Minor fixups (#801)

* CMake: Set include directory for template files

* README: fix typos, formatting, update

* Fix python package description

* Fix formatting

* Update README, remove obsolete type hint issues

* Remove superfluous const from declaration

* Update doc

* Don't move returned value

CMakeLists.txt

@@ -194,6 +194,8 @@ add_custom_target(
     swig/CMakeLists_model.cmake
     swig/modelname.template.i
     )
+set_target_properties(fileTemplates
+    PROPERTIES INCLUDE_DIRECTORIES "${CMAKE_SOURCE_DIR}/include/")
 
 
 if($ENV{ENABLE_GCOV_COVERAGE})

README.md

@@ -7,7 +7,8 @@ AMICI provides a multi-language (Python, C++, Matlab) interface for the
 [IDAS](https://computing.llnl.gov/projects/sundials/idas)
 (for algebraic differential equations). AMICI allows the user to read
 differential equation models specified as [SBML](http://sbml.org/)
-and automatically compiles such models as `.mex` simulation files
+or [PySB](http://pysb.org/)
+and automatically compiles such models into `.mex` simulation files
 (Matlab), C++ executables or Python modules.
 
 In contrast to the (no longer maintained)
@@ -17,7 +18,7 @@ C++ code, which allows for a significantly faster simulation.
 
 Beyond forward integration, the compiled simulation file also allows for
 forward sensitivity analysis, steady state sensitivity analysis and
-adjoint sensitivity analysis for likelihood based output functions.
+adjoint sensitivity analysis for likelihood-based output functions.
 
 The interface was designed to provide routines for efficient gradient
 computation in parameter estimation of biochemical reaction models but
@@ -28,6 +29,7 @@ constrained optimization problems.
 ## Features
 
 * SBML import (see details below)
+* PySB import
 * Generation of C++ code for model simulation and sensitivity
   computation
 * Access to and high customizability of CVODES and IDAS solver
@@ -40,7 +42,7 @@ constrained optimization problems.
 * Pre-equilibration and pre-simulation conditions
 * Support for
   [discrete events and logical operations](https://academic.oup.com/bioinformatics/article/33/7/1049/2769435)
-
+  (Matlab-only)
 
 ## Interfaces & workflow
 
@@ -55,21 +57,21 @@ is then used for model simulation.
 
 ## Getting started
 
-AMICI installation instructions are provided
-[here](http://icb-dcm.github.io/AMICI/md__i_n_s_t_a_l_l.html).
+The AMICI source code is available at https://github.com/ICB-DCM/AMICI/.
+To install AMICI, first read the
+[installation instructions](http://icb-dcm.github.io/AMICI/md__i_n_s_t_a_l_l.html).
 
-To get you started with Python-AMICI the best way might be this
+To get you started with Python-AMICI, the best way might be checking out this
 [Jupyter notebook](https://github.com/ICB-DCM/AMICI/blob/master/python/examples/example_steadystate/ExampleSteadystate.ipynb).
 
-For Matlab, various examples are available
-[here](https://github.com/ICB-DCM/AMICI/tree/master/matlab/examples).
-
+To get started with Matlab-AMICI, various examples are available
+in [matlab/examples/](https://github.com/ICB-DCM/AMICI/tree/master/matlab/examples).
 
 Comprehensive documentation on installation and usage of AMICI is available
 online at [http://icb-dcm.github.io/AMICI/](http://icb-dcm.github.io/AMICI/).
 
-Any contributions to AMICI are welcome, read more contributing
-[here](http://icb-dcm.github.io/AMICI/md__c_o_n_t_r_i_b_u_t_i_n_g.html).
+Any [contributions](http://icb-dcm.github.io/AMICI/md__c_o_n_t_r_i_b_u_t_i_n_g.html)
+to AMICI are welcome (code, bug reports, suggestions for improvements, ...).
 
 
 ### Getting help
@@ -88,18 +90,25 @@ If you used AMICI in your work, we are happy to include
 your project, please let us know via a Github issue.
 
 When using AMICI in your project, please cite
-* [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., 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)
 and/or
-* [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)
+* 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)
 
 
 ## Status of SBML support in Python-AMICI
 
-Python-AMICI currently passes 494 out of the 1780 (~28%) test cases from
+Python-AMICI currently passes 500 out of the 1780 (~28%) test cases from
 the semantic
-[SBML Test Suite](https://github.com/sbmlteam/sbml-test-suite/).
+[SBML Test Suite](https://github.com/sbmlteam/sbml-test-suite/)
+([current status](https://github.com/ICB-DCM/AMICI/actions)).
 
-In additional, we currently plan to add support for the following features
+In addition, we currently plan to add support for the following features
 (see corresponding issues for details and progress):
 
 - Events (currently Matlab-only)
@@ -108,7 +117,6 @@ In additional, we currently plan to add support for the following features
 - Species assignment rules
 - Compartment assignment rules
 - Models without species
-- Logical operators
 
 contributions are welcome.
 

documentation/README.md

@@ -33,11 +33,8 @@ This is configured in `matlab/mtoc/config`.
 
