piegy 1.1.2__py3-none-any.whl → 1.1.4__py3-none-any.whl

piegy/test_var.py

@@ -31,7 +31,7 @@ Additional tools (can be called directly):
 - var_convergence2: Find the simulatoin results of test_var2 that diverge.
 '''
 
-from . import model as model
+from . import simulation
 from .tools import figure_tools as figure_t
 from . import analysis as analysis
 from . import data_tools as data_t
@@ -45,7 +45,7 @@ import numpy as np
 # can be 'o-', 'x-', ...
 DOTTED_CURVE_TYPE = 'o-'
 
-# map patch_var name to index in the patch class (in stochastic_model.py)
+# map patch_var name to index in the patch class (in simulation.py)
 PATCH_VAR_DICT = {'mu1': 0, 'mu2': 1, 'w1': 2, 'w2': 3, 'kappa1': 4, 'kappa2': 5}
 
 # display name (in latex)
@@ -54,16 +54,16 @@ PATCH_VAR_DISP = {'mu1': r'$\mu_U$', 'mu2': r'$\mu_V$', 'w1': r'$w_U$', 'w2': r'
 
 
 
-def test_var1(sim, var, values, dirs, compress_itv = None, predict_runtime = False):
+def test_var1(mod, var, values, dirs, compress_itv = None, predict_runtime = False):
     '''
     Test the influence of one patch variable on simulation results.
 
     Inputs::
-    - sim:                a simulation object. All tests will use parameters of sim, except for the variable to test.
+    - sim:                a simulation.model object. All tests will use parameters of mod, except for the variable to test.
     - var:                str, which patch variable to test. e.g. var can be 'mu1', 'w2', 'kappa2', ...
     - values:             1D np.array or list, what values of var to test.
     - dirs:               str, where to save data.
-    - compress_itv:         int, whether to reduce data size (if not 1), passed to model.simulation.compress_data function.
+    - compress_itv:         int, whether to reduce data size (if not 1), passed to simulation.model.compress_data function.
     - predict_runtime:    bool, whether to predict how much time left for each test.          
 
     Returns::
@@ -79,16 +79,16 @@ def test_var1(sim, var, values, dirs, compress_itv = None, predict_runtime = Fal
     var_dirs = []
     
     for k in range(len(values)):
-        sim2 = sim.copy(copy_data = False)
+        sim2 = mod.copy(copy_data = False)
         current_var_str = var + '=' + str(values[k])    # e.g., 'mu1=0.1'
         var_dirs.append(dirs + '/' + current_var_str)
         
-        for i in range(sim.N):
-            for j in range(sim.M):
+        for i in range(mod.N):
+            for j in range(mod.M):
                 sim2.P[i][j][PATCH_VAR_DICT[var]] = values[k]
 
         try:
-            model.run(sim2, predict_runtime, message = current_var_str + ', ')
+            simulation.run(sim2, predict_runtime, message = current_var_str + ', ')
             if compress_itv != None:
                 sim2.compress_data(compress_itv)
             data_t.save_data(sim2, var_dirs[k], print_msg = False)
@@ -100,12 +100,12 @@ def test_var1(sim, var, values, dirs, compress_itv = None, predict_runtime = Fal
 
 
 
-def test_var2(sim, var1, var2, values1, values2, dirs, compress_itv = None, predict_runtime = False):
+def test_var2(mod, var1, var2, values1, values2, dirs, compress_itv = None, predict_runtime = False):
     '''
     Two-variable version of test_var1. Test the influence of two varibles on simulation results.
 
     Inputs:
-    - sim:      a simulation object. All tests will use the parameters of sim, except for the two vars to be tested.
+    - sim:      a simulation.model object. All tests will use the parameters of mod, except for the two vars to be tested.
     - var1:     str, the first variable to test.
     - var2:     str, the second variable to test.
     - values1:  1D list or np.array, values for var1.
@@ -125,17 +125,17 @@ def test_var2(sim, var1, var2, values1, values2, dirs, compress_itv = None, pred
 
     for k1 in range(len(values1)):
         for k2 in range(len(values2)):
-            sim2 = sim.copy(copy_data = False)
+            sim2 = mod.copy(copy_data = False)
             current_var_str = var1 + '=' + str(values1[k1]) + ', ' + var2 + '=' + str(values2[k2])   # e.g., mu1=0.1, mu2=0.2
             var_dirs[k1].append(dirs + '/' + current_var_str)
 
