Committing clang-format changes

docs/source/conf.py

@@ -13,7 +13,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-
 import os
 
 # -- Project information -----------------------------------------------------
@@ -40,15 +39,9 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.doctest',
-    'sphinx.ext.intersphinx',
-    'sphinx.ext.todo',
-    'sphinx.ext.coverage',
-    'sphinx.ext.mathjax',
-    'sphinx.ext.githubpages',
-    'sphinx_togglebutton',
-    'sphinxcontrib.bibtex',
+    'sphinx.ext.autodoc', 'sphinx.ext.doctest', 'sphinx.ext.intersphinx',
+    'sphinx.ext.todo', 'sphinx.ext.coverage', 'sphinx.ext.mathjax',
+    'sphinx.ext.githubpages', 'sphinx_togglebutton', 'sphinxcontrib.bibtex',
     'sphinx_rtd_theme'
 ]
 
@@ -90,7 +83,7 @@
 pygments_style = 'sphinx'
 
 # Enable/disable numbered figures
-numfig  = True
+numfig = True
 
 # -- Options for HTML output -------------------------------------------------
 
@@ -103,15 +96,13 @@
 # further.  For a list of options available for each theme, see the
 # documentation.
 #
-html_theme_options = {
-    'vcs_pageview_mode' : 'edit'
-}
+html_theme_options = {'vcs_pageview_mode': 'edit'}
 
 html_context = {
-  'display_github': True,
-  'github_user': 'rmrresearch',
-  'github_repo': 'ghostfragment',
-  'github_version': 'master/docs/source/',
+    'display_github': True,
+    'github_user': 'rmrresearch',
+    'github_repo': 'ghostfragment',
+    'github_version': 'master/docs/source/',
 }
 
 # Add any paths that contain custom static files (such as style sheets) here,
@@ -129,13 +120,11 @@
 #
 # html_sidebars = {}
 
-
 # -- Options for HTMLHelp output ---------------------------------------------
 
 # Output file base name for HTML help builder.
 htmlhelp_basename = project + 'doc'
 
-
 # -- Options for LaTeX output ------------------------------------------------
 
 latex_elements = {
@@ -160,17 +149,13 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, project + '.tex',project + ' Documentation', author, 'manual'),
+    (master_doc, project + '.tex', project + ' Documentation', author,
+     'manual'),
 ]
 
-
-
-
 # -- Extension configuration -------------------------------------------------
 
 # -- Options for intersphinx extension ---------------------------------------
 
 # Example configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {'python' : ('https://docs.python.org/', None) }
-
-
+intersphinx_mapping = {'python': ('https://docs.python.org/', None)}

scripts/equations/generate_gmbe.py

@@ -19,6 +19,7 @@
 
 
 class Term:
+
     def __init__(self, coeff, value):
         self.coeff = coeff
         self.value = value
@@ -48,6 +49,7 @@ def make_fragments(n_fragments):
         fragments.append(Index(some_letters[i]))
     return fragments
 
+
 def make_nmers(trunc_order, frags):
     nmers = []
     if trunc_order == 1:
@@ -76,13 +78,15 @@ def make_intersections(nmers):
 
     return ovps
 
+
 def diff_ovps(old_nmers, new_nmer):
     old_ovps = make_intersections(old_nmers)
     new_nmers = old_nmers + [new_nmer]
     new_ovps = make_intersections(new_nmers)
     return [x for x in new_ovps if x not in old_ovps]
 
-def print_equation(nmers, ovps, clean_up = False):
+
+def print_equation(nmers, ovps, clean_up=False):
     rv = ""
     for nmer in nmers:
         rv += str(nmer)
@@ -93,20 +97,23 @@ def print_equation(nmers, ovps, clean_up = False):
             rv += str(ovp)
     return rv
 
