reference file
         ref_file = self.get_reference_file(datamodel, "refpix")
 
-       # Check for a valid reference file
+        # Check for a valid reference file
         if ref_file == "N/A":
             self.log.warning("No REFPIX reference file found")
             self.log.warning("Reference pixel correction step will be skipped")
             result = datamodel
             result.meta.cal_step.refpix = "SKIPPED"
             return result
 
-
         log.debug(f"Opening the reference file: {ref_file}")
         with rdm.open(ref_file) as refs:
             # Run the correction

romancal/refpix/tests/test_step.py

@@ -1,5 +1,3 @@
-import os
-
 import pytest
 
 from romancal.refpix import RefPixStep
@@ -60,15 +58,14 @@ def test_refpix_step(
         result.border_ref_pix_right.value == regression.border_ref_pix_right.value
     ).all()
     assert result.border_ref_pix_right.unit == regression.border_ref_pix_right.unit
-#
+    #
     # Run the step with reffile = N/A
     result = RefPixStep.call(
         datamodel,
-        override_refpix='N/A',
+        override_refpix="N/A",
         remove_offset=remove_offset,
         remove_trends=remove_trends,
         cosine_interpolate=cosine_interpolate,
         fft_interpolate=fft_interpolate,
     )
-    assert result.meta.cal_step.refpix == 'SKIPPED'
-
+    assert result.meta.cal_step.refpix == "SKIPPED"

romancal/saturation/saturation_step.py

@@ -31,7 +31,7 @@ def process(self, input):
                 return result
 
             # Open the reference file data model
-        # Test for reference file
+            # Test for reference file
             self.log.info("Using SATURATION reference file: %s", self.ref_name)
             ref_model = SaturationRefModel(self.ref_name)
 

romancal/saturation/tests/test_saturation.py

@@ -11,8 +11,9 @@
 from roman_datamodels.datamodels import ScienceRawModel
 
 from romancal.lib import dqflags
-from romancal.saturation.saturation import flag_saturation
 from romancal.saturation import SaturationStep
+from romancal.saturation.saturation import flag_saturation
+
 
 def test_basic_saturation_flagging(setup_wfi_datamodels):
     """Check that the saturation flag is set when a pixel value is above the
@@ -316,29 +317,30 @@ def test_nans_in_mask(setup_wfi_datamodels):
     # Check that output PIXELDQ is set to NO_SAT_CHECK
     assert output.pixeldq[5, 5] == dqflags.pixel["NO_SAT_CHECK"]
 
+
 def test_saturation_getbestref(setup_wfi_datamodels):
     """Check that when CRDS returns N/A for the reference file the
     step is skipped"""
 
-     # Set test size
+    # Set test size
     shape = (2, 20, 20)
 
     # Create test science raw model
     wfi_sci_raw = maker_utils.mk_level1_science_raw(shape=shape)
-    wfi_sci_raw.meta.instrument.name = 'WFI'
+    wfi_sci_raw.meta.instrument.name = "WFI"
     wfi_sci_raw.meta.instrument.detector = "WFI01"
     wfi_sci_raw.meta.instrument.optical_element = "F158"
     wfi_sci_raw.meta["guidestar"]["gw_window_xstart"] = 1012
     wfi_sci_raw.meta["guidestar"]["gw_window_xsize"] = 16
-    wfi_sci_raw.meta.exposure.type = 'WFI_IMAGE'
+    wfi_sci_raw.meta.exposure.type = "WFI_IMAGE"
     wfi_sci_raw.data = u.Quantity(
         np.ones(shape, dtype=np.uint16), u.DN, dtype=np.uint16
     )
     wfi_sci_raw_model = ScienceRawModel(wfi_sci_raw, dq=True)
-    
+
     # Run the pipeline
-    result = SaturationStep.call(wfi_sci_raw_model, override_saturation='N/A')
-    assert result.meta.cal_step.saturation == 'SKIPPED'
+    result = SaturationStep.call(wfi_sci_raw_model, override_saturation="N/A")
+    assert result.meta.cal_step.saturation == "SKIPPED"
 
 
 @pytest.fixture(scope="function")

romancal/stpipe/tests/test_core.py

@@ -1,5 +1,3 @@
-import os
-
 import asdf
 import pytest
 from astropy.time import Time