From eb51ea025c97350d1122cea3483901ddc2ebe92a Mon Sep 17 00:00:00 2001
From: Sourcery AI <>
Date: Thu, 16 Nov 2023 01:43:44 +0000
Subject: [PATCH] 'Refactored by Sourcery'

---
 tests/io/orca/singles/test_sp.py | 21 ---------------
 tests/io/orca/test_io.py         |  7 -----
 wailord/_utils.py                | 11 ++++----
 wailord/exp/cookies.py           |  6 +----
 wailord/io/inp.py                | 42 +++++++----------------------
 wailord/io/orca.py               | 46 +++++++++++++++-----------------
 6 files changed, 37 insertions(+), 96 deletions(-)

diff --git a/tests/io/orca/singles/test_sp.py b/tests/io/orca/singles/test_sp.py
index 1dc026b..8957c22 100644
--- a/tests/io/orca/singles/test_sp.py
+++ b/tests/io/orca/singles/test_sp.py
@@ -22,7 +22,6 @@
 def test_orca_get_sp_e(datadir):
     sEnerg = waio.orca.orcaVis(ofile=datadir / "orca_qcisdt.out")
     np.testing.assert_almost_equal(sEnerg.fin_sp_e.m, -1.01010039)
-    pass
 
 
 def test_orca_runinfo(datadir):
@@ -35,7 +34,6 @@ def test_orca_runinfo(datadir):
         "theory": "QCISD",
         "slug": "H2_test",
     }
-    pass
 
 
 ##########################
@@ -47,14 +45,12 @@ def test_orca_mdci_e_bounds(datadir):
     sEnerg = waio.orca.orcaVis(ofile=datadir / "orca_qcisdt.out")
     with pytest.raises(ValueError):
         sEnerg.single_energy_surface(npoints=34)
-    pass
 
 
 def test_orca_energ_error(datadir):
     sEnerg = waio.orca.orcaVis(ofile=datadir / "orca_qcisdt.out")
     with pytest.raises(NotImplementedError):
         sEnerg.single_energy_surface(etype="Squid")
-    pass
 
 
 def test_orca_energ_empty(datadir):
@@ -64,7 +60,6 @@ def test_orca_energ_empty(datadir):
         sEnerg.single_energy_surface("MDCI", 33)
     with pytest.raises(ValueError):
         sEnerg.single_energy_surface("MDCI w/o Triples")
-    pass
 
 
 def test_orca_mdci_e_xvals(datadir):
@@ -76,7 +71,6 @@ def test_orca_mdci_e_xvals(datadir):
         blength,
         np.linspace(0.4, 2, 33),
     )
-    pass
 
 
 def test_orca_mdci_e_yvals(datadir):
@@ -125,7 +119,6 @@ def test_orca_mdci_e_yvals(datadir):
         energy,
         exp_e,
     )
-    pass
 
 
 def test_orca_mdci_e_mtrip_xvals(datadir):
@@ -137,7 +130,6 @@ def test_orca_mdci_e_mtrip_xvals(datadir):
         blength,
         np.linspace(0.4, 2, 33),
     )
-    pass
 
 
 def test_orca_mdci_e_mtrip_energy_evals(datadir):
@@ -146,7 +138,6 @@ def test_orca_mdci_e_mtrip_energy_evals(datadir):
     eDat = sEnerg.single_energy_surface(npoints=33)
     eDat1 = sEnerg.single_energy_surface()
     pd.testing.assert_frame_equal(eDat, eDat1)
-    pass
 
 
 def test_orca_mdci_e_mtrip_yvals(datadir):
@@ -195,7 +186,6 @@ def test_orca_mdci_e_mtrip_yvals(datadir):
         energy,
         exp_e,
     )
-    pass
 
