update docs

sys-bio · Jul 23, 2014 · 2c85b6b · 2c85b6b
1 parent 2bc49b9
commit 2c85b6b
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Showing 4 changed files with 30 additions and 13 deletions.
diff --git a/make_docs.sh b/make_docs.sh
@@ -14,9 +14,9 @@ doxygen doxygen.conf
 cd "$cwd"
 
 
-cd "$cwd/wrappers/C"
-doxygen core_c_api.doxy
-cd "$cwd"
+#cd "$cwd/wrappers/C"
+#doxygen core_c_api.doxy
+#cd "$cwd"
 
 cd  "$cwd/wrappers/Python/doc"
 make html

diff --git a/source/doxygen.conf b/source/doxygen.conf
@@ -38,7 +38,7 @@ PROJECT_NAME           = "libRoadRunner C++ API"
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = 1.1.0
+PROJECT_NUMBER         = 1.2.3
 
 # 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
@@ -794,9 +794,13 @@ EXCLUDE                = msc_stdint.h	\
                          ./rrSteadyStateSolver.h	\
                          ./rrTestSuiteModelSimulation.h	\
                          ./rrUtils.h	\
+                         ./rrStringUtils.h \
                          ./rrVariableType.h	\
                          ./rrVersionInfo.h \
-                         ./rrConfig.cpp 
+                         ./rrConfig.cpp  \
+                         ./RK4Integrator.h \
+                         ./GillespieIntegrator.h \
+                         ./rrRoadRunner.cpp 
 
 # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
 # directories that are symbolic links (a Unix file system feature) are excluded

diff --git a/source/rrRoadRunner.h b/source/rrRoadRunner.h
@@ -549,9 +549,8 @@ class RR_DECLSPEC RoadRunner : public Configurable
     RR_DEPRECATED(double getReactionRate(const int& index));
 
     /**
-     * @deprecated
      * @internal
-     * Returns the rate of changes of a species by its index
+     * @deprecated
      */
     RR_DEPRECATED(double getRateOfChange(const int& index));
 
@@ -725,11 +724,6 @@ class RR_DECLSPEC RoadRunner : public Configurable
     RR_DEPRECATED(std::vector<std::string> getGlobalParameterIds());
 
     /**
-     * The C back end requires this to be called to update
-     * model variables if anyting is changes. Does nothing
-     * in LLVM back end as everything is automatically handled
-     * with lazy evaluation.
-     *
      * @internal
      * @deprecated
      */

diff --git a/source/rrRoadRunnerOptions.h b/source/rrRoadRunnerOptions.h
@@ -206,7 +206,26 @@ class RR_DECLSPEC SimulateOptions
      */
     enum Integrator
     {
-        CVODE = 0,  GILLESPIE, RK4, INTEGRATOR_END
+        /**
+         * The default CVODE integrator from the Sundials package.
+         */
+        CVODE = 0,  
+
+        /**
+         * Basic Gillespie stochastic integrator. 
+         */
+        GILLESPIE, 
+
+        /**
+         * Basic Runge-Kutta fourth order integrator.
+         */
+        RK4, 
+
+        /**
+         * Always has to be at the end, this way, this value indicates
+         * how many integrators we have. 
+         */
+        INTEGRATOR_END
     };
 
     /**