Enforce PEP8 compliance (#9)

* enforce PEP8 compliance

* apply once more ruff --fix

* one last ruff format call

.github/workflows/quemb_unittest.yml

@@ -52,7 +52,7 @@ jobs:
 
     - name: Check formatting
       run: |
-        ruff format --diff || true    # for the moment we want to report always report success
+        ruff format --diff
 
 
     - name: Static analysis

src/kbe/helper.py

@@ -5,8 +5,6 @@
 import numpy
 
 
-
-
 def get_veff(eri_, dm, S, TA, hf_veff, return_veff0=False):
     from pyscf import scf
 

src/kbe/pbe.py

@@ -13,8 +13,6 @@
 from .pfrag import Frags
 
 
-
-
 class BE:
     """
     Class for handling periodic bootstrap embedding (BE) calculations.

src/kbe/pfrag.py

@@ -13,8 +13,6 @@
 from .solver import schmidt_decomp_svd
 
 
-
-
 class Frags:
     """
     Class for handling fragments in periodic bootstrap embedding.

src/molbe/_opt.py

@@ -177,6 +177,7 @@ def optimize(self, method, J0=None, trust_region=False):
         import sys
 
         from molbe.external.optqn import FrankQN
+
         print("-----------------------------------------------------", flush=True)
         print("             Starting BE optimization ", flush=True)
         print("             Solver : ", self.solver, flush=True)

src/molbe/external/lo_helper.py

@@ -26,7 +26,6 @@ def get_symm_mat_pow(A, p, check_symm=True, thresh=1.0e-8):
 
 
 def get_aoind_by_atom(mol, atomind_by_motif=None):
-
     natom = mol.natm
     aoslice_by_atom = mol.aoslice_by_atom()
     aoshift_by_atom = [0] + [aoslice_by_atom[ia][-1] for ia in range(natom)]

src/molbe/external/unrestricted_utils.py

@@ -6,8 +6,6 @@
 import numpy
 
 
-
-
 def make_uhf_obj(fobj_a, fobj_b, frozen=False):
     from pyscf import scf
 

src/molbe/fragment.py

@@ -6,8 +6,6 @@
 from .helper import get_core
 
 
-
-
 class fragpart:
     """Fragment/partitioning definition
 

src/molbe/lo.py

@@ -365,7 +365,6 @@ def localize(
             self.lmo_coeff = self.W.T @ self.S @ self.C[:, self.ncore :]
 
     elif lo_method == "iao":
-
         loc_type = "SO"
         val_basis = "sto-3g"
 
@@ -468,7 +467,6 @@ def localize(
             self.lmo_coeff = self.W.T @ self.S @ self.C[:, self.ncore :]
 
     elif lo_method == "boys":
-
         es_, vs_ = eigh(self.S)
         edx = es_ > 1.0e-15
         W_ = numpy.dot(vs_[:, edx] / numpy.sqrt(es_[edx]), vs_[:, edx].T)

src/molbe/mbe.py

@@ -5,7 +5,6 @@
 
 import h5py
 import numpy
-import pyscf
 
 import molbe.be_var as be_var
 
@@ -67,6 +66,7 @@ class BE:
     lo_method : str
         Method for orbital localization, default is 'lowdin'.
     """
+
     def __init__(
         self,
         mf,

src/molbe/misc.py

@@ -410,7 +410,6 @@ def be2puffin(
                 use_df = False
                 jk = None
             elif use_df and jk is None:
-
                 mf = scf.RHF(mol).density_fit(auxbasis=df_aux_basis)
             else:
                 mf = scf.RHF(mol)

src/molbe/pfrag.py

@@ -235,7 +235,6 @@ def scf(
             Alpha (0) or beta (1) spin for unrestricted calculation, by default None
         """
 
-
         if self._mf is not None:
             self._mf = None
         if self._mc is not None:

src/molbe/solver.py

@@ -133,7 +133,6 @@ def be_func(
                 rdm1_tmp = make_rdm1_ccsd_t1(fobj.t1)
 
         elif solver == "FCI":
-
             mc = fci.FCI(fobj._mf, fobj._mf.mo_coeff)
             efci, civec = mc.kernel()
             rdm1_tmp = mc.make_rdm1(civec, mc.norb, mc.nelec)

src/molbe/ube.py

@@ -22,8 +22,6 @@
 from .pfrag import Frags
 
 
-
-
 class UBE(BE):  # 🍠
     def __init__(
         self,
@@ -457,8 +455,16 @@ def oneshot(
         print(flush=True)
 
