piegy 1.1.5__tar.gz → 2.0.0__tar.gz

{piegy-1.1.5/src/piegy.egg-info → piegy-2.0.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: piegy
-Version: 1.1.5
+Version: 2.0.0
 Summary: Payoff-Driven Stochastic Spatial Model for Evolutionary Game Theory
 Author-email: Chenning Xu <cxu7@caltech.edu>
 License: BSD 3-Clause License

{piegy-1.1.5 → piegy-2.0.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = 'setuptools.build_meta'
 
 [project]
 name = 'piegy'
-version = '1.1.5'
+version = '2.0.0'
 description = 'Payoff-Driven Stochastic Spatial Model for Evolutionary Game Theory'
 readme = 'README.md'
 requires-python = '>=3.6'

{piegy-1.1.5 → piegy-2.0.0}/src/piegy/__version__.py

@@ -19,5 +19,7 @@ version history:
 1.1.3: update README.
 1.1.4: changed name: ``model`` module to ``simulation``, and ``model.simulation`` class to ``simulation.model``. Bug fix in videos.
 1.1.5: update README.
+1.1.6: change name of variables in model class -- for compatability with the new C core. 1.1.6 is the last verion of v1. From v2 on, the piegy package has C core.
 
+2.0.0: update simulation core to C-based.
 '''

{piegy-1.1.5 → piegy-2.0.0}/src/piegy/analysis.py

@@ -183,7 +183,7 @@ def combine_sim(mod1, mod2):
 
     Returns:
 
-    - sim3:     a new model object whose U, V, U_pi, V_pi are weighted averages of mod1 and mod2
+    - sim3:     a new model object whose U, V, Upi, Vpi are weighted averages of mod1 and mod2
                 (weighted by sim_time). 
                 sim3.print_pct is set to mod1's, seed set to None, sim_time set to sum of mod1's and mod2's. All other params same as mod1
     '''
@@ -213,8 +213,8 @@ def combine_sim(mod1, mod2):
             for k in range(sim3.max_record):
                 sim3.U[i][j][k] = (mod1.U[i][j][k] * mod1.sim_time + mod2.U[i][j][k] * mod2.sim_time) / combined_sim_time
                 sim3.V[i][j][k] = (mod1.V[i][j][k] * mod1.sim_time + mod2.V[i][j][k] * mod2.sim_time) / combined_sim_time
-                sim3.U_pi[i][j][k] = (mod1.U_pi[i][j][k] * mod1.sim_time + mod2.U_pi[i][j][k] * mod2.sim_time) / combined_sim_time
-                sim3.V_pi[i][j][k] = (mod1.V_pi[i][j][k] * mod1.sim_time + mod2.V_pi[i][j][k] * mod2.sim_time) / combined_sim_time
+                sim3.Upi[i][j][k] = (mod1.Upi[i][j][k] * mod1.sim_time + mod2.Upi[i][j][k] * mod2.sim_time) / combined_sim_time
+                sim3.Vpi[i][j][k] = (mod1.Vpi[i][j][k] * mod1.sim_time + mod2.Vpi[i][j][k] * mod2.sim_time) / combined_sim_time
 
     return sim3
 

{piegy-1.1.5 → piegy-2.0.0}/src/piegy/data_tools.py

@@ -38,24 +38,19 @@ def save_data(mod, dirs = '', print_msg = True):
         
     data = []
     
