fixed many bugs and started migrating to pyproject.toml

fccoelho · Dec 18, 2024 · d9761ac · d9761ac
1 parent 5a94cbc
commit d9761ac
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Showing 10 changed files with 431 additions and 130 deletions.
diff --git a/.idea/misc.xml b/.idea/misc.xml
diff --git a/.idea/workspace.xml b/.idea/workspace.xml
diff --git a/.python-version b/.python-version
@@ -0,0 +1 @@
+3.12
diff --git a/Epigrass/epigdal.py b/Epigrass/epigdal.py
@@ -73,8 +73,7 @@ def _check_map(self):
             assert map_size == unique_gcs
         except AssertionError as e:
             print(f"Column {self.geocfield} should have {map_size} unique values, but it has {unique_gcs}.")
-            raise(e)
-
+            raise (e)
 
     def get_layer_list(self):
         return self.layers
@@ -87,7 +86,7 @@ def draw_layer(self, l):
         else:
             print(f'Layer {l} not available.')
 
-    def get_hex_color(self, value, cmap="YlOrRd" ):
+    def get_hex_color(self, value, cmap="YlOrRd"):
         cols = cm.get_cmap(cmap, 256)
         rgba = cols(value * 256)
         bgrcol = list(rgba[:-1])  # rgb(list)
@@ -123,13 +122,11 @@ def create_node_layer(self):
             self.get_node_list()
         if not self.nodesource:
             centroids = self.map.geometry.centroid
-            nodes = gpd.GeoDataFrame(columns=[self.geocfield, self.namefield, 'x', 'y'])
-            for gc, xy in self.centdict.items():
-                nodes = nodes.append({self.geocfield: gc,
-                                      self.namefield: self.namedict[gc],
-                                      'x': xy[0],
-                                      'y': xy[1]
-                                      }, ignore_index=True)
+            nodes = gpd.GeoDataFrame(columns=[self.geocfield, self.namefield, 'x', 'y'],
+                                     data=[
+                                         {self.geocfield: gc, self.namefield: self.namedict[gc], 'x': xy[0], 'y': xy[1]}
+                                         for gc, xy in self.centdict.items()]
+                                     )
 
             nodes['geometry'] = gpd.points_from_xy(nodes.x, nodes.y)
             nodes.to_file(os.path.join(self.outdir, 'Nodes.gpkg'), driver='GPKG')
@@ -181,13 +178,13 @@ def create_data_layer(self, varlist, data):
             os.remove(os.path.join(self.outdir, 'Data.gpkg'))
         # Creates a new shape file to hold the data
         if not self.datasource:
-            dsd = gpd.GeoDataFrame(columns=['geocode', 'name', 'colors']+varlist+['geometry'])
+            dsd = gpd.GeoDataFrame(columns=['geocode', 'name', 'colors'] + varlist + ['geometry'])
 
             dsd['geocode'] = data[:, 0]
             dsd['name'] = [self.namedict[int(gc)] for gc in data[:, 0]]
             dsd['colors'] = [str([self.get_hex_color(norms[i](v)) for i, v in enumerate(l[1:])]) for l in data]
             for i, v in enumerate(varlist):
-                dsd[v] = data[:, i+1]
+                dsd[v] = data[:, i + 1]
             for i, row in dsd.iterrows():
                 geom = self.map[self.map[self.geocfield] == row.geocode].geometry.values[0]
                 dsd.at[i, 'geometry'] = geom
@@ -821,7 +818,6 @@ def writeToFile(self, dir):
         f.write(self.kmldoc.toxml())
         f.close()
 
-
 # def gdal_error_handler(err_class, err_num, err_msg):
 #     errtype = {
 #         gdal.CE_None: 'None',

diff --git a/Epigrass/models.py b/Epigrass/models.py
@@ -12,8 +12,8 @@
 import sys
 import redis
 from epimodels.continuous.models import SIR, SEIR
-import numba
-from numba.typed import List
+# import numba
+# from numba.typed import List
 
 redisclient = redis.StrictRedis()
 