+
 if __name__ == "__main__":
     n_fragments = 4
     trunc_order = 2
     frags = make_fragments(n_fragments)
     nmers = make_nmers(trunc_order, frags)
-    ovps  = make_intersections(nmers)
+    ovps = make_intersections(nmers)
     for x in ovps:
         if len(x.value.associate()) == 3:
             print(x, x.clean_up())
     #print(print_equation(nmers, ovps, True))
-    nmers = [Term(1.0, Union(Index("I"), Index("J"))),
-             Term(1.0, Union(Index("I"), Index("K"))),
-             Term(1.0, Union(Index("J"), Index("K"))),
-             Term(1.0, Union(Index("I"), Index("L"))),
-             Term(1.0, Union(Index("J"), Index("L")))]
+    nmers = [
+        Term(1.0, Union(Index("I"), Index("J"))),
+        Term(1.0, Union(Index("I"), Index("K"))),
+        Term(1.0, Union(Index("J"), Index("K"))),
+        Term(1.0, Union(Index("I"), Index("L"))),
+        Term(1.0, Union(Index("J"), Index("L")))
+    ]
     diff = diff_ovps(nmers, Term(1.0, Union(Index("K"), Index("L"))))
     #print(print_equation(nmers, diff, True))

scripts/equations/index.py

@@ -12,7 +12,9 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+
 class Index:
+
     def __init__(self, value):
         self.value = value
 

scripts/equations/intersection.py

@@ -14,6 +14,8 @@
 
 from set_base import SetBase
 from union import Union
+
+
 class Intersection(SetBase):
     """ Class representing a symbolic intersection of indices.
     """
@@ -36,20 +38,18 @@ def is_proper_subset(self, rhs):
             return self.count(rhs) == 1
         elif rhs.is_union():
             for x in self.terms:
-               if rhs.count(x):
-                   return True
+                if rhs.count(x):
+                    return True
             return False
         elif rhs.is_intersection():
-            if len(rhs) >=  len(self):
+            if len(rhs) >= len(self):
                 return False
             # Every term in rhs, must be in us
             for x in rhs.terms:
                 if self.count(x) == 0:
                     return False
             return True
 
-
-
     def clean_up(self):
         new_terms = [x.clean_up() for x in self.terms]
         final_terms = new_terms
@@ -71,7 +71,6 @@ def associate(self):
                 new_terms.append(new_term)
         return Intersection(*new_terms)
 
-
     def distribute(self):
         new_terms = self.associate()
         nterms = len(new_terms)
@@ -80,8 +79,8 @@ def distribute(self):
             newi = new_terms[i].distribute()
             if newi.is_union():
                 lhs = rv
-                rhs = new_terms[i + 1 : nterms]
-                rv = [ ]
+                rhs = new_terms[i + 1:nterms]
+                rv = []
                 for x in new_terms[i].terms:
                     rv.append(Intersection(*lhs, x, *rhs).distribute())
                 return Union(*rv).associate()

scripts/equations/set_base.py

@@ -12,7 +12,9 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+
 class SetBase:
+
     def __init__(self, *args):
         self.terms = []
         # This makes sure we only add unique elements

scripts/equations/tests/test_index.py

@@ -15,13 +15,16 @@
 import unittest
 import sys
 import os
+
 sys.path.insert(0, os.path.join(os.getcwd(), ".."))
 
 from union import Union
 from intersection import Intersection
 from index import Index
 
+
 class IndexTest(unittest.TestCase):
+
     def setUp(self):
         self.i = Index("I")
         self.j = Index("J")

scripts/equations/tests/test_intersection.py

@@ -15,6 +15,7 @@
 import unittest
 import sys
 import os
+
 sys.path.insert(0, os.path.join(os.getcwd(), ".."))
 
 from union import Union
@@ -23,6 +24,7 @@
 
 
 class IntersectionTest(unittest.TestCase):
+
     def setUp(self):
         i, j, k, l = Index("I"), Index("J"), Index("K"), Index("L")
         self.icj = Intersection(i, j)
@@ -35,7 +37,7 @@ def test_is_union(self):
         self.assertFalse(self.icjck.is_union())
         self.assertFalse(self.icjckcl.is_union())
         self.assertFalse(self.icjk.is_union())
-    
+
     def test_is_intersection(self):
         self.assertTrue(self.icj.is_intersection())
         self.assertTrue(self.icjck.is_intersection())
@@ -48,12 +50,12 @@ def test_is_index(self):
         self.assertFalse(self.icjckcl.is_index())
         self.assertFalse(self.icjk.is_index())
 
