update get_integrator function, documentation, ode_plotter

LICENSE

@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright (c) 2017 Stefan Badelt <badelt@dna.caltech.edu>
+Copyright (c) 2017-2020 Stefan Badelt <stefan.badelt@gmail.com>
 
 Permission is hereby granted, free of charge, to any person obtaining a copy of
 this software and associated documentation files (the "Software"), to deal in

README.md

@@ -8,17 +8,18 @@ equations (ODEs).
 
 Create a test file with your CRN:
 
-File: ozzy.crn
+File: [oscillator.crn]
 ```
-# Oscillator Test
+# Rock-Paper-Scissors Oscillator
+
 A + B -> B + B [k = 0.2]
-B + C -> C + C [k = 0.3]
-C + A -> A + A [k = 1]
+B + C -> C + C [k = 0.4]
+C + A -> A + A [k = 0.7]
 ```
 
 And pipe it into the crnsimulator:
 ```sh
-~$ crnsimulator -o ozzy < ozzy.crn
+~$ crnsimulator -o ozzy < oscillator.crn
 ```
 This writes the ODE system to an executable python script: `ozzy.py`
 
@@ -35,7 +36,7 @@ You can pass the command line options for ozzy.py directly to `crnsimulator`.
 This will automatically simulate your ODE system. Use --force to overwrite an
 existing `ozzy.py` script.
 ```sh
-~$ crnsimulator --p0 A=0.1 B=1e-2 C=1e-3 --t8 10000 -o ozzy --pyplot ozzy.pdf < ozzy.crn
+~$ crnsimulator --p0 A=0.1 B=1e-2 C=1e-3 --t8 10000 -o ozzy --pyplot ozzy.pdf < oscillator.crn
 ```
 
