piegy 1.1.1__py3-none-any.whl → 1.1.3__py3-none-any.whl

piegy/__version__.py

@@ -1,4 +1,4 @@
-__version__ = '1.0.0'
+__version__ = '1.1.2'
 
 '''
 version history:
@@ -12,8 +12,10 @@ version history:
 0.1.8: updated installation in README
 0.1.9: first round of full debugging
 
-1.0.0: first version in PyPI
+1.0.0: first version in PyPI.
 1.1.0: debugging. Updated a range of functions, in the following modules: figures, videos, test_var, model, figure_tools
 1.1.1: minor debugging in model module.
+1.1.2: fix text bad location in figure_tools, update labeling and titling in figures and test_var. Add dpi param to make_video in videos. Remove reset_data function in model.
+1.1.3: update README.
 
 '''

piegy/figures.py

@@ -72,9 +72,9 @@ def UV_heatmap(sim, ax_U = None, ax_V = None, U_color = 'Purples', V_color = 'Gr
     
     #### plot ####
     
-    U_title = figure_t.gen_title('U', start, end)
+    U_title = figure_t.gen_title('Popu U', start, end)
     U_text = figure_t.gen_text(np.mean(U_ave), np.std(U_ave))
-    V_title = figure_t.gen_title('V', start, end)
+    V_title = figure_t.gen_title('Popu V', start, end)
     V_text = figure_t.gen_text(np.mean(V_ave), np.std(V_ave))
 
     ax_U = figure_t.heatmap(U_ave, ax_U, U_color, annot, fmt, U_title, U_text)
@@ -110,9 +110,9 @@ def UV_bar(sim, ax_U = None, ax_V = None, U_color = 'purple', V_color = 'green',
 
     #### plot ####
 
-    U_title = figure_t.gen_title('U', start, end)
+    U_title = figure_t.gen_title('Population U', start, end)
     U_text = figure_t.gen_text(np.mean(U_ave), np.std(U_ave))
-    V_title = figure_t.gen_title('V', start, end)
+    V_title = figure_t.gen_title('Population V', start, end)
     V_text = figure_t.gen_text(np.mean(V_ave), np.std(V_ave))
 
     ax_U = figure_t.bar(U_ave, ax = ax_U, color = U_color, xlabel = 'patches', ylabel = 'U', title = U_title, text = U_text)
@@ -405,7 +405,6 @@ def pi_dyna(sim, ax = None, interval = 20, grid = True):
     ax.plot(xaxis, U_curve, CURVE_TYPE, label = r'$p_U$')
     ax.plot(xaxis, V_curve, CURVE_TYPE, label = r'$p_V$')
     ax.plot(xaxis, total_curve, CURVE_TYPE, label = 'total')
-    ax.set_xlim(0, sim.maxtime)
     ax.set_xlabel('Time')
     ax.set_ylabel('Payoff')
     ax.set_title('Payoff ' + r'$p_U$' + ' & ' + r'$p_V$' + ' over time')
@@ -492,7 +491,7 @@ def pi_std(sim, ax = None, interval = 20, grid = True):
 
 
 
-def UV_pi(sim, ax_U = None, ax_V = None, U_color = 'violet', V_color = 'yellowgreen', alpha = 0.4, start = 0.95, end = 1.0):
+def UV_pi(sim, ax_U = None, ax_V = None, U_color = 'violet', V_color = 'yellowgreen', alpha = 0.5, start = 0.95, end = 1.0):
     '''
     Make two scatter plots: x-axes are population and y-axes are payoff in a specified time interval.
     Reveals relationship between population and payoff.

piegy/model.py

@@ -33,7 +33,7 @@ from timeit import default_timer as timer
 
 
 # data type used by simulation.U and simulation.V
-UV_DTYPE = 'float32'
+UV_DTYPE = 'float64'
 
 # data type used by simulation.U_pi and V_pi
 PI_DTYPE = 'float64'
@@ -282,7 +282,7 @@ class simulation:
 
     def __init__(self, N, M, maxtime, record_itv, sim_time, boundary, I, X, P, print_pct = 25, seed = None, UV_dtype = UV_DTYPE, pi_dtype = PI_DTYPE):
 
-        self.check_valid_input(N, M, maxtime, record_itv, sim_time, boundary, I, X, P, print_pct, seed)
+        self.check_valid_input(N, M, maxtime, record_itv, sim_time, boundary, I, X, P, print_pct)
         
         self.N = N                      # int, N x M is spatial dimension
         self.M = M                      # int, can't be 1. If want to make 1D space, use N = 1. And this model doesn't work for 1x1 space (causes NaN)
@@ -318,7 +318,7 @@ class simulation:
         self.V_pi = np.zeros((self.N, self.M, self.max_record), dtype = self.pi_dtype)
 
 
-    def check_valid_input(self, N, M, maxtime, record_itv, sim_time, boundary, I, X, P, print_pct, seed):
+    def check_valid_input(self, N, M, maxtime, record_itv, sim_time, boundary, I, X, P, print_pct):
         # check whether the inputs are valid
         # seed, UV_dtype, pi_dtype is handled by numpy
 
@@ -355,10 +355,8 @@ class simulation:
         if print_pct <= 0:
             raise ValueError('Please use an int > 0 for print_pct or None for not printing progress.')
         
