refactor np.isclose(...).all() -> np.allclose(...)

ramannoodle/io/io_utils.py

@@ -135,7 +135,7 @@ def _read_polarizability_dataset(
             read_structure_and_polarizability_fn(filepath)
         )
         if file_index != 0:
-            if not np.isclose(lattice, read_lattice, atol=1e-5).all():
+            if not np.allclose(lattice, read_lattice, atol=1e-5):
                 raise IncompatibleStructureException(
                     f"incompatible lattice: {filepath}"
                 )

ramannoodle/polarizability/art.py

@@ -211,7 +211,7 @@ def add_art_from_files(
         _displacement = displacements[0].copy()
         atom_index = int(np.argmax(np.sum(_displacement**2, axis=1)))
         _displacement[atom_index] = np.zeros(3)
-        if not np.isclose(_displacement, 0.0, atol=1e-6).all():
+        if not np.allclose(_displacement, 0.0, atol=1e-6):
             raise InvalidDOFException("multiple atoms displaced simultaneously")
 
         # Checks displacement
@@ -288,7 +288,7 @@ def get_dof_indexes(
         for atom_index in atom_indexes:
             for index, basis_vector in enumerate(self._cart_basis_vectors):
                 direction = basis_vector[atom_index]
-                if not np.isclose(direction, 0, atol=1e-5).all():
+                if not np.allclose(direction, 0, atol=1e-5):
                     dof_indexes.append(index)
         return dof_indexes
 

ramannoodle/polarizability/interpolation.py

@@ -59,7 +59,7 @@ def find_duplicates(vectors: Iterable[ArrayLike]) -> NDArray | None:
         raise get_type_error("vectors", vectors, "Iterable") from exc
     try:
         for vector_1, vector_2 in combinations:
-            if np.isclose(vector_1, vector_2).all():
+            if np.allclose(vector_1, vector_2):
                 return np.array(vector_1)
         return None
     except TypeError as exc:
@@ -368,12 +368,12 @@ def _construct_and_add_interpolations(
             # Warn user if amplitudes don't span zero
             max_amplitude = np.max(interpolation_x)
             min_amplitude = np.min(interpolation_x)
-            if np.isclose(max_amplitude, 0, atol=1e-3).all() or max_amplitude <= 0:
+            if np.allclose(max_amplitude, 0, atol=1e-3) or max_amplitude <= 0:
                 warn(
                     "max amplitude <= 0, when usually it should be > 0",
                     DOFWarning,
                 )
-            if np.isclose(min_amplitude, 0, atol=1e-3).all() or min_amplitude >= 0:
+            if np.allclose(min_amplitude, 0, atol=1e-3) or min_amplitude >= 0:
                 warn(
                     "min amplitude >= 0, when usually it should be < 0",
                     DOFWarning,

ramannoodle/structure/symmetry_utils.py

@@ -36,7 +36,7 @@ def are_collinear(vector_1: NDArray[np.float64], vector_2: NDArray[np.float64])
         raise ValueError(
             f"vector_1 and vector_2 have different lengths: {length_expr}"
         ) from exc
-    return bool(np.isclose(dot_product, 1).all() or np.isclose(dot_product, -1).all())
+    return bool(np.allclose(dot_product, 1) or np.isclose(dot_product, -1))
 
 
 def is_orthogonal_to_all(
@@ -69,7 +69,7 @@ def is_orthogonal_to_all(
         except TypeError as exc:
             raise get_type_error(f"vectors[{index}]", vector_2, "ndarray") from exc
 
-        if not np.isclose(np.dot(vector_1.flatten(), vector_2.flatten()) + 1, 1).all():
+        if not np.allclose(np.dot(vector_1.flatten(), vector_2.flatten()) + 1, 1):
             return index
 
     return -1

test/tests/test_outcar.py

@@ -46,15 +46,15 @@ def test_read_phonons_from_outcar(
 
     known_degrees_of_freedom = known_num_atoms * 3
     assert phonons.wavenumbers.shape == (known_degrees_of_freedom,)
-    assert np.isclose(phonons.wavenumbers[0:4], known_wavenumbers).all()
+    assert np.allclose(phonons.wavenumbers[0:4], known_wavenumbers)
     assert phonons.displacements.shape == (
         known_degrees_of_freedom,
         known_num_atoms,
         3,
     )
-    assert np.isclose(phonons.displacements[0, 0], known_first_displacement).all()
+    assert np.allclose(phonons.displacements[0, 0], known_first_displacement)
     print(phonons.displacements[-1, -1])
-    assert np.isclose(phonons.displacements[-1, -1], known_last_displacement).all()
+    assert np.allclose(phonons.displacements[-1, -1], known_last_displacement)
 