-    def test_associate(self):      
+    def test_associate(self):
         i, j, k, l = Index("I"), Index("J"), Index("K"), Index("L")
 
         corr = Intersection(i, j)
         self.assertEqual(self.icj.associate(), corr)
-        
+
         corr = Intersection(i, j, k)
         self.assertEqual(self.icjck.associate(), corr)
 
@@ -75,7 +77,7 @@ def test_distribute(self):
 
         corr = Intersection(i, j)
         self.assertEqual(self.icj.distribute(), corr)
-        
+
         corr = Intersection(i, j, k)
         self.assertEqual(self.icjck.distribute(), corr)
 
@@ -94,13 +96,12 @@ def test_distribute(self):
         self.assertEqual(i_jck_jk.distribute(), corr)
 
         ijcikcjk = Intersection(Union(i, j), Union(i, k), Union(j, k))
-        corr = Union(Intersection(i, i, j), Intersection(i, i, k), 
+        corr = Union(Intersection(i, i, j), Intersection(i, i, k),
                      Intersection(i, k, j), Intersection(i, k, k),
-                     Intersection(j, i, j), Intersection(j, i, k), 
+                     Intersection(j, i, j), Intersection(j, i, k),
                      Intersection(j, k, j), Intersection(j, k, k))
         self.assertEqual(ijcikcjk.distribute(), corr)
 
-
     def test_equal(self):
         i, j, k, l = Index("I"), Index("J"), Index("K"), Index("L")
         self.assertEqual(self.icj, Intersection(i, j))
@@ -116,4 +117,4 @@ def test_str(self):
 
 
 if __name__ == "__main__":
-    unittest.main()
+    unittest.main()

scripts/equations/tests/test_union.py

@@ -15,6 +15,7 @@
 import unittest
 import sys
 import os
+
 sys.path.insert(0, os.path.join(os.getcwd(), ".."))
 
 from union import Union
@@ -23,6 +24,7 @@
 
 
 class UnionTest(unittest.TestCase):
+
     def setUp(self):
         i, j, k, l = Index("I"), Index("J"), Index("K"), Index("L")
         self.ij = Union(i, j)
@@ -35,7 +37,7 @@ def test_is_union(self):
         self.assertTrue(self.ijk.is_union())
         self.assertTrue(self.ijkl.is_union())
         self.assertTrue(self.i_jck.is_union())
-    
+
     def test_is_intersection(self):
         self.assertFalse(self.ij.is_intersection())
         self.assertFalse(self.ijk.is_intersection())
@@ -48,12 +50,12 @@ def test_is_index(self):
         self.assertFalse(self.ijkl.is_index())
         self.assertFalse(self.i_jck.is_index())
 
-    def test_associate(self):      
+    def test_associate(self):
         i, j, k, l = Index("I"), Index("J"), Index("K"), Index("L")
 
         corr = Union(i, j)
         self.assertEqual(self.ij.associate(), corr)
-        
+
         corr = Union(i, j, k)
         self.assertEqual(self.ijk.associate(), corr)
 
@@ -70,13 +72,12 @@ def test_associate(self):
         i_jck_jk = Union(i, jck, Union(j, k))
         self.assertEqual(i_jck_jk.associate(), Union(i, jck, j, k))
 
-
     def test_distribute(self):
         i, j, k, l = Index("I"), Index("J"), Index("K"), Index("L")
 
         corr = Union(i, j)
         self.assertEqual(self.ij.distribute(), corr)
-        
+
         corr = Union(i, j, k)
         self.assertEqual(self.ijk.distribute(), corr)
 
@@ -97,7 +98,6 @@ def test_distribute(self):
         corr = Union(i, Intersection(j, l), Intersection(k, l))
         self.assertEqual(i_jkcl.distribute(), corr)
 
-
     def test_equal(self):
         i, j, k, l = Index("I"), Index("J"), Index("K"), Index("L")
         self.assertEqual(self.ij, Union(i, j))