         self.ebe_tot = E + self.uhf_full_e
-        print("Total Energy : {:>12.8f} Ha".format((self.ebe_tot), ))
-        print("Corr  Energy : {:>12.8f} Ha".format((E), ))
+        print(
+            "Total Energy : {:>12.8f} Ha".format(
+                (self.ebe_tot),
+            )
+        )
+        print(
+            "Corr  Energy : {:>12.8f} Ha".format(
+                (E),
+            )
+        )
 
         if clean_eri == True:
             try:

tests/chem_dm_kBE_test.py

@@ -13,8 +13,6 @@
 from kbe import BE, fragpart
 
 
-
-
 class Test_kBE_Full(unittest.TestCase):
     try:
         import libdmet

tests/chempot_molBE_test.py

@@ -12,8 +12,6 @@
 from molbe import BE, fragpart
 
 
-
-
 class TestBE_restricted(unittest.TestCase):
     def test_h8_sto3g_ben(self):
         # Linear Equidistant (r=1Å) H8 Chain, STO-3G

tests/dm_molBE_test.py

@@ -11,8 +11,6 @@
 from molbe import BE, fragpart
 
 
-
-
 class TestBE_restricted(unittest.TestCase):
     # TODO: Add test against known values (molecular_restrict_test)
     def test_h8_sto3g_ben_trustRegion(self):

tests/dmrg_molBE_test.py

@@ -12,16 +12,16 @@
 from molbe import BE, fragpart
 
 
-
-
 class TestBE_DMRG(unittest.TestCase):
     try:
         from pyscf import dmrgscf
     except ImportError:
         dmrgscf = None
 
-    @unittest.skipIf(not os.getenv("QUEMB_DO_KNOWN_TO_FAIL_TESTS") == "true",
-                     reason="This test is known to fail.")
+    @unittest.skipIf(
+        not os.getenv("QUEMB_DO_KNOWN_TO_FAIL_TESTS") == "true",
+        reason="This test is known to fail.",
+    )
     def test_h8_sto3g_pipek(self):
         mol = gto.M()
         mol.atom = [["H", (0.0, 0.0, i * 1.2)] for i in range(8)]

tests/eri_onthefly_test.py

@@ -12,8 +12,6 @@
 from molbe import BE, fragpart
 
 
-
-
 class TestDF_ontheflyERI(unittest.TestCase):
     @unittest.skipIf(
         os.getenv("QUEMB_SKIP_EXPENSIVE_TESTS") == "true",

tests/hf-in-hf_BE_test.py

@@ -12,8 +12,6 @@
 from molbe import BE, fragpart
 
 
-
-
 class TestHFinHF_restricted(unittest.TestCase):
     def test_h8_sto3g_ben(self):
         # Linear Equidistant (r=1Å) H8 Chain, STO-3G

tests/molbe_h8_test.py

@@ -31,7 +31,7 @@ def prepare_system():
     return mol, mf
 
 
-def do_BE(mol, mf, be_type : str, only_chem : bool):
+def do_BE(mol, mf, be_type: str, only_chem: bool):
     fobj = fragpart(be_type=be_type, mol=mol)
     mybe = BE(mf, fobj)
     mybe.optimize(solver="FCI", only_chem=only_chem)
@@ -64,6 +64,6 @@ def test_BE_chemical_potential():
     assert np.isclose(BE3.ebe_tot - BE3.ebe_hf, -0.1332017928466369)
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     test_BE_chemical_potential()
-    test_BE_density_matching()
+    test_BE_density_matching()

tests/molbe_io_fcidump_test.py

@@ -19,8 +19,10 @@ def prepare_system():
     # Read in molecular integrals expressed in libint basis ordering
     # numpy.loadtxt takes care of the input under the hood
     mol, mf = libint2pyscf(
-        "data/distorted_octane.xyz", "data/hcore_libint_octane.dat",
-        "STO-3G", hcore_skiprows=1
+        "data/distorted_octane.xyz",
+        "data/hcore_libint_octane.dat",
+        "STO-3G",
+        hcore_skiprows=1,
     )
     with with_omp_threads(1):
         # multi-threaded HF execution can lead to non-deterministic
@@ -34,7 +36,7 @@ def prepare_system():
     return oct_be
 