-        # seed is checked by number
-        
 
-    def check_valid_data(self, data_empty, max_record, compress_itv, U, V, U_pi, V_pi):
+    def check_valid_data(self, data_empty, max_record, compress_itv):
         # check whether a set of data is valid, used when reading a saved model
         if type(data_empty) != bool:
             raise TypeError('data_empty not a bool')
@@ -482,21 +480,16 @@ class simulation:
         # set seed
         self.seed = seed
 
-    
-    def reset_data(self):
-        # clear all data stored, set all to 0
-        self.init_storage()
-
 
     def clear(self):
-        # clear data by simply reseting
-        self.reset_data()
+        # clear all data stored, set all to 0
+        self.init_storage()
 
 
     def set_data(self, data_empty, max_record, compress_itv, U, V, U_pi, V_pi):
         # set data to the given data values
         # copies are made
-        self.check_valid_data(data_empty, max_record, compress_itv, U, V, U_pi, V_pi)
+        self.check_valid_data(data_empty, max_record, compress_itv)
 
         self.data_empty = data_empty
         self.max_record = max_record

piegy/test_var.py

@@ -193,12 +193,12 @@ def var_UV1(var, values, var_dirs, ax_U = None, ax_V = None, start = 0.95, end =
     var_disp = PATCH_VAR_DISP[var]
     
     ax_U.set_xlabel(var_disp)
-    ax_U.set_ylabel(r'$U$')
+    ax_U.set_ylabel('Population ' + r'$U$')
     ax_U.plot(values, U_ave, DOTTED_CURVE_TYPE, color = U_color)
     ax_U.set_title(figure_t.gen_title(var_disp + r'$\,-\,U$', start, end))
     
     ax_V.set_xlabel(var_disp)
-    ax_V.set_ylabel(r'$V$')
+    ax_V.set_ylabel('Population ' + r'$V$')
     ax_V.plot(values, V_ave, DOTTED_CURVE_TYPE, color = V_color)
     ax_V.set_title(figure_t.gen_title(var_disp + r'$\,-\,V$', start, end))
     
@@ -277,7 +277,7 @@ def var_UV2(var1, var2, values1, values2, var_dirs, ax_U = None, ax_V = None, va
             color_k = cmap_U(k / len(values1))[:3] + (rgb_alpha,)
             ax_U.plot(values2, U_ave[k], DOTTED_CURVE_TYPE, label = label, color = color_k)
             ax_U.set_xlabel(var2_disp)
-    ax_U.set_ylabel(r'$U$')
+    ax_U.set_ylabel('Population ' + r'$U$')
     ax_U.set_title(figure_t.gen_title(var1_disp + ',' + var2_disp + r'$\,-\,U$', start, end))
     ax_U.legend()
     
@@ -294,7 +294,7 @@ def var_UV2(var1, var2, values1, values2, var_dirs, ax_U = None, ax_V = None, va
             color_k = cmap_V(k / len(values1))[:3] + (rgb_alpha,)
             ax_V.plot(values2, V_ave[k], DOTTED_CURVE_TYPE, label = label, color = color_k)
             ax_V.set_xlabel(var2_disp)
-    ax_V.set_ylabel(r'$V$')
+    ax_V.set_ylabel('Population ' + r'$V$')
     ax_V.set_title(figure_t.gen_title(var1_disp + ',' + var2_disp + r'$\,-\,V$', start, end))
     ax_V.legend()
     
