piegy 2.0.3__py3-none-any.whl → 2.0.5__py3-none-any.whl

piegy/__version__.py

@@ -1,4 +1,4 @@
-__version__ = '2.0.3'
+__version__ = '2.0.5'
 
 '''
 version history:
@@ -25,4 +25,6 @@ version history:
 2.0.1: re-upload, the C core is not included in package.
 2.0.2: update version number in __version__.py and update README.
 2.0.3: speed boost & debugging in C core. Add check_overflow feature in simulation module, checks whether overflow/too large numbers might be encountered in simulation.
+2.0.4: minor debuggings.
+2.0.5: fix error in random number generator.
 '''

piegy/simulation.py

@@ -5,10 +5,11 @@ Main Module of Stochastic Simulation
 Contains all the necessary tools to build a model and run models based on Gillespie Algorithm.
 
 Class & Functions:
-- model:            creates a stochastic mode. Run the model by ``simulation.run(mod)``
-- run:              runs stochastic simulation on a model.
-- demo_model:       returns a demo model.
-- UV_expected_val:  calculates the expected population of U, V at steady state, assuming no migration and any stochastic process.
+- model:                creates a stochastic mode. Run the model by ``simulation.run(mod)``
+- run:                  runs stochastic simulation on a model.
+- demo_model:           returns a demo model.
+- UV_expected_val:      calculates the expected population of U, V at steady state, assuming no migration and any stochastic process.
+- check_overflow_func:  check whether an overflow might happen in simulation. This is usually done automatically when init-ing a model.
 '''
 
 
@@ -25,8 +26,8 @@ C_LIB_PATH = os.path.join(os.path.dirname(__file__), 'C_core', 'piegyc.so')
 
 # check whether overflow / too large values might be encountered
 # these values are considered as exponents in exp()
-EXP_OVERFLOW_BOUND = 700  # where exp(x) reaches overflow bound
-EXP_TOO_LARGE_BOUND = 87  # where exp(x) reaches 1e20
+EXP_OVERFLOW_BOUND = 709  # where exp(x) reaches overflow bound
+EXP_TOO_LARGE_BOUND = 88  # where exp(x) reaches 1e20
 
 
 '''
@@ -134,7 +135,10 @@ class model:
         self.I = np.array(I)            # N x M x 2 np.array, initial population. Two init-popu for every patch (U and V)
         self.X = np.array(X)            # N x M x 4 np.array, matrices. The '4' comes from 2x2 matrix flattened to 1D
         self.P = np.array(P)            # N x M x 6 np.array, 'patch variables', i.e., mu1&2, w1&2, kappa1&2
-        self.print_pct = print_pct      # int, print how much percent is done, need to be non-zero
+        if print_pct == None:
+            self.print_pct = -1
+        else:
+            self.print_pct = print_pct      # int, print how much percent is done, need to be non-zero
         if seed == None:
             self.seed = -1                # non-negative int, seed for random number generation
         else:
@@ -195,11 +199,12 @@ class model:
         if np.array(P).shape != (N, M, 6):
             raise ValueError('Please set P as a N x M x 6 shape list or array. 6 is for mu1, mu2, w1, w2, kappa1, kappa2')
         
-        if print_pct <= 0:
+        if not ((print_pct == None) or (isinstance(print_pct, int) and (print_pct >= -1))):
+            # if not the two acceptable values: None or >= -1 int
             raise ValueError('Please use an int > 0 for print_pct or None for not printing progress.')
         
-        if (not isinstance(seed, int)) or (seed < 0):
-            raise ValueError('Please use a non-negative int as seed')
+        if not ((seed == None) or (isinstance(seed, int) and (seed >= -1))):
+            raise ValueError('Please use a non-negative int as seed, or use None for no seed.')
         
         if not isinstance(check_overflow, bool):
             raise ValueError('Please use a bool for check_overflow')
@@ -391,6 +396,9 @@ def run(mod, message = ""):
     C-cored simulation
     '''
 
+    if not mod.data_empty:
+        raise ValueError('mod has non-empty data.')
+
     msg_len = len(message)
     msg_bytes = message.encode('utf-8')
     msg_buffer = ctypes.create_string_buffer(msg_bytes, msg_len) 
@@ -404,15 +412,14 @@ def run(mod, message = ""):
                            mod.N, mod.M, mod.maxtime, mod.record_itv, mod.sim_time, mod.boundary,
                            I, X, P, mod.print_pct, mod.seed)
     if not success:
-        raise RuntimeError("mod_init failed")
+        raise RuntimeError('mod_init failed')
     
     lib.run(ctypes.byref(mod_c), msg_buffer, msg_len)
     
-    mod.data_empty = False
-    mod.U = mod_c.get_array('U1d').reshape(mod.N, mod.M, mod.max_record)
-    mod.V = mod_c.get_array('V1d').reshape(mod.N, mod.M, mod.max_record)
-    mod.Upi = mod_c.get_array('Upi_1d').reshape(mod.N, mod.M, mod.max_record)
-    mod.Vpi = mod_c.get_array('Vpi_1d').reshape(mod.N, mod.M, mod.max_record)
+    mod.set_data(False, mod.max_record, 1, mod_c.get_array('U1d').reshape(mod.N, mod.M, mod.max_record), 
+                 mod_c.get_array('V1d').reshape(mod.N, mod.M, mod.max_record), 
+                 mod_c.get_array('Upi_1d').reshape(mod.N, mod.M, mod.max_record), 
+                 mod_c.get_array('Vpi_1d').reshape(mod.N, mod.M, mod.max_record))
 
     lib.mod_free_py(ctypes.byref(mod_c))
     del mod_c
@@ -438,7 +445,7 @@ def demo_model():
     X = [[[-1, 4, 0, 2] for _ in range(M)] for _ in range(N)]
     
