Merge branch '15-file-reads-non-array-data' into 'master'

Resolve "File reads non-array data"

Closes orest-d#15

See merge request schlipf/py4vasp!13

src/py4vasp/data/band.py

@@ -15,8 +15,8 @@ def __init__(self, raw_band):
         self._spin_polarized = len(self._bands) == 2
         scale = raw_band.cell.scale
         lattice_vectors = raw_band.cell.lattice_vectors
-        self._cell = scale * np.array(lattice_vectors)
-        self._line_length = np.array(raw_band.line_length)
+        self._cell = scale * lattice_vectors
+        self._line_length = raw_band.line_length
         self._num_lines = len(self._kpoints) // self._line_length
         self._indices = raw_band.label_indices
         self._labels = raw_band.labels
@@ -62,7 +62,7 @@ def _kpoint_distances(self, kpoints=None):
         if self._kdists is not None:
             return self._kdists
         if kpoints is None:
-            kpoints = self._kpoints
+            kpoints = self._kpoints[:]
         cartesian_kpoints = np.linalg.solve(self._cell, kpoints.T).T
         kpoint_lines = np.split(cartesian_kpoints, self._num_lines)
         kpoint_norms = [np.linalg.norm(line - line[0], axis=1) for line in kpoint_lines]

src/py4vasp/data/dos.py

@@ -42,7 +42,7 @@ def to_dict(self, selection=None):
 
     def to_frame(self, selection=None):
         df = pd.DataFrame(self._read_data(selection))
-        df.fermi_energy = np.array(self._fermi_energy)
+        df.fermi_energy = self._fermi_energy
         return df
 
     def _read_data(self, selection):

src/py4vasp/raw/file.py

@@ -8,7 +8,7 @@ def __init__(self, filename="vaspout.h5"):
 
     def dos(self):
         return raw.Dos(
-            fermi_energy=self._h5f["results/electron_dos/efermi"],
+            fermi_energy=self._h5f["results/electron_dos/efermi"][()],
             energies=self._h5f["results/electron_dos/energies"],
             dos=self._h5f["results/electron_dos/dos"],
             projectors=self.projectors(),
@@ -17,8 +17,8 @@ def dos(self):
 
     def band(self):
         return raw.Band(
-            fermi_energy=self._h5f["results/electron_dos/efermi"],
-            line_length=self._h5f["input/kpoints/number_kpoints"],
+            fermi_energy=self._h5f["results/electron_dos/efermi"][()],
+            line_length=self._h5f["input/kpoints/number_kpoints"][()],
             kpoints=self._h5f["results/electron_eigenvalues/kpoint_coords"],
             eigenvalues=self._h5f["results/electron_eigenvalues/eigenvalues"],
             labels=self._safe_get_key("input/kpoints/labels_kpoints"),
@@ -35,12 +35,12 @@ def projectors(self):
             ion_types=self._h5f["results/positions/ion_types"],
             number_ion_types=self._h5f["results/positions/number_ion_types"],
             orbital_types=self._h5f["results/projectors/lchar"],
-            number_spins=self._h5f["results/electron_eigenvalues/ispin"],
+            number_spins=self._h5f["results/electron_eigenvalues/ispin"][()],
         )
 
     def cell(self):
         return raw.Cell(
-            scale=self._h5f["results/positions/scale"],
+            scale=self._h5f["results/positions/scale"][()],
             lattice_vectors=self._h5f["results/positions/lattice_vectors"],
         )
 

tests/raw/test_file.py

@@ -8,6 +8,7 @@
 import itertools
 from tempfile import TemporaryFile
 from collections import namedtuple
+from numbers import Number, Integral
 
 num_spins = 2
 num_energies = 20
@@ -18,7 +19,7 @@
 fermi_energy = 0.123
 
 SetupTest = namedtuple(
-    "SetupTest", "directory, options, create_reference, write_reference, attribute"
+    "SetupTest", "directory, options, create_reference, write_reference, check_actual"
 )
 
 
@@ -43,8 +44,7 @@ def generic_test(setup):
             setup.write_reference(h5f, reference)
             h5f.close()
             file = open_vasp_file(use_default, filename)
-            actual = getattr(file, setup.attribute)()
-            assert actual == reference
+            setup.check_actual(file, reference)
             file.close()  # must be after comparison, because file is read lazily
 
 
@@ -63,7 +63,7 @@ def test_dos(tmpdir):
         options=itertools.product((True, False), repeat=2),
         create_reference=reference_dos,
         write_reference=write_dos,
-        attribute="dos",
+        check_actual=check_dos,
     )
     generic_test(setup)
 
@@ -88,13 +88,19 @@ def write_dos(h5f, dos):
         h5f["results/electron_dos/dospar"] = proj.dos
 
 
+def check_dos(file, reference):
+    actual = file.dos()
+    assert actual == reference
+    assert isinstance(actual.fermi_energy, Number)
+
+
 def test_band(tmpdir):
     setup = SetupTest(
         directory=tmpdir,
         options=itertools.product((True, False), repeat=3),
         create_reference=reference_band,
         write_reference=write_band,
-        attribute="band",
+        check_actual=check_band,
     )
     generic_test(setup)
 
@@ -134,13 +140,20 @@ def write_band(h5f, band):
         h5f["results/projectors/par"] = band.projections
 
 
+def check_band(file, reference):
+    actual = file.band()
+    assert actual == reference
+    assert isinstance(actual.fermi_energy, Number)
+    assert isinstance(actual.line_length, Integral)
+
+
 def test_projectors(tmpdir):
     setup = SetupTest(
         directory=tmpdir,
         options=((True,), (False,)),
         create_reference=reference_projectors,
         write_reference=write_projectors,
-        attribute="projectors",
+        check_actual=check_projectors,
     )
     generic_test(setup)
 
@@ -162,13 +175,19 @@ def write_projectors(h5f, proj):
     h5f["results/electron_eigenvalues/ispin"] = proj.number_spins
 
 
+def check_projectors(file, reference):
+    actual = file.projectors()
+    assert actual == reference
+    assert isinstance(actual.number_spins, Integral)
+
+
 def test_cell(tmpdir):
     setup = SetupTest(
         directory=tmpdir,
         options=((True,), (False,)),
         create_reference=reference_cell,
         write_reference=write_cell,
-        attribute="cell",
+        check_actual=check_actual,
     )
     generic_test(setup)
 
@@ -180,3 +199,9 @@ def reference_cell():
 def write_cell(h5f, cell):
     h5f["results/positions/scale"] = cell.scale
     h5f["results/positions/lattice_vectors"] = cell.lattice_vectors
+
+
+def check_actual(file, reference):
+    actual = file.cell()
+    assert actual == reference
+    assert isinstance(actual.scale, Number)