 
-def verify_fcidump_writing(kind_of_MO : str):
+def verify_fcidump_writing(kind_of_MO: str):
     oct_be = prepare_system()
     tmp_dir = Path(mkdtemp())
     data_dir = Path("data/octane_FCIDUMPs/")
@@ -44,27 +46,32 @@ def verify_fcidump_writing(kind_of_MO : str):
     be2fcidump(oct_be, str(tmp_dir / kind_of_MO / "octane"), kind_of_MO)
 
     for i in range(6):
-        reference = fcidump.read(data_dir / kind_of_MO / f'octanef{i}')
-        new = fcidump.read(tmp_dir / kind_of_MO / f'octanef{i}')
+        reference = fcidump.read(data_dir / kind_of_MO / f"octanef{i}")
+        new = fcidump.read(tmp_dir / kind_of_MO / f"octanef{i}")
 
-        for key in ['H1', 'H2']:
+        for key in ["H1", "H2"]:
             if not np.allclose(new[key], reference[key]):
                 print(abs(new[key] - reference[key]).max())
                 raise ValueError("too large difference")
     rmtree(tmp_dir)
 
 
-@pytest.mark.skipif(not os.getenv("QUEMB_DO_KNOWN_TO_FAIL_TESTS") == "true",
-                    reason="This test is known to fail.")
+@pytest.mark.skipif(
+    not os.getenv("QUEMB_DO_KNOWN_TO_FAIL_TESTS") == "true",
+    reason="This test is known to fail.",
+)
 def test_embedding():
     verify_fcidump_writing("embedding")
 
 
-@pytest.mark.skipif(not os.getenv("QUEMB_DO_KNOWN_TO_FAIL_TESTS") == "true",
-                    reason="This test is known to fail.")
+@pytest.mark.skipif(
+    not os.getenv("QUEMB_DO_KNOWN_TO_FAIL_TESTS") == "true",
+    reason="This test is known to fail.",
+)
 def test_fragment_mo():
     verify_fcidump_writing("fragment_mo")
 
-if __name__ == '__main__':
+
+if __name__ == "__main__":
     test_embedding()
     test_fragment_mo()

tests/molbe_octane_get_rdms_test.py

@@ -11,8 +11,11 @@
 #   energies etc.
 #   At the moment the test fails already for technical reasons.
 
-@pytest.mark.skipif(not os.getenv("QUEMB_DO_KNOWN_TO_FAIL_TESTS") == "true",
-                    reason="This test is known to fail.")
+
+@pytest.mark.skipif(
+    not os.getenv("QUEMB_DO_KNOWN_TO_FAIL_TESTS") == "true",
+    reason="This test is known to fail.",
+)
 def test_rdm():
     # Perform pyscf HF calculation to get mol & mf objects
     mol = gto.M(
@@ -48,7 +51,6 @@ def test_rdm():
         charge=0,
     )
 
-
     mf = scf.RHF(mol)
     mf.conv_tol = 1e-12
     mf.kernel()

tests/molbe_octane_test.py

@@ -11,8 +11,11 @@
 # TODO: actually add meaningful tests for energies etc.
 #   At the moment the test fails already for technical reasons.
 
-@pytest.mark.skipif(not os.getenv("QUEMB_DO_KNOWN_TO_FAIL_TESTS") == "true",
-                    reason="This test is known to fail.")
+
+@pytest.mark.skipif(
+    not os.getenv("QUEMB_DO_KNOWN_TO_FAIL_TESTS") == "true",
+    reason="This test is known to fail.",
+)
 def test_octane_molbe():
     # Perform pyscf HF calculation to get mol & mf objects
     mol = gto.M(
@@ -48,7 +51,6 @@ def test_octane_molbe():
         charge=0,
     )
 
-
     mf = scf.RHF(mol)
     mf.conv_tol = 1e-12
     mf.kernel()

tests/molbe_oneshot_rbe_qmmm-fromchk_test.py

@@ -19,10 +19,10 @@
 # misc/be2puffin
 
 
-
-@pytest.mark.skipif(not os.getenv("QUEMB_DO_KNOWN_TO_FAIL_TESTS") == "true",
-                    reason="This test is known to fail because the check file "
-                           "does not exist.")
+@pytest.mark.skipif(
+    not os.getenv("QUEMB_DO_KNOWN_TO_FAIL_TESTS") == "true",
+    reason="This test is known to fail because the check file " "does not exist.",
+)
 def test_rbe_qmmm_fromchk():
     charges = [-0.2, -0.1, 0.15, 0.2]
     coords = [(-3, -8, -2), (-2, 6, 1), (2, -5, 2), (1, 8, 1.5)]