Release 0.11.11 (#1363)

* Fix: Don't require code context for call stack (fixes #1347) (#1348)

* Fix Intel compiler warnings (#1349)

'type qualifier on return type is meaningless'

Closes #1346

* Avoid segfault in CVODES CVAdataStore (#1351)

Does not fix the root cause of occassional segfaults, but turns them into exceptions / integration failues.

* CI: Move windows tests from TravisCI to GitHub Actions (#1354)

Closes #1350

Removes obsolete .travis.yml

* Fix cxxcode import for SymPy 1.6 (#1356)

* Piecewise to heaviside (#1352)

* parse piecewise into heaviside functions

* Add Events as model quantity, parse Heavisides slightly differently

* bugfix

* rename symbols of root to h and switch order of functions to make sure h is known when dxdotdx_explicit is generated, to have the header file of h included

* rename root symbols to HeavisideFunction_ to have things more indicative

* tell AMICI about root, stau, and deltasx functions

* heavisides without sensitivities should be working

* need to change generation of stau to generration via inverse function theorem

* compute stau via inverse function theorem

* added functionality for deltasx, but segfaulting

* bugfixing

* remove debug output

* get indentations right

* Update python/amici/ode_export.py

Co-authored-by: Fabian Fröhlich <[email protected]>

* Update python/amici/ode_export.py

Co-authored-by: Fabian Fröhlich <[email protected]>

* Update python/amici/ode_export.py

Co-authored-by: Fabian Fröhlich <[email protected]>

* Update python/amici/ode_export.py

Co-authored-by: Fabian Fröhlich <[email protected]>

* Update python/amici/ode_export.py

Co-authored-by: Fabian Fröhlich <[email protected]>

* Update python/amici/sbml_import.py

Co-authored-by: Fabian Fröhlich <[email protected]>

* add a test for trajectories

* fix sroot and test

* cosmetic

* add analytical expressions for sensitivities

* add test for a complex condition

* add test for many conditions

* fix test

* improve documentation

* rename tests and refactor test for iterated piecewise, to check SBML piecewise logic a bit further

* cleanup for code review

* further cleanup

* quarter way done with parsing heavisides into piecewise

* fix logic parsing

* monkeypatch sympy printer

* enable more tests

* implement denesting of piecewise

* fix SBML nonsense

* fix boolean triggers

* simplify logic checks

* fix code smells

* add events to variable prototypes

* cleanup

* report details for skipped tests durin GHA run

* better skip printing

* resubstitution of non-optimized RHS into stau

* add sensitivity tests

* refactor tests

* remove skipping display code

* update test stats

* Update python/amici/ode_export.py

* Apply suggestions from code review

Co-authored-by: Daniel Weindl <[email protected]>

* document and simplify _collect_heaviside_roots

* address review comments

* reduce complexity

* misplaced docstrings

Co-authored-by: Fabian Fröhlich <[email protected]>
Co-authored-by: dilpath <[email protected]>
Co-authored-by: Daniel Weindl <[email protected]>

* restore support for species references (#1358)

* restore support for species references

* fixup and improve error message

* extend support for sbml functions (#1357)

* add more function mappings

* fixup min/max

* fix rem

* add Mod to unsupported functions

* more trigonometric functions

* more functions, fix xref

* fix xref with init assignment

* extend unsupported functions

* fix plus with empty arguments, update statistics

* update test stats

* fix stats

* Refactor: introduce import_utils.py (#1361)

* Refactor: introduce import_utils.py

To collect format-independent functions for model import.

* add additional file to SBML Testsuite path check

* Include new module in doc

Co-authored-by: Fabian Fröhlich <[email protected]>

* CI: Show all compiler warnings and treat as error (#1362)

* CI: Show all compiler errors and treat as error

Closes #1167

* Fix unused arguments

* Fix deprecated-copy

* Fix NVector (non-)const mess

* Fix CMake deprecation warning

* Fix doxygen

* Fix some typos

* Simplify / reduce number of const_casts

* Add support for different noise models for PySB import (#1360)

* Add support for different noise models for PySB import

.. as already the case for SBML import.

Closes #1176

* Respect noise model selection for PySB-PEtab import (#1339)

* doc, import

* Respect observable transformation for PySB-PEtab import (Fixes #1339)

* Set ODEModel._has_quadratic_nllh

Co-authored-by: Fabian Fröhlich <[email protected]>

* version bump

* fix some code smells to trigger GHA builds again?

