Add symbol names to python-wrapped models and make them available in …

…python (Closes #64) (#346)

* core() Add symbol names to python-wrapped models and make them available in python (Closes #64)

* feature(core) add functions to check for set symbol names

* Rewrap test models

* ci(osx) Let osx build fail until #348 is resolved

* ci(osx) go back to standard brew python

* ci() move buildAmici to script

.travis.yml

@@ -7,6 +7,7 @@ branches:
     - staging
 
 matrix:
+  fast_finish: true
   include: 
     - os: linux
       dist: xenial
@@ -38,9 +39,9 @@ matrix:
         - brew update # without this homebrew can stumble over wrong ruby version
         - travis_wait brew install gcc || brew link --overwrite gcc # fix linker warning regarding /usr/local/include/c++
         - brew install hdf5 cppcheck swig doxygen ragel graphviz homebrew/cask/mactex
-        - brew install zoidbergwill/python/python36
+        - brew upgrade python
       after_success: 
-        - cd $BASE_DIR # cd to base dir for correct relative pah in deploy
+        - cd $BASE_DIR # cd to base dir for correct relative path in deploy
       deploy:
         provider: pages
         local-dir: doc
@@ -50,24 +51,46 @@ matrix:
         verbose: true
         on:
           branch: master
-
+
+  allow_failures:
+  # allow osx build to fail until symengine/homebrew/python3.7 issue is resolved
+    - os: osx
+      osx_image: xcode9.3
+      compiler: clang
+      before_install: 
+        - brew update # without this homebrew can stumble over wrong ruby version
+        - travis_wait brew install gcc || brew link --overwrite gcc # fix linker warning regarding /usr/local/include/c++
+        - brew install hdf5 cppcheck swig doxygen ragel graphviz homebrew/cask/mactex
+        - brew upgrade python
+      after_success: 
+        - cd $BASE_DIR # cd to base dir for correct relative path in deploy
+      deploy:
+        provider: pages
+        local-dir: doc
+        skip-cleanup: true
+        github-token: $GITHUB_TOKEN  # Set in the settings page of your repository, as a secure variable
+        keep-history: false
+        verbose: true
+        on:
+          branch: master
+
 install:
     # Python distutils only looks for `swig` and does not find `swig3.0`
     - export BASE_DIR=`pwd`
     - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then mkdir -p ~/bin/ && ln -s /usr/bin/swig3.0 ~/bin/swig && export PATH=~/bin/:$PATH; fi
-    - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then pyenv versions; fi
+    - pyenv versions
     - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then pyenv shell 2.7 3.6; fi
     - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then export PATH=/Users/travis/Library/Python/3.6/bin:$PATH; fi
     - pip3 install --user --upgrade pip setuptools wheel pkgconfig doxypypy coverage scipy
     - ./scripts/buildSuiteSparse.sh
     - ./scripts/buildSundials.sh
     - ./scripts/buildCpputest.sh
-    - ./scripts/buildAmici.sh
 
 script:  
 #    - cd $BASE_DIR/python/sdist
 #    - python3 setup.py sdist --dist-dir=$BASE_DIR/build/python/
 #    - python3 -m pip install $BASE_DIR/build/python/amici-*.tar.gz --verbose
+    - ./scripts/buildAmici.sh
     - cd $BASE_DIR
     - ./scripts/run-cpputest.sh
     - ./scripts/run-cppcheck.sh

include/amici/model.h

@@ -504,6 +504,56 @@ namespace amici {
          */
         int checkFinite(const int N,const realtype *array, const char* fun) const;
 
+
+        /**
+         * @brief Reports whether the model has parameter names set.
+         * @return
+         */
+        virtual bool hasParameterNames() const { return np() && !getParameterNames().empty(); }
+
+        /**
+         * @brief Get names of the model parameters
+         * @return the names
+         */
+        virtual std::vector<std::string> getParameterNames() const { return std::vector<std::string>(); }
+
+
+        /**
+         * @brief Reports whether the model has state names set.
+         * @return
+         */
+        virtual bool hasStateNames() const { return nx && !getStateNames().empty(); }
+
+        /**
+         * @brief Get names of the model states
+         * @return the names
+         */
+        virtual std::vector<std::string> getStateNames() const { return std::vector<std::string>(); }
+
+        /**
+         * @brief Reports whether the model has fixed parameter names set.
+         * @return
+         */
+        virtual bool hasFixedParameterNames() const { return nk() && !getFixedParameterNames().empty(); }
+
+        /**
+         * @brief Get names of the fixed model parameters
+         * @return the names
+         */
+        virtual std::vector<std::string> getFixedParameterNames() const { return std::vector<std::string>(); }
+
+        /**
+         * @brief Reports whether the model has observable names set.
+         * @return
+         */
+        virtual bool hasObservableNames() const { return ny && !getObservableNames().empty(); }
+
+        /**
+         * @brief Get names of the observables
+         * @return the names
+         */
+        virtual std::vector<std::string> getObservableNames() const { return std::vector<std::string>(); }
+
         /** number of states */
         const int nx;
         /** number of states in the unaugmented system */