 
 ############################
@@ -211,7 +201,6 @@ def test_mult_energy_surf(datadir):
     pd.testing.assert_frame_equal(eDat, eDatAll[["bond_length", "MDCI w/o Triples"]])
     pd.testing.assert_frame_equal(eDatMDCI, eDatAll[["bond_length", "MDCI"]])
     assert len(eDatAll) == len(eDat)
-    pass
 
 
 def test_mult_energy_surf_subset(datadir):
@@ -220,7 +209,6 @@ def test_mult_energy_surf_subset(datadir):
     assert "Actual Energy" not in eDatAll.columns
     assert "MDCI" in eDatAll.columns
     assert "SCF Energy" in eDatAll.columns
-    pass
 
 
 def test_mult_energy_surf_single(datadir):
@@ -230,7 +218,6 @@ def test_mult_energy_surf_single(datadir):
     pd.testing.assert_frame_equal(eDatMDCI, eDatSingleL.loc[:, ["bond_length", "MDCI"]])
     eDatSingle = sEnerg.mult_energy_surface(etype="MDCI")
     pd.testing.assert_frame_equal(eDatMDCI, eDatSingle.loc[:, ["bond_length", "MDCI"]])
-    pass
 
 
 ##############################
@@ -246,7 +233,6 @@ def test_orca_single_chargepop(datadir):
     sdat2 = spop.single_population_analysis("Loewdin")
     assert sdat2.shape == (4, 5)
     np.testing.assert_equal(sdat2.pcharge.to_numpy(), np.zeros(4))
-    pass
 
 
 def test_orca_single_fullpop(datadir):
@@ -258,7 +244,6 @@ def test_orca_single_fullpop(datadir):
     sdat2 = spop.single_population_analysis("Loewdin")
     assert sdat2.shape == (2, 6)
     np.testing.assert_equal(sdat2.pcharge.to_numpy(), np.zeros(2))
-    pass
 
 
 def test_orca_nstep_pop(datadir):
@@ -268,7 +253,6 @@ def test_orca_nstep_pop(datadir):
     assert (popdat >> si.filter(_.step == 1)).shape == (
         popdat >> si.filter(_.step == 2)
     ).shape
-    pass
 
 
 ################################
@@ -281,7 +265,6 @@ def test_orca_mult_chargepop(datadir):
     sdat = spop.mult_population_analysis()
     assert sdat.shape == (8, 10)
     np.testing.assert_equal(sdat.pcharge.to_numpy(), np.zeros(8))
-    pass
 
 
 def test_orca_mult_fullpop(datadir):
@@ -290,7 +273,6 @@ def test_orca_mult_fullpop(datadir):
     assert sdat.shape == (4, 11)
     np.testing.assert_equal(sdat.pcharge.to_numpy(), np.zeros(4))
     np.testing.assert_equal(sdat.pspin.to_numpy(), np.zeros(4))
-    pass
 
 
 ###############
@@ -308,7 +290,6 @@ def test_orca_irspec(datadir):
         sdat.freq.pint.m.to_numpy(), np.array([1639.47, 3807.28, 3903.73])
     )
     np.testing.assert_equal(sdat.Mode.to_numpy(), np.array([6, 7, 8]))
-    pass
 
 
 ######################
@@ -326,7 +307,6 @@ def test_orca_vpt2(datadir):
         sdat.harmonic_freq.pint.m.to_numpy(), np.array([1638.78, 3808.09, 3904.51])
     )
     np.testing.assert_equal(sdat.Mode.to_numpy(), np.array([1, 2, 3]))
-    pass
 
 
 #########################
@@ -360,4 +340,3 @@ def test_calc_htst(datadir):
     assert kf.u == "1/second"
     np.testing.assert_almost_equal(kf.m, 2.80583587e-07)
     np.testing.assert_almost_equal(kb.m, 3.31522447e-29)
-    pass
diff --git a/tests/io/orca/test_io.py b/tests/io/orca/test_io.py
index 520771f..57e1d90 100644
--- a/tests/io/orca/test_io.py
+++ b/tests/io/orca/test_io.py
@@ -92,7 +92,6 @@ def test_get_final_sp_energy(datadir):
             dtype=object,
         ),
     )
-    pass
 
