Merge branch 'master' into pip_list_after_override

CHANGES.rst

@@ -54,6 +54,8 @@ flat_field
 
 - Refactored NIRSpec 1D flat interpolation for improved performance. [#7550]
 
+- Added log messages for reporting flat reference file(s) used. [#7592]
+
 cube_build
 ----------
 
@@ -71,6 +73,8 @@ other
 
 - Override package dependencies with requirements file when requested [#7557]
 
+- Close files left open in test suite [#7599]
+
 pathloss
 --------
 

jwst/assign_wcs/nirspec.py

@@ -674,6 +674,7 @@ def get_open_msa_slits(msa_file, msa_metadata_id, dither_position,
             log.warning(message)
             message = ("MSA configuration file has more than 1 shutter with primary source")
             log.warning(message)
+            msa_file.close()
             raise MSAFileError(message)
 
         # subtract 1 because shutter numbers in the MSA reference file are 1-based.

jwst/assign_wcs/tests/test_nirspec.py

@@ -166,17 +166,17 @@ def test_nirspec_ifu_against_esa(wcs_ifu_grating):
     """
     Test Nirspec IFU mode using CV3 reference files.
     """
-    ref = fits.open(get_file_path('Trace_IFU_Slice_00_SMOS-MOD-G1M-17-5344175105_30192_JLAB88.fits'))
+    with fits.open(get_file_path('Trace_IFU_Slice_00_SMOS-MOD-G1M-17-5344175105_30192_JLAB88.fits')) as ref:
+        # Test NRS1
+        pyw = astwcs.WCS(ref['SLITY1'].header)
+        # Test evaluating the WCS (slice 0)
+        im, refs = wcs_ifu_grating("G140M", "OPAQUE")
+        w0 = nirspec.nrs_wcs_set_input(im, 0)
 
-    # Test NRS1
-    pyw = astwcs.WCS(ref['SLITY1'].header)
-    # Test evaluating the WCS (slice 0)
-    im, refs = wcs_ifu_grating("G140M", "OPAQUE")
-    w0 = nirspec.nrs_wcs_set_input(im, 0)
+        # get positions within the slit and the corresponding lambda
+        slit1 = ref['SLITY1'].data  # y offset on the slit
+        lam = ref['LAMBDA1'].data
 
-    # get positions within the slit and the corresponding lambda
-    slit1 = ref['SLITY1'].data  # y offset on the slit
-    lam = ref['LAMBDA1'].data
     # filter out locations outside the slit
     cond = np.logical_and(slit1 < .5, slit1 > -.5)
     y, x = cond.nonzero()  # 0-based

jwst/associations/tests/test_mkpool.py

@@ -22,10 +22,10 @@
 
 
 def test_hdu(exposures):
-    hdus = [
-        fits.open(exposure)[0]
-        for exposure in exposures
-    ]
+    hdus = []
+    for exposure in exposures:
+        with fits.open(exposure) as hdulist:
+            hdus.append(hdulist[0])
     pool = mkpool(hdus)
     assert isinstance(pool, AssociationPool)
     assert REQUIRED_PARAMS.issubset(pool.colnames)
@@ -41,6 +41,7 @@ def test_hdulist(exposures):
     assert isinstance(pool, AssociationPool)
     assert REQUIRED_PARAMS.issubset(pool.colnames)
     assert len(pool) == len(exposures)
+    [h.close() for h in hduls]
 
 
 def test_mkpool(exposures):

jwst/flatfield/flat_field_step.py

@@ -104,9 +104,9 @@ def process(self, input):
 
             # Record the user-supplied flat as the FLAT reference type for recording
             # in the result header.
-            self._reference_files_used.append(
-                ('flat', reference_file_models['user_supplied_flat'].meta.filename)
-            )
+            flat_ref_file = reference_file_models['user_supplied_flat'].meta.filename
+            self._reference_files_used.append(('flat', flat_ref_file))
+            self.log.info('Using flat field reference file: ', flat_ref_file)
         elif self.use_correction_pars:
             self.log.info(f'Using flat field from correction pars {self.correction_pars["flat"]}')
             reference_file_models = {
@@ -197,9 +197,9 @@ def _get_references(self, data, exposure_type):
         for reftype, reffile in reference_file_names.items():
             if reffile is not None:
                 reference_file_models[reftype] = model_type[reftype](reffile)
-                self.log.debug('Using %s reference file: %s', reftype.upper(), reffile)
+                self.log.info('Using %s reference file: %s', reftype.upper(), reffile)
             else:
-                self.log.debug('No reference found for type %s', reftype.upper())
+                self.log.info('No reference found for type %s', reftype.upper())
                 reference_file_models[reftype] = None
 
         return reference_file_models

jwst/outlier_detection/tests/test_outlier_detection.py

@@ -251,6 +251,9 @@ def test_outlier_step_square_source_no_outliers(we_three_sci, _jail):
         np.testing.assert_allclose(image.data, corrected.data)
         np.testing.assert_allclose(image.dq, corrected.dq)
 
+    container.close()
+    pristine.close()
+
 
 @pytest.mark.parametrize("exptype", IMAGE_MODES)
 def test_outlier_step_image_weak_CR_dither(exptype, _jail):

jwst/residual_fringe/tests/test_background_fit.py

@@ -19,14 +19,14 @@ def read_fit_column(file):
     file_dir = Path(__file__).parent.resolve()
     file_path = str(file_dir / file)
 
-    hdu = fits.open(file_path)
-    col_data = hdu[1].data
-    col_weight = hdu[2].data
-    col_wnum = hdu[3].data
-    bg_fit = hdu[4].data
-    store_freq = hdu[0].header['FFREQ']
-
-    return col_data, col_weight, col_wnum, bg_fit, store_freq
+    with fits.open(file_path) as hdu:
+        col_data = hdu[1].data
+        col_weight = hdu[2].data
+        col_wnum = hdu[3].data
+        bg_fit = hdu[4].data
+        store_freq = hdu[0].header['FFREQ']
+
+        return col_data, col_weight, col_wnum, bg_fit, store_freq
 
 
 @pytest.mark.parametrize("file", ['good_col.fits', 'edge_col.fits'])