Prevent unit test of boltztrap2 from modifying files in place (mate…

…rialsproject#4095)

* rename setup method

* use temp dir for TestBztTransportProperties

* revert to setup method

* revert previous changes, but split tests by sp/non-sp

* use temp dir

* Revert "use temp dir"

This reverts commit f403974.

* Revert "revert previous changes, but split tests by sp/non-sp"

This reverts commit 950ac97.

* properly capture bt2 import exception

* properly setup

* try to revert to HEAD

* also revert testcase

* typo, that's the reason

* add back TestCase inherit

* extract tests from setup method

* use temp dir

* use a global skip mark

* use temp dir for TestBztInterpolator as well

* NEED CONFIRM: replace BoltztrapError with more semantic exception

* pre-commit auto-fixes

---------

Signed-off-by: Shyue Ping Ong <[email protected]>
Co-authored-by: Shyue Ping Ong <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

src/pymatgen/electronic_structure/boltztrap2.py

@@ -35,7 +35,6 @@
 from tqdm import tqdm
 
 from pymatgen.electronic_structure.bandstructure import BandStructure, BandStructureSymmLine, Spin
-from pymatgen.electronic_structure.boltztrap import BoltztrapError
 from pymatgen.electronic_structure.dos import CompleteDos, Dos, Orbital
 from pymatgen.electronic_structure.plotter import BSPlotter, DosPlotter
 from pymatgen.io.ase import AseAtomsAdaptor
@@ -52,7 +51,7 @@
     from BoltzTraP2 import bandlib as BL
     from BoltzTraP2 import fite, sphere, units
 except ImportError as exc:
-    raise BoltztrapError("BoltzTraP2 has to be installed and working") from exc
+    raise ImportError("BoltzTraP2 has to be installed and working") from exc
 
 
 __author__ = "Francesco Ricci"
@@ -85,7 +84,7 @@ def __init__(self, obj, structure=None, nelect=None) -> None:
         elif isinstance(obj, BandStructure):
             bs_obj = obj
         else:
-            raise BoltztrapError("The object provided is neither a Bandstructure nor a Vasprun.")
+            raise TypeError("The object provided is neither a Bandstructure nor a Vasprun.")
 
         self.kpoints = np.array([kp.frac_coords for kp in bs_obj.kpoints])
 
@@ -94,7 +93,7 @@ def __init__(self, obj, structure=None, nelect=None) -> None:
         elif structure:
             self.structure = structure
         else:
-            raise BoltztrapError("A structure must be given.")
+            raise ValueError("A structure must be given.")
 
         self.atoms = AseAtomsAdaptor.get_atoms(self.structure)
         self.proj_all = None
@@ -131,7 +130,7 @@ def __init__(self, obj, structure=None, nelect=None) -> None:
         elif self.vbm_idx:
             self.nelect_all = self.vbm_idx + self.cbm_idx + 1
         else:
-            raise BoltztrapError("nelect must be given.")
+            raise ValueError("nelect must be given.")
 
     @classmethod
     def from_file(cls, vasprun_file: str | Path) -> Self:
@@ -322,7 +321,7 @@ def __init__(self, vrun_obj=None) -> None:
                     self.proj = next(iter(vrun_obj.projected_eigenvalues.values()))
 
             elif len(vrun_obj.eigenvalues) == 2:
-                raise BoltztrapError("spin bs case not implemented")
+                raise NotImplementedError("spin bs case not implemented")
 
             self.lattvec = self.atoms.get_cell().T * units.Angstrom
 
@@ -466,7 +465,7 @@ def load(self, fname="bztInterp.json.gz"):
             self.equivalences, coeffs = loadfn(fname)
             bands_loaded = False
         else:
-            raise BoltztrapError("Something wrong reading the data file!")
+            raise RuntimeError("Something wrong reading the data file!")
         self.coeffs = coeffs[0] + coeffs[1] * 1j
         return bands_loaded
 
@@ -588,7 +587,7 @@ def get_partial_doses(self, tdos, eband_ud, spins, enr, npts_mu, T, progress):
             progress: Default False, If True a progress bar is shown.
         """
         if not self.data.proj:
-            raise BoltztrapError("No projections loaded.")
+            raise ValueError("No projections loaded.")
 
