try fixing paths again

src/aspired/spectrum_oneD.py

@@ -5447,6 +5447,7 @@ def save_fits(
         overwrite=False,
         recreate=True,
         empty_primary_hdu=True,
+        create_folder=False,
     ):
         """
         Save the reduced data to disk, with a choice of any combination of the
@@ -5522,19 +5523,41 @@ def save_fits(
             Set to True to overwrite the FITS data and header.
         empty_primary_hdu: boolean (Default: True)
             Set to True to leave the Primary HDU blank (Default: True)
+        create_folder: boolean (Default: False)
+            Create folder if not exist. Use with caution.
 
         """
 
         self.create_fits(
             output, recreate=recreate, empty_primary_hdu=empty_primary_hdu
         )
 
+        # create the director if not exist
+        if create_folder:
+            if not os.path.exists(os.path.dirname(filename)):
+                os.makedirs(os.path.dirname(filename))
+
         # Save file to disk
-        self.hdu_output.writeto(
-            filename + ".fits", overwrite=overwrite, output_verify="fix+ignore"
-        )
+        if os.path.splitext(filename)[-1].lower() in [".fits", ".fit", ".fts"]:
+            self.hdu_output.writeto(
+                filename, overwrite=overwrite, output_verify="fix+ignore"
+            )
 
-    def save_csv(self, output, filename, overwrite, recreate):
+        else:
+            self.hdu_output.writeto(
+                filename + ".fits",
+                overwrite=overwrite,
+                output_verify="fix+ignore",
+            )
+
+    def save_csv(
+        self,
+        output,
+        filename,
+        overwrite=False,
+        recreate=True,
+        create_folder=False,
+    ):
         """
         Save the reduced data to disk, with a choice of any combination of the
         5 sets of data, see below the 'output' parameters for details.
@@ -5607,11 +5630,18 @@ def save_csv(self, output, filename, overwrite, recreate):
             Default is False.
         recreate: boolean (Default: False)
             Set to True to overwrite the FITS data and header.
+        create_folder: boolean (Default: False)
+            Create folder if not exist. Use with caution.
 
         """
 
         self.create_fits(output, recreate=recreate, empty_primary_hdu=False)
 
+        # create the director if not exist
+        if create_folder:
+            if not os.path.exists(os.path.dirname(filename)):
+                os.makedirs(os.path.dirname(filename))
+
         output_split = output.split("+")
 
         start = 0

test/test_onedspec.py

@@ -443,7 +443,7 @@ def test_add_wavelength_science_two_spec():
 
 @pytest.mark.xfail(raises=ValueError)
 # science add_wavelengthcalibration to two traces
-def test_add_wavelength_science_expect_fail():
+def test_add_wavelength_science_expect_fail_wrong_specid():
     onedspec = spectral_reduction.OneDSpec(
         log_file_name=None, log_level="ERROR"
     )
@@ -453,11 +453,10 @@ def test_add_wavelength_science_expect_fail():
 
 @pytest.mark.xfail(raises=ValueError)
 # science add_wavelengthcalibration to two traces
-def test_add_wavelength_science_expect_fail():
+def test_add_wavelength_science_expect_fail_wrong_shape():
     onedspec = spectral_reduction.OneDSpec(
         log_file_name=None, log_level="ERROR"
     )
-
     onedspec.add_spec(np.arange(100), spec_id=0, stype="science+standard")
     onedspec.add_wavelength(
         [np.arange(100), np.arange(200)], spec_id=[0], stype="science+standard"
@@ -901,7 +900,7 @@ def test_add_fit_coeff_science_fail_type():
 
 
 @pytest.mark.xfail(raises=ValueError)
-def test_add_fit_coeff_science_fail_type():
+def test_add_fit_coeff_science_fail_wrong_shape():
     onedspec = spectral_reduction.OneDSpec(
         log_file_name=None, log_level="ERROR"
     )

test/test_twodspec.py

@@ -16,9 +16,7 @@
 HERE = os.path.dirname(os.path.realpath(__file__))
 
 img = image_reduction.ImageReduction(log_file_name=None)
-img.add_filelist(
-    filelist=os.path.join(HERE, "test_data", "sprat_LHS6328.list")
-)
+img.add_filelist(filelist=os.path.join(HERE, "test_data", "sprat_LHS6328.list"))
 img.load_data()
 img.reduce()
 
@@ -458,7 +456,7 @@ def test_add_arc_hdulist():
     assert twodspec.arc_header == arc_fits.header
 
 
-def test_add_arc_hdulist():
+def test_add_arc_CCDData():
     twodspec = spectral_reduction.TwoDSpec(log_file_name=None)
     twodspec.add_arc(arc_in_CCDData)
     assert (twodspec.arc == arc_fits.data).all()