pre release (#178)

* fixes bad dtype conversion through loc / append * pre-release, bump version number, update changelog
DamCB · Feb 24, 2020 · 5f13a7e · 5f13a7e
1 parent cb6cee9
commit 5f13a7e
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diff --git a/changelog.md b/changelog.md
@@ -4,6 +4,19 @@
 
 - Added periodic boundary conditions support
 
+## Generation
+
+- adds spherical sheet and monolayers from CGAL
+
+## Install
+
+- CGAL-less version installable with pip
+
+## Geometry & Dynamics
+
+- New geometry classes
+- BorderElasticity, RadialTension, and  BarrierElasticity effectors
+- Cell division on periodic boundary conditions
 
 # What's new in 0.6.0
 

diff --git a/setup.py b/setup.py
@@ -28,9 +28,9 @@
 # Version management copied form numpy
 # Thanks to them!
 MAJOR = 0
-MINOR = 6
-MICRO = 9
-ISRELEASED = True
+MINOR = 7
+MICRO = 0
+ISRELEASED = False
 VERSION = "%d.%d.%s" % (MAJOR, MINOR, MICRO)
 
 
@@ -117,12 +117,16 @@ def run(self):
         try:
             out = subprocess.check_output(["cmake", "--version"])
         except OSError:
-            raise RuntimeError("CMake must be installed to build the following extensions: " +
-                               ", ".join(e.name for e in self.extensions))
+            raise RuntimeError(
+                "CMake must be installed to build the following extensions: "
+                + ", ".join(e.name for e in self.extensions)
+            )
 
         if platform.system() == "Windows":
-            cmake_version = LooseVersion(re.search(r'version\s*([\d.]+)', out.decode()).group(1))
-            if cmake_version < '3.1.0':
+            cmake_version = LooseVersion(
+                re.search(r"version\s*([\d.]+)", out.decode()).group(1)
+            )
+            if cmake_version < "3.1.0":
                 raise RuntimeError("CMake >= 3.1.0 is required on Windows")
 
         for ext in self.extensions:

diff --git a/setup_noarch.py b/setup_noarch.py
@@ -28,8 +28,8 @@
 ## Version management copied form numpy
 ## Thanks to them!
 MAJOR = 0
-MINOR = 6
-MICRO = 8
+MINOR = 7
+MICRO = 0
 ISRELEASED = True
 VERSION = "%d.%d.%s" % (MAJOR, MINOR, MICRO)
 

diff --git a/tyssue/core/history.py b/tyssue/core/history.py
@@ -334,12 +334,15 @@ def record(self, to_record=None, time_stamp=None, sheet=None):
                     )
                 )
             else:
-                if dtypes_[element].to_dict() != self.dtypes[element].to_dict():
-                    change_type = {k: self.dtypes[element].to_dict()[k] for k in self.dtypes[element].to_dict() if k in dtypes_[
-                        element].to_dict() and self.dtypes[element].to_dict()[k] != dtypes_[element].to_dict()[k]}
+                old_types = self.dtypes[element].to_dict()
+                new_types = dtypes_[element].to_dict()
+                if new_types != old_types:
+                    changed_type = {
+                        k: old_types[k] for k in old_types
+                        if k in new_types and old_types[k] != new_types[k]}
                     raise ValueError(
                         "There is a change of datatype in {} table in {} columns".format(
-                            element, change_type)
+                            element, changed_type)
                     )
 
         if (self.save_every is None) or (
@@ -381,4 +384,4 @@ def retrieve(self, time):
 def _retrieve(dset, time):
     times = dset["time"].values
     t = times[np.argmin(np.abs(times - time))]
-    return dset[dset["time"] == t]
+    return dset[dset["time"] == t]
diff --git a/tyssue/core/objects.py b/tyssue/core/objects.py
@@ -51,14 +51,14 @@ def __init__(self, identifier, datasets, specs=None, coords=None, maxbackup=5):
                         ## Topology
                         "num_sides": 6,
                         ## Masks
-                        "is_alive": True},
+                        "is_alive": 1},
                     "vert": {
                         ## Coordinates
                         "x": 0.,
                         "y": 0.,
                         "z": 0.,
                         ## Masks
-                        "is_active": True},
+                        "is_active": 1},
                     "edge": {
                         ## Connections
                         "srce": 0,

diff --git a/tyssue/topology/base_topology.py b/tyssue/topology/base_topology.py
@@ -34,7 +34,9 @@ def split_vert(sheet, vert, face, to_rewire, epsilon, recenter=False):
 