-            for i in range(sim.N):
-                for j in range(sim.M):
+            for i in range(mod.N):
+                for j in range(mod.M):
                     sim2.P[i][j][PATCH_VAR_DICT[var1]] = values1[k1]
                     sim2.P[i][j][PATCH_VAR_DICT[var2]] = values2[k2]
 
             try:
-                model.run(sim2, predict_runtime, message = current_var_str + ', ')
+                simulation.run(sim2, predict_runtime, message = current_var_str + ', ')
                 if compress_itv != None:
                     sim2.compress_data(compress_itv)
                 data_t.save_data(sim2, var_dirs[k1][k2], print_msg = False)
@@ -488,11 +488,11 @@ def var_convergence1(var_dirs, interval = 20, start = 0.8, fluc = 0.07):
 
     Inputs:
     - var_dirs:       Return value of test_var1
-    - interval:       int. One of the inputs of model_analysis.check_convergence.
+    - interval:       int. One of the inputs of analysis.check_convergence.
                     The size of interval to take average over.
-    - start:          (0,1) float. One of the inputs of model_analysis.check_convergence. 
+    - start:          (0,1) float. One of the inputs of analysis.check_convergence. 
                     Convergence is expected to start from at least this point.
-    - fluc:           (0,1) float. One of the inputs of model_analysis.check_convergence. 
+    - fluc:           (0,1) float. One of the inputs of analysis.check_convergence. 
                     Expect the difference between any two small intervals (a quotient-form difference) should be less than fluc.
 
     Returns:
@@ -503,11 +503,11 @@ def var_convergence1(var_dirs, interval = 20, start = 0.8, fluc = 0.07):
 
     for dirs in var_dirs:
         try:
-            sim = data_t.read_data(dirs)
+            mod = data_t.read_data(dirs)
         except FileNotFoundError:
             print(dirs + ' data not found, skipped')
             continue
-        if not analysis.check_convergence(sim, interval, start, fluc):
+        if not analysis.check_convergence(mod, interval, start, fluc):
             diverge_list.append(dirs)
 
     return diverge_list
@@ -554,11 +554,11 @@ def var_convergence2(var_dirs, interval = 20, start = 0.8, fluc = 0.07):
 
     Inputs:
     - var_dirs:       Return value of test_var2
-    - interval:       int. One of the inputs of model_analysis.check_convergence.
+    - interval:       int. One of the inputs of analysis.check_convergence.
                     The size of interval to take average over.
-    - start:          (0,1) float. One of the inputs of model_analysis.check_convergence. 
+    - start:          (0,1) float. One of the inputs of analysis.check_convergence. 
                     Convergence is expected to start from at least this point.
-    - fluc:           (0,1) float. One of the inputs of model_analysis.check_convergence. 
+    - fluc:           (0,1) float. One of the inputs of analysis.check_convergence. 
                     Expect the difference between any two small intervals (a quotient-form difference) should be less than fluc.
 
     Returns:
@@ -570,11 +570,11 @@ def var_convergence2(var_dirs, interval = 20, start = 0.8, fluc = 0.07):
     for sublist in var_dirs:
         for dirs in sublist:
             try:
-                sim = data_t.read_data(dirs)
+                mod = data_t.read_data(dirs)
             except FileNotFoundError:
                 print(dirs + ' data not found, skipped')
                 continue
-            if not analysis.check_convergence(sim, interval, start, fluc):
+            if not analysis.check_convergence(mod, interval, start, fluc):
                 diverge_list.append(dirs)
 
     return diverge_list

piegy/tools/figure_tools.py

@@ -7,7 +7,7 @@ Functions:
 - scatter:          Make a scatter plot. Sets title, text ... as well.
 - gen_title:        Generates a title when the plot is about an interval of time.
 - gen_text:         Generates a text about standard deviation info.
-- scale_interval:   scale interval if sim's data was already reduced.
+- scale_interval:   scale interval if mod's data was already reduced.
 - ave_interval:     Calculates average value of data over a time interval.
 - ave_interval_1D:  Return in a 1D format.
 - config_mpl:       Configure Matplotlib parameters in a nice format
@@ -201,13 +201,13 @@ def ave_interval_1D(data, start_index, end_index):
 
 
 def scale_interval(interval, compress_itv):
-    # scale interval if sim's data was already reduced.
+    # scale interval if mod's data was already reduced.
     if compress_itv < 1:
         raise ValueError('figures.scale_interval has compress_itv < 1:', compress_itv)
 
     interval = int(interval / compress_itv)
     if interval == 0:
-        print('Warning: data already smoothed by an interval: sim.compress_itv =', compress_itv, 'which is coarser than your', interval)
+        print('Warning: data already smoothed by an interval: mod.compress_itv =', compress_itv, 'which is coarser than your', interval)
         interval = 1
 
     return interval

piegy/videos.py

@@ -106,12 +106,12 @@ def get_max_lim(lims):
 