@@ -347,14 +347,14 @@ def var_pi1(var, values, var_dirs, ax_U = None, ax_V = None, start = 0.95, end =
     var_disp = PATCH_VAR_DISP[var]
     
     ax_U.set_xlabel(var_disp)
-    ax_U.set_ylabel(r'$\pi_U$')
+    ax_U.set_ylabel('Payoff ' + r'$p_U$')
     ax_U.plot(values, U_ave, DOTTED_CURVE_TYPE, color = U_color)
-    ax_U.set_title(figure_t.gen_title(var_disp + r'$\,-\,\pi_U$', start, end))
+    ax_U.set_title(figure_t.gen_title(var_disp + r'$\,-\,p_U$', start, end))
     
     ax_V.set_xlabel(var_disp)
-    ax_V.set_ylabel(r'$\pi_V$')
+    ax_V.set_ylabel('Payoff ' + r'$p_V$')
     ax_V.plot(values, V_ave, DOTTED_CURVE_TYPE, color = V_color)
-    ax_V.set_title(figure_t.gen_title(var_disp  + r'$\,-\,\pi_V$', start, end))
+    ax_V.set_title(figure_t.gen_title(var_disp  + r'$\,-\,p_V$', start, end))
 
     return ax_U, ax_V
 
@@ -428,8 +428,8 @@ def var_pi2(var1, var2, values1, values2, var_dirs, ax_U = None, ax_V = None, va
             color_k = cmap_U(k / len(values1))[:3] + (rgb_alpha,)
             ax_U.plot(values2, U_ave[k], DOTTED_CURVE_TYPE, label = label, color = color_k)
             ax_U.set_xlabel(var2_disp)
-    ax_U.set_ylabel(r'$\pi_{V}$')
-    ax_U.set_title(figure_t.gen_title(var1_disp + ',' + var2_disp + r'$\,-\,\pi_U$', start, end))
+    ax_U.set_ylabel('Payoff ' + r'$p_{V}$')
+    ax_U.set_title(figure_t.gen_title(var1_disp + ',' + var2_disp + r'$\,-\,p_U$', start, end))
     ax_U.legend()
     
     cmap_V = plt.get_cmap(V_color)
@@ -445,8 +445,8 @@ def var_pi2(var1, var2, values1, values2, var_dirs, ax_U = None, ax_V = None, va
             color_k = cmap_V(k / len(values1))[:3] + (rgb_alpha,)
             ax_V.plot(values2, V_ave[k], DOTTED_CURVE_TYPE, label = label, color = color_k)
             ax_V.set_xlabel(var2_disp)
-    ax_V.set_ylabel(r'$\pi_{U}$')
-    ax_V.set_title(figure_t.gen_title(var1_disp + ',' + var2_disp + r'$\,-\,\pi_V$', start, end))
+    ax_V.set_ylabel('Payoff ' + r'$p_{U}$')
+    ax_V.set_title(figure_t.gen_title(var1_disp + ',' + var2_disp + r'$\,-\,p_V$', start, end))
     ax_V.legend()
     
     return ax_U, ax_V

piegy/tools/figure_tools.py

@@ -43,10 +43,10 @@ def heatmap(data, ax = None, cmap = "Greens", annot = False, fmt = '.3g', title
         _, ax = plt.subplots()
 
     if text != None:
-        ax.text(0.66, 0.9, text, size = 10, linespacing = 1.5, transform = plt.gcf().transFigure)
+        ax.text(0.8, 1.025, text, size = 10, linespacing = 1.5, transform = ax.transAxes)
 
     ax = sns.heatmap(data, ax = ax, cmap = cmap, annot = annot, fmt = fmt)
-    ax.set_title(title)
+    ax.set_title(title, x = 0.5, y = 1)
     
     return ax
 
@@ -80,12 +80,12 @@ def bar(data, ax = None, color = "green", xlabel = None, ylabel = None, title =
             _, ax = plt.subplots()
 
     if text != None:
-        ax.text(0.66, 0.9, text, size = 10, linespacing = 1.5, transform = plt.gcf().transFigure)
+        ax.text(0.7, 1.025, text, size = 10, linespacing = 1.5, transform = ax.transAxes)
 
     ax.bar(x = xaxis, height = data, color = color)
     ax.set_xlabel(xlabel)
     ax.set_ylabel(ylabel)
-    ax.set_title(title)
+    ax.set_title(title, x = 0.5, y = 1)
     
     return ax
 
@@ -121,7 +121,7 @@ def gen_title(title, start, end):
     '''
     Generate a title for plot when it's about an interval of time.
     '''
-    title += ", " + str(round(start * 100, 1)) + " ~ " + str(round(end * 100, 1)) + "%"
+    title += ", " + str(round(start * 100, 1)) + "~" + str(round(end * 100, 1)) + "%"
     return title
 
 

piegy/videos.py

@@ -201,7 +201,7 @@ def make_mp4(video_dir, frame_dir, fps):
 
 
 
-def make_video(sim, func_name = 'UV_heatmap', frames = 100, fps = 30, U_color = 'Greens', V_color = 'Purples', annot = False, fmt = '.3g', del_frames = False, dirs = 'videos'):
+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'):
     '''
     Make a mp4 video based on simulation results.
 
