skpkg: apply black line-length 79 to all files in the project directory

src/diffpy/__init__.py

@@ -12,4 +12,4 @@
 #
 ##############################################################################
 
-# Placeholder until this gets scikit-packaged later
+# Placeholder until this gets scikit-packaged later

src/diffpy/distanceprinter/__init__.py

@@ -16,7 +16,7 @@
 Blank namespace package.
 """
 
-__import__('pkg_resources').declare_namespace(__name__)
+__import__("pkg_resources").declare_namespace(__name__)
 
 
 # End of file

src/diffpy/distanceprinter/distanceprinter.py

@@ -18,23 +18,29 @@
 from diffpy.pdffit2 import PdfFit
 from diffpy.structure import PDFFitStructure
 
+
 def calDistance(strufile, atomi, atomj, lb, ub, complete):
-    
+
     stru = PDFFitStructure(filename=strufile)
     pdffit = PdfFit()
     pdffit.add_structure(stru)
     ele = stru.element
-        
+
     rv = pdffit.bond_length_types(atomi, atomj, lb, ub)
-    dij = np.around(rv['dij'], 6)
-    ddij = np.around(rv['ddij'], 10)
-    rv['all0ddij'] = np.all(ddij == 0)
-    ij0 = rv['ij0']
-
-    chardtype = 'S8' if complete else 'S4'
-    dtypec = [('distance', float), ('dd', float), ('i', chardtype), ('j', chardtype)]
+    dij = np.around(rv["dij"], 6)
+    ddij = np.around(rv["ddij"], 10)
+    rv["all0ddij"] = np.all(ddij == 0)
+    ij0 = rv["ij0"]
+
+    chardtype = "S8" if complete else "S4"
+    dtypec = [
+        ("distance", float),
+        ("dd", float),
+        ("i", chardtype),
+        ("j", chardtype),
+    ]
     distlist = np.zeros(len(dij), dtype=dtypec)
-    
+
     if not complete:
         for i, dist, dd, ij in zip(range(len(dij)), dij, ddij, ij0):
             if ij[0] > ij[1]:
@@ -44,55 +50,82 @@ def calDistance(strufile, atomi, atomj, lb, ub, complete):
         distlist = np.unique(distlist)
     else:
         for i, dist, dd, ij in zip(range(len(dij)), dij, ddij, ij0):
-            distlist[i] = (dist, dd, '%s.%i' % (ele[ij[0]], ij[0]), '%s.%i' % (ele[ij[1]], ij[1]))
-
-    distlist.sort(order='distance')
-    rv['distlist'] = distlist
-    rv['atomi'] = atomi
-    rv['atomj'] = atomj
-    rv['lb'] = lb
-    rv['ub'] = ub
-    rv['complete'] = complete
-    rv['stru'] = stru
-    rv['strufile'] = strufile
+            distlist[i] = (
+                dist,
+                dd,
+                "%s.%i" % (ele[ij[0]], ij[0]),
+                "%s.%i" % (ele[ij[1]], ij[1]),
+            )
+
+    distlist.sort(order="distance")
+    rv["distlist"] = distlist
+    rv["atomi"] = atomi
+    rv["atomj"] = atomj
+    rv["lb"] = lb
+    rv["ub"] = ub
+    rv["complete"] = complete
+    rv["stru"] = stru
+    rv["strufile"] = strufile
     return rv
-
+
+
 def formatResults(stru, distlist, complete, all0ddij, **kw):
-    '''
+    """
     format the distlist to string
-    '''
+    """
     lines = []
     # header
-    lines.append("# Structure file: %s" % kw['strufile'])
-    lines.append('# ')
+    lines.append("# Structure file: %s" % kw["strufile"])
+    lines.append("# ")
     strustr = stru.__str__().splitlines()
-    lines.append('# ' + strustr[0])
+    lines.append("# " + strustr[0])
     for i in range(1, len(strustr)):
-        lines.append('# %2i ' % (i - 1) + strustr[i])
-    lines.append('# ')
-    lines.append('# Inter-atomic distance of (%s, %s) in (%2.2f, %2.2f) A' 
-                 % (kw['atomi'], kw['atomj'], kw['lb'], kw['ub']))
-    lines.append('')
-
+        lines.append("# %2i " % (i - 1) + strustr[i])
+    lines.append("# ")
+    lines.append(
+        "# Inter-atomic distance of (%s, %s) in (%2.2f, %2.2f) A"
+        % (kw["atomi"], kw["atomj"], kw["lb"], kw["ub"])
+    )
+    lines.append("")
+
     if complete:
         for dist in distlist:
             try:
-                lines.append('%s-%s:\t%2.6f' % (dist[2].decode('utf-8'), dist[3].decode('utf-8'), dist[0]))
+                lines.append(
+                    "%s-%s:\t%2.6f"
+                    % (
+                        dist[2].decode("utf-8"),
+                        dist[3].decode("utf-8"),
+                        dist[0],
+                    )
+                )
             except AttributeError:
-                lines.append('%s-%s:\t%2.6f' % (dist[2], dist[3], dist[0]))
+                lines.append("%s-%s:\t%2.6f" % (dist[2], dist[3], dist[0]))
     else:
         for dist in distlist:
             try:
-                lines.append('%s-%s:\t%2.6f (%1.1e)' % (dist[2].decode('utf-8'), dist[3].decode('utf-8'), dist[0], dist[1]))
+                lines.append(
+                    "%s-%s:\t%2.6f (%1.1e)"
+                    % (
+                        dist[2].decode("utf-8"),
+                        dist[3].decode("utf-8"),
+                        dist[0],
+                        dist[1],
+                    )
+                )
             except AttributeError:
-                lines.append('%s-%s:\t%2.6f (%1.1e)' % (dist[2], dist[3], dist[0], dist[1]))
-    rv = '\n'.join(lines)
+                lines.append(
+                    "%s-%s:\t%2.6f (%1.1e)"
+                    % (dist[2], dist[3], dist[0], dist[1])
+                )
+    rv = "\n".join(lines)
     return rv
 
