Update tests

doped/chemical_potentials.py

@@ -1219,12 +1219,23 @@ def from_vaspruns(self, path="competing_phases", folder="vasp_std", csv_path=Non
         else:
             raise ValueError("Path should either be a list of paths, a string or a pathlib Path object")
 
-        if skipped_folders and verbose:
+        # only warn about skipped folders that are recognised calculation folders (containing a material
+        # composition in the name, or 'EaH' in the name)
+        skipped_folders_for_warning = []
+        for folder_name in skipped_folders:
+            comps = []
+            for i in folder_name.split(" or ")[0].split("_"):
+                with contextlib.suppress(ValueError):
+                    comps.append(Composition(i))
+            if "EaH" in folder_name or comps:
+                skipped_folders_for_warning.append(folder_name)
+
+        if skipped_folders_for_warning and verbose:
             parent_folder_string = f" (in {path})" if isinstance(path, (PurePath, str)) else ""
-            print(
+            warnings.warn(
                 f"vasprun.xml files could not be found in the following "
                 f"directories{parent_folder_string}, and so they will be skipped for parsing:\n"
-                + "\n".join(skipped_folders)
+                + "\n".join(skipped_folders_for_warning)
             )
 
         # Ignore POTCAR warnings when loading vasprun.xml
@@ -1690,13 +1701,20 @@ def intrinsic_phase_diagram(self) -> dict:
             self.calculate_chempots()
         return self._intrinsic_phase_diagram
 
-    def cplap_input(self, dependent_variable=None, filename="input.dat"):
-        """For completeness' sake, automatically saves to input.dat for cplap
+    def _cplap_input(self, dependent_variable=None, filename="input.dat"):
+        """
+        Generates an ``input.dat`` file for the ``CPLAP`` ``FORTRAN`` code
+        (legacy code for computing and analysing chemical potential limits, no
+        longer recommended).
+
         Args:
-            dependent_variable (str) Pick one of the variables as dependent, the first element is
-                chosen from the composition if this isn't set
-            filename (str): filename, should end in .dat
-        Returns
+            dependent_variable (str):
+                Pick one of the variables as dependent, the first element in
+                the composition is chosen if this isn't set.
+            filename (str):
+                Filename, should end in ``.dat``.
+
+        Returns:
             None, writes input.dat file.
         """
         if not hasattr(self, "chempots"):

tests/test_chemical_potentials.py

@@ -266,15 +266,15 @@ def test_vaspruns_none_parsed(self):
         with warnings.catch_warnings(record=True) as w, pytest.raises(FileNotFoundError) as e:
             cpa.from_vaspruns(path=path, folder="relax", csv_path=self.csv_path)
         print([str(warning.message) for warning in w])  # for debugging
-        assert len(w) == 1
-        assert "Failed to parse the following `vasprun.xml` files:\n(files: error)\n" in str(w[0].message)
-        assert "Is a directory" in str(w[0].message)
+        assert "vasprun.xml files could not be found in the following directories (in" in str(w[0].message)
+        assert "ZrO2 or ZrO2/relax" in str(w[0].message)
+        print(e.value)
         assert "No vasprun files have been parsed," in str(e.value)
 
     def test_cplap_input(self):
         cpa = chemical_potentials.CompetingPhasesAnalyzer(self.stable_system)
         cpa.from_csv(self.csv_path)
-        cpa.cplap_input(dependent_variable="O")
+        cpa._cplap_input(dependent_variable="O")
 
         assert Path("input.dat").is_file()
 
@@ -688,8 +688,10 @@ def test_init_ytos(self):
 
     def test_api_keys_errors(self):
         nonvalid_api_key_error = ValueError(
-            "API key test is not a valid legacy Materials Project API key. These are "
-            "available at https://legacy.materialsproject.org/open"
+            "The supplied API key (``api_key`` or 'PMG_MAPI_KEY' in your ``.pmgrc.yaml`` "
+            "file) test is not a valid legacy Materials Project API key, which is "
+            "required by doped. See the doped installation instructions for details:\n"
+            "https://doped.readthedocs.io/en/latest/Installation.html#setup-potcars-and-materials-project-api"
         )
         with pytest.raises(ValueError) as e:
             chemical_potentials.CompetingPhases(
@@ -699,8 +701,11 @@ def test_api_keys_errors(self):
         assert str(nonvalid_api_key_error) in str(e.value)
 
         new_api_key_error = ValueError(
-            "You are trying to use the new Materials Project (MP) API which is not supported "
-            "by doped. Please use the legacy MP API (https://legacy.materialsproject.org/open)."
+            "The supplied API key (``api_key`` or 'PMG_MAPI_KEY' in your ``.pmgrc.yaml`` "
+            "file) corresponds to the new Materials Project (MP) API, which is not "
+            "supported by doped. Please use the legacy MP API as detailed on the doped "
+            "installation instructions:\n"
+            "https://doped.readthedocs.io/en/latest/Installation.html#setup-potcars-and-materials-project-api"
         )
         with pytest.raises(ValueError) as e:
             chemical_potentials.CompetingPhases(