-    inputs1 = []
-    inputs1.append(mod.N)
-    inputs1.append(mod.M)
-    inputs1.append(mod.maxtime)
-    inputs1.append(mod.record_itv)
-    inputs1.append(mod.sim_time)
-    inputs1.append(mod.boundary)
-    inputs1.append(mod.I.tolist())
-    inputs1.append(mod.X.tolist())
-    inputs1.append(mod.P.tolist())
-    data.append(inputs1)
-
-    inputs2 = []
-    inputs2.append(mod.print_pct)
-    inputs2.append(mod.seed)
-    inputs2.append(mod.UV_dtype)
-    inputs2.append(mod.pi_dtype)
-    data.append(inputs2)
+    inputs = []
+    inputs.append(mod.N)
+    inputs.append(mod.M)
+    inputs.append(mod.maxtime)
+    inputs.append(mod.record_itv)
+    inputs.append(mod.sim_time)
+    inputs.append(mod.boundary)
+    inputs.append(mod.I.tolist())
+    inputs.append(mod.X.tolist())
+    inputs.append(mod.P.tolist())
+    inputs.append(mod.print_pct)
+    inputs.append(mod.seed)
+    data.append(inputs)
 
     # skipped rng
     
@@ -64,9 +59,9 @@ def save_data(mod, dirs = '', print_msg = True):
     outputs.append(mod.compress_itv)
     outputs.append(mod.U.tolist())
     outputs.append(mod.V.tolist())
-    outputs.append(mod.U_pi.tolist())
-    outputs.append(mod.V_pi.tolist())
-    # H&V_pi_total are not saved, will be calculated when reading the data
+    outputs.append(mod.Upi.tolist())
+    outputs.append(mod.Vpi.tolist())
+    # H&Vpi_total are not saved, will be calculated when reading the data
     data.append(outputs)
     
     data_json = json.dumps(data)
@@ -112,14 +107,14 @@ def read_data(dirs):
     try:
         mod = simulation.model(N = data[0][0], M = data[0][1], maxtime = data[0][2], record_itv = data[0][3],
                             sim_time = data[0][4], boundary = data[0][5], I = data[0][6], X = data[0][7], P = data[0][8], 
-                            print_pct = data[1][0], seed = data[1][1], UV_dtype = data[1][2], pi_dtype = data[1][3])
+                            print_pct = data[0][9], seed = data[0][10])
     except:
         raise ValueError('Invalid input parameters saved in data')
 
     # outputs
     try:
-        mod.set_data(data_empty = False, max_record = data[2][0], compress_itv = data[2][1], 
-                    U = data[2][2], V = data[2][3], U_pi = data[2][4], V_pi = data[2][5])
+        mod.set_data(data_empty = False, max_record = data[1][0], compress_itv = data[1][1], 
+                    U = data[1][2], V = data[1][3], Upi = data[1][4], Vpi = data[1][5])
     except:
         raise ValueError('Invalid model results saved in data')
     

{piegy-1.1.5 → piegy-2.0.0}/src/piegy/figures.py

@@ -14,13 +14,13 @@ Plots for population:
 
 
 Plots for payoff:
-- pi_heatmap:       Used for 2D space, plot distribution of U_pi & V_pi within a specified time interval.
+- pi_heatmap:       Used for 2D space, plot distribution of Upi & Vpiwithin a specified time interval.
                     Average payoff over that interval is taken.
 - pi_bar:           Used for 1D space, counterpart of pi_heatmap.
-                    Plot average distribution of U_pi & V_pi in a specified time interval in a bar plot.
-- pi_dyna:         Plot change of total U_pi, V_pi overtime.
-- pi_hist:          Make a histogram of U_pi, V_pi in a specified time interval.
-- pi_std:           Plot change of standard deviation of U_pi, V_pi over time.
+                    Plot average distribution of Upi & Vpiin a specified time interval in a bar plot.
+- pi_dyna:         Plot change of total Upi, Vpiovertime.
+- pi_hist:          Make a histogram of Upi, Vpiin a specified time interval.
+- pi_std:           Plot change of standard deviation of Upi, Vpiover time.
 
