Beta release

.github/workflows/main.yml

@@ -9,7 +9,7 @@ on:
   workflow_dispatch:
 
 jobs:
-  build:
+  unit-tests:
     runs-on: ubuntu-latest
 
     steps:

AUTHORS

@@ -0,0 +1,7 @@
+Brian Drawert
+Bruno Jacob
+Bryan Rumsey
+Evie Hilton
+Mason Kidwell
+Matthew Geiger
+Sean Matthew

COPYRIGHT

@@ -1,16 +1,15 @@
-SpatialPy is a Python 3 package for simulation of 
+SpatialPy is a Python 3 package for simulation of
 spatial deterministic/stochastic reaction-diffusion-advection problems
 Copyright (C) 2020 SpatialPy developers.
 
 This program is free software: you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation, either version 3 of the License, or
-(at your option) any later version.
+it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as
+published by the Free Software Foundation.
 
 This program is distributed in the hope that it will be useful,
 but WITHOUT ANY WARRANTY; without even the implied warranty of
 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-GNU General Public License for more details.
+GNU GENERAL PUBLIC LICENSE Version 3 for more details.
 
 You should have received a copy of the GNU General Public License
 along with this program.  If not, see <http://www.gnu.org/licenses/>.

RELEASE_NOTES

@@ -1,4 +1,17 @@
-1.0.0
-------------
-- First release. 
+                                 RELEASE NOTES
+                             	   SpatialPy
 
+These are release notes for SpatialPy.
+----------------------------------------
+Date: 2/25/2021
+Version: 0.5.0+beta
+----------------------------------------
+- Initial beta release
+----------------------------------------
+Date: 3/9/2021
+Version: 0.5.1+beta
+----------------------------------------
+- Added pickling Results
+- Added add_mesh() function
+- timespan() now includes option to set timestep size
+- Added ability to read StochSS domains

examples/coral_reef/coral.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 import os
 import numpy
 import sys

examples/coral_reef/old/coral.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 import math
 import matplotlib.pyplot as plt
 import numpy

examples/cylinderDemo/SpatialPy_cylinderDemo3D.ipynb

@@ -223,23 +223,6 @@
     "%time result = sol.run()\n"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": 60,
-   "metadata": {},
-   "outputs": [
-    {
-     "output_type": "stream",
-     "name": "stdout",
-     "text": [
-      "{'Status': 'Success'}\n"
-     ]
-    }
-   ],
-   "source": [
-    "print(result)"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": 12,

examples/cylinderDemo/old/cylinder_demo3D.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 """ pyURDME model file for the annihilation cylinder 3D example. """
 
 import os

examples/cylinderDemo/old/ensemble_test.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 from cylinder_demo3D import cylinderDemo3D
 from pyurdme.nsmsolver import NSMSolver
 import matplotlib.pyplot as plt

examples/cylinderDemo/old/pickle_test.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 from cylinder_demo3D import cylinderDemo3D
 from pyurdme.nsmsolver import NSMSolver
 import matplotlib.pyplot as plt

examples/mincde/old/mincde.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 import numpy
 import os.path

examples/simple_diffusion/simple_diffusion2.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 """ PyURDME model with one species diffusing in the unit circle and one
     species diffusing on the boundary of the circle. Subdomains are 
     here handled by Dolfin's native subdomain model. """

