Fix remaining pycodestyle issues

abipy/__init__.py

@@ -20,8 +20,8 @@
 # Release data
 __author__ = ''
 for author, email in release.authors.values():
-  __author__ += author + ' <' + email + '>\n'
+    __author__ += author + ' <' + email + '>\n'
 del author, email
 
-__license__  = release.license
-__version__  = release.version
+__license__ = release.license
+__version__ = release.version

abipy/abilab.py

@@ -84,6 +84,7 @@ def _straceback():
     import traceback
     return traceback.format_exc()
 
+
 # Abinit text files. Use OrderedDict for nice output in show_abiopen_exc2class.
 ext2file = collections.OrderedDict([
     (".abi", AbinitInputFile),

abipy/abio/abivars.py

@@ -20,6 +20,7 @@
     "AbinitInputParser",
 ]
 
+
 def is_anaddb_var(varname):
     """True if varname is a valid Anaddb variable."""
     return varname in get_codevars()["anaddb"]
@@ -44,6 +45,7 @@ def is_abivar(varname):
         "T", "Tesla",)
 }
 
+
 def is_abiunit(s):
     """
     True if string is one of the units supported by the ABINIT parser
@@ -218,7 +220,7 @@ def to_string(self, post=None, mode="text", verbose=0):
             if mode == "html": vname = var_database[k].html_link(label=vname)
             app("%s %s" % (vname, str(self[k])))
 
-        return "\n".join(lines) if mode=="text" else "\n".join(lines).replace("\n", "<br>")
+        return "\n".join(lines) if mode == "text" else "\n".join(lines).replace("\n", "<br>")
 
     def _repr_html_(self):
         """Integration with jupyter_ notebooks."""
@@ -428,7 +430,7 @@ def parse(self, s):
 
         varpos.append(len(tokens))
 
-	# Build dict {varname --> value_string}
+        # Build dict {varname --> value_string}
         dvars = {}
         for i, pos in enumerate(varpos[:-1]):
             varname = tokens[pos]
@@ -452,7 +454,7 @@ def parse(self, s):
         if udtset is not None:
             raise NotImplementedError("udtset is not supported")
 
-	# Build list of datasets.
+        # Build list of datasets.
         datasets = [Dataset() for i in range(ndtset)]
 
         # Treat all variables without a dataset index
@@ -483,7 +485,7 @@ def parse(self, s):
             vname = k[:-1]
             start = str2array(dvars.pop(k))
 
-	    # Handle ecut+ or ecut*
+            # Handle ecut+ or ecut*
             incr = dvars.pop(vname + "+", None)
             if incr is not None:
                 incr = str2array(incr)
@@ -498,12 +500,12 @@ def parse(self, s):
                     dt[vname] = start.copy()
                     start *= mult
 
-	# Consistency check
-	# 1) dvars should be empty
+        # Consistency check
+        # 1) dvars should be empty
         if dvars:
             raise ValueError("Don't know how handle variables in:\n%s" % pformat(dvars), indent=4)
 
-	# 2) Keys in datasets should be valid Abinit input variables.
+        # 2) Keys in datasets should be valid Abinit input variables.
         wrong = []
         for i, dt in enumerate(datasets):
             wlist = [k for k in dt if not is_abivar(k)]
@@ -512,7 +514,7 @@ def parse(self, s):
         if wrong:
             raise ValueError("Found variables that are not registered in the abipy database:\n%s" % pformat(wrong, indent=4))
 
-	# 3) We don't support spg builder: dataset.structure will fail or, even worse,
+        # 3) We don't support spg builder: dataset.structure will fail or, even worse,
         #    spglib will segfault so it's better to raise here!
         for dt in datasets:
             if "spgroup" in dt or "nobj" in dt:
@@ -531,9 +533,9 @@ def eval_abinit_operators(tokens):
         Receive a list of strings, find the occurences of operators supported
         in the input file (e.g. sqrt), evalute the expression and return new list of strings.
 