         bkp_data_ebands = np.copy(self.data.ebands)
 
@@ -1053,13 +1052,13 @@ def plot_props(
         props_short = tuple(p[: len(prop_y)] for p in props)
 
         if prop_y not in props_short:
-            raise BoltztrapError("prop_y not valid")
+            raise ValueError("prop_y not valid")
 
         if prop_x not in {"mu", "doping", "temp"}:
-            raise BoltztrapError("prop_x not valid")
+            raise ValueError("prop_x not valid")
 
         if prop_z not in {"doping", "temp"}:
-            raise BoltztrapError("prop_z not valid")
+            raise ValueError("prop_z not valid")
 
         idx_prop = props_short.index(prop_y)
 
@@ -1095,7 +1094,7 @@ def plot_props(
                 plt.xlabel(r"$\mu$ (eV)", fontsize=30)
                 plt.xlim(xlim)
             else:
-                raise BoltztrapError(
+                raise ValueError(
                     "only prop_x=mu and prop_z=temp are \
                     available for c.c. and Hall c.c.!"
                 )
@@ -1172,7 +1171,7 @@ def plot_props(
     def plot_bands(self):
         """Plot a band structure on symmetry line using BSPlotter()."""
         if self.bzt_interp is None:
-            raise BoltztrapError("BztInterpolator not present")
+            raise ValueError("BztInterpolator not present")
 
         sbs = self.bzt_interp.get_band_structure()
 
@@ -1181,7 +1180,7 @@ def plot_bands(self):
     def plot_dos(self, T=None, npoints=10000):
         """Plot the total Dos using DosPlotter()."""
         if self.bzt_interp is None:
-            raise BoltztrapError("BztInterpolator not present")
+            raise ValueError("BztInterpolator not present")
 
         tdos = self.bzt_interp.get_dos(T=T, npts_mu=npoints)
         dosPlotter = DosPlotter()

tests/electronic_structure/test_boltztrap2.py

@@ -1,13 +1,14 @@
 from __future__ import annotations
 
+import shutil
 from unittest import TestCase
 
 import numpy as np
 import pytest
 from monty.serialization import loadfn
+from monty.tempfile import ScratchDir
 from pytest import approx
 
-from pymatgen.electronic_structure.boltztrap import BoltztrapError
 from pymatgen.electronic_structure.core import OrbitalType, Spin
 from pymatgen.io.vasp import Vasprun
 from pymatgen.util.testing import TEST_FILES_DIR
@@ -22,9 +23,8 @@
         VasprunLoader,
     )
 
-except BoltztrapError:
-    pytest.skip("No boltztrap2.", allow_module_level=True)
-
+except ImportError:
+    pytest.skip("No boltztrap2", allow_module_level=True)
 
 TEST_DIR = f"{TEST_FILES_DIR}/electronic_structure/boltztrap2"
 
@@ -33,6 +33,7 @@
 
 VASP_RUN_FILE_SPIN = f"{TEST_DIR}/vasprun_spin.xml"
 VASP_RUN_SPIN = Vasprun(VASP_RUN_FILE_SPIN, parse_projected_eigen=True)
+
 BAND_STRUCT = loadfn(f"{TEST_DIR}/PbTe_bandstructure.json")
 BAND_STRUCT_SPIN = loadfn(f"{TEST_DIR}/N2_bandstructure.json")
 
@@ -127,22 +128,24 @@ def test_from_file(self):
 