 
 Popu-payoff correlation:
@@ -329,15 +329,15 @@ def pi_heatmap(mod, ax_U = None, ax_V = None, U_color = 'BuPu', V_color = 'YlGn'
     start_index = int(mod.max_record * start)
     end_index = int(mod.max_record * end)
     
-    U_pi_ave = figure_t.ave_interval(mod.U_pi, start_index, end_index)
-    V_pi_ave = figure_t.ave_interval(mod.V_pi, start_index, end_index)
+    Upi_ave = figure_t.ave_interval(mod.Upi, start_index, end_index)
+    V_pi_ave = figure_t.ave_interval(mod.Vpi, start_index, end_index)
     
     U_title = figure_t.gen_title('Payoff ' + r'$p_U$', start, end)
-    U_text = figure_t.gen_text(np.mean(U_pi_ave), np.std(U_pi_ave))
+    U_text = figure_t.gen_text(np.mean(Upi_ave), np.std(Upi_ave))
     V_title = figure_t.gen_title('Payoff ' + r'$p_V$', start, end)
     V_text = figure_t.gen_text(np.mean(V_pi_ave), np.std(V_pi_ave))
     
-    ax_U = figure_t.heatmap(U_pi_ave, ax_U, U_color, annot, fmt, U_title, U_text)
+    ax_U = figure_t.heatmap(Upi_ave, ax_U, U_color, annot, fmt, U_title, U_text)
     ax_V = figure_t.heatmap(V_pi_ave, ax_V, V_color, annot, fmt, V_title, V_text)
 
     return ax_U, ax_V
@@ -357,15 +357,15 @@ def pi_bar(mod, ax_U = None, ax_V = None, U_color = 'violet', V_color = 'yellowg
     start_index = int(mod.max_record * start)
     end_index = int(mod.max_record * end)
     
-    U_pi_ave = figure_t.ave_interval_1D(mod.U_pi, start_index, end_index)
-    V_pi_ave = figure_t.ave_interval_1D(mod.V_pi, start_index, end_index)
+    Upi_ave = figure_t.ave_interval_1D(mod.Upi, start_index, end_index)
+    V_pi_ave = figure_t.ave_interval_1D(mod.Vpi, start_index, end_index)
     
     U_title = figure_t.gen_title(r'$p_U$', start, end)
-    U_text = figure_t.gen_text(np.mean(U_pi_ave), np.std(U_pi_ave))
+    U_text = figure_t.gen_text(np.mean(Upi_ave), np.std(Upi_ave))
     V_title = figure_t.gen_title(r'$p_V$', start, end)
     V_text = figure_t.gen_text(np.mean(V_pi_ave), np.std(V_pi_ave))
     
-    ax_U = figure_t.bar(U_pi_ave, ax_U, U_color, 'Patches', 'Payoff ' + r'$p_U$', U_title, U_text)
+    ax_U = figure_t.bar(Upi_ave, ax_U, U_color, 'Patches', 'Payoff ' + r'$p_U$', U_title, U_text)
     ax_V = figure_t.bar(V_pi_ave, ax_V, V_color, 'Patches', 'Payoff ' + r'$p_V$', V_title, V_text)
 
     return ax_U, ax_V
@@ -389,8 +389,8 @@ def pi_dyna(mod, ax = None, interval = 20, grid = True):
     interval_num = int(mod.max_record / interval)
     
     for i in range(interval_num):
-        U_ave = figure_t.ave_interval(mod.U_pi, i * interval, (i + 1) * interval)
-        V_ave = figure_t.ave_interval(mod.V_pi, i * interval, (i + 1) * interval)
+        U_ave = figure_t.ave_interval(mod.Upi, i * interval, (i + 1) * interval)
+        V_ave = figure_t.ave_interval(mod.Vpi, i * interval, (i + 1) * interval)
     
         U_curve.append(np.sum(U_ave))
         V_curve.append(np.sum(V_ave))
@@ -427,8 +427,8 @@ def pi_hist(mod, ax_U = None, ax_V = None, U_color = 'violet', V_color = 'yellow
     start_index = int(start * mod.max_record)
     end_index = int(end * mod.max_record)
 