-	.. note:
+        .. note:
 
-	    This function is not recursive hence expr like sqrt(1/2) are not supported
+            This function is not recursive hence expr like sqrt(1/2) are not supported
         """
         import math
         import re

abipy/abio/factories.py

@@ -63,6 +63,7 @@
     kppa=1000,
 )
 
+
 class ShiftMode(Enum):
     """
     Class defining the mode to be used for the shifts.
@@ -1416,6 +1417,7 @@ def dfpt_from_gsinput(gs_inp, ph_ngqpt=None, qpoints=None, do_ddk=True, do_dde=T
 
     return multi
 
+
 #FIXME if the pseudos are passed as a PseudoTable the whole table will be serialized,
 # it would be better to filter on the structure elements
 class InputFactory(MSONable):

abipy/abio/input_tags.py

@@ -8,7 +8,7 @@
 NSCF = "nscf"
 BANDS = "bands"
 DOS = "dos"
-MOLECULAR_DYNACMICS="molecular_dynamics"
+MOLECULAR_DYNACMICS = "molecular_dynamics"
 DFPT = "dfpt"
 PHONON = "phonon"
 DDK = "ddk"

abipy/abio/inputs.py

@@ -582,9 +582,11 @@ def to_string(self, sortmode="section", post=None, with_mnemonics=False, mode="t
         """
         if mode == "html":
             import html
+
             def escape(text):
                 return html.escape(text, quote=True)
         else:
+
             def escape(text):
                 return text
 
@@ -988,7 +990,7 @@ def product(self, *items):
         varnames, values = items[:i], items[i:]
         if len(varnames) != len(values):
             raise self.Error("The number of variables must equal the number of lists\n"
-                              "varnames: %s\nvalues %s" % (str(varnames), str(values)))
+                             "varnames: %s\nvalues %s" % (str(varnames), str(values)))
 
         # TODO: group varnames and varvalues!
         #varnames = [t[0] for t in items]
@@ -1117,8 +1119,8 @@ def new_with_structure(self, new_structure, scdims=None, verbose=1):
                 raise NotImplementedError("kptrlatt in new_with_structure")
                 #new["kptrlatt"] = (np.rint(np.array(new["kptrlatt"]) / iscale)).astype(int)
             else:
-               # Single k-point
-               pass
+                # Single k-point
+                pass
 
             # Add chkprim if not yet done.
             new.set_vars_ifnotin(chkprim=0)
@@ -1217,7 +1219,7 @@ def make_ph_inputs_qpoint(self, qpt, tolerance=None, prtwf=-1, prepgkk=0, manage
         # Note: this will work for phonons, but not for the other types of perturbations.
         for pert, ph_input in zip(perts, ph_inputs):
             rfdir = 3 * [0]
-            rfdir[pert.idir -1] = 1
+            rfdir[pert.idir - 1] = 1
 
             ph_input.set_vars(
                 rfphon=1,                           # Will consider phonon-type perturbation
@@ -1402,10 +1404,10 @@ def make_dte_inputs(self, phonon_pert=False, skip_permutations=False, ixc=None,
                 d3e_pert1_dir=rfdir1,  # Direction of the dte perturbation.
                 d3e_pert2_dir=rfdir2,
                 d3e_pert3_dir=rfdir3,
-                d3e_pert1_phon = 1 if pert.i1pert <= na else 0,
-                d3e_pert2_phon = 1 if pert.i2pert <= na else 0,
-                d3e_pert3_phon = 1 if pert.i3pert <= na else 0,
-                d3e_pert1_atpol = atpol,
+                d3e_pert1_phon=1 if pert.i1pert <= na else 0,
+                d3e_pert2_phon=1 if pert.i2pert <= na else 0,
+                d3e_pert3_phon=1 if pert.i3pert <= na else 0,
+                d3e_pert1_atpol=atpol,
                 nqpt=1,         # One wavevector is to be considered
                 qpt=(0, 0, 0),  # q-wavevector.
                 optdriver=5,    # non-linear response functions, using the 2n+1 theorem.
@@ -1437,7 +1439,7 @@ def make_bec_inputs(self, tolerance=None, manager=None):
         # See tutorespfn/Input/trf1_5.in dataset 3
         for pert, inp in zip(perts, multi):
             rfdir = 3 * [0]
-            rfdir[pert.idir -1] = 1
+            rfdir[pert.idir - 1] = 1
 
             inp.set_vars(
                 rfphon=1,             # Activate the calculation of the atomic dispacement perturbations
@@ -1480,7 +1482,7 @@ def make_strain_perts_inputs(self, tolerance=None, phonon_pert=True, kptopt=2, m
 