 class TestBztInterpolator(TestCase):
     def setUp(self):
-        self.loader = VasprunBSLoader(VASP_RUN)
-        self.bztInterp = BztInterpolator(self.loader, lpfac=2)
-        assert self.bztInterp is not None
-        # TODO: following creates file locally, use temp dir
-        self.bztInterp = BztInterpolator(self.loader, lpfac=2, save_bztInterp=True, fname=BZT_INTERP_FN)
-        assert self.bztInterp is not None
-        self.bztInterp = BztInterpolator(self.loader, load_bztInterp=True, fname=BZT_INTERP_FN)
-        assert self.bztInterp is not None
-
-        self.loader_sp = VasprunBSLoader(VASP_RUN_SPIN)
-        self.bztInterp_sp = BztInterpolator(self.loader_sp, lpfac=2)
-        assert self.bztInterp_sp is not None
-        self.bztInterp_sp = BztInterpolator(self.loader_sp, lpfac=2, save_bztInterp=True, fname=BZT_INTERP_FN)
-        assert self.bztInterp_sp is not None
-        self.bztInterp_sp = BztInterpolator(self.loader_sp, lpfac=2, load_bztInterp=True, fname=BZT_INTERP_FN)
-        assert self.bztInterp_sp is not None
+        with ScratchDir("."):
+            shutil.copy(BZT_INTERP_FN, ".")
+
+            loader = VasprunBSLoader(VASP_RUN)
+            self.bztInterp = BztInterpolator(loader, lpfac=2)
+            assert self.bztInterp is not None
+            self.bztInterp = BztInterpolator(loader, lpfac=2, save_bztInterp=True)
+            assert self.bztInterp is not None
+            self.bztInterp = BztInterpolator(loader, load_bztInterp=True)
+            assert self.bztInterp is not None
+
+            loader_sp = VasprunBSLoader(VASP_RUN_SPIN)
+            self.bztInterp_sp = BztInterpolator(loader_sp, lpfac=2)
+            assert self.bztInterp_sp is not None
+            self.bztInterp_sp = BztInterpolator(loader_sp, lpfac=2, save_bztInterp=True)
+            assert self.bztInterp_sp is not None
+            self.bztInterp_sp = BztInterpolator(loader_sp, lpfac=2, load_bztInterp=True)
+            assert self.bztInterp_sp is not None
 
     def test_properties(self):
         assert self.bztInterp.cband.shape == (6, 3, 3, 3, 29791)
@@ -204,105 +207,122 @@ def test_tot_proj_dos(self):
 
 class TestBztTransportProperties(TestCase):
     def setUp(self):
+        with ScratchDir("."):
+            shutil.copy(BZT_TRANSP_FN, ".")
+
+            # non spin polarized
+            loader = VasprunBSLoader(VASP_RUN)
+            bztInterp = BztInterpolator(loader, lpfac=2)
+
+            self.bztTransp = BztTransportProperties(
+                bztInterp,
+                temp_r=np.arange(300, 600, 100),
+                save_bztTranspProps=True,
+            )
+            assert self.bztTransp is not None
+
+            bztInterp = BztInterpolator(loader, lpfac=2)
+            self.bztTransp = BztTransportProperties(
+                bztInterp,
+                load_bztTranspProps=True,
+            )
+            assert self.bztTransp is not None
+
+            # spin polarized
+            loader_sp = VasprunBSLoader(VASP_RUN_SPIN)
+            bztInterp_sp = BztInterpolator(loader_sp, lpfac=2)
+
+            self.bztTransp_sp = BztTransportProperties(
+                bztInterp_sp,
+                temp_r=np.arange(300, 600, 100),
+                save_bztTranspProps=True,
+            )
+            assert self.bztTransp_sp is not None
+
+            bztInterp_sp = BztInterpolator(loader_sp, lpfac=2)
+            self.bztTransp_sp = BztTransportProperties(
+                bztInterp_sp,
+                load_bztTranspProps=True,
+            )
+            assert self.bztTransp_sp is not None
+
+    def test_init(self):
+        # non spin polarized
         loader = VasprunBSLoader(VASP_RUN)
         bztInterp = BztInterpolator(loader, lpfac=2)
         self.bztTransp = BztTransportProperties(bztInterp, temp_r=np.arange(300, 600, 100))
         assert self.bztTransp is not None
 
-        self.bztTransp = BztTransportProperties(
-            bztInterp, doping=10.0 ** np.arange(20, 22), temp_r=np.arange(300, 600, 100)
-        )
-        assert self.bztTransp is not None
-        assert self.bztTransp.contain_props_doping
-
-        bztInterp = BztInterpolator(loader, lpfac=2)
         self.bztTransp = BztTransportProperties(
             bztInterp,
+            doping=10.0 ** np.arange(20, 22),
             temp_r=np.arange(300, 600, 100),
-            save_bztTranspProps=True,
-            fname=BZT_TRANSP_FN,
         )
         assert self.bztTransp is not None
+        assert self.bztTransp.contain_props_doping
 