 ## Python documentation
 
-Python documentation is processed by doxygen using the script and filters
-in `scripts/`.
-
-**NOTE:** Unfortunately, the current doxygen Python filter is unable to deal
-with Python type hints (https://github.com/ICB-DCM/AMICI/issues/613).
+Python documentation is processed by doxygen and doxypypy using the script and
+filters in `scripts/`.
 
 
 ## Out-of-source documentation
@@ -60,7 +57,7 @@ Some guidelines:
 
 * Please stick to the limit of 80 characters per line for readability of raw
   Markdown files where possible. 
-  
+
   However, note that some Markdown interpreters can handle line breaks within
   links and headings, whereas others cannot. Here, compatibility is preferred
   over linebreaks. 

documentation/development.md

@@ -19,7 +19,7 @@ and deploy a new release on [PyPI](https://pypi.org/project/amici/).
 
 We try to keep a clean git history. Therefore, feature pull requests are
 squash-merged to `develop`. Merging of release branches to master is done via
-merge commits.   
+merge commits.
 
 
 ## When starting to work on some issue
@@ -127,6 +127,9 @@ described below:
 
 * We want to maintain compatibility with g++, clang and the Intel C++ compiler 
 
+* For code formatting, we use the settings from `.clang-format` in the root
+  directory
+
 * *Details to be defined*
 
 

include/amici/misc.h

@@ -11,7 +11,7 @@
 #include <gsl/gsl-lite.hpp>
 
 namespace amici {
-    
+
 /**
  * @brief creates a slice from existing data
  *
@@ -20,9 +20,9 @@ namespace amici {
  * @param size slice size
  * @return span of the slice
  */
- 
- gsl::span<realtype> slice(std::vector<realtype> &data, const int index,
-                           const unsigned size);
+
+ gsl::span<realtype> slice(std::vector<realtype> &data, int index,
+                           unsigned size);
 
 /**
  * @brief Checks the values in an array for NaNs and Infs

include/amici/model.h

@@ -524,7 +524,7 @@ class Model : public AbstractModel {
      * @param it time index
      * @return t timepoint
      */
-    realtype getTimepoint(const int it) const;
+    realtype getTimepoint(int it) const;
 
     /**
      * @brief Set the timepoint vector

python/sdist/setup.py

@@ -163,7 +163,7 @@ def main():
             'develop': my_develop,
         },
         version=__version__,
-        description='Advanced multi-language Interface to CVODES and IDAS (%s)',
+        description='Advanced multi-language Interface to CVODES and IDAS',
         long_description=long_description,
         long_description_content_type="text/markdown",
         url='https://github.com/ICB-DCM/AMICI',

src/interface_matlab.cpp

@@ -2,8 +2,8 @@
  * @file   interface_matlab.cpp
  * @brief  core routines for mex interface
  *
- * This file defines the fuction mexFunction which is executed upon calling the
- * mex file from matlab
+ * This file defines the function `mexFunction` which is executed upon calling
+ * the `.mex` file from Matlab.
  */
 
 #include "amici/interface_matlab.h"
@@ -23,7 +23,7 @@ namespace amici {
     int dbl2int(const double x);
 
 /**
- * @brief The mexFunctionArguments enum takes care of the ordering of mex file
+ * @brief The mexRhsArguments enum takes care of the ordering of mex file
  * arguments (indexing in prhs)
  */
 enum mexRhsArguments {
@@ -41,8 +41,7 @@ enum mexRhsArguments {
 
 
 /*!
- * amici_blasCBlasTransToBlasTrans translates AMICI_BLAS_TRANSPOSE values to
- * CBlas readable strings
+ * Translates AMICI_BLAS_TRANSPOSE values to CBLAS readable strings
  *
  * @param trans       flag indicating transposition and complex conjugation
  *
@@ -480,7 +479,7 @@ void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[]) {
     std::unique_ptr<amici::ExpData> edata;
     if (nrhs > amici::RHS_DATA && mxGetPr(prhs[amici::RHS_DATA])) {
         try {
-            edata = std::move(amici::expDataFromMatlabCall(prhs, *model));
+            edata = amici::expDataFromMatlabCall(prhs, *model);
         } catch (amici::AmiException const& ex) {
             amici::errMsgIdAndTxt("AMICI:mex:setup","Failed to read experimental data:\n%s",ex.what());
         }

src/main.template.cpp

@@ -10,8 +10,7 @@
 #include "wrapfunctions.h"  /* model-provided functions */
 
 /* This is a scaffold for a stand-alone AMICI simulation executable
- * demonstrating
- * use of the AMICI C++ API.
+ * demonstrating the use of the AMICI C++ API.
  *
  * This program reads AMICI options from an HDF5 file, prints some results
  * and writes additional results to an HDF5 file. The name of the HDF5 file