 You can specify the CRN in a single line:
@@ -69,21 +70,38 @@ However, here is a small example using the above oscillating CRN.
             [['B', 'C'],['C','C'],0.8],
             [['C', 'A'],['A','A'],0.9]]
 >>> RG = ReactionGraph(crn)
->>> filename, odename = RG.write_ODE_lib(filename='ozzy.py')
+>>> svars = ['B', 'C', 'A'] # let's enforce the order of species, because we can!
+>>> filename, odename = RG.write_ODE_lib(filename='ozzy.py', sorted_vars = svars)
 >>> print('Wrote ODE system file:', filename)
 Wrote ODE system file: ozzy.py
 ```
 
-Then go ahead and execute `ozzy.py`
+Then go ahead and execute `ozzy.py`:
 ```sh
-~$ python ./ozzy.py --p0 1=1e-6 2=2e-6 3=5e-6 --t8 1e8 --pyplot ozzy.pdf
+~$ python ./ozzy.py --p0 1=1e-6 2=2e-6 3=5e-6 --t8 1e8 --pyplot ozzy.pdf --atol 1e-10 --rtol 1e-10
 ```
 
-... or load it as python library.
+... or load its functions by treating it as a python library:
+
+```py
+# Import
+>>> import numpy as np
+>>> from scipy.integrate import odeint
+>>> from crnsimulator import get_integrator
+>>> odesys = get_integrator(filename, function = odename)
+>>> odeplt = get_integrator(filename, function = 'ode_plotter')
+# Simulate
+>>> p0 = [1e-6, 2e-6, 5e-6] # order of svars
+>>> time = np.linspace(0, 1e8, num = 10_000)
+>>> ny = odeint(odesys, p0, time, (None,), atol = 1e-10, rtol = 1e-10).T
+# Plot
+>>> odeplt(`ozzy.pdf`, time, ny, svars)
+```
 
+... or include the prebuilt integrator in you own script (like the crnsimulator exectuable):
 ```py
 >>> from crnsimulator import get_integrator
->>> integrate = get_integrator(odename, filename)
+>>> integrate = get_integrator(filename)
 >>> integrate(args) # args = <argparse.ArgumentParser()>
 ```
 
@@ -92,12 +110,8 @@ Then go ahead and execute `ozzy.py`
 ```sh
 ~$ python setup.py install
 ```
-
-### local installation
-```sh
-~$ python setup.py install --user
-```
 
 ## Version
-0.7
+0.7.1
 
+[oscillator.crn]: <https://github.com/bad-ants-fleet/crnsimulator/blob/master/tests/crns/oscillator.crn>

crnsimulator/__init__.py

@@ -6,7 +6,7 @@
 # Use at your own risk.
 #
 #
-__version__ = "v0.7"
+__version__ = "v0.7.1"
 
 from crnsimulator.crn_parser import parse_crn_string, parse_crn_file
 from crnsimulator.reactiongraph import ReactionGraph

crnsimulator/odelib_template.py

@@ -26,8 +26,8 @@
 sns.set(style="darkgrid", font_scale=1, rc={"lines.linewidth": 2.0})
 
 
-def ode_plotter(name, t, ny, svars, log=False, labels=None,
-        xlim=None, ylim=None):
+def ode_plotter(name, t, ny, svars, log = False, labels = None,
+        xlim = None, ylim = None, plim = None):
     """ Plots the ODE trajectories.
 
     Args:
@@ -37,6 +37,9 @@ def ode_plotter(name, t, ny, svars, log=False, labels=None,
       svars (list[str]): A list of names for every trajectory in ny
       log (bool,optional): Plot data on a logarithmic time scale
       labels (set(),optional): Define species that appear labelled in the plot
+      xlim ((float,float), optional): matplotlib xlim.
+      ylim ((float,float), optional): matplotlib ylim.
+      plim (float, optional): Minimal occupancy to plot a trajectory. Defaults to None.
 
     Prints:
       A file containing the plot (Format *.pdf, *.png, etc.)
@@ -74,7 +77,7 @@ def ode_plotter(name, t, ny, svars, log=False, labels=None,
                 ax.plot(t, y, '--', lw=0.1, color='gray', zorder=1)
     else:
         for e, y in enumerate(ny):
-            if max(y) > 0.05:
+            if plim is None or max(y) > plim:
                 ax.plot(t, y, '-', label=svars[e])
             else:
                 ax.plot(t, y, '--', lw=0.1, color='gray', zorder=1)

crnsimulator/solver.py

@@ -11,13 +11,31 @@
 
 import crnsimulator.odelib_template
 
-def get_integrator(odename, filename):
-    """Workaround to avoid deprecation warnings for the imp module.
+def get_integrator(filename, function = 'integrate'):
+    """ Wrapper for the jit import of a function from a python script.
+    
+    Note: The intended usage is to import the integrate function from the
+    executable produced by crnsimulator. However, it can be used to import
+    arbitrary functions from arbitrary python scripts.
+
+    Args:
+        filename (str): The autogenerated python executable containing the odesystem. 
+        function (str, optional): The name of the function to be imported. Defaults
+            to 'integrate', which is the main function of the file, but it can also 
+            be used to import low-level functions such as 'odesystem' or 'ode_plotter'.
+
+    Returns:
+        A jit import of the requested function.
     """
-    loader = importlib.machinery.SourceFileLoader(odename, filename)
-    mod = types.ModuleType(loader.name)
-    loader.exec_module(mod)
-    return getattr(mod, 'integrate')
+    try:
+        loader = importlib.machinery.SourceFileLoader('my_loader', filename)
+        mod = types.ModuleType(loader.name)
+        loader.exec_module(mod)
+    except FileNotFoundError as err:
+        print(Warning('DEPRECATED - crnsimulator: Please note that the crnsimulator.solver.get_integrator function interface changed.'))
+        raise err
+
+    return getattr(mod, function)
 
 def writeODElib(svars, odeM, jacobian=None, rdict=None, concvect=None,
                 odename='odesystem', filename='./odesystem', template=None):

scripts/crnsimulator

@@ -130,7 +130,7 @@ def main(args):
         print('# Simulating the ODE system, change parameters using:')
         print("#  python {} --help ".format(filename))
 
-        integrate = get_integrator(odename, filename)
+        integrate = get_integrator(filename)
 
         # ********************* #
         # ARGUMENT PROCESSING 2 #

setup.py

@@ -9,13 +9,13 @@
 
 setup(
     name = 'crnsimulator',
-    version = "0.7",
+    version = "0.7.1",
     description = 'Simulate CRNs using ODEs.',
     long_description = LONG_DESCRIPTION,
     author = 'Stefan Badelt',
     author_email = 'badelt@caltech.edu',
     url = 'https://github.com/bad-ants-fleet/crnsimulator',
-    download_url = 'https://github.com/bad-ants-fleet/crnsimulator/archive/v0.7.tar.gz',
+    download_url = 'https://github.com/bad-ants-fleet/crnsimulator/archive/v0.7.1.tar.gz',
     license = 'MIT',
     classifiers = [
         'Development Status :: 3 - Alpha',

tests/test_solver.py

@@ -46,7 +46,7 @@ def test_crn(self):
         RG = ReactionGraph(crn)
 
         filename, odename = RG.write_ODE_lib(filename=self.filename)
-        integrate = get_integrator(odename, filename)
+        integrate = get_integrator(filename)
 
         self.args.p0 = ['1=0.5']
         self.args.t_log = 10
@@ -85,7 +85,7 @@ def test_crn_sympy_imports(self):
         RG = ReactionGraph(crn)
 
         filename, odename = RG.write_ODE_lib(filename=self.filename)
-        integrate = get_integrator(odename, filename)
+        integrate = get_integrator(filename)
 
         self.args.p0 = ['S=0.5', 'cos=0.2']
         self.args.t_log = 10