 
 
-def frame_lim(sim, func, frames):
+def frame_lim(mod, func, frames):
     '''
     Find a large enough xlim and ylim for frames, if not heatmaps.
 
     Inputs:
-        sim:        A stochastic_model.simulation object, the simulation results.
+        mod:        A simulation.model object, the simulation results.
         frames:     How many frame to make for the video.
     
     Returns:
@@ -125,15 +125,17 @@ def frame_lim(sim, func, frames):
     V_ylist = []
     
     for i in range(10):
-        U_fig, V_fig = func(sim, start = i / 10, end = (i / 10 + 1 / frames))
+        fig_U, ax_U = plt.subplots()
+        fig_V, ax_V = plt.subplots()
+        ax_U, ax_V = func(mod, ax_U = ax_U, ax_V = ax_V, start = i / 10, end = (i / 10 + 1 / frames))
 
-        U_xlist.append(U_fig.get_axes()[0].get_xlim())
-        U_ylist.append(U_fig.get_axes()[0].get_ylim())
-        V_xlist.append(V_fig.get_axes()[0].get_xlim())
-        V_ylist.append(V_fig.get_axes()[0].get_ylim())
+        U_xlist.append(ax_U.get_xlim())
+        U_ylist.append(ax_U.get_ylim())
+        V_xlist.append(ax_V.get_xlim())
+        V_ylist.append(ax_V.get_ylim())
 
-        plt.close(U_fig)
-        plt.close(V_fig)
+        plt.close(fig_U)
+        plt.close(fig_V)
     
     # get the largest 'range' based on the lists
     U_xlim = get_max_lim(U_xlist)
@@ -146,12 +148,12 @@ def frame_lim(sim, func, frames):
 
 
 
-def frame_heatmap_lim(sim, func, frames):
+def frame_heatmap_lim(mod, func, frames):
     '''
     Find a large enough color bar lim for frames, if heatmaps.
 
     Inputs:
-        sim:        A stochastic_model.simulation object, the simulation results.
+        mod:        A simulation.model object, the simulation results.
         frames:     How many frame to make for the video.
     
     Returns:
@@ -164,7 +166,7 @@ def frame_heatmap_lim(sim, func, frames):
     for i in range(10):
         fig_U, ax_U = plt.subplots()
         fig_V, ax_V = plt.subplots()
-        ax_U, ax_V = func(sim, ax_U = ax_U, ax_V = ax_V, start = i / 10, end = (i / 10 + 1 / frames))
+        ax_U, ax_V = func(mod, ax_U = ax_U, ax_V = ax_V, start = i / 10, end = (i / 10 + 1 / frames))
 
         U_list.append(ax_U.collections[0].get_clim())
         V_list.append(ax_V.collections[0].get_clim())
@@ -201,14 +203,15 @@ def make_mp4(video_dir, frame_dir, fps):
 
 
 
-def make_video(sim, func_name = 'UV_heatmap', frames = 100, dpi = 200, fps = 30, U_color = 'Greens', V_color = 'Purples', annot = False, fmt = '.3g', del_frames = False, dirs = 'videos'):
+def make_video(mod, func_name = 'UV_heatmap', frames = 100, dpi = 200, fps = 30, U_color = 'Greens', V_color = 'Purples', annot = False, fmt = '.3g', del_frames = False, dirs = 'videos'):
     '''
     Make a mp4 video based on simulation results.
 