models/model_dirac/model_dirac.h

@@ -1,6 +1,6 @@
 #ifndef _amici_model_dirac_h
 #define _amici_model_dirac_h
-/* Generated by amiwrap (R2017b) 413f6c54d956e878a95406f02808fafd1272c1cd */
+/* Generated by amiwrap (R2017b) f1e875655d8b056a0adf3c71f583fe988f257a06 */
 #include <cmath>
 #include <memory>
 #include "amici/defines.h"
@@ -62,7 +62,7 @@ class Model_model_dirac : public amici::Model_ODE {
 
     virtual amici::Model* clone() const override { return new Model_model_dirac(*this); };
 
-    const  char* getAmiciVersion() const { return "413f6c54d956e878a95406f02808fafd1272c1cd"; };
+    const  char* getAmiciVersion() const { return "f1e875655d8b056a0adf3c71f583fe988f257a06"; };
 
     virtual void fJ(realtype *J, const realtype t, const realtype *x, const double *p, const double *k, const realtype *h, const realtype *w, const realtype *dwdx) override {
         J_model_dirac(J, t, x, p, k, h, w, dwdx);

models/model_events/model_events.h

@@ -1,6 +1,6 @@
 #ifndef _amici_model_events_h
 #define _amici_model_events_h
-/* Generated by amiwrap (R2017b) 413f6c54d956e878a95406f02808fafd1272c1cd */
+/* Generated by amiwrap (R2017b) f1e875655d8b056a0adf3c71f583fe988f257a06 */
 #include <cmath>
 #include <memory>
 #include "amici/defines.h"
@@ -76,7 +76,7 @@ class Model_model_events : public amici::Model_ODE {
 
     virtual amici::Model* clone() const override { return new Model_model_events(*this); };
 
-    const  char* getAmiciVersion() const { return "413f6c54d956e878a95406f02808fafd1272c1cd"; };
+    const  char* getAmiciVersion() const { return "f1e875655d8b056a0adf3c71f583fe988f257a06"; };
 
     virtual void fJ(realtype *J, const realtype t, const realtype *x, const double *p, const double *k, const realtype *h, const realtype *w, const realtype *dwdx) override {
         J_model_events(J, t, x, p, k, h, w, dwdx);

models/model_jakstat_adjoint/model_jakstat_adjoint.h

@@ -1,6 +1,6 @@
 #ifndef _amici_model_jakstat_adjoint_h
 #define _amici_model_jakstat_adjoint_h
-/* Generated by amiwrap (R2017b) 413f6c54d956e878a95406f02808fafd1272c1cd */
+/* Generated by amiwrap (R2017b) f1e875655d8b056a0adf3c71f583fe988f257a06 */
 #include <cmath>
 #include <memory>
 #include "amici/defines.h"
@@ -65,7 +65,7 @@ class Model_model_jakstat_adjoint : public amici::Model_ODE {
 
     virtual amici::Model* clone() const override { return new Model_model_jakstat_adjoint(*this); };
 
-    const  char* getAmiciVersion() const { return "413f6c54d956e878a95406f02808fafd1272c1cd"; };
+    const  char* getAmiciVersion() const { return "f1e875655d8b056a0adf3c71f583fe988f257a06"; };
 
     virtual void fJ(realtype *J, const realtype t, const realtype *x, const double *p, const double *k, const realtype *h, const realtype *w, const realtype *dwdx) override {
         J_model_jakstat_adjoint(J, t, x, p, k, h, w, dwdx);

models/model_jakstat_adjoint_o2/model_jakstat_adjoint_o2.h

@@ -1,6 +1,6 @@
 #ifndef _amici_model_jakstat_adjoint_o2_h
 #define _amici_model_jakstat_adjoint_o2_h
-/* Generated by amiwrap (R2017b) 413f6c54d956e878a95406f02808fafd1272c1cd */
+/* Generated by amiwrap (R2017b) f1e875655d8b056a0adf3c71f583fe988f257a06 */
 #include <cmath>
 #include <memory>
 #include "amici/defines.h"
@@ -65,7 +65,7 @@ class Model_model_jakstat_adjoint_o2 : public amici::Model_ODE {
 
     virtual amici::Model* clone() const override { return new Model_model_jakstat_adjoint_o2(*this); };
 