examples/tests/Spatial_Birth_Death.ipynb

@@ -0,0 +1,255 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import os\n",
+    "import numpy\n",
+    "import matplotlib.pyplot as plt"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%load_ext autoreload\n",
+    "%autoreload 2"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "'../../spatialpy/__init__.py'"
+      ]
+     },
+     "execution_count": 3,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "import sys\n",
+    "sys.path.insert(0,'../..')\n",
+    "import spatialpy\n",
+    "spatialpy.__file__"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "model = spatialpy.Model('Spatial Birth-Death')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "model.mesh = spatialpy.Mesh.create_3D_domain([0,1],[0,1],[0,0.1], 10,10,1, fixed=True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "rabbits = model.add_species(spatialpy.Species('rabbits', D=0.1))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "model.add_initial_condition(spatialpy.ScatterInitialCondition(rabbits, 100, types=None))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "[<spatialpy.Model.Parameter at 0x7f6ade4d9280>,\n",
+       " <spatialpy.Model.Parameter at 0x7f6ade4d98e0>]"
+      ]
+     },
+     "execution_count": 8,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "kb=spatialpy.Parameter('k_birth',10)\n",
+    "kd=spatialpy.Parameter('k_death',0.1)\n",
+    "model.add_parameter([kb,kd])"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "model.add_reaction(spatialpy.Reaction(\n",
+    "    'birth',\n",
+    "    reactants={},\n",
+    "    products={rabbits:1},\n",
+    "    rate=kb))\n",
+    "#model.add_reaction(spatialpy.Reaction(\n",
+    "#    'death',\n",
+    "#    reactants={rabbits:1},\n",
+    "#    products={},\n",
+    "#    rate=kd))\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "True"
+      ]
+     },
+     "execution_count": 10,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "model.staticDomain"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 11,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "model.timespan(numpy.arange(0,10,1))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 12,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "model.timestep_size = 1"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 13,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Reading stdout/stderr from process:\n",
+      "\n",
+      "make: *** No rule to make target 'Birth-Death_generated_model.c'.  Stop.\n",
+      "\n"
+     ]
+    },
+    {
+     "ename": "SimulationError",
+     "evalue": "Compilation of solver failed, return_code=2",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mSimulationError\u001b[0m                           Traceback (most recent call last)",
+      "\u001b[0;32m<timed exec>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n",
+      "\u001b[0;32m~/Desktop/research/SpatialPy/spatialpy/Model.py\u001b[0m in \u001b[0;36mrun\u001b[0;34m(self, number_of_trajectories, seed, timeout, number_of_threads, debug_level, debug, profile)\u001b[0m\n\u001b[1;32m    103\u001b[0m         \u001b[0msol\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mSolver\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdebug_level\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mdebug_level\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    104\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 105\u001b[0;31m         return sol.run(number_of_trajectories=number_of_trajectories, seed=seed, timeout=timeout,\n\u001b[0m\u001b[1;32m    106\u001b[0m                        number_of_threads=number_of_threads, debug=debug, profile=profile)\n\u001b[1;32m    107\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;32m~/Desktop/research/SpatialPy/spatialpy/Solver.py\u001b[0m in \u001b[0;36mrun\u001b[0;34m(self, number_of_trajectories, seed, timeout, number_of_threads, debug, profile)\u001b[0m\n\u001b[1;32m    131\u001b[0m         \u001b[0;31m# Check if compiled, call compile() if not.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    132\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mis_compiled\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 133\u001b[0;31m             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcompile\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdebug\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mdebug\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mprofile\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mprofile\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    134\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    135\u001b[0m         \u001b[0;31m# Execute the solver\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;32m~/Desktop/research/SpatialPy/spatialpy/Solver.py\u001b[0m in \u001b[0;36mcompile\u001b[0;34m(self, debug, profile)\u001b[0m\n\u001b[1;32m    103\u001b[0m             \u001b[0;32mexcept\u001b[0m \u001b[0mException\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0me\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    104\u001b[0m                 \u001b[0;32mpass\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 105\u001b[0;31m             raise SimulationError(\n\u001b[0m\u001b[1;32m    106\u001b[0m                 \"Compilation of solver failed, return_code={0}\".format(return_code))\n\u001b[1;32m    107\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;31mSimulationError\u001b[0m: Compilation of solver failed, return_code=2"
+     ]
+    }
+   ],
+   "source": [
+    "%time result = model.run()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 14,
+   "metadata": {},
+   "outputs": [
+    {
+     "ename": "NameError",
+     "evalue": "name 'result' is not defined",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mNameError\u001b[0m                                 Traceback (most recent call last)",
+      "\u001b[0;32m<ipython-input-14-baaa9e3c3437>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mresult\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mplot_property\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'type'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
+      "\u001b[0;31mNameError\u001b[0m: name 'result' is not defined"
+     ]
+    }
+   ],
+   "source": [
+    "result.plot_property('type')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "result.plot_species('rabbits', animated=True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.8.5"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}

examples/yeast_polarization/G_protein_cycle.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 """ pyURDME model file for the polarization 1D example. """
 
 import os

examples/yeast_polarization/polarisome_model.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 """ pyURDME model file for the model found in Lawson et al. PloS Comp Bio (2013). """
 
 import os

setup.cfg

@@ -1,4 +1,4 @@
 [metadata]
-description-file=README.md
+description-file = README.md
 license_files = LICENSE