Fix docs, check ny, more flexible plotting

pyodesys/core.py

@@ -13,7 +13,7 @@
 
 import os
 
-from .util import _ensure_4args
+from .util import _ensure_4args, _default
 from .plotting import plot_result, plot_phase_plane
 
 
@@ -220,6 +220,9 @@ def integrate(self, xout, y0, params=(), **kwargs):
         """
         intern_xout, intern_y0, self.internal_params = self.pre_process(
             xout, y0, params)
+        if hasattr(self, 'ny'):
+            if len(intern_y0) != self.ny:
+                raise ValueError("Incorrect length of intern_y0")
         integrator = kwargs.pop('integrator', None)
         if integrator is None:
             integrator = os.environ.get('PYODESYS_INTEGRATOR', 'scipy')
@@ -458,13 +461,10 @@ def _plot(self, cb, internal_xout=None, internal_yout=None,
 
         if 'names' not in kwargs:
             kwargs['names'] = getattr(self, 'names', None)
-        if (internal_xout, internal_yout, internal_params) == (None,)*3:
-            internal_xout = self.internal_xout
-            internal_yout = self.internal_yout
-            internal_params = self.internal_params
-        elif None in (internal_xout, internal_yout, internal_params):
-            raise ValueError("Pass either all or none of internal_* kwargs")
-        return cb(internal_xout, internal_yout, internal_params, **kwargs)
+
+        return cb(_default(internal_xout, self.internal_xout),
+                  _default(internal_yout, self.internal_yout),
+                  _default(internal_params, self.internal_params), **kwargs)
 
     def plot_result(self, **kwargs):
         """ Plots the integrated dependent variables from last integration.

pyodesys/plotting.py

@@ -55,6 +55,8 @@ def plot_result(x, y, params=(), indices=None, plot=None, plot_kwargs_cb=None,
     post_processors : iterable of callback (default: tuple())
 
     """
+    import matplotlib.pyplot as plt
+
     if plot is None:
         from matplotlib.pyplot import plot
     if plot_kwargs_cb is None:
@@ -106,7 +108,6 @@ def post_process(x, y, params):
                 idx, lines=False, markers=markers, labels=names))
 
     if xlabel is None:
-        import matplotlib.pyplot as plt
         try:
             plt.xlabel(x_post.dimensionality.latex)
         except AttributeError:
@@ -115,7 +116,6 @@ def post_process(x, y, params):
         plt.xlabel(xlabel)
 
     if ylabel is None:
-        import matplotlib.pyplot as plt
         try:
             plt.ylabel(y_post.dimensionality.latex)
         except AttributeError:

pyodesys/symbolic.py

@@ -216,8 +216,6 @@ def from_callback(cls, cb, ny, nparams=0, backend=None, **kwargs):
             length of p
         backend : module (optional)
             default: sympy
-        \*args :
-            arguments passed onto :class:`SymbolicSys`
         \*\*kwargs :
             keyword arguments passed onto :class:`SymbolicSys`
 

pyodesys/tests/test_symbolic.py

@@ -22,6 +22,12 @@ def identity(x):
 logexp = (sp.log, sp.exp)
 
 
+def test_SymbolicSys():
+    odesys = SymbolicSys.from_callback(lambda x, y, p, be: [y[1], -y[0]], 2)
+    with pytest.raises(ValueError):
+        odesys.integrate(1, [0])
+
+
 def decay_rhs(t, y, k):
     ny = len(y)
     dydt = [0]*ny
@@ -97,6 +103,9 @@ def f(t, x, k):
     ref = np.array(bateman_full(y0, k+[0], xout - xout[0], exp=np.exp)).T
     assert np.allclose(yout, ref, rtol=3e-11, atol=3e-11)
 
+    with pytest.raises(TypeError):
+        odesys.integrate([1e-12, 1], [0]*len(k), k, integrator='scipy')
+
 
 def test_ScaledSys_from_callback__exprs():
     def f(t, x, k):

pyodesys/util.py

@@ -157,3 +157,7 @@ def _ensure_4args(func):
         return lambda x, y, p=(), backend=math: func(x, y)
     else:
         raise ValueError("Incorrect numer of arguments")
+
+
+def _default(arg, default):
+    return default if arg is None else arg