@@ -182,7 +182,7 @@ def selectModel(modtype):
 #                beta='double', alpha='double', E='double', I='double', S='double', N='long',
 #                r='double', b='double', w='double', Lpos='double', Lpos_esp='double', R='double',
 #                Ipos='double', Spos='double', Rpos='double')
-@numba.jit(forceobj=True, cache=True)
+# @numba.jit(forceobj=True, cache=True)
 def stepFlu(inits, simstep, totpop, theta=0, npass=0, bi=None, bp=None, values=None, model=None) -> tuple:
     """
     Flu model with classes S,E,I subclinical, I mild, I medium, I serious, deaths
@@ -295,7 +295,7 @@ def stepFlu(inits, simstep, totpop, theta=0, npass=0, bi=None, bp=None, values=N
 #                beta='double', alpha='double', E='double', I='double', S='double', N='long',
 #                r='double', b='double', w='double', Lpos='double', Lpos_esp='double', R='double',
 #                Ipos='double', Spos='double', Rpos='double')
-@numba.jit(forceobj=True, cache=True)
+# @numba.jit(forceobj=True, cache=True)
 def stepSIS(inits, simstep, totpop, theta=0, npass=0, bi=None, bp=None, values=None, model=None) -> tuple:
     """
     calculates the model SIS, and return its values (no demographics)
@@ -338,7 +338,7 @@ def stepSIS(inits, simstep, totpop, theta=0, npass=0, bi=None, bp=None, values=N
 #                beta='double', alpha='double', E='double', I='double', S='double', N='long',
 #                r='double', b='double', w='double', Lpos='double', Lpos_esp='double', R='double',
 #                Ipos='double', Spos='double', Rpos='double')
-@numba.jit(forceobj=True, cache=True)
+# @numba.jit(forceobj=True, cache=True)
 def stepSIS_s(inits, simstep, totpop, theta=0, npass=0, bi=None, bp=None, values=None, model=None,
               dist='poisson') -> tuple:
     """
@@ -495,7 +495,7 @@ def stepSIR_cont(inits, simstep, totpop, theta=0, npass=0, bi=None, bp=None, val
 #                beta='double', alpha='double', E='double', I='double', S='double', N='long',
 #                r='double', b='double', w='double', Lpos='double', Lpos_esp='double', R='double',
 #                Ipos='double', Spos='double', Rpos='double')
-@numba.jit(forceobj=True, cache=True)
+# @numba.jit(forceobj=True, cache=True)
 def stepSEIS(inits, simstep, totpop, theta=0, npass=0, bi=None, bp=None, values=None, model=None) -> tuple:
     """
     Defines the model SEIS:
@@ -533,7 +533,7 @@ def stepSEIS(inits, simstep, totpop, theta=0, npass=0, bi=None, bp=None, values=
 #                beta='double', alpha='double', E='double', I='double', S='double', N='long',
 #                r='double', b='double', w='double', Lpos='double', Lpos_esp='double', R='double',
 #                Ipos='double', Spos='double', Rpos='double')
-@numba.jit(forceobj=True, cache=True)
+# @numba.jit(forceobj=True, cache=True)
 def stepSEIS_s(inits, simstep, totpop, theta=0, npass=0, bi=None, bp=None, values=None, model=None,
                dist='poisson') -> tuple:
     """
@@ -704,7 +704,7 @@ def stepSEIR_cont(inits, simstep, totpop, theta=0, npass=0, bi=None, bp=None, va
 #                beta='double', alpha='double', E='double', I='double', S='double', N='long',
 #                r='double', b='double', w='double', Lpos='double', Lpos_esp='double', R='double',
 #                Ipos='double', Spos='double', Rpos='double')
-@numba.jit(forceobj=True, cache=True)
+# @numba.jit(forceobj=True, cache=True)
 def stepSIpRpS(inits, simstep, totpop, theta=0, npass=0, bi=None, bp=None, values=None, model=None) -> tuple:
     """
     calculates the model SIpRpS, and return its values (no demographics)
@@ -742,7 +742,7 @@ def stepSIpRpS(inits, simstep, totpop, theta=0, npass=0, bi=None, bp=None, value
 #                beta='double', alpha='double', E='double', I='double', S='double', N='long',
 #                r='double', b='double', w='double', Lpos='double', Lpos_esp='double', R='double',
 #                Ipos='double', Spos='double', Rpos='double')
-@numba.jit(forceobj=True, cache=True)
