Added new names from #60 as alias in cmf.i and bumped version number

cmf/__init__.py

@@ -22,8 +22,8 @@
 from .stopwatch import StopWatch
 
 
-__version__ = '1.3.1'
-__compiletime__ = 'Wed Aug 22 10:53:40 2018'
+__version__ = '1.4'
+__compiletime__ = 'Wed Aug 22 15:25:40 2018'
 
 from .cmf_core import connect_cells_with_flux as __ccwf
 

cmf/cmf_core.py

@@ -13879,4 +13879,10 @@ def to_string(self, *args, **kwargs):
 # SoluteWaterIntegrator end
 
 
+ConstantFlux = TechnicalFlux
+ConstantStateFlux = statecontrol_connection
+WaterBalanceFlux = waterbalance_connection
+ConceptualInfiltration = SimpleInfiltration
+
+
 

cmf/cmf_core_src/cmf.i

@@ -124,5 +124,11 @@ std::string pyrepr(PyObject* o) {
 %include "math/integrators/WaterSoluteIntegrator.h"
 
 
-
+%pythoncode {
+    ConstantFlux = TechnicalFlux
+    ConstantStateFlux = statecontrol_connection
+    WaterBalanceFlux = waterbalance_connection
+    ConceptualInfiltration = SimpleInfiltration
+}
+
 

cmf/cmf_core_src/docstrings.i

@@ -951,14 +951,23 @@ cmf::water::bidirectional_kinematic_exchange::to_string "virtual
 std::string to_string() const ";
 
 
-// File: classcmf_1_1math_1_1_brents_method.xml
-%feature("docstring") cmf::math::BrentsMethod "";
+// File: classcmf_1_1math_1_1root__finding_1_1_bisect.xml
+%feature("docstring") cmf::math::root_finding::Bisect "";
 
-%feature("docstring")  cmf::math::BrentsMethod::BrentsMethod "BrentsMethod(double tolerance=1e-12, unsigned int max_iterations=1000)
+%feature("docstring")  cmf::math::root_finding::Bisect::Bisect "Bisect(double tolerance=1e-12, unsigned int max_iterations=1000) ";
+
+%feature("docstring")  cmf::math::root_finding::Bisect::f "virtual
+double f(double) const =0 ";
+
+
+// File: classcmf_1_1math_1_1root__finding_1_1_brents_method.xml
+%feature("docstring") cmf::math::root_finding::BrentsMethod "";
+
+%feature("docstring")
+cmf::math::root_finding::BrentsMethod::BrentsMethod "BrentsMethod(double tolerance=1e-12, unsigned int max_iterations=1000)
 ";
 
-%feature("docstring")  cmf::math::BrentsMethod::f "virtual double
-f(double) const =0 ";
+%feature("docstring")  cmf::math::root_finding::BrentsMethod::f "virtual double f(double) const =0 ";
 
 
 // File: classcmf_1_1upslope_1_1_brooks_corey_retention_curve.xml
@@ -6463,11 +6472,11 @@ const
 returns the number of state variables ";
 
 
-// File: classcmf_1_1math_1_1_brents_method_1_1iteration__error.xml
-%feature("docstring") cmf::math::BrentsMethod::iteration_error "";
+// File: classcmf_1_1math_1_1root__finding_1_1iteration__error.xml
+%feature("docstring") cmf::math::root_finding::iteration_error "";
 
 %feature("docstring")
-cmf::math::BrentsMethod::iteration_error::iteration_error "iteration_error(std::string msg) ";
+cmf::math::root_finding::iteration_error::iteration_error "iteration_error(std::string msg) ";
 
 
 // File: classcmf_1_1river_1_1_i_volume_height_function.xml
@@ -9991,11 +10000,11 @@ Returns the water balance of each vector as a vector.
 Replaces slow Python code like: ";
 
 
-// File: classcmf_1_1math_1_1_brents_method_1_1not__finite__error.xml
-%feature("docstring") cmf::math::BrentsMethod::not_finite_error "";
+// File: classcmf_1_1math_1_1root__finding_1_1not__finite__error.xml
+%feature("docstring") cmf::math::root_finding::not_finite_error "";
 
 %feature("docstring")
-cmf::math::BrentsMethod::not_finite_error::not_finite_error "not_finite_error(std::string msg) ";
+cmf::math::root_finding::not_finite_error::not_finite_error "not_finite_error(std::string msg) ";
 
 
 // File: classcmf_1_1water_1_1_null_adsorption.xml
@@ -13130,10 +13139,10 @@ transp_from_layer(cmf::upslope::SoilLayer::ptr sl, cmf::math::Time t)
 ";
 
 
-// File: classcmf_1_1math_1_1_brents_method_1_1sign__error.xml
-%feature("docstring") cmf::math::BrentsMethod::sign_error "";
+// File: classcmf_1_1math_1_1root__finding_1_1sign__error.xml
+%feature("docstring") cmf::math::root_finding::sign_error "";
 
-%feature("docstring")  cmf::math::BrentsMethod::sign_error::sign_error
+%feature("docstring")  cmf::math::root_finding::sign_error::sign_error
 "sign_error(std::string msg) ";
 
