rename test_(to->as)_from_dict

janosh · janosh · commit d4c6d432f51a · 2023-08-23T14:15:08.000-07:00
google-style doc str for class Poscar
diff --git a/pymatgen/io/vasp/inputs.py b/pymatgen/io/vasp/inputs.py
@@ -54,48 +54,22 @@
 class Poscar(MSONable):
     """
     Object for representing the data in a POSCAR or CONTCAR file.
-    Please note that this current implementation. Most attributes can be set
-    directly.
 
-    .. attribute:: structure
-
-        Associated Structure.
-
-    .. attribute:: comment
-
-        Optional comment string.
-
-    .. attribute:: true_names
-
-        Boolean indication whether Poscar contains actual real names parsed
-        from either a POTCAR or the POSCAR itself.
-
-    .. attribute:: selective_dynamics
-
-        Selective dynamics attribute for each site if available. A Nx3 array of
-        booleans.
-
-    .. attribute:: velocities
-
-        Velocities for each site (typically read in from a CONTCAR). A Nx3
-        array of floats.
-
-    .. attribute:: predictor_corrector
-
-        Predictor corrector coordinates and derivatives for each site; i.e.
-        a list of three 1x3 arrays for each site (typically read in from a MD
-        CONTCAR).
-
-    .. attribute:: predictor_corrector_preamble
-
-        Predictor corrector preamble contains the predictor-corrector key,
-        POTIM, and thermostat parameters that precede the site-specic predictor
-        corrector data in MD CONTCAR
-
-    .. attribute:: temperature
-
-        Temperature of velocity Maxwell-Boltzmann initialization. Initialized
-        to -1 (MB hasn"t been performed).
+    Attributes:
+        structure: Associated Structure.
+        comment: Optional comment string.
+        true_names: Boolean indication whether Poscar contains actual real names parsed
+            from either a POTCAR or the POSCAR itself.
+        selective_dynamics: Selective dynamics attribute for each site if available.
+            A Nx3 array of booleans.
+        velocities: Velocities for each site (typically read in from a CONTCAR).
+            A Nx3 array of floats.
+        predictor_corrector: Predictor corrector coordinates and derivatives for each site;
+            i.e. a list of three 1x3 arrays for each site (typically read in from a MD CONTCAR).
+        predictor_corrector_preamble: Predictor corrector preamble contains the predictor-corrector key,
+            POTIM, and thermostat parameters that precede the site-specic predictor corrector data in MD CONTCAR.
+        temperature: Temperature of velocity Maxwell-Boltzmann initialization.
+            Initialized to -1 (MB hasn't been performed).
     """
 
     def __init__(
diff --git a/tests/alchemy/test_filters.py b/tests/alchemy/test_filters.py
@@ -47,7 +47,7 @@ def test_filtering(self):
         f8 = ContainsSpecieFilter(species4, strict_compare=False, AND=True)
         assert not f8.test(struct), "Incorrect filter"
 
-    def test_to_from_dict(self):
+    def test_as_from_dict(self):
         species1 = ["Si5+", "Mg2+"]
         f1 = ContainsSpecieFilter(species1, strict_compare=True, AND=False)
         d = f1.as_dict()
@@ -66,7 +66,7 @@ def test_filter(self):
         sf = SpecieProximityFilter({"P": 5})
         assert not sf.test(struct)
 
-    def test_to_from_dict(self):
+    def test_as_from_dict(self):
         sf = SpecieProximityFilter({"Li": 1})
         d = sf.as_dict()
         assert isinstance(SpecieProximityFilter.from_dict(d), SpecieProximityFilter)
@@ -85,7 +85,7 @@ def test_filter(self):
         transmuter.apply_filter(dup_filter)
         assert len(transmuter.transformed_structures) == 11
 
