more cleanups and linting

python/xraydb/xray.py

@@ -1,15 +1,17 @@
-import sys
+"""
+calculations using XrayDB
+"""
 from collections import namedtuple
 import numpy as np
 
-from .utils import (R_ELECTRON_CM, AVOGADRO, PLANCK_HC, E_MASS,
+from .utils import (R_ELECTRON_CM, AVOGADRO, PLANCK_HC,
                     QCHARGE, SI_PREFIXES, index_nearest)
 
-R0 = 1.e8 * R_ELECTRON_CM
-
 from .xraydb import XrayDB,  XrayLine
 from .chemparser import chemparse
 
+R0 = 1.e8 * R_ELECTRON_CM
+
 fluxes = namedtuple('IonChamberFluxes', ('incident', 'transmitted',
                                          'photo', 'incoherent', 'coherent'))
 
@@ -532,8 +534,8 @@ def xray_line(element, line):
                 if lfinal is None:
                     lfinal = val[3][0]
         return XrayLine(value/scale, scale, linit, lfinal)
-    else:
-        return lines.get(line.title(), None)
+
+    return lines.get(line.title(), None)
 
 
 def fluor_yield(element, edge, line, energy):
@@ -564,7 +566,7 @@ def fluor_yield(element, edge, line, energy):
          etc) and probabilities for each of these.
 
     """
-    e0, fyield, jump = xray_edge(element, edge)
+    e0, fyield, _ = xray_edge(element, edge)
     trans  = xray_lines(element, initial_level=edge)
 
     lines = []
@@ -665,7 +667,7 @@ def ionization_potential(gas):
         return 32.0
 
 
-def guess_edge(energy, edges=['K', 'L3', 'L2', 'L1', 'M5']):
+def guess_edge(energy, edges=('K', 'L3', 'L2', 'L1', 'M5')):
     """guess an element and edge based on energy (in eV)
 
     Args:
@@ -676,7 +678,7 @@ def guess_edge(energy, edges=['K', 'L3', 'L2', 'L1', 'M5']):
         a tuple of (atomic symbol, edge) for best guess
 
     Notes:
-        by default, the list of edges is ['K', 'L3', 'L2', 'L1', 'M5']
+        by default, the list of edges is ('K', 'L3', 'L2', 'L1', 'M5')
 
     """
     xdb = get_xraydb()
@@ -692,7 +694,7 @@ def guess_edge(energy, edges=['K', 'L3', 'L2', 'L1', 'M5']):
             maxz = 0
             xquery = xdb.tables['xray_levels'].select()
             for row in xdb.session.execute(xquery).fetchall():
-                ir, elem, edgename, en, eyield, xjump = row
+                ir, elem, edgename, en, eyield, _ = row
                 iz = xdb.atomic_number(elem)
                 maxz = max(iz, maxz)
                 if ename == edgename.lower():
@@ -710,8 +712,7 @@ def guess_edge(energy, edges=['K', 'L3', 'L2', 'L1', 'M5']):
             diff = 0.25*diff
         elif edge in ('L1', 'M5'): # penalize L1 and M5 edges
             diff = 2.0*diff
-        if diff < min_diff:
-            min_diff = diff
+        min_diff = min(diff, min_diff)
         ret.append((edge, iz, diff))
 
     for edge, iz, diff in ret:
@@ -917,7 +918,6 @@ def ionchamber_fluxes(gas='nitrogen', volts=1.0, length=100.0, energy=10000.0,
     from .materials import material_mu
 
     xdb = get_xraydb()
-    fin = fout = fphoto = 0.0
 
     units = sensitivity_units.replace('Volts', 'V').replace('Volt', 'V')
     units = units.replace('Amperes', 'A').replace('Ampere', 'A')
@@ -1009,11 +1009,11 @@ def dynamical_theta_offset(energy, crystal='Si', hkl=(1, 1, 1), a=None,
     """
     lattice_constants = {'Si': 5.4309, 'Ge': 5.6578, 'C': 3.567}
     h_, k_, l_ = hkl
-    hklsum = (h_ + k_ + l_)
+    hklsum = h_ + k_ + l_
     if hklsum % 4 == 0 and (h_ % 2 == 0 and k_ % 2 == 0 and l_ % 2 == 0):
-        eqr = 8
+        pass
     elif (h_ % 2 == 1 and k_ % 2 == 1 and l_ % 2 == 1): # all odd
-        eqr =4*np.sqrt(2)
+        pass
     else:
         raise ValueError("hkl must sum to 4 or be all odd")
 