     """
     # Add a vertex
-    sheet.vert_df = sheet.vert_df.append(sheet.vert_df.loc[vert], ignore_index=True)
+    this_vert = sheet.vert_df.loc[vert:vert] # avoid type munching
+    sheet.vert_df = sheet.vert_df.append(this_vert, ignore_index=True)
+    # reset datatypes
     new_vert = sheet.vert_df.index[-1]
     # Move it towards the face center
     r_ia = sheet.face_df.loc[face, sheet.coords] - sheet.vert_df.loc[vert, sheet.coords]
@@ -103,9 +105,11 @@ def add_vert(eptm, edge):
         (eptm.edge_df["srce"] == srce) & (eptm.edge_df["trgt"] == trgt)
     ]
 
-    new_vert = eptm.vert_df.loc[[srce, trgt]].mean()
+    new_vert = eptm.vert_df.loc[srce:srce]
     eptm.vert_df = eptm.vert_df.append(new_vert, ignore_index=True)
     new_vert = eptm.vert_df.index[-1]
+    eptm.vert_df.loc[new_vert, eptm.coords] = eptm.vert_df.loc[[srce, trgt], eptm.coords].mean()
+
     new_edges = []
 
     for p, p_data in parallels.iterrows():
@@ -155,7 +159,7 @@ def close_face(eptm, face):
         print("Closing only possible with exactly two dangling vertices")
         raise err
 
-    eptm.edge_df = eptm.edge_df.append(face_edges.iloc[0], ignore_index=True)
+    eptm.edge_df = eptm.edge_df.append(face_edges.iloc[0:1], ignore_index=True)
     eptm.edge_df.index.name = "edge"
     new_edge = eptm.edge_df.index[-1]
     eptm.edge_df.loc[new_edge, ["srce", "trgt"]] = single_trgt, single_srce

diff --git a/tyssue/topology/bulk_topology.py b/tyssue/topology/bulk_topology.py
@@ -78,7 +78,7 @@ def remove_cell(eptm, cell):
 def close_cell(eptm, cell):
     """Closes the cell by adding a face. Assumes a single face is missing
     """
-    eptm.face_df = eptm.face_df.append(eptm.face_df.iloc[0], ignore_index=True)
+    eptm.face_df = eptm.face_df.append(eptm.face_df.loc[0:0], ignore_index=True)
 
     new_face = eptm.face_df.index[-1]
 
@@ -301,7 +301,7 @@ def cell_division(eptm, mother, geom, vertices=None):
             plane_center=None,
         )
 
-    cell_cols = eptm.cell_df.loc[mother]
+    cell_cols = eptm.cell_df.loc[mother:mother]
     eptm.cell_df = eptm.cell_df.append(cell_cols, ignore_index=True)
     eptm.cell_df.index.name = "cell"
     daughter = eptm.cell_df.index[-1]

diff --git a/tyssue/topology/sheet_topology.py b/tyssue/topology/sheet_topology.py
@@ -117,22 +117,22 @@ def cell_division(sheet, mother, geom, angle=None):
 
     Parameters
     ----------
-    
+
     sheet : a 'Sheet' instance
-    mother : face index of target dividing cell 
+    mother : face index of target dividing cell
     geom : a 2D geometry
     angle : division angle for newly formed edge
-    
+
     Returns
     -------
-    daughter: face index of new cell 
-    
+    daughter: face index of new cell
+
     Notes
     -----
-    - Function checks for perodic boundaries if there are, it checks if dividing cell 
-      rests on an edge of the periodic boundaries if so, it displaces the boundaries 
-      by a half a period and moves the target cell in the bulk of the tissue. It then 
-      performs cell division normally and reverts the periodic boundaries to the original 
+    - Function checks for perodic boundaries if there are, it checks if dividing cell
+      rests on an edge of the periodic boundaries if so, it displaces the boundaries
+      by a half a period and moves the target cell in the bulk of the tissue. It then
+      performs cell division normally and reverts the periodic boundaries to the original
       configuration
     """
 
@@ -207,12 +207,12 @@ def face_division(sheet, mother, vert_a, vert_b):
     """
     # mother = sheet.edge_df.loc[edge_a, 'face']
 
-    face_cols = sheet.face_df.loc[mother]
+    face_cols = sheet.face_df.loc[mother:mother]
     sheet.face_df = sheet.face_df.append(face_cols, ignore_index=True)
     sheet.face_df.index.name = "face"
     daughter = int(sheet.face_df.index[-1])
 
-    edge_cols = sheet.edge_df[sheet.edge_df["face"] == mother].iloc[0]
+    edge_cols = sheet.edge_df[sheet.edge_df["face"] == mother].iloc[0:1]
     sheet.edge_df = sheet.edge_df.append(edge_cols, ignore_index=True)
     new_edge_m = sheet.edge_df.index[-1]
     sheet.edge_df.loc[new_edge_m, "srce"] = vert_b