+# @numba.jit(forceobj=True, cache=True)
 def stepSIpRpS_s(inits, simstep, totpop, theta=0, npass=0, bi=None, bp=None, values=None, model=None,
                  dist='poisson') -> tuple:
     """
@@ -787,7 +787,7 @@ def stepSIpRpS_s(inits, simstep, totpop, theta=0, npass=0, bi=None, bp=None, val
 #                beta='double', alpha='double', E='double', I='double', S='double', N='long',
 #                r='double', b='double', w='double', Lpos='double', Lpos_esp='double', R='double',
 #                Ipos='double', Spos='double', Rpos='double')
-@numba.jit(forceobj=True)
+# @numba.jit(forceobj=True)
 def stepSEIpRpS(inits, simstep, totpop, theta=0, npass=0, bi=None, bp=None, values=None, model=None) -> tuple:
     """
     Defines the model SEIpRpS:
@@ -825,7 +825,7 @@ def stepSEIpRpS(inits, simstep, totpop, theta=0, npass=0, bi=None, bp=None, valu
 #                beta='double', alpha='double', E='double', I='double', S='double', N='long',
 #                r='double', b='double', w='double', Lpos='double', Lpos_esp='double', R='double',
 #                Ipos='double', Spos='double', Rpos='double')
-@numba.jit(forceobj=True, cache=True)
+# @numba.jit(forceobj=True, cache=True)
 def stepSEIpRpS_s(inits, simstep, totpop, theta=0, npass=0, bi=None, bp=None, values=None, model=None,
                   dist='poisson') -> tuple:
     """
@@ -870,7 +870,7 @@ def stepSEIpRpS_s(inits, simstep, totpop, theta=0, npass=0, bi=None, bp=None, va
 #                beta='double', alpha='double', E='double', I='double', S='double', N='long',
 #                r='double', b='double', w='double', Lpos='double', Lpos_esp='double', R='double',
 #                Ipos='double', Spos='double', Rpos='double')
-@numba.jit(forceobj=True, cache=True)
+# @numba.jit(forceobj=True, cache=True)
 def stepSIpR(inits, simstep, totpop, theta=0, npass=0, bi=None, bp=None, values=None, model=None) -> tuple:
     """
     calculates the model SIpR, and return its values (no demographics)
@@ -962,7 +962,7 @@ def stepSIpR_s(inits, simstep, totpop, theta=0, npass=0, bi=None, bp=None, value
 #                beta='double', alpha='double', E='double', I='double', S='double', N='long',
 #                r='double', b='double', w='double', Lpos='double', Lpos_esp='double', R='double',
 #                Ipos='double', Spos='double', Rpos='double')
-@numba.jit(forceobj=True, cache=True)
+# @numba.jit(forceobj=True, cache=True)
 def stepSEIpR(inits, simstep, totpop, theta=0, npass=0, bi=None, bp=None, values=None, model=None) -> tuple:
     """
     calculates the model SEIpR, and return its values (no demographics)
@@ -1059,7 +1059,7 @@ def stepSEIpR_s(inits, simstep, totpop, theta=0, npass=0, bi=None, bp=None, valu
 #                beta='double', alpha='double', E='double', I='double', S='double', N='long',
 #                r='double', b='double', w='double', Lpos='double', Lpos_esp='double', R='double',
 #                Ipos='double', Spos='double', Rpos='double')
-@numba.jit(forceobj=True, cache=True)
+# @numba.jit(forceobj=True, cache=True)
 def stepSIRS(inits, simstep, totpop, theta=0, npass=0, bi=None, bp=None, values=None, model=None) -> tuple:
     """
     calculates the model SIRS, and return its values (no demographics)

diff --git a/Epigrass/simobj.py b/Epigrass/simobj.py
@@ -176,8 +176,8 @@ def runModel(self, parallel=True):
         pipe.rpush("{}:ts".format(self.geocode), str(inits))
         pipe.set("{}:npass".format(self.geocode), float(npass))
         pipe.set("{}:theta".format(self.geocode), int(nan_to_num(theta)))
-        pipe.hmset("{}:bi".format(self.geocode), self.bi)
-        pipe.hmset("{}:bp".format(self.geocode), self.bp)
+        pipe.hset("{}:bi".format(self.geocode), mapping=self.bi)
+        pipe.hset("{}:bp".format(self.geocode), mapping=self.bp)
         pipe.execute()
         # ------------------------
         if parallel: