Release 0.11.28

Merge pull request #1777 from AMICI-dev/release_0.11.28

Author: dweindl

.github/workflows/test_petab_test_suite.yml

@@ -63,9 +63,10 @@ jobs:
       # retrieve test models
       - name: Download and install PEtab test suite
         run: |
-          git clone --depth 1  --branch develop https://github.com/PEtab-dev/petab_test_suite \
+          git clone --depth 1 --branch develop \
+            https://github.com/PEtab-dev/petab_test_suite \
             && source ./build/venv/bin/activate \
-            && cd petab_test_suite && pip3 install -e . && cd ..
+            && cd petab_test_suite && pip3 install -e .
 
       - name: Run PEtab-related unit tests
         run: |

.github/workflows/test_sbml_semantic_test_suite.yml

@@ -13,6 +13,7 @@ on:
       - python/amici/import_utils.py
       - scripts/run-SBMLTestsuite.sh
       - tests/testSBMLSuite.py
+      - tests/conftest.py
   check_suite:
    types: [requested]
   workflow_dispatch:
@@ -25,8 +26,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        cases: ["1 - 250", "251 - 500", "501 - 750", "751 - 1000",
-                "1000-1250", "1251-1780"]
+        cases: ["1-250", "251-500", "501-750", "751-1000",
+                "1000-1250", "1251-"]
         python-version: [ 3.8 ]
 
     steps:

CHANGELOG.md

@@ -2,6 +2,41 @@
 
 ## v0.X Series
 
+### v0.11.28 (2022-04-08)
+
+New features:
+* Added `Solver.setSteadyStateToleranceFactor` and
+  `Solver.setSteadyStateSensiToleranceFactor` to specify a steady state
+  tolerance factor by @dilpath in https://github.com/AMICI-dev/AMICI/pull/1758
+
+  **NOTE: This also relaxed the default steady state (sensitivity)**
+  **tolerances by a factor of 100.**
+* Added support for `pathlib.Path` by @dweindl in
+  https://github.com/AMICI-dev/AMICI/pull/1769
+* Allow specifying initial timepoint with `ExpData` by @dilpath in
+  https://github.com/AMICI-dev/AMICI/pull/1776
+
+Performance:
+* Speedup for models with conservation laws by @FFroehlich in
+  https://github.com/AMICI-dev/AMICI/pull/1765
+* Improved efficiency of newton step convergence check by @FFroehlich in
+  https://github.com/AMICI-dev/AMICI/pull/1775
+
+Fixes:
+* Fixed deprecation warning for pandas.DataFrame.append in
+  `rdatas_to_measurement_df` by @dweindl in
+  https://github.com/AMICI-dev/AMICI/pull/1770
+* Fixed Rule-target handling in PEtab import by @dweindl in
+  https://github.com/AMICI-dev/AMICI/pull/1753
+
+Removed functionality:
+* Removed long deprecated `sbml2amici` arguments `modelName`
+  and `constantParameters` by @dweindl in
+  https://github.com/AMICI-dev/AMICI/pull/1774
+
+**Full Changelog**:
+https://github.com/AMICI-dev/AMICI/compare/v0.11.27...v0.11.28
+
 ### v0.11.27 (2022-04-04)
 
 New features:
@@ -24,7 +59,6 @@ Performance:
 * Optional parallel computation of derivatives during model import by @dweindl
   in https://github.com/AMICI-dev/AMICI/pull/1740
 * Sparsify jacobian by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1766
-* Speedup for models with conservation laws by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1765
 * Speedup conservation law computation by @FFroehlich in
   https://github.com/AMICI-dev/AMICI/pull/1754
 * Exploit stoichiometric matrix in pysb import by @FFroehlich in

documentation/python_interface.rst

@@ -26,7 +26,7 @@ AMICI can import :term:`SBML` models via the
 Status of SBML support in Python-AMICI
 ++++++++++++++++++++++++++++++++++++++
 
-Python-AMICI currently **passes 996 out of the 1780 (~56%) test cases** from
+Python-AMICI currently **passes 1014 out of the 1821 (~56%) test cases** from
 the semantic
 `SBML Test Suite <https://github.com/sbmlteam/sbml-test-suite/>`_
 (`current status <https://github.com/AMICI-dev/AMICI/actions>`_).
@@ -60,6 +60,7 @@ The following SBML test suite tags are currently supported
 * Concentration
 * ConstantSpecies
 * ConversionFactors
+* DefaultValue
 * EventT0Firing
 * HasOnlySubstanceUnits
 * InitialValueReassigned

include/amici/edata.h

@@ -519,6 +519,7 @@ class ConditionContext : public ContextManager {
     std::vector<realtype> original_sx0_;
     std::vector<realtype> original_parameters_;
     std::vector<realtype> original_fixed_parameters_;
+    realtype original_tstart_;
     std::vector<realtype> original_timepoints_;
     std::vector<int> original_parameter_list_;
     std::vector<amici::ParameterScaling> original_scaling_;

include/amici/serialization.h

@@ -62,8 +62,10 @@ void serialize(Archive &ar, amici::Solver &s, const unsigned int /*version*/) {
     ar &s.rtol_fsa_;
     ar &s.quad_atol_;
     ar &s.quad_rtol_;
+    ar &s.ss_tol_factor_;
     ar &s.ss_atol_;
     ar &s.ss_rtol_;
+    ar &s.ss_tol_sensi_factor_;
     ar &s.ss_atol_sensi_;
     ar &s.ss_rtol_sensi_;
     ar &s.maxsteps_;

include/amici/solver.h

@@ -44,7 +44,7 @@ namespace amici {
  *
  * NOTE: Any changes in data members here must be propagated to copy ctor,
  * equality operator, serialization functions in serialization.h, and
- * amici::hdf5::readSolverSettingsFromHDF5 in hdf5.cpp.
+ * amici::hdf5::(read/write)SolverSettings(From/To)HDF5 in hdf5.cpp.
  */
 class Solver {
   public:
@@ -384,6 +384,26 @@ class Solver {
      */
     void setAbsoluteToleranceQuadratures(double atol);
 
+    /**
+     * @brief returns the steady state simulation tolerance factor.
+     *
+     * Steady state simulation tolerances are the product of the simulation
+     * tolerances and this factor, unless manually set with
+     * `set(Absolute/Relative)ToleranceSteadyState()`.
+     * @return steady state simulation tolerance factor
+     */
+    double getSteadyStateToleranceFactor() const;
+
+    /**
+     * @brief set the steady state simulation tolerance factor.
+     *
+     * Steady state simulation tolerances are the product of the simulation
+     * tolerances and this factor, unless manually set with
+     * `set(Absolute/Relative)ToleranceSteadyState()`.
+     * @param factor tolerance factor (non-negative number)
+     */
+    void setSteadyStateToleranceFactor(double factor);
+
     /**
      * @brief returns the relative tolerance for the steady state problem
      * @return relative tolerance
@@ -408,6 +428,26 @@ class Solver {
      */
     void setAbsoluteToleranceSteadyState(double atol);
 
+    /**
+     * @brief returns the steady state sensitivity simulation tolerance factor.
+     *
+     * Steady state sensitivity simulation tolerances are the product of the
+     * sensitivity simulation tolerances and this factor, unless manually set
+     * with `set(Absolute/Relative)ToleranceSteadyStateSensi()`.
+     * @return steady state simulation tolerance factor
+     */
+    double getSteadyStateSensiToleranceFactor() const;
+
+    /**
+     * @brief set the steady state sensitivity simulation tolerance factor.
+     *
+     * Steady state sensitivity simulation tolerances are the product of the
+     * sensitivity simulation tolerances and this factor, unless manually set
+     * with `set(Absolute/Relative)ToleranceSteadyStateSensi()`.
+     * @param factor tolerance factor (non-negative number)
+     */
+    void setSteadyStateSensiToleranceFactor(double factor);
+
     /**
      * @brief returns the relative tolerance for the sensitivities of the
      * steady state problem
@@ -855,31 +895,32 @@ class Solver {
     std::vector<int> const& getLastOrder() const {
         return order_;
     }
-    
+
     /**
-     * @brief Returns how convergence checks for steadystate computation are performed.
+     * @brief Returns how convergence checks for steadystate computation are performed. If activated,
+     * convergence checks are limited to every 25 steps in the simulation solver to limit performance impact.
      * @return boolean flag indicating newton step (true) or the right hand side (false)
      */
     bool getNewtonStepSteadyStateCheck() const {
         return newton_step_steadystate_conv_;
     }
-    
+
     /**
      * @brief Returns how convergence checks for steadystate computation are performed.
      * @return boolean flag indicating state and sensitivity equations (true) or only state variables (false).
      */
     bool getSensiSteadyStateCheck() const {
         return check_sensi_steadystate_conv_;
     }
-    
+
     /**
      * @brief Sets how convergence checks for steadystate computation are performed.
      * @param flag boolean flag to pick newton step (true) or the right hand side (false, default)
      */
     void setNewtonStepSteadyStateCheck(bool flag) {
         newton_step_steadystate_conv_ = flag;
     }
-    
+
     /**
      * @brief Sets for which variables convergence checks for steadystate computation are performed.
      * @param flag boolean flag to pick state and sensitivity equations (true, default) or only state variables (false).
@@ -1753,23 +1794,29 @@ class Solver {
     /** relative tolerances for backward quadratures */
     realtype quad_rtol_ {1e-8};
 
+    /** steady state simulation tolerance factor */
+    realtype ss_tol_factor_ {1e2};
+
     /** absolute tolerances for steadystate computation */
     realtype ss_atol_ {NAN};
 
     /** relative tolerances for steadystate computation */
     realtype ss_rtol_ {NAN};
 
-    /** absolute tolerances for steadystate computation */
+    /** steady state sensitivity simulation tolerance factor */
+    realtype ss_tol_sensi_factor_ {1e2};
+
+    /** absolute tolerances for steadystate sensitivity computation */
     realtype ss_atol_sensi_ {NAN};
 
-    /** relative tolerances for steadystate computation */
+    /** relative tolerances for steadystate sensitivity computation */
     realtype ss_rtol_sensi_ {NAN};
 
     RDataReporting rdata_mode_ {RDataReporting::full};
-    
+
     /** whether newton step should be used for convergence steps */
     bool newton_step_steadystate_conv_ {false};
-    
+
     /** whether sensitivities should be checked for convergence to steadystate */
     bool check_sensi_steadystate_conv_ {true};
 

python/amici/__init__.py

@@ -24,8 +24,9 @@
 import os
 import re
 import sys
+from pathlib import Path
 from types import ModuleType as ModelModule
-from typing import Optional
+from typing import Optional, Union
 
 
 def _get_amici_path():
@@ -127,8 +128,8 @@ def getModel(self) -> amici.Model:
 class add_path:
     """Context manager for temporarily changing PYTHONPATH"""
 
-    def __init__(self, path: str):
-        self.path: str = path
+    def __init__(self, path: Union[str, Path]):
+        self.path: str = str(path)
 
     def __enter__(self):
         if self.path:
@@ -141,8 +142,10 @@ def __exit__(self, exc_type, exc_value, traceback):
             pass
 
 
-def import_model_module(module_name: str,
-                        module_path: Optional[str] = None) -> ModelModule:
+def import_model_module(
+        module_name: str,
+        module_path: Optional[Union[Path, str]] = None
+) -> ModelModule:
     """
     Import Python module of an AMICI model
 
@@ -153,6 +156,7 @@ def import_model_module(module_name: str,
     :return:
         The model module
     """
+    module_path = str(module_path)
 
     # ensure we will find the newly created module
     importlib.invalidate_caches()