Merge branch 'master' into parallel_odeint

pysb/examples/cupsoda/run_michment_cupsoda.py

@@ -21,7 +21,8 @@ def run():
     tspan = np.linspace(0, 50, 501)
     # run_cupsoda returns a 3D array of species and observables trajectories
     trajectories = run_cupsoda(model, tspan, initials=initials,
-                               atol=1e-10, rtol=1e-4, verbose=True)
+                               integrator_options={'atol': 1e-10, 'rtol': 1e-4},
+                               verbose=True)
     # extract the trajectories for the 'Product' into a numpy array and
     # transpose to aid in plotting
     x = np.array([tr['Product'] for tr in trajectories]).T

pysb/examples/cupsoda/run_tyson_oscillator_cupsoda.py

@@ -8,9 +8,10 @@ def run():
     n_sims = 100
     vol = model.parameters['vol'].value
     tspan = np.linspace(0, 500, 501)
-    sim = CupSodaSimulator(model, tspan, vol=vol, verbose=True,
+    sim = CupSodaSimulator(model, tspan, verbose=True,
                            integrator_options={'atol' : 1e-12,
                                                'rtol' : 1e-6,
+                                               'vol': vol,
                                                'max_steps' :20000})
 
     # Rate constants

pysb/examples/run_robertson.py

@@ -14,7 +14,7 @@
 t = linspace(0, 40)
 # Simulate the model
 print("Simulating...")
-y = ScipyOdeSimulator(model, rtol=1e-4, atol=[1e-8, 1e-14, 1e-6]).run(
+y = ScipyOdeSimulator(model, integrator_options=dict(rtol=1e-4, atol=[1e-8, 1e-14, 1e-6])).run(
     tspan=t).all
 # Gather the observables of interest into a matrix
 yobs = array([y[obs] for obs in ('A_total', 'B_total', 'C_total')]).T

pysb/examples/run_tutorial_a.py

@@ -5,4 +5,4 @@
 t = [0, 10, 20, 30, 40, 50, 60]
 simulator = ScipyOdeSimulator(model, tspan=t)
 simresult = simulator.run()
-print(simresult.species[:, 1])
+print(simresult.species)

pysb/pathfinder.py

@@ -2,6 +2,9 @@
 import sys
 import sysconfig
 
+# Set to False to not utilize the system PATH environment variable
+use_path = 'PYSB_PATHFINDER_IGNORE_PATH' not in os.environ
+
 _path_config = {
     'bng': {
         'name': 'BioNetGen',
@@ -126,14 +129,13 @@ def get_path(prog_name):
                                 path_conf['name'],
                                 _get_executable(prog_name)))
 
-    # If this is anaconda, check the anaconda binary dir
-    if _is_anaconda():
-        try:
-            _path_cache[prog_name] = _validate_path(prog_name,
-                                                    _get_anaconda_bindir())
-            return _path_cache[prog_name]
-        except ValueError:
-            pass
+    # Check the Anaconda environment, if applicable, or BINDIR
+    try:
+        _path_cache[prog_name] = _validate_path(prog_name,
+                                                _get_anaconda_bindir())
+        return _path_cache[prog_name]
+    except ValueError:
+        pass
 
     # Check default paths for this operating system
     if os.name not in path_conf['search_paths'].keys():
@@ -147,6 +149,10 @@ def get_path(prog_name):
                                      set_path.__name__))
 
     search_paths = path_conf['search_paths'][os.name]
+    if use_path:
+        search_paths = list(search_paths) + os.environ.get('PATH', '').split(
+            os.pathsep)
+
     for search_path in search_paths:
         try:
             _path_cache[prog_name] = _validate_path(prog_name, search_path)
@@ -186,10 +192,6 @@ def set_path(prog_name, full_path):
     _path_cache[prog_name] = _validate_path(prog_name, full_path)
 
 
-def _is_anaconda():
-    """ Identify if this is an anaconda environment """
-    return 'conda' in sys.version
-
 
 def _get_anaconda_bindir():
     """ Get the binary path from python build time (for anaconda) """
@@ -198,7 +200,7 @@ def _get_anaconda_bindir():
     if conda_env:
         return os.path.join(conda_env, 'Scripts' if os.name == 'nt' else 'bin')
 
-    # Otherwise, use the default anaconda bin directory
+    # Otherwise, try the default anaconda/python bin directory
     bindir = sysconfig.get_config_var('BINDIR')
     if os.name == 'nt':
         # bindir doesn't point to scripts directory on Windows
@@ -236,7 +238,7 @@ def _validate_path(prog_name, full_path):
     if not os.path.isfile(full_path):
         # On anaconda, check batch file on Windows, if applicable
         batch_file = _get_batch_file(prog_name)
-        if _is_anaconda() and os.name == 'nt' and batch_file:
+        if os.name == 'nt' and batch_file:
             try:
                 return _validate_path(prog_name,
                                       os.path.join(full_path, batch_file))

pysb/simulator/scipyode.py

@@ -176,7 +176,7 @@ def __init__(self, model, tspan=None, initials=None, param_values=None,
                     "installing a package for compiling the ODEs to C code: "
                     "'weave' (recommended for Python 2) or "
                     "'cython' (recommended for Python 3). This warning can "
-                    "be suppressed by specifying compiler_mode='python'.")
+                    "be suppressed by specifying compiler='python'.")
             self._logger.debug('Equation mode set to "%s"' % self._compiler)
         else:
             self._compiler = compiler_mode

setup.py

@@ -28,7 +28,7 @@ def main():
           setup_requires=['nose'],
           tests_require=['coverage', 'pygraphviz', 'matplotlib', 'pexpect',
                          'pandas', 'theano', 'h5py', 'mock', 'cython',
-                         'libsbml', 'roadrunner'],
+                         'python-libsbml', 'roadrunner'],
           cmdclass=cmdclass,
           keywords=['systems', 'biology', 'model', 'rules'],
           classifiers=[