@@ -209,6 +209,7 @@ def make_video(sim, func_name = 'UV_heatmap', frames = 100, fps = 30, U_color =
     - sim:            a stochastic_model.simulation 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.
@@ -274,8 +275,8 @@ def make_video(sim, func_name = 'UV_heatmap', frames = 100, fps = 30, U_color =
                 ax_V.set_xlim(U_xlim)
                 ax_V.set_xlim(V_xlim)
 
-        fig_U.savefig(U_frame_dirs + '/' + 'U_frame_' + str(i) + '.png', pad_inches = 0.25)
-        fig_V.savefig(V_frame_dirs + '/' + 'V_frame_' + str(i) + '.png', pad_inches = 0.25)
+        fig_U.savefig(U_frame_dirs + '/' + 'U_frame_' + str(i) + '.png', pad_inches = 0.25, dpi = dpi)
+        fig_V.savefig(V_frame_dirs + '/' + 'V_frame_' + str(i) + '.png', pad_inches = 0.25, dpi = dpi)
         
         plt.close(fig_U)
         plt.close(fig_V)

{piegy-1.1.1.dist-info → piegy-1.1.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: piegy
-Version: 1.1.1
+Version: 1.1.3
 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-1.1.3.dist-info/RECORD

@@ -0,0 +1,16 @@
+piegy/__init__.py,sha256=Lrh6NegSvo6LOCXg_tBTu804eicnHpQY2zmE0FchjKE,3241
+piegy/__version__.py,sha256=bfx1My4_mpMZlHLCS9hPCp888d56dz178h1mb2itmNo,724
+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=ReLrMwwgZfOgtsXPW5q29AAyFv0_E4A3DKo6BUFzups,10213
+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-1.1.3.dist-info/licenses/LICENSE.txt,sha256=wfzEht_CxOcfGGmg3f3at4mWJb9rTBjA51mXLl_3O3g,1498
+piegy-1.1.3.dist-info/METADATA,sha256=HhWIqo8y685rQPZv-fZnDhz-n1O4gW4aZZ4FfcF3UHE,5291
+piegy-1.1.3.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+piegy-1.1.3.dist-info/top_level.txt,sha256=k4QLYL8PqdqDuy95-4NZD_FVLqJDsmq67tpKkBn4vMw,6
+piegy-1.1.3.dist-info/RECORD,,

piegy-1.1.1.dist-info/RECORD

@@ -1,16 +0,0 @@
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-piegy/__version__.py,sha256=8IfclnXlmVE5p-odcoFI_9v7RIOmz2Cxd8Dvx1dMjNc,526
-piegy/analysis.py,sha256=1cF06igQMGJGVjLiyhtgepGk8fYhzvL0orI48tOK1qY,8713
-piegy/data_tools.py,sha256=lNFOX4H0o_WfRSNQoC9QGCK66-IdrZ0zCnz12N-Ael4,3599
-piegy/figures.py,sha256=xR4NKuHc-7E3ld6NjyAAVcJG8CtIoKoM4mqd8qPOXsg,19063
-piegy/model.py,sha256=NkP_Apnun3MhATSihR4_irnA-8p4FW879xQjCXVEPMA,45502
-piegy/test_var.py,sha256=PDtCCou-kFXumEe2EdAQNKJohwHH58ifLSsp5xQraVI,23532
-piegy/videos.py,sha256=vPl1aTIOaWxIUsxX5yL3JPiuf-Um0bPo7qYIHZP0bo0,10143
-piegy/tools/__init__.py,sha256=eYOl_HJHDonYexfrmKh3koOlxvtSo46vH6jHvCEEB4k,300
-piegy/tools/figure_tools.py,sha256=tAI5sBMsxN_1BN5_G_3UoMcDeYTj2DXr8l4HpPl9FSs,6961
-piegy/tools/file_tools.py,sha256=ncxFWeHfIE-GYLQlOrahFlhBgqPyuY3R5_93fpQeCEs,630
-piegy-1.1.1.dist-info/licenses/LICENSE.txt,sha256=wfzEht_CxOcfGGmg3f3at4mWJb9rTBjA51mXLl_3O3g,1498
-piegy-1.1.1.dist-info/METADATA,sha256=qawzMEDrKZITzujlqMf_9WJoEklAGFYcOw3I2u8plbQ,5097
-piegy-1.1.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-piegy-1.1.1.dist-info/top_level.txt,sha256=k4QLYL8PqdqDuy95-4NZD_FVLqJDsmq67tpKkBn4vMw,6
-piegy-1.1.1.dist-info/RECORD,,