Add seekpath to requirements

Author: gmatteo

abipy/abio/tests/test_abivars.py

@@ -188,7 +188,7 @@ def test_tricky_inputs(self):
         self.assert_equal(inp.structure[1].specie.symbol, "As")
         mat = 5.6533 * np.array([0, 1/2, 1/2, 1/2, 0, 1/2, 1/2, 1/2, 0])
         mat.shape = (3, 3)
-        self.assert_equal(inp.structure[1].lattice.matrix, mat)
+        self.assert_almost_equal(inp.structure[1].lattice.matrix, mat)
 
         # tutorial/input/tbase2_1
         # 2 datasets with different natom (should use typat[:1] in 2nd dataset)

abipy/dfpt/tests/test_msqdos.py

@@ -42,7 +42,7 @@ def test_from_ddb(self):
         assert np.all(abipy_indsym == msqd_dos.structure.indsym)
 
         cif_string = msqd_dos.get_cif_string(temp=300)
-        #print("cif_string:\n", cif_string)
+        print("cif_string:\n", cif_string)
 
         self.assertMultiLineEqual(cif_string, """\
 # generated using pymatgen
@@ -98,16 +98,6 @@ def test_from_ddb(self):
 O7    0.01126    0.01922    0.01356    0.00412   -0.00249    0.00765
 O8    0.01922    0.01518    0.01356   -0.00661   -0.00412    0.01157""")
 
-#Si0    0.00850    0.00695    0.00611   -0.00019   -0.00009    0.00348
-#Si1    0.00850    0.00850    0.00611    0.00009   -0.00009    0.00502
-#Si2    0.00695    0.00850    0.00611    0.00009    0.00019    0.00348
-#O3    0.01916    0.01120    0.01353    0.00249   -0.00411    0.00762
-#O4    0.01120    0.01512    0.01353   -0.00660   -0.00249    0.00358
-#O5    0.01512    0.01916    0.01353    0.00411    0.00660    0.01153
-#O6    0.01512    0.01120    0.01353    0.00249    0.00660    0.00358
-#O7    0.01120    0.01916    0.01353    0.00411   -0.00249    0.00762
-#O8    0.01916    0.01512    0.01353   -0.00660   -0.00411    0.01153""")
-
         # Write CIF file with U_cif tensor
         filepath = msqd_dos.write_cif_file(filepath=None, temp=300)
         assert filepath.endswith(".cif")

abipy/dfpt/tests/test_vzsisa.py

@@ -70,7 +70,7 @@ def test_vzsisa(self):
         self.assert_almost_equal(vols, [40.2445043, 40.4564043])
 
         vols, fits = qha.vol_Einf_Vib2(tstop=tstop, tstart=tstart, num=2)
-        self.assert_almost_equal(vols, [40.2457091, 40.4461412])
+        self.assert_almost_equal(vols, [40.2457091, 40.4461412], decimal=5)
 
         vols, fits = qha.vol_Einf_Vib4(tstop=tstop, tstart=tstart, num=2)
         self.assert_almost_equal(vols, [40.2456922, 40.4467746])

abipy/dynamics/analyzer.py

@@ -42,9 +42,6 @@
 e2s = 1.602188**2 # electron charge in Coulomb scaled by 10.d-19**2
 kbs = 1.38066     # Boltzmann constant in Joule/K scaled by 10.d-23
 
-#bohr2a = 0.529177
-#kBoltzAng10m9 = 1.38066e-02
-#kBoltz = 1.38066e-23
 kBoltzEv = 8.617333e-05
 #nCar = 56  # FIXME: Harcoded
 
@@ -420,6 +417,7 @@ def __init__(self,
             cart_positions: Cartesian positions in Ang. Default shape: (nt, natom, 3).
             ucmats: Array of lattice matrix of every step. Used for NPT.
                 For NVT-AIMD, the lattice at each time step is set to the lattice in the "structure" argument.
+            engine: String defining the engine used to produce the MD trajectory.
             pos_order: "tac" if cart_positions has shape (nt, natom, 3).
                        "atc" if cart_positions has shape (natom, nt, 3).
             evp_df:
@@ -1761,9 +1759,10 @@ class ArrheniusEntry:
 
     @classmethod
     def from_file(cls, filepath: PathLike, key, mpl_style) -> ArrheniusEntry:
-
-        # Read data in CSV format. Assuming header with at least the following entries:
-        #   temperature,diffusion,err_diffusion,volume,symbol,composition
+        """
+        Read data in CSV format. Assuming header with at least the following entries:
+        temperature,diffusion,err_diffusion,volume,symbol,composition
+        """
         try:
             df = pd.read_csv(filepath, skipinitialspace=True)
 
@@ -1993,7 +1992,7 @@ def plot(self, thinvt_arange=None, what="diffusion", ncar=None, colormap="jet",
             what: Selects the quantity to plot. Possibile values: "diffusion", "sigma", "tsigma".
             ncar: Number of carriers. Required if what is "sigma" or "tsigma".
             colormap: Colormap used to select the color if entry.mpl_style does not provide it.
-            with_t: True to dd a twin axes with the value of T
+            with_t: True to add a twin axes with the value of T
             text:
             ax: |matplotlib-Axes| or None if a new figure should be created.
             fontsize: fontsize for legends and titles.

pyproject.toml

@@ -58,6 +58,7 @@ dependencies = [
     "packaging",
     "pandas",
     "phonopy<=2.31.2",
+    "seekpath",
     "plotly",
     "pydispatcher>=2.0.5",
     #"pymatgen==v2024.10.29",

requirements.txt

@@ -23,6 +23,7 @@ ipython
 chart-studio
 click
 phonopy<=2.31.2
+seekpath
 ase
 # TODO remove after https://github.com/materialsproject/emmet/issues/768 is fixed
 pydantic<2.0.0

setup.py

@@ -168,6 +168,7 @@ def cleanup():
     "chart-studio",
     "click",
     "phonopy<=2.31.2",
+    "seekpath",
     "ase",
     #"custodian",
     #pydantic,