-    def test_to_from_dict(self):
+    def test_as_from_dict(self):
         fil = RemoveDuplicatesFilter()
         d = fil.as_dict()
         assert isinstance(RemoveDuplicatesFilter().from_dict(d), RemoveDuplicatesFilter)
diff --git a/tests/analysis/test_energy_models.py b/tests/analysis/test_energy_models.py
@@ -31,7 +31,7 @@ def test_get_energy(self):
         s2 = Structure.from_file(f"{TEST_FILES_DIR}/Li2O.cif")
         assert m.get_energy(s2) == approx(-145.39050015844839, abs=1e-4)
 
-    def test_to_from_dict(self):
+    def test_as_from_dict(self):
         m = EwaldElectrostaticModel()
         d = m.as_dict()
         assert isinstance(EwaldElectrostaticModel.from_dict(d), EwaldElectrostaticModel)
@@ -43,7 +43,7 @@ def test_get_energy(self):
         s2 = Structure.from_file(f"{TEST_FILES_DIR}/Li2O.cif")
         assert m.get_energy(s2) == approx(-225)
 
-    def test_to_from_dict(self):
+    def test_as_from_dict(self):
         m = SymmetryModel(symprec=0.2)
         d = m.as_dict()
         o = SymmetryModel.from_dict(d)
@@ -63,7 +63,7 @@ def test_get_energy(self):
         struct[5] = Species("Fe", 2, spin=-4)
         assert m.get_energy(struct) == approx(51.97424405382921)
 
-    def test_to_from_dict(self):
+    def test_as_from_dict(self):
         m = IsingModel(5, 4)
         d = m.as_dict()
         o = IsingModel.from_dict(d)
diff --git a/tests/analysis/test_graphs.py b/tests/analysis/test_graphs.py
@@ -390,7 +390,7 @@ def test_draw(self):
         }
         assert pdfs == expected_pdfs
 
-    def test_to_from_dict(self):
+    def test_as_from_dict(self):
         d = self.mos2_sg.as_dict()
         sg = StructureGraph.from_dict(d)
         d2 = sg.as_dict()
diff --git a/tests/analysis/test_phase_diagram.py b/tests/analysis/test_phase_diagram.py
@@ -72,7 +72,7 @@ def test_is_element(self):
         assert not self.entry.is_element
         assert not self.gp_entry.is_element
 
-    def test_to_from_dict(self):
+    def test_as_from_dict(self):
         d = self.entry.as_dict()
         gpd = self.gp_entry.as_dict()
         entry = PDEntry.from_dict(d)
@@ -142,7 +142,7 @@ def test_is_element(self):
         iron = Composition("Fe")
         assert TransformedPDEntry(PDEntry(iron, 0), {iron: iron}).is_element is True
 
-    def test_to_from_dict(self):
+    def test_as_from_dict(self):
         dct = self.transformed_entry.as_dict()
         entry = TransformedPDEntry.from_dict(dct)
         assert entry.name == "LiFeO2" == self.transformed_entry.name
@@ -599,7 +599,7 @@ def test_get_all_chempots(self):
     def test_get_plot(self):
         self.pd.get_plot()  # PDPlotter functionality is tested separately
 
-    def test_to_from_dict(self):
+    def test_as_from_dict(self):
         # test round-trip for other entry types such as ComputedEntry
         entry = ComputedEntry("H", 0.0, 0.0, entry_id="test")
         pd = PhaseDiagram([entry])
@@ -768,7 +768,7 @@ def test_get_decomp_and_e_above_hull(self):
     def test_repr(self):
         assert repr(self.ppd) == str(self.ppd) == "PatchedPhaseDiagram covering 15 sub-spaces"
 
-    def test_to_from_dict(self):
+    def test_as_from_dict(self):
         ppd_dict = self.ppd.as_dict()
         assert ppd_dict["@module"] == self.ppd.__class__.__module__
         assert ppd_dict["@class"] == self.ppd.__class__.__name__
diff --git a/tests/analysis/test_pourbaix_diagram.py b/tests/analysis/test_pourbaix_diagram.py
@@ -51,7 +51,7 @@ def test_calc_coeff_terms(self):
         assert self.PxSol.nPhi == -6, "Wrong nPhi!"
         assert self.PxSol.nH2O == 3, "Wrong nH2O!"
 