 
 ##############################
@@ -121,7 +120,6 @@ def test_get_energy_surface_shape(datadir):
     assert len(edat[edat.isin(["3-21G"]).any(axis=1)]) == 3 * 33  #: 3 levels of theory
     assert len(edat[edat.isin(["UHF"]).any(axis=1)]) == 9 * 33  #: 9 basis sets
     assert edat.shape == (891, 8)  #: Rows = basis (9) * theory (3) * npoints (33)
-    pass
 
 
 @pytest.mark.filterwarnings("ignore::UserWarning")
@@ -129,7 +127,6 @@ def test_get_energy_surface_empty(datadir):
     expt = waio.orca.orcaExp(expfolder=datadir / "h2")
     with pytest.raises(ValueError):
         expt.get_energy_surface(etype=["MDCI", "Actual Energy"])
-    pass
 
 
 def test_get_energy_surface_shape_more(datadir):
@@ -159,7 +156,6 @@ def test_get_energy_surface_shape_more(datadir):
         edat.theory.value_counts().to_numpy(),
         np.repeat(33, 5),
     )
-    pass
 
 
 #######################
@@ -193,7 +189,6 @@ def test_get_pop(datadir):
         popdat.theory.value_counts().to_numpy(),
         np.array([60, 50, 40]),
     )
-    pass
 
 
 ###############
@@ -207,7 +202,6 @@ def test_get_ir_freq(datadir):
     vdat = expt.get_ir_spec()
     assert vdat.shape == (63, 11)
     assert (vdat >> si.filter(_.slug == "O1H2_h2o")).shape == (9, 11)
-    pass
 
 
 ######################
@@ -220,4 +214,3 @@ def test_vpt2_transitions(datadir):
     expt = waio.orca.orcaExp(expfolder=datadir / "vpt2_h2o", order_theory=oth)
     vdat = expt.get_vpt2_transitions()
     assert vdat.shape == (9, 9)
-    pass
diff --git a/wailord/_utils.py b/wailord/_utils.py
index dc1a3c6..01dbb2b 100644
--- a/wailord/_utils.py
+++ b/wailord/_utils.py
@@ -38,13 +38,12 @@ def __init__(self, *args, **kwargs):
                 self[key] = DotDict(self[key])
 
     def __getitem__(self, key):
-        if isinstance(key, str):
-            try:
-                return super().__getitem__(key)
-            except KeyError:
-                raise MissingVariableError(f"No such variable '{key}' exists") from None
-        else:
+        if not isinstance(key, str):
             raise TypeError("Key must be a string")
+        try:
+            return super().__getitem__(key)
+        except KeyError:
+            raise MissingVariableError(f"No such variable '{key}' exists") from None
 
     def __setitem__(self, key, value):
         if isinstance(value, dict) and not isinstance(value, DotDict):
diff --git a/wailord/exp/cookies.py b/wailord/exp/cookies.py
index e606a4d..e0ed95b 100644
--- a/wailord/exp/cookies.py
+++ b/wailord/exp/cookies.py
@@ -12,11 +12,7 @@
 
 def gen_base(filen=None, /, template="basicExperiment", *, absolute=False):
     """Generate a base template"""
-    if absolute:
-        template = str(template)
-    else:
-        template = str(TEMPLATE_DIR / template)
-
+    template = str(template) if absolute else str(TEMPLATE_DIR / template)
     if filen is not None:
         with open(filen, "r") as ymlfile:
             config = yaml.safe_load(ymlfile)
diff --git a/wailord/io/inp.py b/wailord/io/inp.py
index 76aa671..db80bae 100644
--- a/wailord/io/inp.py
+++ b/wailord/io/inp.py
@@ -93,8 +93,7 @@ def read_yml(self):
 