         for pert, inp in zip(perts, multi):
             rfdir = 3 * [0]
-            rfdir[pert.idir -1] = 1
+            rfdir[pert.idir - 1] = 1
 
             if pert.ipert <= len(self.structure):
                 inp.set_vars(rfphon=1,             # Activate the calculation of the atomic dispacement perturbations
@@ -1550,11 +1552,12 @@ def abiget_spacegroup(self, tolsym=None, retdict=False, workdir=None, manager=No
             retdict: True to return dictionary with space group information instead of Structure.
             workdir: Working directory of the fake task used to compute the ibz. Use None for temporary dir.
             manager: |TaskManager| of the task. If None, the manager is initialized from the config file.
-	    verbose: Verbosity level.
+            verbose: Verbosity level.
 
         Return:
             |Structure| object with AbinitSpaceGroup obtained from the main output file if retdict is False
-	    else dict with e.g. {'bravais': 'Bravais cF (face-center cubic)', 'spg_number': 227, 'spg_symbol': 'Fd-3m'}.
+            else dict with e.g.
+            {'bravais': 'Bravais cF (face-center cubic)', 'spg_number': 227, 'spg_symbol': 'Fd-3m'}.
         """
         # Avoid modifications in self.
         inp = self.deepcopy()
@@ -1658,7 +1661,7 @@ def _handle_task_exception(self, task, prev_exc):
         # 1) Abinit cannot be executed or runtime errors due e.g to libraries
         # 2) IO buffering (Abinit called MPI_ABORT but files are not flushed before aborting.
         # Try to return as much iformation as possible to aid debugging
-        errors = ["Problem in temp Task executed in %s" %  task.workdir,
+        errors = ["Problem in temp Task executed in %s" % task.workdir,
                   "Previous exception %s" % prev_exc]
 
         try:
@@ -2227,7 +2230,7 @@ def has_same_variable(kref, vref, other_inp):
 
             for i, inp in enumerate(self):
                 header = "### DATASET %d ###" % (i + 1)
-                is_last = (i==self.ndtset - 1)
+                is_last = (i == self.ndtset - 1)
                 s = inp.to_string(post=str(i + 1), with_pseudos=is_last and with_pseudos, mode=mode,
                                   with_structure=not has_same_structures, exclude=global_vars)
                 if s:
@@ -2236,7 +2239,7 @@ def has_same_variable(kref, vref, other_inp):
 
                 lines.append(s)
 
-            return "\n".join(lines) if mode=="text" else "\n".join(lines).replace("\n", "<br>")
+            return "\n".join(lines) if mode == "text" else "\n".join(lines).replace("\n", "<br>")
 
         else:
             # single datasets ==> don't append the dataset index to the variables.
@@ -2566,15 +2569,16 @@ def phbands_and_dos(cls, structure, ngqpt, nqsmall, qppa=None, ndivsm=20, line_d
 
         if lo_to_splitting:
             directions = []
+            rl = structure.lattice.reciprocal_lattice_crystallographic
             for i, qpt in enumerate(qptbounds):
                 if np.array_equal(qpt, (0, 0, 0)):
                     # anaddb expects cartesian coordinates for the qph2l list
                     if i > 0:
-                        directions.extend(structure.lattice.reciprocal_lattice_crystallographic.get_cartesian_coords(qptbounds[i-1]))
+                        directions.extend(rl.get_cartesian_coords(qptbounds[i-1]))
                         directions.append(0)
 
                     if i < len(qptbounds) - 1:
-                        directions.extend(structure.lattice.reciprocal_lattice_crystallographic.get_cartesian_coords(qptbounds[i+1]))
+                        directions.extend(rl.get_cartesian_coords(qptbounds[i+1]))
                         directions.append(0)
 
             if directions:
@@ -2872,7 +2876,6 @@ def html_link(self, label=None):
         return '<a href="%s" target="_blank">%s</a>' % (self.url, self.name if label is None else label)
 
 
-
 class OpticError(Exception):
     """Error class raised by OpticInput."""
 
