Update AMICI to v0.29.0

``` git subrepo clone (merge) --branch=v0.29.0 --force git@github.com:AMICI-dev/AMICI.git deps/AMICI subrepo: subdir: "deps/AMICI" merged: "d2fbf917" upstream: origin: "git@github.com:AMICI-dev/AMICI.git" branch: "v0.29.0" commit: "d2fbf917" git-subrepo: version: "0.4.8" origin: "https://github.com/ingydotnet/git-subrepo" commit: "3a53c20" ```
ICB-DCM · Nov 28, 2024 · 9e2a53c · 9e2a53c
1 parent d553b18
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diff --git a/deps/AMICI/.github/actions/install-macos-dependencies/action.yml b/deps/AMICI/.github/actions/install-macos-dependencies/action.yml
@@ -27,5 +27,8 @@ runs:
 
     # install amici dependencies
     - name: homebrew
-      run: brew install hdf5 swig gcc libomp boost
+      # install hdf5 without dependencies, because pkgconf installation fails,
+      # because it's already installed on the runners. install the other
+      # hdf5 dependencies (libaec) manually
+      run: brew install libaec && brew install --ignore-dependencies hdf5 && brew install swig libomp boost
       shell: bash
diff --git a/deps/AMICI/.github/workflows/test_benchmark_collection_models.yml b/deps/AMICI/.github/workflows/test_benchmark_collection_models.yml
@@ -50,7 +50,7 @@ jobs:
       run: |
         pip3 install --user petab[vis] && \
         AMICI_PARALLEL_COMPILE="" pip3 install -v --user \
-            $(ls -t python/sdist/dist/amici-*.tar.gz | head -1)[petab,test,vis]
+            $(ls -t python/sdist/dist/amici-*.tar.gz | head -1)[petab,test,vis,jax]
 
     - name: Install test dependencies
       run: |
@@ -60,14 +60,27 @@ jobs:
 
     - name: Download benchmark collection
       run: |
-        git clone --depth 1 https://github.com/benchmarking-initiative/Benchmark-Models-PEtab.git \
-          && python3 -m pip install -e Benchmark-Models-PEtab/src/python
+        pip install git+https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab.git@master#subdirectory=src/python
 
     - name: Run tests
       env:
         AMICI_PARALLEL_COMPILE: ""
       run: |
-          cd tests/benchmark-models && pytest --durations=10
+          cd tests/benchmark-models && pytest \
+              --durations=10
+              --cov=amici \
+              --cov-report=xml:"coverage_py.xml" \
+              --cov-append \
+
+    - name: Codecov Python
+      if: github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev'
+      uses: codecov/codecov-action@v5
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        file: coverage_py.xml
+        flags: python
+        fail_ci_if_error: true
+        verbose: true
 
     # collect & upload results
     - name: Aggregate results

diff --git a/deps/AMICI/.github/workflows/test_install.yml b/deps/AMICI/.github/workflows/test_install.yml
@@ -96,14 +96,8 @@ jobs:
 
     - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
 
-    # install amici dependencies
-    - name: homebrew
-      run: |
-        brew install hdf5 swig gcc cppcheck libomp boost \
-          && brew ls -v boost \
-          && brew ls -v libomp \
-          && echo LDFLAGS="-L/usr/local/lib/ -L/usr/local/Cellar/boost/1.81.0_1/lib/" >> $GITHUB_ENV \
-          && echo CPPFLAGS="-I /usr/local/Cellar/boost/1.81.0_1/include/" >> $GITHUB_ENV
+    - name: Install dependencies
+      uses: ./.github/actions/install-macos-dependencies
 
     - name: Create AMICI sdist
       run: scripts/buildSdist.sh

diff --git a/deps/AMICI/.github/workflows/test_petab_test_suite.yml b/deps/AMICI/.github/workflows/test_petab_test_suite.yml
@@ -101,7 +101,7 @@ jobs:
 
       - name: Codecov
         if: github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev'
-        uses: codecov/codecov-action@v4
+        uses: codecov/codecov-action@v5