-    def test_to_from_dict(self):
+    def test_as_from_dict(self):
         d = self.PxIon.as_dict()
         ion_entry = self.PxIon.from_dict(d)
         assert ion_entry.entry.name == "MnO4[-1]", "Wrong Entry!"
diff --git a/tests/analysis/test_reaction_calculator.py b/tests/analysis/test_reaction_calculator.py
@@ -233,7 +233,7 @@ def test_products_reactants(self):
         assert rxn.normalized_repr == "4 Li3Fe2(PO4)3 + 2 Fe2O3 -> 3 O2 + 12 LiFePO4"
         assert rxn.calculate_energy(energies) == approx(-0.48333333, abs=1e-5)
 
-    def test_to_from_dict(self):
+    def test_as_from_dict(self):
         reactants = [Composition("Fe"), Composition("O2")]
         products = [Composition("Fe2O3")]
         rxn = Reaction(reactants, products)
@@ -300,7 +300,7 @@ def test_init(self):
         with pytest.raises(ReactionError, match="Reaction is unbalanced"):
             BalancedReaction(rct, prod)
 
-    def test_to_from_dict(self):
+    def test_as_from_dict(self):
         rct = {Composition("K2SO4"): 3, Composition("Na2S"): 1, Composition("Li"): 24}
         prod = {Composition("KNaS"): 2, Composition("K2S"): 2, Composition("Li2O"): 12}
         rxn = BalancedReaction(rct, prod)
@@ -516,7 +516,7 @@ def test_calculated_reaction_energy_uncertainty_for_nan(self):
     def test_init(self):
         assert str(self.rxn) == "2 Li + O2 -> Li2O2"
 
-    def test_to_from_dict(self):
+    def test_as_from_dict(self):
         d = self.rxn.as_dict()
         new_rxn = ComputedReaction.from_dict(d)
         assert str(new_rxn) == "2 Li + O2 -> Li2O2"
diff --git a/tests/analysis/xas/test_spectrum.py b/tests/analysis/xas/test_spectrum.py
@@ -55,7 +55,7 @@ def test_add_mul(self):
         assert_allclose(scaled_spect2.y, 3 * self.k_xanes.y)
         assert approx(self.k_xanes.get_interpolated_value(7720.422), abs=1e-3) == 0.274302
 
-    def test_to_from_dict(self):
+    def test_as_from_dict(self):
         s = XAS.from_dict(self.k_xanes.as_dict())
         assert_allclose(s.y, self.k_xanes.y)
 
diff --git a/tests/apps/battery/test_insertion_battery.py b/tests/apps/battery/test_insertion_battery.py
@@ -79,7 +79,7 @@ def test_entries(self):
     def test_get_all_entries(self):
         self.ie_LTO.get_all_entries()
 
-    def test_to_from_dict(self):
+    def test_as_from_dict(self):
         d = self.ie_LTO.as_dict()
         ie = InsertionElectrode.from_dict(d)
         assert ie.max_voltage == approx(2.78583901)
diff --git a/tests/apps/borg/test_hive.py b/tests/apps/borg/test_hive.py
@@ -38,7 +38,7 @@ def test_assimilate(self):
         assert entry.structure is not None
         # assert len(entry.parameters["history"]) == 2
 
-    def test_to_from_dict(self):
+    def test_as_from_dict(self):
         d = self.structure_drone.as_dict()
         drone = VaspToComputedEntryDrone.from_dict(d)
         assert isinstance(drone, VaspToComputedEntryDrone)
@@ -54,7 +54,7 @@ def test_get_valid_paths(self):
             if path[0] == TEST_FILES_DIR:
                 assert len(self.drone.get_valid_paths(path)) > 0
 
