Merge branch 'develop' into jax_export

.github/workflows/test_python_ver_matrix.yml

@@ -25,8 +25,15 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.10', '3.11', '3.12', '3.13']
-        experimental: [false]
+        include:
+          - python-version: '3.10'
+            experimental: false
+          - python-version: '3.11'
+            experimental: false
+          - python-version: '3.12'
+            experimental: false
+          - python-version: '3.13'
+            experimental: true
 
     steps:
     - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV

CHANGELOG.md

@@ -4,6 +4,41 @@ See also our [versioning policy](https://amici.readthedocs.io/en/latest/versioni
 
 ## v0.X Series
 
+### v0.27.0 (2024-10-21)
+
+This release comes with an **updated version of the SUNDIALS package (7.1.1)** (https://github.com/AMICI-dev/AMICI/pull/2513).
+  For C++ users of some of AMICI's internal RAII classes, this may include some
+  breaking changes. The Python API is not affected.
+
+*Note regarding **editable** installations (`pip install -e ...`):*
+Due to the SUNDIALS update, it will be necessary to clean out some temporary
+build directories (at least `ThirdParty/sundials/build/`,
+`python/sdist/build/`) before rebuilding the package.
+
+**Fixes**
+
+* Fixed a bug that led to program termination if a root-after-reinitialization
+  error (potentially also others) occurred at an output timepoint
+
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2555
+
+* CMake: Fixes compilation errors for models named `model`
+
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2547
+
+* Updated CMake export config, making it easier to use AMICI in CMake projects
+  and fixing some potential issues with interferring packages
+
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2540
+
+* CMake: Set policies for CMake 3.31
+
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2539
+
+* Documentation fixes by @FFroehlich, @ChocolateCharlie, @dweindl
+
+**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.26.3...v0.27.0
+
 
 ### v0.26.3 (2024-10-03)
 

documentation/amici_refs.bib

@@ -1403,6 +1403,38 @@ @Article{JakstaiteZho2024
   publisher        = {American Chemical Society (ACS)},
 }
 
+@InBook{BarthelKun2024,
+  author           = {Barthel, Lars and Kunz, Philipp and King, Rudibert and Meyer, Vera},
+  editor           = {Kwade, Arno and Kampen, Ingo},
+  pages            = {467--490},
+  publisher        = {Springer Nature Switzerland},
+  title            = {Harnessing Genetic and Microfluidic Approaches to Model Shear Stress Response in Cell Wall Mutants of the Filamentous Cell Factory Aspergillus niger},
+  year             = {2024},
+  address          = {Cham},
+  isbn             = {978-3-031-63164-1},
+  abstract         = {Aspergillus niger is an efficient biotechnological cell factory harnessed for the production of proteins, enzymes, platform chemicals and secondary metabolites. Critical for productivity of filamentous fungi such as A. niger is their hyphal growth and the ability of their cell walls to withstand shear stress conditions during submerged bioreactor cultivations. As chitin is thought to be fundamental for the rigidity of fungal hyphae, we generated a chitin synthase knock-out library for A. niger and studied the impact of these genetic modifications on its ability to withstand shear stress during submerged bioreactor cultivations. We isolated a double deletion mutant in which the genes chsE and chsD were inactivated and observed a reduction in chitin content by 60{\%}, cell wall thickness by 20{\%}, hyphal diameter by 60{\%} and maximum growth rate by 25{\%}. We furthermore developed a parallelized microfluidic growth chamber system that enabled us to track the growth of the double mutant and the respective control strain using a confocal laser scanning microscope, and, additionally, to compare their growth responses when subjected to different shear stress conditions. A newly developed mathematical model allowed us to compute and evaluate lag-phase, maximum growth rate and shear stress response based on the microscopic images obtained. Overall, this microfluidic approach clearly identified differences in shear stress response between both strains and has high potential as scale-down screening tool to predict growth characteristics under submerged bioreactor cultivations.},
+  booktitle        = {Dispersity, Structure and Phase Changes of Proteins and Bio Agglomerates in Biotechnological Processes},
+  creationdate     = {2024-09-29T16:46:24},
+  doi              = {10.1007/978-3-031-63164-1_15},
+  modificationdate = {2024-09-29T16:46:24},
+  url              = {https://doi.org/10.1007/978-3-031-63164-1_15},
+}
+
+@Article{ArmisteadHoe2024,
+  author           = {Armistead, Joy and Höpfl, Sebastian and Goldhausen, Pierre and Müller-Hartmann, Andrea and Fahle, Evelin and Hatzold, Julia and Franzen, Rainer and Brodesser, Susanne and Radde, Nicole E. and Hammerschmidt, Matthias},
+  journal          = {Cell Death & Disease},
+  title            = {A sphingolipid rheostat controls apoptosis versus apical cell extrusion as alternative tumour-suppressive mechanisms},
+  year             = {2024},
+  issn             = {2041-4889},
+  month            = oct,
+  number           = {10},
+  volume           = {15},
+  creationdate     = {2024-10-17T16:27:55},
+  doi              = {10.1038/s41419-024-07134-2},
+  modificationdate = {2024-10-17T16:28:08},
+  publisher        = {Springer Science and Business Media LLC},
+}
+
 @Comment{jabref-meta: databaseType:bibtex;}
 
 @Comment{jabref-meta: grouping:

documentation/references.md

@@ -1,6 +1,6 @@
 # References
 
-List of publications using AMICI. Total number is 92.
+List of publications using AMICI. Total number is 94.
 
 If you applied AMICI in your work and your publication is missing, please let us know via a new
 [GitHub issue](https://github.com/AMICI-dev/AMICI/issues/new?labels=documentation&title=Add+publication&body=AMICI+was+used+in+this+manuscript:+DOI).
@@ -15,13 +15,32 @@ If you applied AMICI in your work and your publication is missing, please let us
 <h1 class="unnumbered" id="section">2024</h1>
 <div id="refs" class="references csl-bib-body hanging-indent"
 role="list">
+<div id="ref-ArmisteadHoe2024" class="csl-entry" role="listitem">
+Armistead, Joy, Sebastian Höpfl, Pierre Goldhausen, Andrea
+Müller-Hartmann, Evelin Fahle, Julia Hatzold, Rainer Franzen, Susanne
+Brodesser, Nicole E. Radde, and Matthias Hammerschmidt. 2024. <span>“A
+Sphingolipid Rheostat Controls Apoptosis Versus Apical Cell Extrusion as
+Alternative Tumour-Suppressive Mechanisms.”</span> <em>Cell Death &amp;
+Disease</em> 15 (10). <a
+href="https://doi.org/10.1038/s41419-024-07134-2">https://doi.org/10.1038/s41419-024-07134-2</a>.
+</div>
 <div id="ref-BaltussenJon2024" class="csl-entry" role="listitem">
 Baltussen, Mathieu G., Thijs J. de Jong, Quentin Duez, William E.
 Robinson, and Wilhelm T. S. Huck. 2024. <span>“Chemical Reservoir
 Computation in a Self-Organizing Reaction Network.”</span>
 <em>Nature</em>, June. <a
 href="https://doi.org/10.1038/s41586-024-07567-x">https://doi.org/10.1038/s41586-024-07567-x</a>.
 </div>
+<div id="ref-BarthelKun2024" class="csl-entry" role="listitem">
+Barthel, Lars, Philipp Kunz, Rudibert King, and Vera Meyer. 2024.
+<span>“Harnessing Genetic and Microfluidic Approaches to Model Shear
+Stress Response in Cell Wall Mutants of the Filamentous Cell Factory
+Aspergillus Niger.”</span> In <em>Dispersity, Structure and Phase
+Changes of Proteins and Bio Agglomerates in Biotechnological
+Processes</em>, edited by Arno Kwade and Ingo Kampen, 467–90. Cham:
+Springer Nature Switzerland. <a
+href="https://doi.org/10.1007/978-3-031-63164-1_15">https://doi.org/10.1007/978-3-031-63164-1_15</a>.
+</div>
 <div id="ref-DoresicGre2024" class="csl-entry" role="listitem">
 Dorešić, Domagoj, Stephan Grein, and Jan Hasenauer. 2024.
 <span>“Efficient Parameter Estimation for ODE Models of Cellular

include/amici/forwardproblem.h

@@ -2,6 +2,7 @@
 #define AMICI_FORWARDPROBLEM_H
 
 #include "amici/defines.h"
+#include "amici/edata.h"
 #include "amici/misc.h"
 #include "amici/model.h"
 #include "amici/vector.h"
@@ -195,7 +196,7 @@ class ForwardProblem {
         if (model->getTimepoint(it) == initial_state_.t)
             return getInitialSimulationState();
         auto map_iter = timepoint_states_.find(model->getTimepoint(it));
-        assert(map_iter != timepoint_states_.end());
+        Ensures(map_iter != timepoint_states_.end());
         return map_iter->second;
     };
 
@@ -441,8 +442,20 @@ class FinalStateStorer : public ContextManager {
      * @brief destructor, stores simulation state
      */
     ~FinalStateStorer() {
-        if (fwd_)
+        if (fwd_) {
             fwd_->final_state_ = fwd_->getSimulationState();
+            // if there is an associated output timepoint, also store it in
+            // timepoint_states if it's not present there.
+            // this may happen if there is an error just at
+            // (or indistinguishably before) an output timepoint
+            auto final_time = fwd_->getFinalTime();
+            auto const timepoints = fwd_->model->getTimepoints();
+            if (!fwd_->timepoint_states_.count(final_time)
+                && std::find(timepoints.cbegin(), timepoints.cend(), final_time)
+                       != timepoints.cend()) {
+                fwd_->timepoint_states_[final_time] = fwd_->final_state_;
+            }
+        }
     }
 
   private:

include/amici/logging.h

@@ -80,7 +80,7 @@ struct LogItem {
     )
         : severity(severity)
         , identifier(identifier)
-        , message(message){};
+        , message(message) {};
 
     /** Severity level */
     LogSeverity severity = LogSeverity::error;

scripts/run-valgrind-cpp.sh

@@ -10,4 +10,4 @@ set -eou pipefail
 # run tests
 cd "${AMICI_PATH}/build/"
 VALGRIND_OPTS="--leak-check=full --error-exitcode=1 --trace-children=yes --show-leak-kinds=definite"
-valgrind ${VALGRIND_OPTS} ctest
+CTEST_OUTPUT_ON_FAILURE=1 valgrind ${VALGRIND_OPTS} ctest

src/rdata.cpp

@@ -241,7 +241,7 @@ void ReturnData::processForwardProblem(
     if (edata)
         initializeObjectiveFunction(model.hasQuadraticLLH());
 
-    auto initialState = fwd.getInitialSimulationState();
+    auto const& initialState = fwd.getInitialSimulationState();
     if (initialState.x.getLength() == 0 && model.nx_solver > 0)
         return; // if x wasn't set forward problem failed during initialization
 
@@ -259,7 +259,7 @@ void ReturnData::processForwardProblem(
     realtype tf = fwd.getFinalTime();
     for (int it = 0; it < model.nt(); it++) {
         if (model.getTimepoint(it) <= tf) {
-            auto simulation_state = fwd.getSimulationStateTimepoint(it);
+            auto const simulation_state = fwd.getSimulationStateTimepoint(it);
             model.setModelState(simulation_state.state);
             getDataOutput(it, model, simulation_state, edata);
         } else {
@@ -273,7 +273,7 @@ void ReturnData::processForwardProblem(
     if (nz > 0) {
         auto rootidx = fwd.getRootIndexes();
         for (int iroot = 0; iroot <= fwd.getEventCounter(); iroot++) {
-            auto simulation_state = fwd.getSimulationStateEvent(iroot);
+            auto const simulation_state = fwd.getSimulationStateEvent(iroot);
             model.setModelState(simulation_state.state);
             getEventOutput(
                 simulation_state.t, rootidx.at(iroot), model, simulation_state,

src/solver_cvodes.cpp

@@ -91,8 +91,7 @@ static_assert(
     "AMICI_FIRST_QRHSFUNC_ERR != CV_FIRST_QRHSFUNC_ERR"
 );
 static_assert(
-    amici::AMICI_WARNING == CV_WARNING,
-    "AMICI_WARNING != CV_WARNING"
+    amici::AMICI_WARNING == CV_WARNING, "AMICI_WARNING != CV_WARNING"
 );
 
 /*

src/solver_idas.cpp

@@ -71,8 +71,7 @@ static_assert(
     "AMICI_IDAS_CONSTR_FAIL != IDA_CONSTR_FAIL"
 );
 static_assert(
-    amici::AMICI_WARNING == IDA_WARNING,
-    "AMICI_WARNING != IDA_WARNING"
+    amici::AMICI_WARNING == IDA_WARNING, "AMICI_WARNING != IDA_WARNING"
 );
 
 /*

tests/cpp/unittests/testMisc.cpp

@@ -360,10 +360,9 @@ TEST_F(SolverTest, SettersGettersWithSetup)
     ASSERT_EQ(static_cast<int>(solver.getSensitivityMethod()),
               static_cast<int>(sensi_meth));
 
-    sundials::Context sunctx;
     auto rdata = std::make_unique<ReturnData>(solver, testModel);
-    AmiVector x(nx, sunctx), dx(nx, sunctx);
-    AmiVectorArray sx(nx, 1, sunctx), sdx(nx, 1, sunctx);
+    AmiVector x(nx, solver.getSunContext()), dx(nx, solver.getSunContext());
+    AmiVectorArray sx(nx, 1, solver.getSunContext()), sdx(nx, 1, solver.getSunContext());
 
     testModel.setInitialStates(std::vector<realtype>{ 0 });
 

version.txt

@@ -1 +1 @@
-0.26.3
+0.27.0