-        bztInterp = BztInterpolator(loader, lpfac=2)
-        self.bztTransp = BztTransportProperties(bztInterp, load_bztTranspProps=True, fname=BZT_TRANSP_FN)
-        assert self.bztTransp is not None
-
+        # spin polarized
         loader_sp = VasprunBSLoader(VASP_RUN_SPIN)
         bztInterp_sp = BztInterpolator(loader_sp, lpfac=2)
         self.bztTransp_sp = BztTransportProperties(bztInterp_sp, temp_r=np.arange(300, 600, 100))
         assert self.bztTransp_sp is not None
 
-        bztInterp_sp = BztInterpolator(loader_sp, lpfac=2)
-        # TODO: following creates file locally, use temp dir
-        self.bztTransp_sp = BztTransportProperties(
-            bztInterp_sp,
-            temp_r=np.arange(300, 600, 100),
-            save_bztTranspProps=True,
-            fname=BZT_TRANSP_FN,
-        )
-        assert self.bztTransp_sp is not None
-
-        bztInterp_sp = BztInterpolator(loader_sp, lpfac=2)
-        self.bztTransp_sp = BztTransportProperties(bztInterp_sp, load_bztTranspProps=True, fname=BZT_TRANSP_FN)
-        assert self.bztTransp_sp is not None
-
     def test_properties(self):
-        for p in [
+        for p in (
             self.bztTransp.Conductivity_mu,
             self.bztTransp.Seebeck_mu,
             self.bztTransp.Kappa_mu,
             self.bztTransp.Effective_mass_mu,
             self.bztTransp.Power_Factor_mu,
-        ]:
+        ):
             assert p.shape == (3, 3686, 3, 3)
 
-        for p in [
+        for p in (
             self.bztTransp.Carrier_conc_mu,
             self.bztTransp.Hall_carrier_conc_trace_mu,
-        ]:
+        ):
             assert p.shape == (3, 3686)
 
-        for p in [
+        for p in (
             self.bztTransp_sp.Conductivity_mu,
             self.bztTransp_sp.Seebeck_mu,
             self.bztTransp_sp.Kappa_mu,
             self.bztTransp_sp.Effective_mass_mu,
             self.bztTransp_sp.Power_Factor_mu,
-        ]:
+        ):
             assert p.shape == (3, 3252, 3, 3)
 
-        for p in [
+        for p in (
             self.bztTransp_sp.Carrier_conc_mu,
             self.bztTransp_sp.Hall_carrier_conc_trace_mu,
-        ]:
+        ):
             assert p.shape == (3, 3252)
 
     def test_compute_properties_doping(self):
         self.bztTransp.compute_properties_doping(doping=10.0 ** np.arange(20, 22))
-        for p in [
+        for p in (
             self.bztTransp.Conductivity_doping,
             self.bztTransp.Seebeck_doping,
             self.bztTransp.Kappa_doping,
             self.bztTransp.Effective_mass_doping,
             self.bztTransp.Power_Factor_doping,
-        ]:
+        ):
             assert p["n"].shape == (3, 2, 3, 3)
             assert self.bztTransp.contain_props_doping
 
         self.bztTransp_sp.compute_properties_doping(doping=10.0 ** np.arange(20, 22))
-        for p in [
+        for p in (
             self.bztTransp_sp.Conductivity_doping,
             self.bztTransp_sp.Seebeck_doping,
             self.bztTransp_sp.Kappa_doping,
             self.bztTransp_sp.Effective_mass_doping,
             self.bztTransp_sp.Power_Factor_doping,
-        ]:
+        ):
             assert p["n"].shape == (3, 2, 3, 3)
             assert self.bztTransp_sp.contain_props_doping
 
 
-class TestBztPlotter(TestCase):
+class TestBztPlotter:
     def test_plot(self):
         loader = VasprunBSLoader(VASP_RUN)
         bztInterp = BztInterpolator(loader, lpfac=2)