     def parse_geom(self, geom):
         """Rework the geometry into output"""
-        textlines = []
-        textlines.append("\n%geom")
+        textlines = ["\n%geom"]
         if "scan" in geom:
             textlines.append(f"\n  Scan\n")
             for scanthing in geom.scan.keys():
@@ -106,7 +105,7 @@ def parse_geom(self, geom):
                     raise TypeError(
                         f"Only dihedral, bond and angle scan types are supported, got {scanthing} instead"
                     )
-            textlines.append(f"  end")
+            textlines.append("  end")
         if "constrain" in geom:
             textlines.append(f"\n  Constraints\n")
             for consthing in geom.constrain.keys():
@@ -120,7 +119,7 @@ def parse_geom(self, geom):
                     raise TypeError(
                         f"Only dihedral, bond, angle, and cartesian constraints are supported, got {consthing} instead"
                     )
-            textlines.append(f"  end")
+            textlines.append("  end")
         if "maxiter" in geom:
             string = f"""
             maxiter {geom.maxiter}
@@ -135,10 +134,7 @@ def geom_constrain(self, cons, constype):
         constype = constype[0][0].upper()
         for constraint in cons:
             btwn = constraint["between"]
-            if "value" in constraint.keys():
-                value = float(constraint["value"])
-            else:
-                value = ""
+            value = float(constraint["value"]) if "value" in constraint.keys() else ""
             if constype != "C":
                 btwn_num = btwn.split(" ")
                 # TODO Handle the other types as tuples (B,2)
@@ -150,9 +146,7 @@ def geom_constrain(self, cons, constype):
                 )
                 # if constype == 'B' and len(btwn_num) == 2:
             else:
-                warnings.warn(
-                    f"Cartesian comments have not been implemented", UserWarning
-                )
+                warnings.warn("Cartesian comments have not been implemented", UserWarning)
                 comment = ""
             linesthing.append(f"    {{ {constype} {btwn} {value} C }} # {comment}\n")
         return "".join(linesthing)
@@ -232,7 +226,6 @@ def parse_xyz(self):
                         if "blocks" in self.config.keys():
                             self.blocks = self.parse_blocks(self.config.blocks)
                         self.gendir_qc(extra=None)
-        pass
 
     def parse_blocks(self, blocks):
         """Generic Block Handler
@@ -268,9 +261,7 @@ def parse_blocks(self, blocks):
         return "".join(blines)
 
     def parse_keywords(self, keywords):
-        keylines = []
-        for kl in keywords:
-            keylines.append(f"\n! {kl}")
+        keylines = [f"\n! {kl}" for kl in keywords]
         return "".join(keylines)
 
     def parse_yml(self):
@@ -281,7 +272,6 @@ def parse_yml(self):
         self.parse_xyz()
         if self.qc.active is True:
             self.parse_qc()
-        pass
 
     def parse_viz(self, viz):
         if viz.chemcraft is True:
@@ -296,8 +286,7 @@ def parse_viz(self, viz):
             return textwrap.dedent(string)
 
     def parse_scf(self, scf):
-        textlines = []
-        textlines.append("\n%scf\n")
+        textlines = ["\n%scf\n"]
         if "brokensym" in scf:
             textlines.append(
                 f"  BrokenSym {scf.brokensym.more_unpaired}, {scf.brokensym.less_unpaired}"
@@ -314,8 +303,7 @@ def parse_params(self, params):
         """Rework the parameters into output. Recall that these do not require
         relaxation, and can also take fixed variables. On the other hand, these
         need more information to set up."""
-        textlines = []
-        textlines.append("%paras\n")
+        textlines = ["%paras\n"]
         for param in params:
             if param.get("value"):
                 param["slot"]["name"] = param["name"]
@@ -326,14 +314,12 @@ def parse_params(self, params):
                 self.xyzlines[-1], comment = self.params_slot(param["slot"])
                 textlines.append(self.params_range(param, comment))
             else:
-                raise TypeError(
-                    f"Currently only value and range variables are supported"
-                )
+                raise TypeError("Currently only value and range variables are supported")
         textlines.append("end\n")
         return "".join(textlines)
 