-    const  char* getAmiciVersion() const { return "413f6c54d956e878a95406f02808fafd1272c1cd"; };
+    const  char* getAmiciVersion() const { return "f1e875655d8b056a0adf3c71f583fe988f257a06"; };
 
     virtual void fJ(realtype *J, const realtype t, const realtype *x, const double *p, const double *k, const realtype *h, const realtype *w, const realtype *dwdx) override {
         J_model_jakstat_adjoint_o2(J, t, x, p, k, h, w, dwdx);

models/model_nested_events/model_nested_events.h

@@ -1,6 +1,6 @@
 #ifndef _amici_model_nested_events_h
 #define _amici_model_nested_events_h
-/* Generated by amiwrap (R2017b) 413f6c54d956e878a95406f02808fafd1272c1cd */
+/* Generated by amiwrap (R2017b) f1e875655d8b056a0adf3c71f583fe988f257a06 */
 #include <cmath>
 #include <memory>
 #include "amici/defines.h"
@@ -65,7 +65,7 @@ class Model_model_nested_events : public amici::Model_ODE {
 
     virtual amici::Model* clone() const override { return new Model_model_nested_events(*this); };
 
-    const  char* getAmiciVersion() const { return "413f6c54d956e878a95406f02808fafd1272c1cd"; };
+    const  char* getAmiciVersion() const { return "f1e875655d8b056a0adf3c71f583fe988f257a06"; };
 
     virtual void fJ(realtype *J, const realtype t, const realtype *x, const double *p, const double *k, const realtype *h, const realtype *w, const realtype *dwdx) override {
         J_model_nested_events(J, t, x, p, k, h, w, dwdx);

models/model_neuron/model_neuron.h

@@ -1,6 +1,6 @@
 #ifndef _amici_model_neuron_h
 #define _amici_model_neuron_h
-/* Generated by amiwrap (R2017b) 413f6c54d956e878a95406f02808fafd1272c1cd */
+/* Generated by amiwrap (R2017b) f1e875655d8b056a0adf3c71f583fe988f257a06 */
 #include <cmath>
 #include <memory>
 #include "amici/defines.h"
@@ -79,7 +79,7 @@ class Model_model_neuron : public amici::Model_ODE {
 
     virtual amici::Model* clone() const override { return new Model_model_neuron(*this); };
 
-    const  char* getAmiciVersion() const { return "413f6c54d956e878a95406f02808fafd1272c1cd"; };
+    const  char* getAmiciVersion() const { return "f1e875655d8b056a0adf3c71f583fe988f257a06"; };
 
     virtual void fJ(realtype *J, const realtype t, const realtype *x, const double *p, const double *k, const realtype *h, const realtype *w, const realtype *dwdx) override {
         J_model_neuron(J, t, x, p, k, h, w, dwdx);

models/model_neuron_o2/model_neuron_o2.h

@@ -1,6 +1,6 @@
 #ifndef _amici_model_neuron_o2_h
 #define _amici_model_neuron_o2_h
-/* Generated by amiwrap (R2017b) 413f6c54d956e878a95406f02808fafd1272c1cd */
+/* Generated by amiwrap (R2017b) f1e875655d8b056a0adf3c71f583fe988f257a06 */
 #include <cmath>
 #include <memory>
 #include "amici/defines.h"
@@ -81,7 +81,7 @@ class Model_model_neuron_o2 : public amici::Model_ODE {
 
     virtual amici::Model* clone() const override { return new Model_model_neuron_o2(*this); };
 
-    const  char* getAmiciVersion() const { return "413f6c54d956e878a95406f02808fafd1272c1cd"; };
+    const  char* getAmiciVersion() const { return "f1e875655d8b056a0adf3c71f583fe988f257a06"; };
 
     virtual void fJ(realtype *J, const realtype t, const realtype *x, const double *p, const double *k, const realtype *h, const realtype *w, const realtype *dwdx) override {
         J_model_neuron_o2(J, t, x, p, k, h, w, dwdx);

models/model_robertson/model_robertson.h

@@ -1,6 +1,6 @@
 #ifndef _amici_model_robertson_h
 #define _amici_model_robertson_h
-/* Generated by amiwrap (R2017b) 413f6c54d956e878a95406f02808fafd1272c1cd */
+/* Generated by amiwrap (R2017b) f1e875655d8b056a0adf3c71f583fe988f257a06 */
 #include <cmath>
 #include <memory>
 #include "amici/defines.h"
@@ -63,7 +63,7 @@ class Model_model_robertson : public amici::Model_DAE {
 
     virtual amici::Model* clone() const override { return new Model_model_robertson(*this); };
 
