Release 0.10.12

Merge pull request #817 from ICB-DCM/develop

.cppcheck-exitcode-suppressions

@@ -0,0 +1 @@
+alloca:*:*

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 In contrast to the (no longer maintained)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

@@ -183,15 +183,15 @@ class Model : public AbstractModel {
      * @param sx pointer to state variable sensititivies
      * @param x pointer to state variables
      */
-    void initializeStateSensitivities(AmiVectorArray &sx, AmiVector &x);
+    void initializeStateSensitivities(AmiVectorArray &sx, const AmiVector &x);
 
     /**
      * Initialises the heaviside variables h at the intial time t0
      * heaviside variables activate/deactivate on event occurences
      * @param x pointer to state variables
      * @param dx pointer to time derivative of states (DAE only)
      */
-    void initHeaviside(AmiVector &x, AmiVector &dx);
+    void initHeaviside(const AmiVector &x, const AmiVector &dx);
 
     /**
      * @brief Number of parameters wrt to which sensitivities are computed
@@ -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/amici/__init__.py

@@ -32,6 +32,38 @@
 import sys
 from contextlib import suppress
 
+
+def _get_amici_path():
+    """
+    Determine package installation path, or, if used directly from git
+    repository, get repository root
+    """
+    basedir = os.path.dirname(os.path.dirname(os.path.dirname(__file__)))
+    if os.path.exists(os.path.join(basedir, '.git')):
+        return os.path.abspath(basedir)
+    return os.path.dirname(__file__)
+
+
+def _get_commit_hash():
+    """Get commit hash from file"""
+    basedir = os.path.dirname(os.path.dirname(os.path.dirname(amici_path)))
+    commitfile = next(
+        (
+            file for file in [
+                os.path.join(basedir, '.git', 'FETCH_HEAD'),
+                os.path.join(basedir, '.git', 'ORIG_HEAD'),
+            ]
+            if os.path.isfile(file)
+        ),
+        None
+    )
+
+    if commitfile:
+        with open(commitfile) as f:
+            return str(re.search(r'^([\w]*)', f.read().strip()).group())
+    return 'unknown'
+
+
 # redirect C/C++ stdout to python stdout if python stdout is redirected,
 # e.g. in ipython notebook
 capture_cstdout = suppress
@@ -57,14 +89,8 @@
     except (ImportError, ModuleNotFoundError, AttributeError):
         pass
 
-# determine package installation path, or, if used directly from git
-# repository, get repository root
-if os.path.exists(os.path.join(os.path.dirname(__file__), '..', '..', '.git')):
-    amici_path = os.path.abspath(os.path.join(
-        os.path.dirname(__file__), '..', '..'))
-else:
-    amici_path = os.path.dirname(__file__)
-
+# Initialize AMICI paths
+amici_path = _get_amici_path()
 amiciSwigPath = os.path.join(amici_path, 'swig')
 amiciSrcPath = os.path.join(amici_path, 'src')
 amiciModulePath = os.path.dirname(__file__)
@@ -73,24 +99,7 @@
 with open(os.path.join(amici_path, 'version.txt')) as f:
     __version__ = f.read().strip()
 
-# get commit hash from file
-_commitfile = next(
-    (
-        file for file in [
-            os.path.join(amici_path, '..', '..', '..', '.git', 'FETCH_HEAD'),
-            os.path.join(amici_path, '..', '..', '..', '.git', 'ORIG_HEAD'),
-        ]
-        if os.path.isfile(file)
-    ),
-    None
-)
-
-if _commitfile:
-    with open(_commitfile) as f:
-        __commit__ = str(re.search(r'^([\w]*)', f.read().strip()).group())
-else:
-    __commit__ = 'unknown'
-
+__commit__ = _get_commit_hash()
 
 try:
     # These module require the swig interface and other dependencies which will