     def params_slot(self, thing):
-        if not "xyz" in thing or thing["xyz"] is not True:
+        if "xyz" not in thing or thing["xyz"] is not True:
             raise TypeError("Currently only supports xyz")
         atype, anum, axis, name = itemgetter("atype", "anum", "axis", "name")(thing)
         xyztmp = self.xyzlines[-1].split("\n")
@@ -393,7 +379,6 @@ def parse_qc(self):
             itertt.chain(self.qc.style, self.qc.calculations, self.qc.basis_sets)
         )
         self.qcopts = qcList
-        pass
 
     def gendir_qc(self, basename=None, extra=None):
         """Function to generate QC folder structure recursively"""
@@ -406,20 +391,17 @@ def gendir_qc(self, basename=None, extra=None):
             styl = styl.replace(" ", "_")
             self.gendir_qcspin(basename / styl)
         self.genharness(basename)
-        pass
 
     def gendir_qcspin(self, path):
         """Generates the style folders"""
         for sp in self.spin:
             sp = sp.replace(" ", "")
             self.gendir_qccalc(path / Path(f"spin_{sp}"))
-        pass
 
     def gendir_qccalc(self, path):
         """Generates set of calculation folders"""
         for cal in self.config.qc.calculations:
             self.gendir_qcbasis(path / cal)
-        pass
 
     def gendir_qcbasis(self, path):
         """Generates the directory of input files. Note that the folders will have +
@@ -428,7 +410,6 @@ def gendir_qcbasis(self, path):
             bas = base.replace("+", "P").replace("*", "8")
             Path.mkdir(path / bas, parents=True, exist_ok=True)
             self.geninp(path / bas)
-        pass
 
     def geninp(self, path):
         """Uses the path to generate details for an input file"""
@@ -453,7 +434,6 @@ def geninp(self, path):
             from_loc=self.conf_path.parent / self.config.jobscript,
             slug=f"{tmpconf['basis']}_{tmpconf['style']}",
         )
-        pass
 
     def putscript(self, from_loc, to_loc, slug):
         """Copies the jobscript"""
@@ -473,7 +453,6 @@ def putscript(self, from_loc, to_loc, slug):
                     $orcadir/orca_2mkl orca -molden"""
                     script.writelines(textwrap.dedent(string))
         self.scripts.append(scriptname)
-        pass
 
     def writeinp(self, confobj, extralines=None):
         """Writes an input file. Minimally should have:
@@ -511,7 +490,6 @@ def writeinp(self, confobj, extralines=None):
             op.write("\n")
             op.write(self.xyzlines[-1])
             op.write("*")
-        pass
 
 
 class simpleInput:
diff --git a/wailord/io/orca.py b/wailord/io/orca.py
index 347b0ac..c936b73 100644
--- a/wailord/io/orca.py
+++ b/wailord/io/orca.py
@@ -133,9 +133,7 @@ def parseOut(filename, plotter=False):
         spin = "triplet"
     else:
         raise (NotImplementedError(f"Not yet implemented {runinfo['spin']}"))
-    finGeom = []
-    for i in reversed(range(1, num_species + 1)):
-        finGeom.append(allAtoms[-i])
+    finGeom = [allAtoms[-i] for i in reversed(range(1, num_species + 1))]
     #  Creates a dictionary of the system H num O num
     systr = pd.DataFrame(finGeom).atype.value_counts().to_dict()
     # Flattens the dictionary to a list
@@ -151,10 +149,7 @@ def parseOut(filename, plotter=False):
         spin=spin,
         theory=runinfo["theory"],
     )
-    if plotter == True:
-        return oout, energ
-    else:
-        return oout
+    return (oout, energ) if plotter == True else oout
 