 
@@ -18252,15 +18261,13 @@ p2) ";
 
 
 // File: namespacecmf_1_1math.xml
-%feature("docstring")  cmf::math::get_parallel_threads "int
-cmf::math::get_parallel_threads()
+%feature("docstring")  cmf::math::root_finding::get_parallel_threads "int cmf::math::get_parallel_threads()
 
 Returns the max number of threads used by OpenMP in parallel sections
 of the code. ";
 
-%feature("docstring")  cmf::math::nash_sutcliffe "double
-cmf::math::nash_sutcliffe(const cmf::math::timeseries &model, const
-cmf::math::timeseries &observation)
+%feature("docstring")  cmf::math::root_finding::nash_sutcliffe "double cmf::math::nash_sutcliffe(const cmf::math::timeseries &model,
+const cmf::math::timeseries &observation)
 
 Calculates the Nash-Sutcliffe efficiency of a modeled timeseries in
 comparison with an observed timeseries.
@@ -18282,16 +18289,18 @@ steps
 
 :math:`\\\\overline{O}` is the arithmetic mean of observations ";
 
-%feature("docstring")  cmf::math::set_parallel_threads "int
-cmf::math::set_parallel_threads(int numthreads)
+%feature("docstring")  cmf::math::root_finding::set_parallel_threads "int cmf::math::set_parallel_threads(int numthreads)
 
 Set the number of threads used by OpenMP in parallel sections of the
 code. ";
 
-%feature("docstring")  cmf::math::timespan "Time
+%feature("docstring")  cmf::math::root_finding::timespan "Time
 cmf::math::timespan(long long ms) ";
 
 
+// File: namespacecmf_1_1math_1_1root__finding.xml
+
+
 // File: namespacecmf_1_1river.xml
 %feature("docstring")  cmf::river::make_river_gap "double
 cmf::river::make_river_gap(Reach::ptr root_reach)
@@ -18536,6 +18545,9 @@ boundary condition, providing the potential of the lower node. ";
 // File: namespacestd.xml
 %feature("docstring")  std::isfinite "bool std::isfinite(double v) ";
 
+%feature("docstring")  std::to_string "std::string std::to_string(T
+val) ";
+
 
 // File: ____init_____8py.xml
 

setup.py

@@ -30,7 +30,7 @@
 from distutils.sysconfig import customize_compiler
 from distutils.command.build_py import build_py
 
-version = '1.3.1'
+version = '1.4'
 branchversion = version
 try:
     from pygit2 import Repository

test/abstract_fluxes.py

@@ -0,0 +1,62 @@
+"""
+Tests the functionality of the rather abstract connection types
+
+"""
+import cmf
+import numpy as np
+import unittest
+
+def get_project():
+    p = cmf.project()
+    w = p.NewStorage('source')
+    o = p.NewOutlet('out')
+
+    return p, w, o
+
+
+class TestAbstractFluxes(unittest.TestCase):
+
+    def test_constant_flux(self):
+        p, w, o = get_project()
+        cmf.ConstantFlux(w, o, 1.0, 1.0, cmf.day)
+        t0 = cmf.Time()
+
+        def assert_flux(vol, flux):
+            w.volume = vol
+            self.assertAlmostEqual(w.flux_to(o, t0), flux)
+
+        for vol, flux in [(3, 1), (2, 1), (1.5, 0.5), (1.0, 0.0), (0.0, 0.0)]:
+            assert_flux(vol, flux)
+
+    def test_constant_state_flux(self):
+        p, w, o = get_project()
+        o.is_source = True
+        cmf.ConstantStateFlux(w, o, 1.0, cmf.day)
+        t0 = cmf.Time()
+
+        def assert_flux(vol, flux):
+            w.volume = vol
+            self.assertAlmostEqual(w.flux_to(o, t0), flux)
+
+        for vol, flux in [(2, 1), (1, 0), (1.5, 0.5), (0.0, -1.0)]:
+            assert_flux(vol, flux)
+
+    def test_balance_flux(self):
+        p, w, o = get_project()
+        i = p.NewNeumannBoundary('input', w)
+        o.is_source = True
+        cmf.WaterBalanceFlux(w, o)
+        t0 = cmf.Time()
+
+        def assert_flux(influx, outflux):
+            i.flux = influx
+            self.assertAlmostEqual(w.flux_to(o, t0), outflux)
+
+        for flux in np.arange(0, 10, 0.1):
+            assert_flux(flux, flux)
+
+
+if __name__ == '__main__':
+    unittest.main()
+
+

test/reachtypes.py

@@ -35,3 +35,6 @@ def test_depth(self):
 
         for a in np.arange(0., 2., 0.01):
             self.assertAlmostEquals(cr.get_depth(a), tr.get_depth(a))
+
+if __name__ == '__main__':
+    unittest.main()

tools/Doxyfile

@@ -38,7 +38,7 @@ PROJECT_NAME           = cmf
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = 1.3.1
+PROJECT_NUMBER         = 1.4
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a