Fixed bug when picking divisor basis and other small bugs. Bumped to …

…version 0.3.2

cytools/__init__.py

@@ -19,7 +19,7 @@
 from cytools.utils import read_polytopes, fetch_polytopes
 
 # Latest version
-version = "0.3.1"
+version = "0.3.2"
 versions_with_serious_bugs = []
 
 # Check for more recent versions of CYTools

cytools/calabiyau.py

@@ -1258,7 +1258,7 @@ def intersection_numbers(self, in_basis=False, format="dok",
  # Let's print the output and see how to interpret it
  print(intnum_nobasis)
  # {(1, 2, 3): 18, (2, 3, 4): 18, (1, 3, 4): 2, (1, 2, 4): 3, (1, 2, 5): 3, (2, 3, 5): 18, [the output is too long so we truncate it]
- # The above output means that the intersection number of divisors 1, 2, 3 is 13, and so on
+ # The above output means that the intersection number of divisors 1, 2, 3 is 18, and so on
  # Let us now compute the intersection numbers in a given basis of divisors
  # First, let's check the current basis of divisors
  cy.divisor_basis()
@@ -1489,9 +1489,7 @@ def is_smooth(self):
  if self._is_smooth is not None:
  return self._is_smooth
  if self._is_hypersurface:
- sm = (True if self.dim() <= 3 else
- all(c.is_smooth() for c in self.ambient_variety().fan_cones(self.dim(),self.dim()-1)))
- self._is_smooth = sm
+ self._is_smooth = self.ambient_variety().canonical_divisor_is_smooth()
  else:
  self.intersection_numbers() # The variable is set while computing intersection numbers
  return self._is_smooth

cytools/polytope.py

@@ -604,8 +604,8 @@ def _points_saturated(self):
  - Points are sorted so that interior points are first, and then the
  rest are arranged by decreasing number of saturated inequalities and
  lexicographically. For reflexive polytopes this is useful since the
- origin will be at index 0 and boundary points not interior to facets
- will be last.
+ origin will be at index 0 and boundary points interior to facets will
+ be last.
  - Typically this function should not be called by the user. Instead, it
  is called by various other functions in the Polytope class.
  :::
@@ -761,10 +761,11 @@ def points(self, as_indices=False):
  Returns the lattice points of the polytope.
 
  :::note
- Points are sorted so that interior points are first, and then the rest
- are arranged by decreasing number of saturated inequalities.
- For reflexive polytopes this is useful since the origin will be at
- index 0 and boundary points not interior to facets will be last.
+ Points are sorted so that interior points are first, and then the
+ rest are arranged by decreasing number of saturated inequalities and
+ lexicographically. For reflexive polytopes this is useful since the
+ origin will be at index 0 and boundary points interior to facets will
+ be last.
  :::
 
  **Arguments:**
@@ -1811,6 +1812,8 @@ def glsm_charge_matrix(self, include_origin=True,
  glsm = np.insert(glsm, pp, extra_columns[p], axis=1)
  origin_column = -np.sum(glsm, axis=1)
  glsm = np.insert(glsm, 0, origin_column, axis=1)
+ glsm_rref = fmpz_mat(glsm.tolist()).rref()
+ glsm = np.array(glsm_rref[0].tolist(),dtype=int) // int(glsm_rref[1])
  linear_relations = extra_rows
  extra_linear_relation_columns = -1*np.diag(row_scalings)
  for p,pp in enumerate(good_lattice_basis):

cytools/toricvariety.py

@@ -1565,7 +1565,7 @@ def canonical_divisor_is_smooth(self):
  pts_mpcp = {tuple(pt) for pt in self.polytope().points_not_interior_to_facets()}
  ind_triang = list(set.union(*[set(s) for s in self._triang.simplices()]))
  pts_triang = {tuple(pt) for pt in self._triang.points()[ind_triang]}
- sm = (pts_triang.issubset(pts_mpcp) and
+ sm = (pts_mpcp.issubset(pts_triang) and
  (True if self.dim() <= 4 else
  all(c.is_smooth() for c in self.fan_cones(self.dim()-1,self.dim()-2))))
  self._canon_div_is_smooth = sm

cytools/triangulation.py

@@ -164,15 +164,15 @@ def __init__(self, triang_pts, poly=None, heights=None, make_star=False,
  # A fine, regular, star triangulation of a 4-dimensional point configuration with 7 points in ZZ^4
  ```
  """
- tmp_triang_pts = [tuple(pt) for pt in np.array(triang_pts, dtype=int)]
+ tmp_triang_pts = {tuple(pt) for pt in np.array(triang_pts, dtype=int)}
  heights = copy.deepcopy(heights)
  if poly is None:
  from cytools.polytope import Polytope
- self._poly = Polytope(tmp_triang_pts)
+ self._poly = Polytope(list(tmp_triang_pts))
  else:
  self._poly = poly
  if (not self._poly.is_solid()
- or np.linalg.matrix_rank([pt+(1,) for pt in tmp_triang_pts]) != len(tmp_triang_pts[0])+1):
+ or np.linalg.matrix_rank([pt+(1,) for pt in tmp_triang_pts]) != len(next(iter(tmp_triang_pts)))+1):
  raise Exception("Only triangulations of full-dimensional point "
  "configurations are supported.")
  # Now we reorder the points to make sure they match the ordering of

scripts/linux/cytools

@@ -106,7 +106,7 @@ cat << EOF
  ░░█████████ █████ █████ ░░██████ ░░██████ █████ ██████
  ░░░░░░░░░ ░░░░░ ░░░░░ ░░░░░░ ░░░░░░ ░░░░░ ░░░░░░
 
- Developed by Liam McAllister's Group | Version 0.3.1
+ Developed by Liam McAllister's Group | Version 0.3.2
  https://cytools.liammcallistergroup.com
 
 EOF

scripts/macos/cytools

@@ -100,7 +100,7 @@ cat << EOF
  ░░█████████ █████ █████ ░░██████ ░░██████ █████ ██████
  ░░░░░░░░░ ░░░░░ ░░░░░ ░░░░░░ ░░░░░░ ░░░░░ ░░░░░░
 
- Developed by Liam McAllister's Group | Version 0.3.1
+ Developed by Liam McAllister's Group | Version 0.3.2
  https://cytools.liammcallistergroup.com
 
 EOF

scripts/windows/launcher.ps1

@@ -38,7 +38,7 @@ $banner=@"
  ░░█████████ █████ █████ ░░██████ ░░██████ █████ ██████
  ░░░░░░░░░ ░░░░░ ░░░░░ ░░░░░░ ░░░░░░ ░░░░░ ░░░░░░
 
- Developed by Liam McAllister's Group | Version 0.3.1
+ Developed by Liam McAllister's Group | Version 0.3.2
  https://cytools.liammcallistergroup.com
 
 "@

setup.py

@@ -5,7 +5,7 @@
 
 setuptools.setup(
  name="cytools",
- version="0.3.1",
+ version="0.3.2",
  author="Liam McAllister Group",
  author_email="",
  description="A software package for analyzing Calabi-Yau hypersurfaces in toric varieties.",