* update docker to 20.04

* pin breathe

Co-authored-by: Daniel Weindl <[email protected]>
Co-authored-by: Lorenzo Contento <[email protected]>
Co-authored-by: Paul Stapor <[email protected]>
Co-authored-by: dilpath <[email protected]>

.github/workflows/test_sbml_semantic_test_suite.yml

@@ -9,6 +9,7 @@ on:
       - .github/workflows/test_sbml_semantic_test_suite.yml
       - python/amici/ode_export.py
       - python/amici/sbml_import.py
+      - python/amici/import_utils.py
       - scripts/run-SBMLTestsuite.sh
       - tests/testSBMLSuite.py
   check_suite:

.github/workflows/test_windows.yml

@@ -0,0 +1,52 @@
+name: Windows Tests
+on: [push, pull_request, workflow_dispatch]
+
+jobs:
+  build:
+    name: Tests Windows
+
+    runs-on: windows-2019
+
+    env:
+      AMICI_SKIP_CMAKE_TESTS: "TRUE"
+      openBLAS_version: "0.3.12"
+
+    steps:
+    - uses: actions/checkout@master
+    - run: git fetch --prune --unshallow
+
+    - shell: bash
+      run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
+    - shell: bash
+      run: echo "C:\\BLAS\\bin" >> $GITHUB_PATH
+    - shell: bash
+      run: echo "BLAS_LIBS=/LIBPATH:C:/BLAS/lib openblas.lib" >> $GITHUB_ENV
+    - shell: bash
+      run: echo "BLAS_CFLAGS=-IC:/BLAS/OpenBLAS-${openBLAS_version}/OpenBLAS-${openBLAS_version}" >> $GITHUB_ENV
+
+    # Developer Command Prompt for Microsoft Visual C++
+    - uses: ilammy/msvc-dev-cmd@v1
+
+    - name: Install deps
+      shell: bash
+      run: |
+        python -m pip install --upgrade pip \
+          && pip install pytest petab \
+          && choco install -y ninja \
+          && choco install -y swig --version=4.0.1
+
+    - name: Install OpenBLAS
+      shell: powershell
+      run: scripts/installOpenBLAS
+
+    - name: Create sdist
+      working-directory: python/sdist
+      run: python setup.py sdist
+
+    - name: Install sdist
+      working-directory: python/sdist
+      shell: bash
+      run: pip install -v $(ls -t dist/amici-*.tar.gz | head -1)
+
+    - name: Run Python tests
+      run: python -m pytest --ignore-glob=*petab* --ignore-glob=*special* python/tests

.gitignore

@@ -153,6 +153,7 @@ python/examples/example_presimulation/model_presimulation/*
 python/examples/example_presimulation/model_presimulation_re/*
 python/examples/example_constant_species/model_constant_species_reduced/*
 python/examples/example_constant_species/model_constant_species/*
+python/tests/sbml_test_models/*
 
 python/sdist/amici.egg-info/*
 python/sdist/amici/version.txt
@@ -191,3 +192,4 @@ tests/performance/CS_Signalling_ERBB_RAS_AKT_petab/*
 coverage_SBMLSuite.xml
 Benchmark-Models-PEtab/
 
+

ThirdParty/sundials/src/cvodes/cvodea.c

@@ -2026,6 +2026,9 @@ static int CVAdataStore(CVodeMem cv_mem, CkpntMem ck_mem)
   /* Run CVode to set following structures in dt_mem[i] */
   i = 1;
   do {
+    // Modified for AMICI
+    // (dt_mem has dimension ca_mem->ca_nsteps)
+    if (i > ca_mem->ca_nsteps) return(CV_FWD_FAIL);
 
     flag = CVode(cv_mem, ck_mem->ck_t1, ca_mem->ca_ytmp, &t, CV_ONE_STEP);
     if (flag < 0) return(CV_FWD_FAIL);

docker/Dockerfile

@@ -1,4 +1,4 @@
-FROM ubuntu:19.10
+FROM ubuntu:20.04
 
 RUN apt update \
     && apt-get install -y \

documentation/python_interface.rst

@@ -25,7 +25,7 @@ AMICI can import :term:`SBML` models via the
 Status of SBML support in Python-AMICI
 ++++++++++++++++++++++++++++++++++++++
 
-Python-AMICI currently **passes 850 out of the 1780 (~48%) test cases** from
+Python-AMICI currently **passes 862 out of the 1780 (~48%) test cases** from
 the semantic
 `SBML Test Suite <https://github.com/sbmlteam/sbml-test-suite/>`_
 (`current status <https://github.com/AMICI-dev/AMICI/actions>`_).
@@ -35,7 +35,6 @@ In addition, we currently plan to add support for the following features
 
 - Events (currently Matlab-only)
 - Algebraic rules
-- Models without species
 
 contributions are welcome.
 

documentation/python_modules.rst

@@ -13,6 +13,7 @@ AMICI Python API
    amici.petab_import
    amici.petab_import_pysb
    amici.petab_objective
+   amici.import_utils
    amici.ode_export
    amici.plotting
    amici.pandas

documentation/rtd_requirements.txt

@@ -12,7 +12,7 @@ sphinx-autodoc-typehints>=1.10.3
 git+https://github.com/readthedocs/sphinx-hoverxref@master
 prompt-toolkit<=3.0.0
 ipython>=7.17.0
-breathe>=4.20.0
+breathe==4.24.1
 #exhale>=0.2.3
 git+https://github.com/dweindl/exhale@ea77a313777c1382a7830ce9ee6c405ce47f5f3b#egg=exhale
 # Newer versions cause trouble with including notebooks:

include/amici/abstract_model.h

@@ -626,7 +626,7 @@ class AbstractModel {
     virtual void fdJydy(realtype *dJydy, int iy, const realtype *p,
                         const realtype *k, const realtype *y,
                         const realtype *sigmay, const realtype *my);
-                        
+
     /**
      * @brief Model-specific implementation of fdJydy colptrs
      * @param dJydy sparse matrix to which colptrs will be written
@@ -800,15 +800,15 @@ class AbstractModel {
      * @param dwdx sparse matrix to which rowvals will be written
      */
     virtual void fdwdx_rowvals(SUNMatrixWrapper &dwdx);
-    
+
     /**
      * @brief Model specific implementation of fdwdw, no w chainrule (Py)
      * @param dwdw partial derivative w wrt w
      * @param t timepoint
      * @param x Vector with the states
      * @param p parameter vector
      * @param k constants vector
-     * @param h heavyside vector
+     * @param h Heaviside vector
      * @param w vector with helper variables
      * @param tcl Total abundances for conservation laws
      */

include/amici/edata.h

@@ -174,7 +174,7 @@ class ExpData {
      * @brief set function that copies observed data for specific observable
      *
      * @param observedData observed data (dimension: nt)
-     * @param iy oberved data index
+     * @param iy observed data index
      */
     void setObservedData(const std::vector<realtype> &observedData, int iy);
 

include/amici/hdf5.h

@@ -243,7 +243,7 @@ void createAndWriteDouble3DDataset(H5::H5File const &file,
 /**
  * @brief Read scalar native double attribute from HDF5 object.
  * @param file HDF5 file
- * @param optionsObject Object to read attribute frin
+ * @param optionsObject Object to read attribute from
  * @param attributeName Name of attribute to read
  * @return Attribute value
  */

include/amici/model.h

@@ -210,7 +210,7 @@ class Model : public AbstractModel {
     using AbstractModel::fx0_fixedParameters;
     using AbstractModel::fy;
     using AbstractModel::fz;
-    
+
     /**
      * @brief Initialize model properties.
      * @param x Reference to state variables
@@ -597,7 +597,7 @@ class Model : public AbstractModel {
      * @return Observable IDs
      */
     virtual std::vector<std::string> getObservableIds() const;
-    
+
     /**
      * @brief Checks whether the defined noise model is gaussian, i.e., the nllh is quadratic
      * @return boolean flag
@@ -1298,13 +1298,13 @@ class Model : public AbstractModel {
 
     /** Flag indicating Matlab- or Python-based model generation */
     bool pythonGenerated;
-    
+
     /**
      * @brief getter for dxdotdp (matlab generated)
      * @return dxdotdp
      */
     const AmiVectorArray &get_dxdotdp() const;
-    
+
     /**
      * @brief getter for dxdotdp (python generated)
      * @return dxdotdp
@@ -1642,7 +1642,7 @@ class Model : public AbstractModel {
      * @param x Array with the states
      */
     void fdwdx(realtype t, const realtype *x);
-    
+
     /**
      * @brief Compute self derivative for recurring terms in xdot.
      * @param t Timepoint
@@ -1736,7 +1736,7 @@ class Model : public AbstractModel {
      * @return State vector with negative values replaced by `0` according to
      * stateIsNonNegative
      */
-    N_Vector computeX_pos(const_N_Vector x);
+    const_N_Vector computeX_pos(const_N_Vector x);
 
     /** All variables necessary for function evaluation */
     ModelState state_;
@@ -1752,13 +1752,13 @@ class Model : public AbstractModel {
 
     /** Sparse dwdx temporary storage (dimension: `ndwdx`) */
     mutable SUNMatrixWrapper dwdx_;
-    
+
     /** Sparse dwdp temporary storage (dimension: `ndwdp`) */
     mutable SUNMatrixWrapper dwdp_;
-    
+
     /** Dense Mass matrix (dimension: `nx_solver` x `nx_solver`) */
     mutable SUNMatrixWrapper M_;
-    
+
     /**
      * Temporary storage of `dxdotdp_full` data across functions (Python only)
      * (dimension: `nplist` x `nx_solver`, nnz: dynamic,
@@ -1780,7 +1780,7 @@ class Model : public AbstractModel {
      * type `CSC_MAT`)
      */
     mutable SUNMatrixWrapper dxdotdp_implicit;
-    
+
     /**
      * Temporary storage of `dxdotdx_explicit` data across functions (Python only)
      * (dimension: `nplist` x `nx_solver`, nnz: 'nxdotdotdx_explicit',
@@ -2005,10 +2005,10 @@ class Model : public AbstractModel {
 
     /** Sparse dwdw temporary storage (dimension: `ndwdw`) */
     mutable SUNMatrixWrapper dwdw_;
-    
+
     /** Sparse dwdx implicit temporary storage (dimension: `ndwdx`) */
     mutable std::vector<SUNMatrixWrapper> dwdx_hierarchical_;
-    
+
     /** Recursion */
     int w_recursion_depth_ {0};
 };