     # patch variables
-    P = [[[0.5, 0.5, 200, 200, 0.001, 0.001] for _ in range(M)] for _ in range(N)]
+    P = [[[0.5, 0.5, 1, 1, 0.001, 0.001] for _ in range(M)] for _ in range(N)]
 
     print_pct = 25           # print progress
     seed = 36               # seed for random number generation
@@ -479,23 +486,15 @@ def UV_expected_val(mod):
 
 
 def check_overflow_func(mod):
-    overflow = False  # flag for might-overflow
-    too_large = False # flag for might-too-large
     _, _, pi_expected = UV_expected_val(mod)
     for i in range(mod.N):
         for j in range(mod.M):
             w1_pi = pi_expected[i][j] * mod.P[i][j][2]  # w1 * U_pi
             w2_pi = pi_expected[i][j] * mod.P[i][j][3]  # w2 * V_pi
             if ((w1_pi > EXP_OVERFLOW_BOUND) or (w2_pi > EXP_OVERFLOW_BOUND)):
-                overflow = True
-                too_large = True
-                break
+                print("Warning: might cause overflow. \n\t w1, w2, or payoff matrix values too large")
+                return
             if ((w1_pi > EXP_TOO_LARGE_BOUND) or (w2_pi > EXP_TOO_LARGE_BOUND)):
-                too_large = True
-                break
-    if overflow:
-        print("Warning: might cause overflow. \n\t w1, w2, or payoff matrix values too large")
-    elif too_large:
-        print("Warning: might encounter large values > 1e38 in simulation. \n\t w1, w2, or payoff matrix values too large")
-
+                print("Warning: might encounter large values > 3e38 in simulation. \n\t w1, w2, or payoff matrix values too large")
+                return
 

{piegy-2.0.3.dist-info → piegy-2.0.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: piegy
-Version: 2.0.3
+Version: 2.0.5
 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. "pi" refers to "payoff, and "egy" are taken from "Evolutionary Game Theory".
+The package full name is: Payoff-Driven Stochastic Spatial Model for Evolutionary Game Theory. "pi" refers to "payoff, and "egy" is 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.
 

{piegy-2.0.3.dist-info → piegy-2.0.5.dist-info}/RECORD

@@ -1,18 +1,18 @@
 piegy/__init__.py,sha256=KlbuIi3_Z9YZ5dWSFTwKxwrX3jdgNO4C8ksDjyDHsbk,2064
-piegy/__version__.py,sha256=7Pl-4GzRC0BYYyqHnr7GEJGnPlMH_a5FmAq5pNsQs7Y,1375
+piegy/__version__.py,sha256=iV5um0EKi2o17CKx28-gNQe2amahfUCmdgLQS_TvQV8,1445
 piegy/analysis.py,sha256=2GBsBbi7LdstSEAM0-F2bfL2kHu3MElcrw8bxZ1x6LI,8719
 piegy/data_tools.py,sha256=auliVb88qKQmCX7LEDgKQvhBcwFTCXBEWKtjJ4_-rTU,3446
 piegy/figures.py,sha256=GwixvD3Flaqg4feSvqr42lDR7CwZK0_2qmZg6N6_1uE,17936
-piegy/simulation.py,sha256=R0f_kzPfuCYiVdxeW07llyCuXOu3Uq6uDqjiq1Uwp3E,19605
+piegy/simulation.py,sha256=t6gusSvqKRMRc9RDEczUC36YMpDptCJEiB3I-NT3Q4o,19900
 piegy/simulation_py.py,sha256=WtWhpHCosKQ457gZ-iJ-7v0N3NtyPqDfgXv4DL3aBKs,29523
 piegy/test_var.py,sha256=EfItIK-FEApJTAW8rs15kdMs5xlv-8Bx6CtfpSoi8ys,23562
 piegy/videos.py,sha256=QfSpOdwfaDsrQYRoiHmZ6gowzRQHom3m8kx1P65_8sM,10218
-piegy/C_core/piegyc.so,sha256=OrUarFXNC4o9viHWwRO7RfcnVeyGoKad0I0ALrQEL2Y,51304
+piegy/C_core/piegyc.so,sha256=Xu3A90PmwpUGtO0tVyW_vtrQs_G0K_o7Fv7wljCHqUI,51080
 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-2.0.3.dist-info/licenses/LICENSE.txt,sha256=wfzEht_CxOcfGGmg3f3at4mWJb9rTBjA51mXLl_3O3g,1498
-piegy-2.0.3.dist-info/METADATA,sha256=stdacrzPZmn1_EVMboRwyZgzQpQnM0VVHBKpzxWEBxc,5453
-piegy-2.0.3.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-piegy-2.0.3.dist-info/top_level.txt,sha256=k4QLYL8PqdqDuy95-4NZD_FVLqJDsmq67tpKkBn4vMw,6
-piegy-2.0.3.dist-info/RECORD,,
+piegy-2.0.5.dist-info/licenses/LICENSE.txt,sha256=wfzEht_CxOcfGGmg3f3at4mWJb9rTBjA51mXLl_3O3g,1498
+piegy-2.0.5.dist-info/METADATA,sha256=xo4jCTouOmBzK_z7pKB6hf32zTOiHzra39hCX4eC2d4,5452
+piegy-2.0.5.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+piegy-2.0.5.dist-info/top_level.txt,sha256=k4QLYL8PqdqDuy95-4NZD_FVLqJDsmq67tpKkBn4vMw,6
+piegy-2.0.5.dist-info/RECORD,,