Merge pull request #419 from ICB-DCM/develop

Release v0.6.0 

## What's Changed

* Update container files by @dweindl in #414
  * activate parpe python environment by default
  * avoid unnecessary full rebuilds when modifying Dockerfile
* Updated amici to v0.30.1 by @dweindl in #417
* Fixed potential issues with `MPI_Finalize` from `~OptimizationApplication` 

**Full Changelog**: v0.5.0...v0.6.0

.gitattributes

@@ -1,3 +1,3 @@
-.git_archival.txt  export-subst
 python/.git_archival.txt  export-subst
+.git_archival.txt  export-subst
 

.github/workflows/deploy_dockerhub.yml

@@ -24,13 +24,13 @@ jobs:
     if: needs.check-secret.outputs.secrets-defined == 'true'
     steps:
     - uses: actions/checkout@master
-    - run: git archive -v -o container/charliecloud/parpe_base/parpe.tar.gz --format=tar.gz HEAD
+    - run: git archive -v -o container/charliecloud/container_files/parpe.tar.gz --format=tar.gz HEAD
     - name: Publish to Registry
       uses: elgohr/Publish-Docker-Github-Action@v5
       with:
         name: dweindl/parpe
         username: ${{ secrets.DOCKER_USERNAME }}
         password: ${{ secrets.DOCKER_PASSWORD }}
-        workdir: container/charliecloud/parpe_base/
+        workdir: container/charliecloud/
         dockerfile: Dockerfile
         tag_names: true

container/charliecloud/parpe_base/Dockerfile → container/charliecloud/Dockerfile

@@ -1,6 +1,6 @@
 FROM ubuntu:24.04
 
-COPY . /container-files
+COPY /container_files /container-files
 
 RUN /container-files/install.sh && rm -rf /tmp && mkdir /tmp
 
@@ -9,7 +9,7 @@ ENV CC clang
 ENV CXX clang++
 ENV OMPI_CC clang
 ENV OMPI_CXX clang++
-RUN /container-files/install_parpe.sh
+RUN /container-files/install_parpe.sh && echo "source /parPE/build/venv/bin/activate" >> /etc/bash.bashrc
 
 ENV PARPE_DIR "/parPE"
 

deps/AMICI/.github/workflows/test_benchmark_collection_models.yml

@@ -67,7 +67,7 @@ jobs:
         AMICI_PARALLEL_COMPILE: ""
       run: |
           cd tests/benchmark-models && pytest \
-              --durations=10
+              --durations=10 \
               --cov=amici \
               --cov-report=xml:"coverage_py.xml" \
               --cov-append \

deps/AMICI/.github/workflows/test_sbml_semantic_test_suite.yml

@@ -58,6 +58,6 @@ jobs:
       uses: codecov/codecov-action@v5
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
-        file: coverage_SBMLSuite.xml
+        files: coverage_SBMLSuite.xml
         flags: sbmlsuite
         fail_ci_if_error: true

deps/AMICI/.gitrepo

@@ -5,8 +5,8 @@
 ;
 [subrepo]
 	remote = git@github.com:ICB-DCM/AMICI.git
-	branch = v0.29.0
-	commit = d2fbf9175502ac0ce5b138a4137d6fb278dbe124
-	parent = d553b182917ab870886077fde8a0b6c5a56d9b92
+	branch = v0.30.1
+	commit = 64bbd800040afa280e8bff1563542497464044a7
+	parent = 87656e656a521c78edc05e4f4ca10d8448e9617d
 	cmdver = 0.4.8
 	method = merge

deps/AMICI/CHANGELOG.md

@@ -4,6 +4,69 @@ See also our [versioning policy](https://amici.readthedocs.io/en/latest/versioni
 
 ## v0.X Series
 
+### v0.30.1 (2025-02-18)
+
+Bugfix-only release.
+
+* Removed `eqx.debug.nan`, fixes #2629
+  by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2630
+* Fixes an SBML import issue that led to incorrect results for models with
+  species-dependent initial assignments (fixes #2642)
+  by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2643
+* Fixed `CVodeGetSensDky` error message
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2644
+* Disabled `CvodeF` checkpointing to prevent certain rare crashes when forward
+  integration takes exactly `maxsteps` integration steps, plus some additional
+  yet unclear condition.
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2645
+* Fixed rare crashes due to uncaught exceptions in `~FinalStateStorer`
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2647
+
+**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.30.0...v0.30.1
+
+
+### v0.30.0 (2024-12-10)
+
+*Please note that the amici JAX model generation introduced in v0.29.0 is
+experimental, the API may substantially change in the future.
+Use at your own risk and do not expect backward compatibility.*
+
+**Features**
+
+* Added serialisation for JAX models
+
+  by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2608
+
+* Disabled building the C++ extension by default when generating a JAX model
+
+  by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2609
+
+* Separate pre-equilibration and dynamic simulation in jax
+
+  by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2617
+
+* State reinitialisation in JAX
+
+  by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2619
+
+**Fixes**
+
+* Fixed ModelStateDerived copy ctor (fixes potential segfaults)
+
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2612
+
+* PEtab parameter mapping: fill in fixed parameter values for initial values
+
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2613
+
+* `nan`-safe log&divide for JAX models
+
+  by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2611
+
+
+**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.29.0...v0.30.0
+
+
 ### v0.29.0 (2024-11-28)
 
 **Fixes**

deps/AMICI/documentation/python_installation.rst

@@ -28,6 +28,17 @@ If this worked, you can now import the Python module via::
 
 If this does not work for you, please follow the full instructions below.
 
+.. note::
+
+  To re-install a previously installed AMICI version with different
+  build options or changed system libraries, pass the ``--no-cache-dir``
+  option to ``pip`` to ensure a clean re-installation:
+
+  .. code-block:: bash
+
+     pip3 install --no-cache-dir amici
+
+
 Installation on Linux
 +++++++++++++++++++++
 

deps/AMICI/include/amici/forwardproblem.h

@@ -441,19 +441,37 @@ class FinalStateStorer : public ContextManager {
     /**
      * @brief destructor, stores simulation state
      */
-    ~FinalStateStorer() {
+    ~FinalStateStorer() noexcept(false) {
         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_;
+            try {
+                // This may throw in `CVodeSolver::getSens`
+                // due to https://github.com/LLNL/sundials/issues/82.
+                // Therefore, this dtor must be `noexcept(false)` to avoid
+                // programm termination.
+                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_;
+                }
+            } catch (std::exception const&) {
+                // We must not throw in case we are already in the stack
+                // unwinding phase due to some other active exception, otherwise
+                // this will also lead to termination.
+                //
+                // In case there is another active exception,
+                // `fwd_->{final_state_,timepoint_states_}` won't be set,
+                // and we assume that they are either not accessed anymore, or
+                // that there is appropriate error handling in place.
+                if(!std::uncaught_exceptions()) {
+                    throw;
+                }
             }
         }
     }

deps/AMICI/include/amici/model_state.h

@@ -175,6 +175,7 @@ struct ModelStateDerived {
             dwdx.set_ctx(sunctx_);
         }
         sspl_.set_ctx(sunctx_);
+        x_pos_tmp_.set_ctx(sunctx_);
         dwdw_.set_ctx(sunctx_);
         dJydy_dense_.set_ctx(sunctx_);
     }

deps/AMICI/pytest.ini

@@ -12,6 +12,7 @@ filterwarnings =
     ignore:Conservation laws for non-constant species in models with Species-AssignmentRules are currently not supported and will be turned off.:UserWarning
     ignore:Conservation laws for non-constant species in combination with parameterized stoichiometric coefficients are not currently supported and will be turned off.:UserWarning
     ignore:Support for PEtab2.0 is experimental!:UserWarning
+    ignore:The JAX module is experimental and the API may change in the future.:ImportWarning
     # hundreds of SBML <=5.17 warnings
     ignore:.*inspect.getargspec\(\) is deprecated.*:DeprecationWarning
     # pysb warnings