@@ -1117,7 +1117,7 @@ def darwin_width(energy, crystal='Si', hkl=(1, 1, 1), a=None,
 
     lattice_constants = {'Si': 5.4309, 'Ge': 5.6578, 'C': 3.567}
     h_, k_, l_ = hkl
-    hklsum = (h_ + k_ + l_)
+    hklsum = h_ + k_ + l_
     if hklsum % 4 == 0 and (h_ % 2 == 0 and k_ % 2 == 0 and l_ % 2 == 0):
         eqr = 8
     elif (h_ % 2 == 1 and k_ % 2 == 1 and l_ % 2 == 1): # all odd

python/xraydb/xraydb.py

@@ -22,10 +22,11 @@
 XrayEdge = namedtuple('XrayEdge', ('energy', 'fyield', 'jump_ratio'))
 XrayLine = namedtuple('XrayLine', ('energy', 'intensity', 'initial_level',
                                    'final_level'))
-ElementData = namedtuple('ElementData', ('Z', 'symbol', 'name', 'mass', 'density'))
-ComptonEnergies = namedtuple('ComptonEnergies', ('incident', 'xray_90deg', 'xray_mean', 'electron_mean'))
-
+ElementData = namedtuple('ElementData',
+                          ('Z', 'symbol', 'name', 'mass', 'density'))
 
+ComptonEnergies = namedtuple('ComptonEnergies',
+                   ('incident', 'xray_90deg', 'xray_mean', 'electron_mean'))
 
 def make_engine(dbname):
     "create engine for sqlite connection, perhaps trying a few sqlachemy variants"
@@ -78,10 +79,10 @@ def __init__(self, dbname='xraydb.sqlite', read_only=True):
             parent, _ = os.path.split(__file__)
             dbname = os.path.join(parent, dbname)
             if not os.path.exists(dbname):
-                raise IOError("Database '%s' not found!" % dbname)
+                raise IOError(f"Database '{dbname}' not found!")
 
         if not isxrayDB(dbname):
-            raise ValueError("'%s' is not a valid X-ray Database file!" % dbname)
+            raise ValueError(f"'{dbname}' is not a valid X-ray Database file!")
         self._cache = {}
         self.dbname = os.path.abspath(dbname)
         self.engine = make_engine(dbname)
@@ -161,14 +162,12 @@ def get_version(self, long=False, with_history=False):
             rows = rows[-1:]
         if long or with_history:
             for row in rows:
-                out.append("XrayDB Version: %s [%s] '%s'" % (row.tag,
-                                                             row.date,
-                                                             row.notes))
-            out.append("Python Version: %s" % __version__)
+                out.append(f"XrayDB Version: {row.tag} [row.date] '{row.notes}'")
+            out.append(f"Python Version: {__version__}")
             out = "\n".join(out)
         else:
-            out = "XrayDB Version: %s, Python Version: %s" % (rows[0].tag,
-                                                              __version__)
+            out = f"XrayDB Version: {rows[0].tag}, Python Version: {__version__}"
+
         return out
 
     def f0_ions(self, element=None):
@@ -409,7 +408,7 @@ def _elem_data(self, element):
             elif element.lower() in self.__atomic_names:
                 row = [r for r in rows if r.name == element.lower()][0]
             else:
-                raise ValueError("unknown element '%s'" % repr(element))
+                raise ValueError(f"unknown element '{repr(element)}'")
         return ElementData(int(row.atomic_number),
                            row.element.title(), row.name,
                            row.molar_mass, row.density)
@@ -699,7 +698,7 @@ def cross_section_elam(self, element, energies, kind='photo'):
         elem = self.symbol(element)
         kind = kind.lower()
         if kind not in ('coh', 'incoh', 'photo'):
-            raise ValueError('unknown cross section kind=%s' % kind)
+            raise ValueError(f'unknown cross section kind={kind}')
 
         tablename = 'photoabsorption' if kind == 'photo' else 'scattering'
 
@@ -757,7 +756,7 @@ def mu_elam(self, element, energies, kind='total'):
         elif kind.lower().startswith('incoh'):
             xsec = calc(element, energies, kind='incoh')
         else:
-            raise ValueError('unknown cross section kind=%s' % kind)
+            raise ValueError(f'unknown cross section kind={kind}')
         return xsec
 
     def coherent_cross_section_elam(self, element, energies):
@@ -808,5 +807,5 @@ def ionization_potential(self, gas):
         itab = self.tables['ionization_potentials']
         out = self.query(itab).filter(itab.c.gas == gas).all()
         if len(out) != 1:
-            raise ValueError('unknown gas for ionization potential: %s' % gas)
+            raise ValueError(f'unknown gas for ionization potential: {gas}')
         return float(out[0].potential)