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           file: coverage.xml

diff --git a/deps/AMICI/.github/workflows/test_python_cplusplus.yml b/deps/AMICI/.github/workflows/test_python_cplusplus.yml
@@ -79,7 +79,7 @@ jobs:
 
     - name: Codecov Python
       if: github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev'
-      uses: codecov/codecov-action@v4
+      uses: codecov/codecov-action@v5
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: build/coverage_py.xml
@@ -99,7 +99,7 @@ jobs:
 
     - name: Codecov CPP
       if: github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev'
-      uses: codecov/codecov-action@v4
+      uses: codecov/codecov-action@v5
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: coverage.info
@@ -161,7 +161,7 @@ jobs:
 
     - name: Codecov Python
       if: github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev'
-      uses: codecov/codecov-action@v4
+      uses: codecov/codecov-action@v5
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: build/coverage_py.xml
@@ -181,7 +181,7 @@ jobs:
 
     - name: Codecov CPP
       if: github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev'
-      uses: codecov/codecov-action@v4
+      uses: codecov/codecov-action@v5
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: coverage.info
@@ -231,11 +231,6 @@ jobs:
     - name: Install python package
       run: scripts/installAmiciSource.sh
 
-    - name: Install notebook dependencies
-      run: |
-        source venv/bin/activate \
-        && pip install jax[cpu]
-
     - name: example notebooks
       run: scripts/runNotebook.sh python/examples/example_*/
 

diff --git a/deps/AMICI/.github/workflows/test_sbml_semantic_test_suite.yml b/deps/AMICI/.github/workflows/test_sbml_semantic_test_suite.yml
@@ -55,7 +55,7 @@ jobs:
 
     - name: Codecov SBMLSuite
       if: github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev'
-      uses: codecov/codecov-action@v4
+      uses: codecov/codecov-action@v5
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: coverage_SBMLSuite.xml

diff --git a/deps/AMICI/.github/workflows/test_valgrind.yml b/deps/AMICI/.github/workflows/test_valgrind.yml
@@ -89,5 +89,9 @@ jobs:
     - name: Install python package
       run: scripts/installAmiciSource.sh
 
+    - name: Remove jax
+      # avoid valgrind errors due to jax et al.
+      run: venv/bin/pip uninstall -y jax
+
     - name: Python tests / Valgrind
       run: scripts/run-valgrind-py.sh
diff --git a/deps/AMICI/.gitignore b/deps/AMICI/.gitignore
@@ -137,6 +137,8 @@ tests/test/*
 */tests/explicit_amici/*
 */tests/fixed_initial_amici/*
 */tests/localfunc_amici/*
+*/tests/conversion/*
+*/tests/dimerization/*
 tests/cpp/writeResults.h5
 tests/cpp/writeResults.h5.bak
 tests/sbml-test-suite/*

diff --git a/deps/AMICI/.gitrepo b/deps/AMICI/.gitrepo
@@ -5,8 +5,8 @@
 ;
 [subrepo]
 	remote = git@github.com:ICB-DCM/AMICI.git
-	branch = v0.28.0
-	commit = c3bbdd9e7261da247ef5e2a648901fd07c2f52fa
-	parent = db859ddeba0094b964aaba66e3aab70746e1eb80
+	branch = v0.29.0
+	commit = d2fbf9175502ac0ce5b138a4137d6fb278dbe124
+	parent = d553b182917ab870886077fde8a0b6c5a56d9b92
 	cmdver = 0.4.8
 	method = merge
diff --git a/deps/AMICI/.readthedocs.yml b/deps/AMICI/.readthedocs.yml
@@ -21,6 +21,7 @@ build:
   os: "ubuntu-22.04"
   apt_packages:
     - libatlas-base-dev
+    - libhdf5-serial-dev
     - swig
   tools:
     python: "3.11"
diff --git a/deps/AMICI/CHANGELOG.md b/deps/AMICI/CHANGELOG.md
@@ -4,6 +4,60 @@ See also our [versioning policy](https://amici.readthedocs.io/en/latest/versioni
 
 ## v0.X Series
 
+### v0.29.0 (2024-11-28)
+
+**Fixes**
+
+* Fixed race conditions in froot, which could have resulted in incorrect
+  simulation results for models with events/heavisides/piecewise, for
+  multi-threaded simulations.