     Inputs:
-    - sim:            a stochastic_model.simulation object, the simulation results.
+    - mod:            a simulation.model object, the simulation results.
     - func_name:      what function to use to make the frames. Should be one of the functions in figures.py
     - frames:         how many frames to make. Use more frames for more smooth evolutions.
+    - dpi:            dots per inch.
     - fps:            frames per second.
     - U_color:        color for U's videos. Color maps or regular colors, based on what function you use.
     - V_color:        color for V's videos.
@@ -231,10 +234,10 @@ def make_video(sim, func_name = 'UV_heatmap', frames = 100, dpi = 200, fps = 30,
     
     if 'heatmap' in func_name:
         # make sure a fixed color bar for all frames
-        U_clim, V_clim = frame_heatmap_lim(sim, func, frames)
+        U_clim, V_clim = frame_heatmap_lim(mod, func, frames)
     else:
         # make sure y axis not changing if not making heatmaps
-        U_xlim, U_ylim, V_xlim, V_ylim = frame_lim(sim, func, frames)
+        U_xlim, U_ylim, V_xlim, V_ylim = frame_lim(mod, func, frames)
 
     
     U_frame_dirs = dirs + '/U-' + func_name
@@ -258,9 +261,9 @@ def make_video(sim, func_name = 'UV_heatmap', frames = 100, dpi = 200, fps = 30,
         fig_V, ax_V = plt.subplots(figsize = (6.4, 4.8))#, constrained_layout = True)
 
         if 'heatmap' in func_name:
-            ax_U, ax_V = func(sim, ax_U = ax_U, ax_V = ax_V, U_color = U_color, V_color = V_color, start = i / frames, end = (i + 1) / frames, annot = annot, fmt = fmt)
+            ax_U, ax_V = func(mod, ax_U = ax_U, ax_V = ax_V, U_color = U_color, V_color = V_color, start = i / frames, end = (i + 1) / frames, annot = annot, fmt = fmt)
         else:
-            ax_U, ax_V = func(sim, ax_U = ax_U, ax_V = ax_V, U_color = U_color, V_color = V_color, start = i / frames, end = (i + 1) / frames)
+            ax_U, ax_V = func(mod, ax_U = ax_U, ax_V = ax_V, U_color = U_color, V_color = V_color, start = i / frames, end = (i + 1) / frames)
         
         if 'heatmap' in func_name:
             ax_U.collections[0].set_clim(U_clim)

{piegy-1.1.2.dist-info → piegy-1.1.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: piegy
-Version: 1.1.2
+Version: 1.1.4
 Summary: Payoff-Driven Stochastic Spatial Model for Evolutionary Game Theory
 Author-email: Chenning Xu <cxu7@caltech.edu>
 License: BSD 3-Clause License
@@ -55,7 +55,7 @@ Dynamic: license-file
 
 # piegy
 
-The package full name is: Payoff-Driven Stochastic Spatial Model for Evolutionary Game Theory
+The package full name is: Payoff-Driven Stochastic Spatial Model for Evolutionary Game Theory. "pi" refers to "payoff, and "egy" are taken from "Evolutionary Game Theory".
 
 Provides a stochastic spatial model for simulating the interaction and evolution of two species in either 1D or 2D space, as well as analytic tools.
 
@@ -69,7 +69,7 @@ pip install piegy
 
 ## Documentation and Source
 
-See source code at: [piegy GitHub repository](https://github.com/Chenning04/piegy.git). 
+See source code at: [piegy GitHub-repo](https://github.com/Chenning04/piegy.git). 
 The *piegy* documentation at: [piegy Documentation](https://piegy.readthedocs.io/en/). 
 
 ## How the Model Works
@@ -80,7 +80,7 @@ We use the Gillepie algorithm as the fundamental event-selection algorithm. At e
 
 ## Analytic Tools
 
-The *piegy* package also provides a wide range of analytic and supportive tools alongside the main model, such as plotting, numerical tools, data saving & reading, etc. We also provide the *piegy.videos* module for more direct visualizations like how population distribution change over time.
+The *piegy* package also provides a wide range of analytic and supportive tools alongside the main model, such as plotting, numerical tools, data saving & reading, etc. We also provide the *piegy.videos* module for more direct visualizations such as how population distribution change over time.
 
 ## Examples
 
@@ -88,15 +88,18 @@ To get started, simply get our demo model and run simulation:
 
 ```python
 from piegy import model, figures
+import matplotlib.pyplot as plt
 
 sim = model.demo_model()
 model.run(sim)
 
-dynamics = figures.UV_dyna(sim)
-U_hmap, V_hmap = figures.UV_heatmap(sim)
+fig1, ax1 = plt.subplots()
+figures.UV_dyna(sim, ax1)
+fig2, ax2 = plt.subplots(1, 2, figsize = (12.8, 4.8))
+U_hmap, V_hmap = figures.UV_heatmap(sim, ax2[0], ax2[1])
 ```
 
-The figures reveal the population dynamics and steady state population distribution.
+The figures reveal population dynamics and steady state population distribution.
 