-    def test_to_from_dict(self):
+    def test_as_from_dict(self):
         d = self.structure_drone.as_dict()
         drone = SimpleVaspToComputedEntryDrone.from_dict(d)
         assert isinstance(drone, SimpleVaspToComputedEntryDrone)
@@ -94,7 +94,7 @@ def test_assimilate(self):
         for p in ["properly_terminated", "stationary_type"]:
             assert p in entry.data
 
-    def test_to_from_dict(self):
+    def test_as_from_dict(self):
         d = self.structure_drone.as_dict()
         drone = GaussianToComputedEntryDrone.from_dict(d)
         assert isinstance(drone, GaussianToComputedEntryDrone)
diff --git a/tests/core/test_lattice.py b/tests/core/test_lattice.py
@@ -284,7 +284,7 @@ def test_mapping_symmetry(self):
         assert len(map) == 3
         assert latt.find_mapping(l2, ltol=0.1) is not None
 
-    def test_to_from_dict(self):
+    def test_as_from_dict(self):
         dct = self.tetragonal.as_dict()
         expected_keys = {"matrix", "@class", "pbc", "@module"}
         assert {*dct} == expected_keys
diff --git a/tests/core/test_operations.py b/tests/core/test_operations.py
@@ -173,7 +173,7 @@ def test_are_symmetrically_related_vectors(self):
         assert self.op.are_symmetrically_related_vectors(to_a, from_a, -r_a, from_b, to_b, r_b)[0]
         assert self.op.are_symmetrically_related_vectors(to_a, from_a, -r_a, from_b, to_b, r_b)[1]
 
-    def test_to_from_dict(self):
+    def test_as_from_dict(self):
         d = self.op.as_dict()
         op = SymmOp.from_dict(d)
         point = np.random.rand(3)
@@ -253,7 +253,7 @@ def test_xyzt_string(self):
         assert magop.time_reversal == -1
         assert magop_str == "3x-2y-z+1/2, -x+12/13, z+1/2, -1"
 
-    def test_to_from_dict(self):
+    def test_as_from_dict(self):
         op = SymmOp(
             [
                 [3, -2, -1, 0.5],
diff --git a/tests/core/test_sites.py b/tests/core/test_sites.py
@@ -36,7 +36,7 @@ def test_properties(self):
         assert self.propertied_site.properties["magmom"] == 5.1
         assert self.propertied_site.properties["charge"] == 4.2
 
-    def test_to_from_dict(self):
+    def test_as_from_dict(self):
         dct = self.disordered_site.as_dict()
         site = Site.from_dict(dct)
         assert site == self.disordered_site
diff --git a/tests/core/test_structure.py b/tests/core/test_structure.py
@@ -71,9 +71,7 @@ def setUp(self):
         assert len(self.struct) == 2, "Wrong number of sites in structure!"
         assert self.struct.is_ordered
         assert self.struct.ntypesp == 1
-        coords = []
-        coords.append([0, 0, 0])
-        coords.append([0.0, 0, 0.0000001])
+        coords = [[0, 0, 0], [0.0, 0, 0.0000001]]
         with pytest.raises(StructureError, match="Structure contains sites that are less than 0.01 Angstrom apart"):
             IStructure(self.lattice, ["Si"] * 2, coords, validate_proximity=True)
         self.propertied_structure = IStructure(self.lattice, ["Si"] * 2, coords, site_properties={"magmom": [5, -5]})
@@ -1135,10 +1133,10 @@ def test_another_supercell(self):
         struct.make_supercell([[0, 2, 0], [1, 0, 0], [0, 0, 1]])
         assert struct.formula == "Si4"
 