 
 @pytest.mark.parametrize(
@@ -91,4 +91,4 @@ def test_read_trajectory_from_outcar(
     """Test read_trajectory for outcar (normal)."""
     trajectory = generic_io.read_trajectory(path_fixture, file_format="outcar")
     assert len(trajectory) == trajectory_length
-    assert np.isclose(last_position, trajectory[-1][-1]).all()
+    assert np.allclose(last_position, trajectory[-1][-1])

test/tests/test_outcar_utils.py

@@ -122,8 +122,8 @@ def test_read_cart_positions_from_outcar(
     cart_positions = vasp_outcar._read_cart_positions(file_fixture, 135)
 
     assert len(cart_positions) == 135
-    assert np.isclose(cart_positions[0], known_first_position).all()
-    assert np.isclose(cart_positions[-1], known_last_position).all()
+    assert np.allclose(cart_positions[0], known_first_position)
+    assert np.allclose(cart_positions[-1], known_last_position)
 
 
 @pytest.mark.parametrize(
@@ -173,8 +173,8 @@ def test_read_positions_from_outcar(
     positions = vasp_outcar._read_positions(file_fixture, 135)
 
     assert len(positions) == 135
-    assert np.isclose(positions[0], known_first_position).all()
-    assert np.isclose(positions[-1], known_last_position).all()
+    assert np.allclose(positions[0], known_first_position)
+    assert np.allclose(positions[-1], known_last_position)
 
 
 @pytest.mark.parametrize(
@@ -227,7 +227,7 @@ def test_read_polarizability_from_outcar(
     """Test _read_polarizability_from_outcar (normal)."""
     polarizability = vasp_outcar._read_polarizability(file_fixture)
 
-    assert np.isclose(polarizability, known_polarizability).all()
+    assert np.allclose(polarizability, known_polarizability)
 
 
 @pytest.mark.parametrize(
@@ -288,7 +288,7 @@ def test_read_lattice_from_outcar(
 ) -> None:
     """Test _read_lattice_from_outcar (normal)."""
     result = vasp_outcar._read_lattice(file_fixture)
-    assert np.isclose(result, known_lattice).all()
+    assert np.allclose(result, known_lattice)
 
 
 @pytest.mark.parametrize(

test/tests/test_phonon_spectrum.py

@@ -38,7 +38,7 @@ def _validate_polarizabilities(model: InterpolationModel, data_directory: str) -
             )
         )
         model_polarizability = model.calc_polarizabilities(np.array([positions]))[0]
-        assert np.isclose(model_polarizability, known_polarizability, atol=1e-4).all()
+        assert np.allclose(model_polarizability, known_polarizability, atol=1e-4)
 
 
 @pytest.mark.parametrize(
@@ -100,8 +100,8 @@ def test_interpolation_spectrum(
         known_wavenumbers = known_spectrum["wavenumbers"]
         known_intensities = known_spectrum["intensities"]
 
-        assert np.isclose(wavenumbers, known_wavenumbers).all()
-        assert np.isclose(intensities, known_intensities, atol=1e-4).all()
+        assert np.allclose(wavenumbers, known_wavenumbers)
+        assert np.allclose(intensities, known_intensities, atol=1e-4)
 
 
 @pytest.mark.parametrize(
@@ -157,8 +157,8 @@ def test_art_spectrum(
         known_wavenumbers = known_spectrum["wavenumbers"]
         known_intensities = known_spectrum["intensities"]
 