 
 ## Acknowledgments

piegy-1.1.4.dist-info/RECORD

@@ -0,0 +1,16 @@
+piegy/__init__.py,sha256=plq8y9IE9ilaKtEFIblJ_QexipAvPBXoalXhXLbs71Q,3244
+piegy/__version__.py,sha256=p8vZzyuX_tcu2qlBukCqdCu3SozzbpVqCUOaVaEe8rE,856
+piegy/analysis.py,sha256=5X6cpEAgFlHiRoaVmqYALlUvkep_LmrqpJHLCtQrd9Q,8727
+piegy/data_tools.py,sha256=Rw1fzeCGbxAB8MqTxZNZnOkVn7FmoUGoRz21scTAvF0,3550
+piegy/figures.py,sha256=bMHS7gTYtWdixUMW_wokBD6NSj_WOjQtnWp0R8VXChw,19059
+piegy/simulation.py,sha256=ngyLGzXAePYlyrcRznxWA7FEvGl9Gad976Sh1gHT0hU,45178
+piegy/test_var.py,sha256=g6BS_G_sewLn-8urUdTnlaVd8LYt_5GDvQQr_4bmNDU,23604
+piegy/videos.py,sha256=QfSpOdwfaDsrQYRoiHmZ6gowzRQHom3m8kx1P65_8sM,10218
+piegy/tools/__init__.py,sha256=eYOl_HJHDonYexfrmKh3koOlxvtSo46vH6jHvCEEB4k,300
+piegy/tools/figure_tools.py,sha256=54vJSJMReXidFnSPE_xFvedtgnJU3d55zQDPNBLGs98,6975
+piegy/tools/file_tools.py,sha256=ncxFWeHfIE-GYLQlOrahFlhBgqPyuY3R5_93fpQeCEs,630
+piegy-1.1.4.dist-info/licenses/LICENSE.txt,sha256=wfzEht_CxOcfGGmg3f3at4mWJb9rTBjA51mXLl_3O3g,1498
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+piegy-1.1.4.dist-info/RECORD,,

piegy-1.1.2.dist-info/RECORD

@@ -1,16 +0,0 @@
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-piegy/__version__.py,sha256=Trj_0I_674hSVhRFZKrxgEPKLEDrFFGr_p7rby3iR5w,701
-piegy/analysis.py,sha256=1cF06igQMGJGVjLiyhtgepGk8fYhzvL0orI48tOK1qY,8713
-piegy/data_tools.py,sha256=lNFOX4H0o_WfRSNQoC9QGCK66-IdrZ0zCnz12N-Ael4,3599
-piegy/figures.py,sha256=xXvr9LcGGhpeVibWTnIiDQlc_kBPibT8qYU5ALKS-zw,19063
-piegy/model.py,sha256=iTC0Ybp4qtrCcX_NcmEEk4bbqIXqUh470eF0CPbeEK0,45311
-piegy/test_var.py,sha256=HpdJf8i90iWteoJaVnYt37NJo1it2cf9srCsuYtwc7k,23628
-piegy/videos.py,sha256=yzZPMvU2wTrBQLnqoQGHuxOWVu-Dxyes7w4UuEB_N6c,10176
-piegy/tools/__init__.py,sha256=eYOl_HJHDonYexfrmKh3koOlxvtSo46vH6jHvCEEB4k,300
-piegy/tools/figure_tools.py,sha256=IWxMF_Yali37l2knzKLAcvrE8ndAQhCixfUu1_sWEf0,6975
-piegy/tools/file_tools.py,sha256=ncxFWeHfIE-GYLQlOrahFlhBgqPyuY3R5_93fpQeCEs,630
-piegy-1.1.2.dist-info/licenses/LICENSE.txt,sha256=wfzEht_CxOcfGGmg3f3at4mWJb9rTBjA51mXLl_3O3g,1498
-piegy-1.1.2.dist-info/METADATA,sha256=VCEwbAo25BkpLu_-b8nmsbisD-cFPy7lwovmG5PKNa0,5097
-piegy-1.1.2.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-piegy-1.1.2.dist-info/top_level.txt,sha256=k4QLYL8PqdqDuy95-4NZD_FVLqJDsmq67tpKkBn4vMw,6
-piegy-1.1.2.dist-info/RECORD,,