@@ -2953,7 +2956,7 @@ def vars(self):
     def _check_varname(self, key):
         if key not in self._VARNAMES:
             raise self.Error("%s is not a valid optic variable.\n"
-                             "If you are sure the name is correct, please change the _VARIABLES list in:\n%s"  %
+                             "If you are sure the name is correct, please change the _VARIABLES list in:\n%s" %
                              (key, __file__))
 
     def get_default(self, key):

abipy/abio/outputs.py

@@ -237,6 +237,7 @@ def get_dtindex_key_value(line):
 
         # (varname, dtindex), [line1, line2 ...]
         stack_var, stack_lines = None, []
+
         def pop_stack():
             if stack_lines:
                 key, dtidx = stack_var
@@ -677,7 +678,6 @@ def yield_figs(self, **kwargs):  # pragma: no cover
             except Exception:
                 print("Abinit output files does not contain timopt data")
 
-
     def compare_gs_scf_cycles(self, others, show=True):
         """
         Produce and returns a list of matplotlib_ figure comparing the GS self-consistent
@@ -974,7 +974,7 @@ class OutNcFile(AbinitNcFile):
     def __init__(self, filepath):
         super().__init__(filepath)
         self.reader = NetcdfReader(filepath)
-        self._varscache= {k: None for k in self.reader.rootgrp.variables}
+        self._varscache = {k: None for k in self.reader.rootgrp.variables}
 
     def __dir__(self):
         """Ipython integration."""

abipy/abio/robots.py

@@ -85,7 +85,7 @@ def from_dir(cls, top, walk=True, abspath=False):
 
         Args:
             top (str): Root directory
-	    walk: if True, directories inside `top` are included as well.
+            walk: if True, directories inside `top` are included as well.
             abspath: True if paths in index should be absolute. Default: Relative to `top`.
         """
         new = cls(*cls._open_files_in_dir(top, walk))
@@ -98,7 +98,7 @@ def from_dirs(cls, dirpaths, walk=True, abspath=False):
         Similar to `from_dir` but accepts a list of directories instead of a single directory.
 
         Args:
-	    walk: if True, directories inside `top` are included as well.
+            walk: if True, directories inside `top` are included as well.
             abspath: True if paths in index should be absolute. Default: Relative to `top`.
         """
         items = []
@@ -119,7 +119,7 @@ def from_dir_glob(cls, pattern, walk=True, abspath=False):
 
         Args:
             pattern: Pattern string
-	    walk: if True, directories inside `top` are included as well.
+            walk: if True, directories inside `top` are included as well.
             abspath: True if paths in index should be absolute. Default: Relative to getcwd().
         """
         import glob
@@ -295,7 +295,7 @@ def scan_dir(self, top, walk=True):
 
         Return:
             Number of files found.
-	"""
+        """
         count = 0
         for filepath, abifile in self.__class__._open_files_in_dir(top, walk):
             count += 1
@@ -692,7 +692,7 @@ def close(self):
             if self._do_close.pop(abifile.filepath, False):
                 try:
                     abifile.close()
-                except:
+                except Exception:
                     print("Exception while closing: ", abifile.filepath)
                     print(exc)
 

abipy/abio/tests/test_factories.py

@@ -147,7 +147,6 @@ def test_g0w0_with_ppmodel_inputs(self):
         flow.register_work(G0W0Work(scf_input, nscf_input, scr_input, sigma_input))
         assert flow.build_and_pickle_dump(abivalidate=True) == 0
 
-
         # The default value of `shifts` changed in v0.3 from (0.5, 0.5, 0.5) to (0.0, 0.0, 0.0)
         multi = g0w0_with_ppmodel_inputs(self.si_structure, self.si_pseudo,
                                         scf_kppa, nscf_nband, ecuteps, ecutsigx,
@@ -301,7 +300,6 @@ def test_phonons_from_gsinput(self):
         self.assert_input_equality('phonons_from_gsinput_ph_q_pert_1.json', inp_ph_q_pert_1_obj)
         self.assert_input_equality('phonons_from_gsinput_ph_q_pert_2.json', inp_ph_q_pert_2_obj)
 
-
     def test_elastic_inputs_from_gsinput(self):
         """Testing elastic_inputs_from_gsinput."""
         gs_inp = gs_input(self.si_structure, self.si_pseudo, kppa=None, ecut=2, spin_mode="unpolarized")