-        assert np.isclose(wavenumbers, known_wavenumbers).all()
-        assert np.isclose(intensities, known_intensities, atol=1e-4).all()
+        assert np.allclose(wavenumbers, known_wavenumbers)
+        assert np.allclose(intensities, known_intensities, atol=1e-4)
 
 
 @pytest.mark.parametrize(
@@ -232,8 +232,8 @@ def test_art_masked_spectrum(
         known_wavenumbers = known_spectrum["wavenumbers"]
         known_intensities = known_spectrum["intensities"]
 
-        assert np.isclose(wavenumbers, known_wavenumbers).all()
-        assert np.isclose(intensities, known_intensities, atol=1e-4).all()
+        assert np.allclose(wavenumbers, known_wavenumbers)
+        assert np.allclose(intensities, known_intensities, atol=1e-4)
 
 
 @pytest.mark.parametrize(
@@ -267,8 +267,8 @@ def test_convolve_intensities(
         with np.load(known_gaussian_spectrum_path) as known_spectrum:
             known_wavenumbers = known_spectrum["wavenumbers"]
             known_intensities = known_spectrum["intensities"]
-            assert np.isclose(gaussian_wavenumbers, known_wavenumbers).all()
-            assert np.isclose(gaussian_intensities, known_intensities).all()
+            assert np.allclose(gaussian_wavenumbers, known_wavenumbers)
+            assert np.allclose(gaussian_intensities, known_intensities)
 
         lorentzian_wavenumbers, lorentzian_intensities = convolve_spectrum(
             wavenumbers, intensities, "lorentzian"
@@ -281,8 +281,8 @@ def test_convolve_intensities(
         with np.load(known_lorentzian_spectrum_path) as known_spectrum:
             known_wavenumbers = known_spectrum["wavenumbers"]
             known_intensities = known_spectrum["intensities"]
-            assert np.isclose(lorentzian_wavenumbers, known_wavenumbers).all()
-            assert np.isclose(lorentzian_intensities, known_intensities).all()
+            assert np.allclose(lorentzian_wavenumbers, known_wavenumbers)
+            assert np.allclose(lorentzian_intensities, known_intensities)
 
 
 @pytest.mark.parametrize(

test/tests/test_poscar.py

@@ -92,9 +92,9 @@ def test_write_read_poscar(
     reference_structure = ramannoodle.io.generic.read_ref_structure(
         "test/data/temp", file_format="poscar"
     )
-    assert np.isclose(reference_structure._lattice, lattice).all()
-    assert np.isclose(reference_structure._atomic_numbers, atomic_numbers).all()
-    assert np.isclose(reference_structure.positions, positions).all()
+    assert np.allclose(reference_structure._lattice, lattice)
+    assert np.allclose(reference_structure._atomic_numbers, atomic_numbers)
+    assert np.allclose(reference_structure.positions, positions)
 
 
 @pytest.mark.parametrize(
@@ -166,8 +166,8 @@ def test_read_cart_poscar(  # pylint: disable=too-many-arguments
     ref_structure = vasp_io.poscar.read_ref_structure(cart_poscar_path)
     known_ref_structure = vasp_io.poscar.read_ref_structure(ref_frac_poscar_path)
 
-    assert np.isclose(ref_structure.lattice, known_ref_structure.lattice).all()
-    assert np.isclose(ref_structure.positions, known_ref_structure.positions).all()
+    assert np.allclose(ref_structure.lattice, known_ref_structure.lattice)
+    assert np.allclose(ref_structure.positions, known_ref_structure.positions)
 
 
 @pytest.mark.parametrize(

test/tests/test_structure.py

@@ -193,7 +193,7 @@ def test_get_positions_permutation_matrix(
 )
 def test_apply_pbc(positions: NDArray[np.float64], known: NDArray[np.float64]) -> None:
     """Test apply_pbc (normal)."""
-    assert np.isclose(apply_pbc(positions), known).all()
+    assert np.allclose(apply_pbc(positions), known)
 
 
 @pytest.mark.parametrize(
@@ -229,7 +229,7 @@ def test_apply_pbc_displacement(
     displacement: NDArray[np.float64], known: NDArray[np.float64]
 ) -> None:
     """Test test_apply_pbc_displacement (normal)."""
-    assert np.isclose(apply_pbc_displacement(displacement), known).all()
+    assert np.allclose(apply_pbc_displacement(displacement), known)
 