-    const  char* getAmiciVersion() const { return "413f6c54d956e878a95406f02808fafd1272c1cd"; };
+    const  char* getAmiciVersion() const { return "f1e875655d8b056a0adf3c71f583fe988f257a06"; };
 
     virtual void fJ(realtype *J, const realtype t, const realtype *x, const double *p, const double *k, const realtype *h, const realtype cj, const realtype *dx, const realtype *w, const realtype *dwdx) override {
         J_model_robertson(J, t, x, p, k, h, cj, dx, w, dwdx);

models/model_steadystate/model_steadystate.h

@@ -1,6 +1,6 @@
 #ifndef _amici_model_steadystate_h
 #define _amici_model_steadystate_h
-/* Generated by amiwrap (R2017b) 413f6c54d956e878a95406f02808fafd1272c1cd */
+/* Generated by amiwrap (R2017b) f1e875655d8b056a0adf3c71f583fe988f257a06 */
 #include <cmath>
 #include <memory>
 #include "amici/defines.h"
@@ -62,7 +62,7 @@ class Model_model_steadystate : public amici::Model_ODE {
 
     virtual amici::Model* clone() const override { return new Model_model_steadystate(*this); };
 
-    const  char* getAmiciVersion() const { return "413f6c54d956e878a95406f02808fafd1272c1cd"; };
+    const  char* getAmiciVersion() const { return "f1e875655d8b056a0adf3c71f583fe988f257a06"; };
 
     virtual void fJ(realtype *J, const realtype t, const realtype *x, const double *p, const double *k, const realtype *h, const realtype *w, const realtype *dwdx) override {
         J_model_steadystate(J, t, x, p, k, h, w, dwdx);

python/amici/sbml_import.py

@@ -1102,10 +1102,28 @@ def writeModelHeader(self):
                         'NK': str(self.n_fixed_parameters),
                         'O2MODE': 'amici::AMICI_O2MODE_NONE',
                         'PARAMETERS': str(self.parameterValues)[1:-1],
-                        'FIXED_PARAMETERS': str(self.fixedParameterValues)[1:-1]}
+                        'FIXED_PARAMETERS': str(self.fixedParameterValues)[1:-1],
+                        'PARAMETER_NAMES_INITIALIZER_LIST': self.getSymbolNameInitializerList('parameter'),
+                        'STATE_NAMES_INITIALIZER_LIST': self.getSymbolNameInitializerList('species'),
+                        'FIXED_PARAMETER_NAMES_INITIALIZER_LIST': self.getSymbolNameInitializerList('fixed_parameter'),
+                        'OBSERVABLE_NAMES_INITIALIZER_LIST': self.getSymbolNameInitializerList('observable'),
+                        }
         applyTemplate(os.path.join(amiciSrcPath, 'model_header.ODE_template.h'),
                       os.path.join(self.modelPath, str(self.modelName) + '.h'), templateData)
 
+    def getSymbolNameInitializerList(self, name):
+        """Get C++ initializer list for vector of names for the given model entity
+        
+        Arguments:
+        name: string, any key present in self.symbols
+
+        Returns:
+
+        Raises:
+
+        """
+        return '\n'.join([ '"%s",' % str(symbol) for symbol in self.symbols[name]['sym'] ])
+
     def writeCMakeFile(self):
         """Write CMake CMakeLists.txt file for this model.
         

src/model_header.ODE_template.h

@@ -697,6 +697,32 @@ class Model_TPL_MODELNAME : public amici::Model_ODE {
     virtual void fz(double *z, const int ie, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h) override {
     }
 
+
+
+    /**
+     * @brief Get names of the model parameters
+     * @return the names
+     */
+    virtual std::vector<std::string> getParameterNames() const { return std::vector<std::string> {TPL_PARAMETER_NAMES_INITIALIZER_LIST}; }
+
+    /**
+     * @brief Get names of the model states
+     * @return the names
+     */
+    virtual std::vector<std::string> getStateNames() const { return std::vector<std::string> {TPL_STATE_NAMES_INITIALIZER_LIST}; }
+
+    /**
+     * @brief Get names of the fixed model parameters
+     * @return the names
+     */
+    virtual std::vector<std::string> getFixedParameterNames() const { return std::vector<std::string> {TPL_FIXED_PARAMETER_NAMES_INITIALIZER_LIST}; }
+
+    /**
+     * @brief Get names of the observables
+     * @return the names
+     */
+    virtual std::vector<std::string> getObservableNames() const { return std::vector<std::string> {TPL_OBSERVABLE_NAMES_INITIALIZER_LIST}; }
+
 };
 
 #endif /* _amici_TPL_MODELNAME_h */

swig/amici.i

@@ -41,3 +41,4 @@ using namespace amici;
 %template(DoubleVector) std::vector<realtype>;
 %template(IntVector) std::vector<int>;
 %template(ParameterScalingVector) std::vector<amici::AMICI_parameter_scaling>;
+%template(StringVector) std::vector<std::string>;