fix: update helper imports after format move

Author: njzjz-bot

dpdata/__init__.py

@@ -1,19 +1,16 @@
 from __future__ import annotations
 
 from .bond_order_system import BondOrderSystem
-from .formats import lammps, md, vasp
 from .system import LabeledSystem, MultiSystems, System
 
 try:
     from ._version import version as __version__
 except ImportError:
     from .__about__ import __version__
 
+
 __all__ = [
     "__version__",
-    "lammps",
-    "md",
-    "vasp",
     "System",
     "LabeledSystem",
     "MultiSystems",

dpdata/formats/cp2k/__init__.py

@@ -0,0 +1,5 @@
+from __future__ import annotations
+
+from . import cell, output
+
+__all__ = ["cell", "output"]

dpdata/formats/gaussian/__init__.py

@@ -0,0 +1,5 @@
+from __future__ import annotations
+
+from . import fchk, gjf, log
+
+__all__ = ["fchk", "gjf", "log"]

dpdata/formats/qe/__init__.py

@@ -0,0 +1,5 @@
+from __future__ import annotations
+
+from . import scf, traj
+
+__all__ = ["scf", "traj"]

tests/test_cell_to_low_triangle.py

@@ -3,12 +3,13 @@
 import unittest
 
 import numpy as np
-from context import dpdata
+
+from dpdata.formats.cp2k.cell import cell_to_low_triangle
 
 
 class TestCellToLowTriangle(unittest.TestCase):
     def test_func1(self):
-        cell_1 = dpdata.cp2k.cell.cell_to_low_triangle(
+        cell_1 = cell_to_low_triangle(
             6, 6, 6, np.pi * 1 / 2, np.pi * 1 / 2, np.pi * 1 / 2
         )
         cell_2 = np.asarray([[6, 0, 0], [0, 6, 0], [0, 0, 6]])
@@ -17,7 +18,7 @@ def test_func1(self):
                 self.assertAlmostEqual(cell_1[ii, jj], cell_2[ii, jj], places=6)
 
     def test_func2(self):
-        cell_1 = dpdata.cp2k.cell.cell_to_low_triangle(
+        cell_1 = cell_to_low_triangle(
             6, 6, 6, np.pi * 1 / 3, np.pi * 1 / 3, np.pi * 1 / 3
         )
         cell_2 = np.asarray(
@@ -28,7 +29,7 @@ def test_func2(self):
                 self.assertAlmostEqual(cell_1[ii, jj], cell_2[ii, jj], places=6)
 
     def test_func3(self):
-        cell_1 = dpdata.cp2k.cell.cell_to_low_triangle(
+        cell_1 = cell_to_low_triangle(
             6, 7, 8, np.pi * 133 / 180, np.pi * 84 / 180, np.pi * 69 / 180
         )
         cell_2 = np.asarray(
@@ -45,21 +46,17 @@ def test_func3(self):
 
     def test_func4(self):
         with self.assertRaises(Exception) as c:
-            dpdata.cp2k.cell.cell_to_low_triangle(
-                0.1, 6, 6, np.pi * 1 / 2, np.pi * 1 / 2, np.pi * 1 / 2
-            )
+            cell_to_low_triangle(0.1, 6, 6, np.pi * 1 / 2, np.pi * 1 / 2, np.pi * 1 / 2)
         self.assertTrue("A==0.1" in str(c.exception))
 
     def test_func5(self):
         with self.assertRaises(Exception) as c:
-            dpdata.cp2k.cell.cell_to_low_triangle(
-                6, 6, 6, np.pi * 3 / 180, np.pi * 1 / 2, np.pi * 1 / 2
-            )
+            cell_to_low_triangle(6, 6, 6, np.pi * 3 / 180, np.pi * 1 / 2, np.pi * 1 / 2)
         self.assertTrue("alpha" in str(c.exception))
 
     def test_func6(self):
         with self.assertRaises(Exception) as c:
-            dpdata.cp2k.cell.cell_to_low_triangle(
+            cell_to_low_triangle(
                 6, 7, 8, np.pi * 153 / 180, np.pi * 84 / 180, np.pi * 69 / 180
             )
         self.assertTrue("lz^2" in str(c.exception))

tests/test_gaussian_driver.py

@@ -9,6 +9,8 @@
 from comp_sys import CompSys, IsNoPBC
 from context import dpdata
 