+
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2587
+
+* Fixed race conditions for the max-time check, which could have resulted in
+  incorrect termination of simulations in case of multi-threaded simulations
+  in combination with a time limit.
+
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2587
+
+* Added missing fields in ExpData HDF5 I/O
+
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2593
+
+* Added missing fields in ReturnData HDF5 output
+
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2602
+
+
+* **Features**
+
+* Generate models in a JAX-compatible format
+  ([example](https://amici.readthedocs.io/en/develop/ExampleJaxPEtab.html))
+
+  by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1861
+
+* Faster `fill_in_parameters_for_condition`
+
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2586
+
+* Added Python function `writeSimulationExpData` for writing ExpData to HDF5
+
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2588
+
+* Improved import of amici-generated models via `amici.import_model_module()`.
+
+  So far, it was not possible to import different model modules with the same
+  name. This is now possible if they are in different directories.
+  Overwriting an already imported module is still not possible (and never
+  was); any attempts to do so will raise a `RuntimeError`.
+  While model packages can, in principle, be imported using regular
+  `import`s, it is strongly recommended to use `amici.import_model_module()`.
+
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2604, https://github.com/AMICI-dev/AMICI/pull/2603, https://github.com/AMICI-dev/AMICI/pull/2596
+
+**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.28.0...v0.29.0
+
+
 ### v0.28.0 (2024-11-11)
 
 **Breaking changes**

diff --git a/deps/AMICI/documentation/ExampleJaxPEtab.ipynb b/deps/AMICI/documentation/ExampleJaxPEtab.ipynb
@@ -0,0 +1 @@
+../python/examples/example_jax_petab/ExampleJaxPEtab.ipynb
diff --git a/deps/AMICI/documentation/conf.py b/deps/AMICI/documentation/conf.py
@@ -206,6 +206,7 @@ def install_doxygen():
     "numpy": ("https://numpy.org/devdocs/", None),
     "sympy": ("https://docs.sympy.org/latest/", None),
     "python": ("https://docs.python.org/3", None),
+    "jax": ["https://jax.readthedocs.io/en/latest/", None],
 }
 
 # Add notebooks prolog with binder links

diff --git a/deps/AMICI/documentation/cpp_installation.rst b/deps/AMICI/documentation/cpp_installation.rst
@@ -18,6 +18,7 @@ Prerequisites:
 * a C++17 compatible compiler
 * a C compiler
 * Optional:
+
   * HDF5 libraries
   * boost for serialization
 

diff --git a/deps/AMICI/documentation/python_examples.rst b/deps/AMICI/documentation/python_examples.rst
@@ -17,5 +17,6 @@ Various example notebooks.
    example_errors.ipynb
    example_large_models/example_performance_optimization.ipynb
    ExampleJax.ipynb
+   ExampleJaxPEtab.ipynb
    ExampleSplines.ipynb
    ExampleSplinesSwameye2003.ipynb
diff --git a/deps/AMICI/documentation/python_installation.rst b/deps/AMICI/documentation/python_installation.rst
@@ -39,7 +39,7 @@ Install the AMICI dependencies via ``apt``
 
 .. code-block:: bash
 
-   sudo apt install libatlas-base-dev swig
+   sudo apt install libatlas-base-dev swig python3-dev
 
    # optionally for HDF5 support:
    sudo apt install libhdf5-serial-dev

diff --git a/deps/AMICI/documentation/python_modules.rst b/deps/AMICI/documentation/python_modules.rst
@@ -25,6 +25,7 @@ AMICI Python API
    amici.petab_objective
    amici.petab_simulate
    amici.import_utils
+   amici.jax
    amici.de_export
    amici.de_model
    amici.de_model_components

diff --git a/deps/AMICI/documentation/rtd_requirements.txt b/deps/AMICI/documentation/rtd_requirements.txt
@@ -3,6 +3,8 @@ sphinx<8
 mock>=5.0.2
 setuptools>=67.7.2
 pysb>=1.11.0
+jax>=0.4.26
+diffrax>=0.5.0
 matplotlib==3.7.1
 nbsphinx==0.9.1
 nbformat==5.8.0

diff --git a/deps/AMICI/include/amici/hdf5.h b/deps/AMICI/include/amici/hdf5.h
@@ -26,6 +26,7 @@ class ReturnData;
 class ExpData;
 class Model;
 class Solver;
+struct LogItem;
 
 namespace hdf5 {
 
@@ -137,6 +138,17 @@ void writeReturnDataDiagnosis(
     std::string const& hdf5Location
 );
 
+/**
+ * @brief Write log message to HDF5 file
+ * @param file HDF5 file to write to
+ * @param logItems Log items to write
+ * @param hdf5Location Full dataset path inside the HDF5 file (will be created)
+ */
+void writeLogItemsToHDF5(
+    H5::H5File const& file, std::vector<amici::LogItem> const& logItems,
+    std::string const& hdf5Location
+);
+
 /**
  * @brief Create the given group and possibly parents.
  * @param file HDF5 file to write to
@@ -164,15 +176,26 @@ std::unique_ptr<ExpData> readSimulationExpData(
 /**
  * @brief Write AMICI experimental data to HDF5 file.
  * @param edata The experimental data which is to be written
- * @param file Name of HDF5 file
- * @param hdf5Location Path inside the HDF5 file to object having ExpData
+ * @param file HDF5 file
+ * @param hdf5Location Path inside the HDF5 file
  */
 
 void writeSimulationExpData(
     ExpData const& edata, H5::H5File const& file,
     std::string const& hdf5Location
 );
 
+/**
+ * @brief Write AMICI experimental data to HDF5 file.
+ * @param edata The experimental data which is to be written
+ * @param file Name of HDF5 file
+ * @param hdf5Location Path inside the HDF5 file
+ */
+void writeSimulationExpData(
+    ExpData const& edata, std::string const& hdf5Filename,
+    std::string const& hdf5Location
+);
+
 /**
  * @brief Check whether an attribute with the given name exists
  * on the given dataset.

diff --git a/deps/AMICI/include/amici/rdata.h b/deps/AMICI/include/amici/rdata.h
@@ -453,7 +453,7 @@ class ReturnData : public ModelDimensions {
 
     /** boolean indicating whether residuals for standard deviations have been
      * added */
-    bool sigma_res;
+    bool sigma_res{false};
 
     /** log messages */
     std::vector<LogItem> messages;
@@ -463,7 +463,7 @@ class ReturnData : public ModelDimensions {
 
   protected:
     /** offset for sigma_residuals */
-    realtype sigma_offset;
+    realtype sigma_offset{0.0};
 
     /** array of number of found roots for a certain event type
      * (shape `ne`) */

diff --git a/deps/AMICI/include/amici/solver.h b/deps/AMICI/include/amici/solver.h
@@ -39,7 +39,8 @@ namespace amici {
  * variables and status flags) are specified as mutable and not included in
  * serialization or equality checks. No solver setting parameter should be
  * marked mutable.
- *
+ */
+/*
  * NOTE: Any changes in data members here must be propagated to copy ctor,
  * equality operator, serialization functions in serialization.h, and
  * amici::hdf5::(read/write)SolverSettings(From/To)HDF5 in hdf5.cpp.
@@ -1868,10 +1869,6 @@ class Solver {
     /** maximum number of allowed Newton steps for steady state computation */
     long int newton_maxsteps_{0L};
 
-    /** maximum number of allowed linear steps per Newton step for steady state
-     * computation */
-    long int newton_maxlinsteps_{0L};
-
     /** Damping factor state used int the Newton method */
     NewtonDampingFactorMode newton_damping_factor_mode_{
         NewtonDampingFactorMode::on
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		../python/examples/example_jax_petab/ExampleJaxPEtab.ipynb