-    U_pi_ave = figure_t.ave_interval_1D(mod.U_pi, start_index, end_index)
-    V_pi_ave = figure_t.ave_interval_1D(mod.V_pi, start_index, end_index)
+    Upi_ave = figure_t.ave_interval_1D(mod.Upi, start_index, end_index)
+    V_pi_ave = figure_t.ave_interval_1D(mod.Vpi, start_index, end_index)
     
     #### plot ####
     
@@ -436,7 +436,7 @@ def pi_hist(mod, ax_U = None, ax_V = None, U_color = 'violet', V_color = 'yellow
         _, ax_U = plt.subplots()
     ax_U.set_xlabel('Payoff ' + r'$p_U$')
     ax_U.set_ylabel('Density')
-    ax_U.hist(U_pi_ave, color = U_color, density = True)
+    ax_U.hist(Upi_ave, color = U_color, density = True)
     ax_U.set_title(figure_t.gen_title('Payoff ' + r'$p_U$' + ' Hist', start, end))
     
     if ax_V == None:
@@ -463,23 +463,23 @@ def pi_std(mod, ax = None, interval = 20, grid = True):
     interval = figure_t.scale_interval(interval, mod.compress_itv)
     interval_num = int(mod.max_record / interval)
     
-    U_pi_std = []
+    Upi_std = []
     V_pi_std = []
     
     for i in range(interval_num):
-        U_pi_ave = figure_t.ave_interval(mod.U_pi, i * interval, (i + 1) * interval)
-        V_pi_ave = figure_t.ave_interval(mod.V_pi, i * interval, (i + 1) * interval)
+        Upi_ave = figure_t.ave_interval(mod.Upi, i * interval, (i + 1) * interval)
+        V_pi_ave = figure_t.ave_interval(mod.Vpi, i * interval, (i + 1) * interval)
         
-        U_pi_std.append(np.std(U_pi_ave))
+        Upi_std.append(np.std(Upi_ave))
         V_pi_std.append(np.std(V_pi_ave))
     
     #### plot ####
-    xaxis = np.linspace(0, mod.maxtime, len(U_pi_std))
+    xaxis = np.linspace(0, mod.maxtime, len(Upi_std))
     
     if ax == None:
         _, ax = plt.subplots()
     ax.grid(grid)
-    ax.plot(xaxis, U_pi_std, CURVE_TYPE, label = r'$p_U$' + ' std')
+    ax.plot(xaxis, Upi_std, CURVE_TYPE, label = r'$p_U$' + ' std')
     ax.plot(xaxis, V_pi_std, CURVE_TYPE, label = r'$p_V$' + ' std')
     ax.legend()
     ax.set_xlabel('Time')
@@ -506,11 +506,11 @@ def UV_pi(mod, ax_U = None, ax_V = None, U_color = 'violet', V_color = 'yellowgr
     U_ave = figure_t.ave_interval_1D(mod.U, start_index, end_index)
     V_ave = figure_t.ave_interval_1D(mod.V, start_index, end_index)
 
-    U_pi_ave = figure_t.ave_interval(mod.U_pi, start_index, end_index)
-    V_pi_ave = figure_t.ave_interval(mod.V_pi, start_index, end_index)
+    Upi_ave = figure_t.ave_interval(mod.Upi, start_index, end_index)
+    V_pi_ave = figure_t.ave_interval(mod.Vpi, start_index, end_index)
     
     
-    ax_U = figure_t.scatter(U_ave, U_pi_ave, ax_U, U_color, alpha, xlabel = 'U', ylabel = 'Payoff ' + r'$p_U$', title = 'U - ' + r'$p_U$')
+    ax_U = figure_t.scatter(U_ave, Upi_ave, ax_U, U_color, alpha, xlabel = 'U', ylabel = 'Payoff ' + r'$p_U$', title = 'U - ' + r'$p_U$')
     ax_V = figure_t.scatter(V_ave, V_pi_ave, ax_V, V_color, alpha, xlabel = 'V', ylabel = 'Payoff ' + r'$p_V$', title = 'V - ' + r'$p_V$')
     
     return ax_U, ax_V