 
 def get_e(orcaoutdat, basis, system):
@@ -207,9 +202,11 @@ def genEBASet(
     geometries. Depreciate this eventually."""
     outs = []
     for root, dirs, files in os.walk(rootdir.resolve()):
-        for filename in files:
-            if "out" in filename and "slurm" not in filename:
-                outs.append(parseOut(f"{root}/{filename}"))
+        outs.extend(
+            parseOut(f"{root}/{filename}")
+            for filename in files
+            if "out" in filename and "slurm" not in filename
+        )
     outdat = pd.DataFrame(data=outs)
     basis_type = CategoricalDtype(categories=order_basis, ordered=True)
     theory_type = CategoricalDtype(categories=order_theory, ordered=True)
@@ -368,9 +365,11 @@ def handle_exp(self, efol):
         with orca_config_path.open(mode="r") as ymlfile:
             self.inpconf = yaml.safe_load(ymlfile)
         for root, dirs, files in os.walk(efol.resolve()):
-            for filename in files:
-                if "out" in filename and "slurm" not in filename:
-                    fnames.append(Path(f"{root}/{filename}"))
+            fnames.extend(
+                Path(f"{root}/{filename}")
+                for filename in files
+                if "out" in filename and "slurm" not in filename
+            )
         self.orclist = fnames
         return
 
@@ -599,7 +598,6 @@ def get_final_e(self, dat=False):
                 raise (
                     ValueError(f"Final single point energy not found for {self.ofile}")
                 )
-        pass
 
     def final_sp_e(self):
         erow = self.runinfo
@@ -677,7 +675,7 @@ def single_energy_surface(self, etype="Actual Energy", npoints=None):
         """
         if etype not in OUT_REGEX:
             raise (NotImplementedError(f"{etype} has not been implemented yet"))
-        if npoints == None:
+        if npoints is None:
             npoints = self.eeval
         xaxis = []
         yaxis = []
@@ -727,7 +725,7 @@ def vib_freq(self):
                                 imaginary=True,
                             )
                         accumulate.append(v)
-                        i = i + 1
+                        i += 1
         vdat = pd.DataFrame(accumulate)
         vdat["freq"] = vdat["freq"].astype("pint[cm_1]")
         # TODO: Add experiment layer
@@ -772,7 +770,7 @@ def vpt2_transitions(self):
                             freq_diff=float(raw[3]),
                         )
                         accumulate.append(v)
-                        i = i + 1
+                        i += 1
         vdat = pd.DataFrame(accumulate)
         vdat["harmonic_freq"] = vdat["harmonic_freq"].astype("pint[cm_1]")
         vdat["vpt2_freq"] = vdat["vpt2_freq"].astype("pint[cm_1]")
@@ -783,9 +781,8 @@ def vpt2_transitions(self):
                     f"Data not found for {self.runinfo['theory']}, did you run VPT2?"
                 )
             )
-        else:
-            for key in self.runinfo.keys():
-                vdat[key] = self.runinfo[key]
+        for key in self.runinfo.keys():
+            vdat[key] = self.runinfo[key]
         return vdat
 
     def ir_spec(self):
@@ -812,7 +809,7 @@ def ir_spec(self):
                             TZ=float(raw[5].replace(")", "")),
                         )
                         accumulate.append(v)
-                        i = i + 1
+                        i += 1
         vdat = pd.DataFrame(accumulate)
         vdat["T2"] = vdat["T2"].astype("pint[km/mol]")
         vdat["freq"] = vdat["freq"].astype("pint[cm_1]")
@@ -822,9 +819,8 @@ def ir_spec(self):
                     f"Spectra not found for {self.runinfo['theory']}, did you run FREQ?"
                 )
             )
-        else:
-            for key in self.runinfo.keys():
-                vdat[key] = self.runinfo[key]
+        for key in self.runinfo.keys():
+            vdat[key] = self.runinfo[key]
         return vdat
 
     def single_population_analysis(self, poptype="Mulliken", /):
@@ -869,7 +865,7 @@ def single_population_analysis(self, poptype="Mulliken", /):
                                 pcharge=float(raw[-1]),
                             )
                         accumulate.append(c)
-                        i = i + 1
+                        i += 1
         popdat = pd.DataFrame(accumulate)
         step = popdat.anum.count() / popdat.anum.nunique()
         popdat["step"] = np.asarray(