+
 def writeToFile(filename, rv):
-    f = open(filename, 'w', encoding="utf-8")
+    f = open(filename, "w", encoding="utf-8")
     try:
-        rv = rv.decode('utf-8')
+        rv = rv.decode("utf-8")
         f.write(rv)
         f.close()
     except AttributeError:
@@ -101,16 +134,18 @@ def writeToFile(filename, rv):
         f.close()
         pass
 
+
 def main():
     sysargv = sys.argv[1:]
     strufile, atomi, atomj, lb, ub, complete, filename = sysargv
     lb = float(lb)
     ub = float(ub)
-    complete = ('1' == complete)
+    complete = "1" == complete
     rv = calDistance(strufile, atomi, atomj, lb, ub, complete)
     strv = formatResults(**rv)
     writeToFile(filename, strv)
     return
 
-if __name__ == '__main__':
+
+if __name__ == "__main__":
     main()

src/diffpy/distanceprinter/version.py

@@ -13,22 +13,22 @@
 ##############################################################################
 
 
-"""Definition of __version__, __date__, __gitsha__.
-"""
+"""Definition of __version__, __date__, __gitsha__."""
 
 from pkg_resources import resource_filename
 from ConfigParser import RawConfigParser
 
 # obtain version information from the version.cfg file
-cp = RawConfigParser(dict(version='', date='', commit='', timestamp=0))
-if not cp.read(resource_filename(__name__, 'version.cfg')):
+cp = RawConfigParser(dict(version="", date="", commit="", timestamp=0))
+if not cp.read(resource_filename(__name__, "version.cfg")):
     from warnings import warn
+
     warn('Package metadata not found, execute "./setup.py egg_info".')
 
-__version__ = cp.get('DEFAULT', 'version')
-__date__ = cp.get('DEFAULT', 'date')
-__gitsha__ = cp.get('DEFAULT', 'commit')
-__timestamp__ = cp.getint('DEFAULT', 'timestamp')
+__version__ = cp.get("DEFAULT", "version")
+__date__ = cp.get("DEFAULT", "date")
+__gitsha__ = cp.get("DEFAULT", "commit")
+__timestamp__ = cp.getint("DEFAULT", "timestamp")
 
 del cp
 

tests/test_distanceprinter.py

@@ -10,26 +10,38 @@ def test_distanceprinter(monkeypatch):
     # must be cif, stru, or xyz file
     strufile = os.path.join(example_file_dir, "Ni-9008476.cif")
     # atoms typically pull from list of elements in stru output of PDFFitStructure. 'all' is always first option
-    atomi = 'all'
-    atomj = 'all'
+    atomi = "all"
+    atomj = "all"
     # lb and ub are lower an upper bound of distance to list in angstroms
     lb = 1
     ub = 10
     #  1 means keep duplicate atom pairs with same inter-atomic distance, 0 means not to
-    comp = '1'
-    monkeypatch.setattr("sys.argv", ['distanceprinter', strufile, atomi, atomj, lb, ub, comp, 'tests\\outputs\\actual.res'])
+    comp = "1"
+    monkeypatch.setattr(
+        "sys.argv",
+        [
+            "distanceprinter",
+            strufile,
+            atomi,
+            atomj,
+            lb,
+            ub,
+            comp,
+            "tests\\outputs\\actual.res",
+        ],
+    )
     cwd = os.getcwd()
     main()
-    generated_file_path = os.path.join(cwd, 'tests\\outputs\\actual.res')
-    f = open(generated_file_path, 'r', encoding="utf-8")
+    generated_file_path = os.path.join(cwd, "tests\\outputs\\actual.res")
+    f = open(generated_file_path, "r", encoding="utf-8")
     rv0 = f.readlines()
-    rv0 = ''.join(rv0)
+    rv0 = "".join(rv0)
     resultstr = rv0
     output_file_dir = os.path.join(current_module_dir, "outputs")
     example_output = os.path.join(output_file_dir, "expected.res")
-    f = open(example_output, 'r', encoding="utf-8")
+    f = open(example_output, "r", encoding="utf-8")
     rv1 = f.readlines()
-    rv1 = ''.join(rv1)
+    rv1 = "".join(rv1)
     teststr = rv1
 
     # Remove structure file path when comparing as it may differ between machines