+from dpdata.formats.gaussian.gjf import detect_multiplicity
+
 
 @unittest.skipIf(shutil.which("g16") is None, "g16 is not installed")
 @unittest.skipIf(
@@ -83,9 +85,7 @@ def test_detect_multiplicity(self):
         self._check_multiplicity(["C", "H"], 2)
 
     def _check_multiplicity(self, symbols, multiplicity):
-        self.assertEqual(
-            dpdata.gaussian.gjf.detect_multiplicity(np.array(symbols)), multiplicity
-        )
+        self.assertEqual(detect_multiplicity(np.array(symbols)), multiplicity)
 
     def tearDown(self):
         if os.path.exists("gaussian/tmp.gjf"):

tests/test_msd.py

@@ -5,6 +5,8 @@
 import numpy as np
 from context import dpdata
 
+from dpdata.formats.md.msd import msd as calc_msd
+
 
 class TestMSD(unittest.TestCase):
     def setUp(self):
@@ -22,9 +24,9 @@ def setUp(self):
 
     def test_msd(self):
         # print(self.system['atom_types'] == 0)
-        msd = dpdata.md.msd.msd(self.system)
-        msd0 = dpdata.md.msd.msd(self.system, self.system["atom_types"] == 0)
-        msd1 = dpdata.md.msd.msd(self.system, self.system["atom_types"] == 1)
+        msd = calc_msd(self.system)
+        msd0 = calc_msd(self.system, self.system["atom_types"] == 0)
+        msd1 = calc_msd(self.system, self.system["atom_types"] == 1)
         # print(msd)
         ncomp = msd.shape[0]
         for ii in range(ncomp):

tests/test_qe_cp_traj.py

@@ -5,6 +5,8 @@
 import numpy as np
 from context import dpdata
 
+from dpdata.formats.qe.traj import convert_celldm
+
 bohr2ang = dpdata.unit.LengthConversion("bohr", "angstrom").value()
 
 
@@ -61,7 +63,7 @@ def setUp(self):
 
 class TestConverCellDim(unittest.TestCase):
     def test_case_null(self):
-        cell = dpdata.qe.traj.convert_celldm(8, [1, 1, 1])
+        cell = convert_celldm(8, [1, 1, 1])
         ref = np.eye(3)
         for ii in range(3):
             for jj in range(3):

tests/test_water_ions.py

@@ -5,6 +5,13 @@
 
 from context import dpdata
 
+from dpdata.formats.md.water import (
+    compute_bonds,
+    compute_bonds_ase,
+    compute_bonds_naive,
+    find_ions,
+)
+
 try:
     import ase  # noqa: F401
     import ase.neighborlist  # noqa: F401
@@ -20,16 +27,14 @@ def setUp(self):
         self.system.from_lammps_lmp(
             os.path.join("poscars", "conf.waterion.lmp"), type_map=["O", "H"]
         )
-        self.bonds = dpdata.md.water.compute_bonds(
+        self.bonds = compute_bonds(
             self.system.data["cells"][0],
             self.system.data["coords"][0],
             self.system.data["atom_types"],
         )
 
     def test_ions_count(self):
-        no, noh, noh2, noh3, nh = dpdata.md.water.find_ions(
-            self.system.data["atom_types"], self.bonds
-        )
+        no, noh, noh2, noh3, nh = find_ions(self.system.data["atom_types"], self.bonds)
         self.assertEqual(len(no), 0)
         self.assertEqual(len(noh), 1)
         self.assertEqual(len(noh2), 125)
@@ -46,12 +51,12 @@ def setUp(self):
         self.system.from_lammps_lmp(
             os.path.join("poscars", "conf.waterion.lmp"), type_map=["O", "H"]
         )
-        self.bonds = dpdata.md.water.compute_bonds_naive(
+        self.bonds = compute_bonds_naive(
             self.system.data["cells"][0],
             self.system.data["coords"][0],
             self.system.data["atom_types"],
         )
-        self.bonds_ase = dpdata.md.water.compute_bonds_ase(
+        self.bonds_ase = compute_bonds_ase(
             self.system.data["cells"][0],
             self.system.data["coords"][0],
             self.system.data["atom_types"],