-    def test_to_from_dict(self):
-        d = self.struct.as_dict()
-        s2 = Structure.from_dict(d)
-        assert isinstance(s2, Structure)
+    def test_as_from_dict(self):
+        dct = self.struct.as_dict()
+        s1 = Structure.from_dict(dct)
+        assert isinstance(s1, Structure)
 
     def test_default_dict_attrs(self):
         d = self.struct.as_dict()
@@ -1810,7 +1808,7 @@ def test_get_centered_molecule(self):
         centered = mol.get_centered_molecule()
         assert_allclose(centered.center_of_mass, [0, 0, 0])
 
-    def test_to_from_dict(self):
+    def test_as_from_dict(self):
         dct = self.mol.as_dict()
         mol2 = IMolecule.from_dict(dct)
         assert isinstance(mol2, IMolecule)
@@ -1933,7 +1931,7 @@ def test_add_site_property(self):
         with pytest.raises(AttributeError, match="attr='magmom' not found on Site"):
             _ = self.mol[0].magmom
 
-    def test_to_from_dict(self):
+    def test_as_from_dict(self):
         self.mol.append("X", [2, 0, 0])
         d = self.mol.as_dict()
         mol2 = Molecule.from_dict(d)
diff --git a/tests/core/test_trajectory.py b/tests/core/test_trajectory.py
@@ -457,7 +457,7 @@ def test_variable_lattice(self):
         self._check_traj_equality(traj, written_traj)
         os.remove("traj_test_XDATCAR")
 
-    def test_to_from_dict(self):
+    def test_as_from_dict(self):
         d = self.traj.as_dict()
         traj = Trajectory.from_dict(d)
         assert isinstance(traj, Trajectory)
diff --git a/tests/electronic_structure/test_boltztrap.py b/tests/electronic_structure/test_boltztrap.py
@@ -259,7 +259,7 @@ def test_extreme(self):
         assert x["p"]["temperature"] == 400
         assert x["n"]["isotropic"] is False
 
-    def test_to_from_dict(self):
+    def test_as_from_dict(self):
         btr_dict = self.btr.as_dict()
         s = json.dumps(btr_dict)
         assert s is not None
diff --git a/tests/electronic_structure/test_dos.py b/tests/electronic_structure/test_dos.py
@@ -146,7 +146,7 @@ def test_get_gap(self):
         with pytest.raises(ValueError, match="x is out of range of provided x_values"):
             dos.get_interpolated_value(1000)
 
-    def test_to_from_dict(self):
+    def test_as_from_dict(self):
         d = self.dos.as_dict()
         dos = CompleteDos.from_dict(d)
         el_dos = dos.get_element_dos()
diff --git a/tests/entries/test_computed_entries.py b/tests/entries/test_computed_entries.py
diff --git a/tests/entries/test_exp_entries.py b/tests/entries/test_exp_entries.py
diff --git a/tests/files/.pytest-split-durations b/tests/files/.pytest-split-durations
diff --git a/tests/io/test_nwchem.py b/tests/io/test_nwchem.py
diff --git a/tests/io/vasp/test_inputs.py b/tests/io/vasp/test_inputs.py
diff --git a/tests/transformations/test_advanced_transformations.py b/tests/transformations/test_advanced_transformations.py
diff --git a/tests/transformations/test_site_transformations.py b/tests/transformations/test_site_transformations.py
diff --git a/tests/util/test_provenance.py b/tests/util/test_provenance.py

Original file line number	Diff line number	Diff line change
`@@ -390,7 +390,7 @@ def test_draw(self):`
`390`	`390`	`}`
`391`	`391`	`assert pdfs == expected_pdfs`
`392`	`392`
`393`		`- def test_to_from_dict(self):`
	`393`	`+ def test_as_from_dict(self):`
`394`	`394`	`d = self.mos2_sg.as_dict()`
`395`	`395`	`sg = StructureGraph.from_dict(d)`
`396`	`396`	`d2 = sg.as_dict()`