 
 @pytest.mark.parametrize(

test/tests/test_trajectory_spectrum.py

@@ -88,8 +88,8 @@ def test_spectrum(
         known_wavenumbers = known_spectrum["wavenumbers"]
         known_intensities = known_spectrum["intensities"]
 
-        assert np.isclose(wavenumbers, known_wavenumbers).all()
-        assert np.isclose(intensities, known_intensities, atol=1e-3).all()
+        assert np.allclose(wavenumbers, known_wavenumbers)
+        assert np.allclose(intensities, known_intensities, atol=1e-3)
 
 
 @pytest.mark.parametrize(

test/tests/test_vasprun.py

@@ -43,8 +43,8 @@ def test_read_positions_and_polarizability(
         path_fixture, file_format="vasprun.xml"
     )
 
-    assert np.isclose(positions[-1], known_last_positions).all()
-    assert np.isclose(polarizability, known_polarizability).all()
+    assert np.allclose(positions[-1], known_last_positions)
+    assert np.allclose(polarizability, known_polarizability)
 
 
 @pytest.mark.parametrize(
@@ -64,7 +64,7 @@ def test_read_positions(
     """Test read_positions (normal)."""
     positions = generic_io.read_positions(path_fixture, file_format="vasprun.xml")
 
-    assert np.isclose(positions[-1], known_last_positions).all()
+    assert np.allclose(positions[-1], known_last_positions)
 
 
 @pytest.mark.parametrize(
@@ -95,7 +95,7 @@ def test_read_ref_structure(
     )
 
     assert ref_structure.atomic_numbers == known_atomic_numbers
-    assert np.isclose(ref_structure.lattice, known_lattice).all()
+    assert np.allclose(ref_structure.lattice, known_lattice)
 
 
 @pytest.mark.parametrize(
@@ -119,7 +119,7 @@ def test_read_trajectory(
     """Test read_ref_structure (normal)."""
     trajectory = generic_io.read_trajectory(path_fixture, file_format="vasprun.xml")
 
-    assert np.isclose(trajectory.positions_ts[-1][-1], known_final_position).all()
+    assert np.allclose(trajectory.positions_ts[-1][-1], known_final_position)
     assert len(trajectory) == known_trajectory_length
     assert np.isclose(trajectory.timestep, known_timestep)
 
@@ -146,8 +146,8 @@ def test_read_phonons(
 
     assert len(phonons.wavenumbers) == len(phonons.displacements)
     assert len(phonons.wavenumbers) == degrees_of_freedom
-    assert np.isclose(phonons.wavenumbers[0:5], known_wavenumbers).all()
-    assert np.isclose(phonons.displacements[-1][-1], known_last_displacement).all()
+    assert np.allclose(phonons.wavenumbers[0:5], known_wavenumbers)
+    assert np.allclose(phonons.displacements[-1][-1], known_last_displacement)
 
 
 @pytest.mark.parametrize(

test/tests/test_xdatcar.py

@@ -37,5 +37,5 @@ def test_read_write_xdatcar(
         overwrite=True,
     )
     written_trajectory = vasp_io.xdatcar.read_trajectory("test/data/temp", 1.0)
-    assert np.isclose(written_trajectory.positions_ts, trajectory.positions_ts).all()
+    assert np.allclose(written_trajectory.positions_ts, trajectory.positions_ts)
     assert written_trajectory.timestep == trajectory.timestep

test/tests/torch/test_gnn.py

@@ -207,7 +207,7 @@ def test_calc_polarizabilities(
 #     for rotation in ref_structure._symmetry_dict["rotations"]:
 #         rotated_polarizability = np.linalg.inv(rotation) @ polarizability @ rotation
 
-#         assert np.isclose(polarizability, rotated_polarizability, atol=1e-5).all()
+#         assert np.allclose(polarizability, rotated_polarizability, atol=1e-5)
 
 
 # def test_symmetry_displaced() -> None: