Add informative error message if no defects parsed, and test

doped/analysis.py

@@ -711,6 +711,9 @@ def __init__(
                     f"files are present and/or specify `bulk_path` manually."
                 )
 
+        # remove trailing '/.' from bulk_path if present:
+        self.bulk_path = self.bulk_path.rstrip("/.")
+
         self.defect_dict = {}
         self.bulk_corrections_data = {  # so we only load and parse bulk data once
             "bulk_locpot_dict": None,
@@ -912,6 +915,15 @@ def _mention_bulk_path_subfolder_for_correction_warnings(warning: str) -> str:
                 if defect_list:
                     warnings.warn(f"Defects: {defect_list} each encountered the same warning:\n{warning}")
 
+        if not parsed_defect_entries:
+            subfolder_string = f" and `subfolder`: '{self.subfolder}'" if self.subfolder != "." else ""
+            raise ValueError(
+                f"No defect calculations in `output_path` '{self.output_path}' were successfully parsed, "
+                f"using `bulk_path`: {self.bulk_path}{subfolder_string}. Please check the correct "
+                f"defect/bulk paths and subfolder are being set, and that the folder structure is as "
+                f"expected (see `DefectsParser` docstring)."
+            )
+
         # get any defect entries in parsed_defect_entries that share the same name (without charge):
         # first get any entries with duplicate names:
         entries_to_rename = [  # TODO: Add test for this:

doped/utils/plotting.py

@@ -727,7 +727,7 @@ def _get_formation_energy_lines(defect_thermodynamics, dft_chempots, xlim):
 
 
 def _get_ylim_from_y_range_vals(y_range_vals, ymin=0, auto_labels=False):
-    window = max(y_range_vals) - min(y_range_vals)
+    window = max(y_range_vals) - min(*y_range_vals, ymin)
     spacer = 0.1 * window
     ylim = (ymin, max(y_range_vals) + spacer)
     if auto_labels:  # need to manually set xlim or ylim if labels cross axes!!

tests/test_analysis.py

@@ -442,7 +442,26 @@ def test_DefectsParser_corrections_errors_warning(self):
         style=f"{module_path}/../doped/utils/doped.mplstyle",
         savefig_kwargs={"transparent": True, "bbox_inches": "tight"},
     )
-    def test_DefectsParser_YTOS(self):
+    def test_DefectsParser_YTOS_default_bulk(self):
+        # bulk path needs to be specified for YTOS as it's not the default name:
+        dp = DefectsParser(
+            output_path=self.YTOS_EXAMPLE_DIR,
+            dielectric=self.ytos_dielectric,
+        )
+        self._check_DefectsParser(dp)
+        thermo = dp.get_defect_thermodynamics()
+        dumpfn(
+            thermo, os.path.join(self.YTOS_EXAMPLE_DIR, "YTOS_example_thermo.json")
+        )  # for test_plotting
+        return thermo.plot()  # no chempots for YTOS formation energy plot test
+
+    @pytest.mark.mpl_image_compare(
+        baseline_dir=f"{data_dir}/remote_baseline_plots",
+        filename="YTOS_example_defects_plot.png",
+        style=f"{module_path}/../doped/utils/doped.mplstyle",
+        savefig_kwargs={"transparent": True, "bbox_inches": "tight"},
+    )
+    def test_DefectsParser_YTOS_explicit_bulk(self):
         # bulk path needs to be specified for YTOS as it's not the default name:
         dp = DefectsParser(
             output_path=self.YTOS_EXAMPLE_DIR,
@@ -456,6 +475,16 @@ def test_DefectsParser_YTOS(self):
         )  # for test_plotting
         return thermo.plot()  # no chempots for YTOS formation energy plot test
 
+    def test_DefectsParser_no_defects_parsed_error(self):
+        with self.assertRaises(ValueError) as exc:
+            DefectsParser(output_path=self.YTOS_EXAMPLE_DIR, subfolder="vasp_gam")
+        assert (
+            f"No defect calculations in `output_path` '{self.YTOS_EXAMPLE_DIR}' were successfully parsed, "
+            f"using `bulk_path`: {self.YTOS_EXAMPLE_DIR}/Bulk and `subfolder`: 'vasp_gam'. Please check "
+            f"the correct defect/bulk paths and subfolder are being set, and that the folder structure is "
+            f"as expected (see `DefectsParser` docstring)." in str(exc.exception)
+        )
+
     @pytest.mark.mpl_image_compare(
         baseline_dir=f"{data_dir}/remote_baseline_plots",
         filename="O_Se_example_defects_plot.png",

tests/test_generation.py

@@ -983,11 +983,11 @@ def _check_editing_defect_gen(self, random_defect_entry_name, defect_gen):
     def _generate_and_test_no_warnings(self, structure, min_image_distance=None, **kwargs):
         original_stdout = sys.stdout  # Save a reference to the original standard output
         sys.stdout = StringIO()  # Redirect standard output to a stringIO object.
+        w = None
         try:
             with warnings.catch_warnings(record=True) as w:
                 warnings.resetwarnings()
                 defect_gen = DefectsGenerator(structure, **kwargs)
-                print([str(warning.message) for warning in w])  # for debugging
                 if min_image_distance is None:
                     assert not w
                 else:
@@ -1003,6 +1003,9 @@ def _generate_and_test_no_warnings(self, structure, min_image_distance=None, **k
         finally:
             sys.stdout = original_stdout  # Reset standard output to its original value.
 
+        if w:
+            print([str(warning.message) for warning in w])  # for debugging
+
         return defect_gen, output
 
     def test_extrinsic(self):