Ensure directories are ignored when using multiple morphs/targets

Author: Sparks29032

news/bugfix.rst

@@ -0,0 +1,24 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* Swap colors for morph and target. Morph is now blue and target red.
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* Multiple morphs/targets used to break given multiple subdirectories.
+* Fixed the Rw calculation. Previously returned an analogue to chi square.
+
+**Security:**
+
+* <news item>

src/diffpy/morph/morphapp.py

@@ -588,14 +588,14 @@ def single_morph(parser, opts, pargs, stdout_flag=True):
         parser.custom_error(save_fail_message)
 
     if opts.plot:
-        pairlist = [chain.xy_morph_out, chain.xy_target_out]
-        labels = [pargs[0], pargs[1]]  # Default is to use file names
+        pairlist = [chain.xy_target_out, chain.xy_morph_out]
+        labels = [pargs[1], pargs[0]]  # Default is to use file names
 
         # If user chooses labels
         if opts.mlabel is not None:
-            labels[0] = opts.mlabel
+            labels[1] = opts.mlabel
         if opts.tlabel is not None:
-            labels[1] = opts.tlabel
+            labels[0] = opts.tlabel
 
         # Plot extent defaults to calculation extent
         pmin = opts.pmin if opts.pmin is not None else opts.rmin
@@ -644,9 +644,12 @@ def multiple_targets(parser, opts, pargs, stdout_flag=True):
 
     # Get list of files from target directory
     target_list = list(target_directory.iterdir())
+    to_remove = []
     for target in target_list:
         if target.is_dir():
-            target_list.remove(target)
+            to_remove.append(target)
+    for target in to_remove:
+        target_list.remove(target)
 
     # Do not morph morph_file against itself if it is in the same directory
     if morph_file in target_list:
@@ -828,9 +831,12 @@ def multiple_morphs(parser, opts, pargs, stdout_flag=True):
 
     # Get list of files from morph directory
     morph_list = list(morph_directory.iterdir())
+    to_remove = []
     for morph in morph_list:
         if morph.is_dir():
-            morph_list.remove(morph)
+            to_remove.append(morph)
+    for morph in to_remove:
+        morph_list.remove(morph)
 
     # Do not morph target_file against itself if it is in the same directory
     if target_file in morph_list:

tests/test_morphapp.py

@@ -18,7 +18,7 @@
 nickel_PDF = testdata_dir.joinpath("nickel_ss0.01.cgr")
 serial_JSON = testdata_dir.joinpath("testsequence_serialfile.json")
 
-testsaving_dir = testdata_dir.joinpath("testsaving")
+testsaving_dir = testsequence_dir.joinpath("testsaving")
 test_saving_succinct = testsaving_dir.joinpath("succinct")
 test_saving_verbose = testsaving_dir.joinpath("verbose")
 tssf = testdata_dir.joinpath("testsequence_serialfile.json")

tests/test_morphio.py

@@ -21,7 +21,7 @@
 testdata_dir = tests_dir.joinpath("testdata")
 testsequence_dir = testdata_dir.joinpath("testsequence")
 
-testsaving_dir = testdata_dir.joinpath("testsaving")
+testsaving_dir = testsequence_dir.joinpath("testsaving")
 test_saving_succinct = testsaving_dir.joinpath("succinct")
 test_saving_verbose = testsaving_dir.joinpath("verbose")
 tssf = testdata_dir.joinpath("testsequence_serialfile.json")

tests/test_tools.py

@@ -60,10 +60,16 @@ def test_nn_value(self, setup):
             pytest.approx(tools.nn_value(-value, name=None), abs(-value))
 
     def test_field_sort(self, setup):
-        sequence_files = [*os.listdir(testsequence_dir)]
+        sequence_files = [file for file in Path(testsequence_dir).iterdir()]
+        to_remove = []
+        for file in sequence_files:
+            if file.is_dir():
+                to_remove.append(file)
+        for d in to_remove:
+            sequence_files.remove(d)
         absolute_sf = []
         for file in sequence_files:
-            absolute_sf.append(os.path.join(testsequence_dir, file))
+            absolute_sf.append(Path(testsequence_dir) / file.name)
 
         # Fisher-Yates randomization
         import random
@@ -87,8 +93,8 @@ def test_field_sort(self, setup):
 
         # Temperature sort should produce same result as alphanumerical if
         # leading character is removed
-        sequence_files.sort(key=lambda entry: entry[2:])
-        assert sequence_files == sorted_sequence
+        sequence_files.sort(key=lambda entry: entry.name[2:])
+        assert [file.name for file in sequence_files] == sorted_sequence
 
         # Check temperatures are correct
         assert fvs == [174, 180, 186, 192, 198, 204, 210]
@@ -103,7 +109,7 @@ def test_field_sort(self, setup):
 
         # Reversed sort should match alphanumerical sort
         sequence_files.sort()
-        assert sequence_files == reversed_sequence
+        assert [file.name for file in sequence_files] == reversed_sequence
 
         # Check we get the same sequence when we load header information from
         # a serial file
@@ -116,7 +122,7 @@ def test_field_sort(self, setup):
         metadata_sequence = []
         for path in metadata_path_sequence:
             metadata_sequence.append(path.name)
-        assert sequence_files == metadata_sequence
+        assert [file.name for file in sequence_files] == metadata_sequence
 
         # Check error thrown when field does not exist
         with pytest.raises(KeyError):