maintenance fixes, fixes #356 (#360)

* remove constant property from observable parameter and change file suffix of steady state example SBML to xml, fixes #351

* improve libSBML error printing and add SBML validation, fixes #343

* add publications to readme.md, fixes #329

* add get{Parameter,State,Observable,...}Ids function and correct respective get...Names function

* proper subscripting in plotting routines, fixes #359

* fix typos

* fix(python) make observable name input optional, add documentation

* documentation(python) added documentation to checkLibSBMLErrors

Author: FFroehlich

.gitignore

@@ -189,4 +189,9 @@ python/testSpeedy.py
 python/test.txt
 
 tests/test/*
+
 coverage_py.xml
+
+.idea/*
+
+python/examples/example_steadystate/model_steadystate_scaled/*

README.md

@@ -5,9 +5,13 @@ AMICI provides a multilanguage (Python, C++, Matlab) interface for the SUNDIALS
 
 The interface was designed to provide routines for efficient gradient computation in parameter estimation of biochemical reaction models but is also applicable to a wider range of differential equation constrained optimization problems.
 
+## Publications
+
+[Fröhlich, F., Kaltenbacher, B., Theis, F. J., & Hasenauer, J. (2017). Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks. Plos Computational Biology, 13(1), e1005331. doi: 10.1371/journal.pcbi.1005331](https://doi.org/10.1371/journal.pcbi.1005331)
+
+[Fröhlich, F., Theis, F. J., Rädler, J. O., & Hasenauer, J. (2017). Parameter estimation for dynamical systems with discrete events and logical operations. Bioinformatics, 33(7), 1049-1056. doi: 10.1093/bioinformatics/btw764](https://doi.org/10.1093/bioinformatics/btw764)
+
 ## Current build status
 
 [![Build Status](https://travis-ci.org/ICB-DCM/AMICI.svg?branch=master)](https://travis-ci.org/ICB-DCM/AMICI)
 [![CodeCov](https://codecov.io/gh/ICB-DCM/AMICI/branch/master/graph/badge.svg)](https://codecov.io/gh/ICB-DCM/AMICI)
-
-

include/amici/model.h

@@ -517,7 +517,6 @@ namespace amici {
          */
         virtual std::vector<std::string> getParameterNames() const { return std::vector<std::string>(); }
 
-
         /**
          * @brief Reports whether the model has state names set.
          * @return
@@ -553,6 +552,54 @@ namespace amici {
          * @return the names
          */
         virtual std::vector<std::string> getObservableNames() const { return std::vector<std::string>(); }
+        
+        /**
+         * @brief Reports whether the model has parameter ids set.
+         * @return
+         */
+        virtual bool hasParameterIds() const { return np() && !getParameterIds().empty(); }
+        
+        /**
+         * @brief Get ids of the model parameters
+         * @return the ids
+         */
+        virtual std::vector<std::string> getParameterIds() const { return std::vector<std::string>(); }
+        
+        /**
+         * @brief Reports whether the model has state ids set.
+         * @return
+         */
+        virtual bool hasStateIds() const { return nx && !getStateIds().empty(); }
+        
+        /**
+         * @brief Get ids of the model states
+         * @return the ids
+         */
+        virtual std::vector<std::string> getStateIds() const { return std::vector<std::string>(); }
+        
+        /**
+         * @brief Reports whether the model has fixed parameter ids set.
+         * @return
+         */
+        virtual bool hasFixedParameterIds() const { return nk() && !getFixedParameterIds().empty(); }
+        
+        /**
+         * @brief Get ids of the fixed model parameters
+         * @return the ids
+         */
+        virtual std::vector<std::string> getFixedParameterIds() const { return std::vector<std::string>(); }
+        
+        /**
+         * @brief Reports whether the model has observable ids set.
+         * @return
+         */
+        virtual bool hasObservableIds() const { return ny && !getObservableIds().empty(); }
+        
+        /**
+         * @brief Get ids of the observables
+         * @return the ids
+         */
+        virtual std::vector<std::string> getObservableIds() const { return std::vector<std::string>(); }
 
         /** number of states */
         const int nx;

python/amici/plotting.py

@@ -20,7 +20,7 @@ def plotStateTrajectories(rdata, state_indices=None, ax = None):
     if not state_indices:
         state_indices = range(rdata['x'].shape[1])
     for ix in state_indices:
-        ax.plot(rdata['t'], rdata['x'][:, ix], label='$x_%d$' % ix)
+        ax.plot(rdata['t'], rdata['x'][:, ix], label='$x_{%d}$' % ix)
         ax.set_xlabel('$t$ (s)')
         ax.set_ylabel('$x_i(t)$ (mmol/ml)')
         ax.legend()
@@ -45,7 +45,7 @@ def plotObservableTrajectories(rdata, observable_indices=None, ax = None):
     if not observable_indices:
         observable_indices = range(rdata['y'].shape[1])
     for iy in observable_indices:
-        ax.plot(rdata['t'], rdata['y'][:, iy], label='$y_%d$' % iy)
+        ax.plot(rdata['t'], rdata['y'][:, iy], label='$y_{%d}$' % iy)
         ax.set_xlabel('$t$ (s)')
         ax.set_ylabel('$y_i(t)$ (AU)')
         ax.legend()