Merge branch 'develop' into makej

ICB-DCM · Nov 11, 2024 · 8fd3ec3 · 8fd3ec3
2 parents c20f7cf + de3ee0b
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diff --git a/README.md b/README.md
@@ -24,11 +24,15 @@ equation (ODE) models.
 parPE offers the following features:
 
 * MPI-based load-balancing of individual simulations
+  (if you don't need this, and don't require a C++ library, consider using
+  the [pypesto](https://pypesto.readthedocs.io/en/latest/) Python package
+  which is more mature and user-friendly)
 * improved load balancing by intermingling multiple optimization runs
   (multi-start local optimization)
-* simple integration with [SBML](http://sbml.org/) models via
+* integration with [SBML](http://sbml.org/) models via
   [AMICI](https://github.com/AMICI-dev/AMICI) and
   [PEtab](https://github.com/PEtab-dev/PEtab)
+  * hierarchical optimization (https://doi.org/10.1093/bioinformatics/btz581)
 * interfaces to [Ipopt](https://www.coin-or.org/Ipopt/),
   [Ceres](http://ceres-solver.org/),
   [FFSQP](https://www.isr.umd.edu/news/news_story.php?id=4088) and
@@ -37,6 +41,12 @@ parPE offers the following features:
 * Good parallel scaling to up to several thousand cores
   (highly problem dependent)
 
+**Note that this library has been developed for specific research questions
+and certain assumptions may not always hold. Use with caution.
+In particular, certain default settings may need adaptation (in particular,
+parallelization settings and AMICI settings such as the sensitivity method).
+PEtab support is patchy. Always verify your simulation results.**
+
 ## Getting started
 
 Although various modules of parPE can be used independently, the most
@@ -109,7 +119,7 @@ Other sample build scripts are provided as `/build*.sh`.
 
 ## Recently tested compilers
 
-* GCC 13.2.0
+* GCC 14.2.0
 * Clang 18.1.3
 
 ## Containers

diff --git a/deps/AMICI/.github/workflows/test_benchmark_collection_models.yml b/deps/AMICI/.github/workflows/test_benchmark_collection_models.yml
@@ -52,25 +52,28 @@ jobs:
         AMICI_PARALLEL_COMPILE="" pip3 install -v --user \
             $(ls -t python/sdist/dist/amici-*.tar.gz | head -1)[petab,test,vis]
 
-    - run: |
+    - name: Install test dependencies
+      run: |
         python3 -m pip uninstall -y petab && python3 -m pip install git+https://github.com/petab-dev/libpetab-python.git@develop \
-        &&  python3 -m pip install -U sympy
+        &&  python3 -m pip install -U sympy \
+        &&  python3 -m pip install git+https://github.com/ICB-DCM/fiddy.git
 
-    # retrieve test models
-    - name: Download and test benchmark collection
+    - name: Download benchmark collection
       run: |
         git clone --depth 1 https://github.com/benchmarking-initiative/Benchmark-Models-PEtab.git \
-          && export BENCHMARK_COLLECTION="$(pwd)/Benchmark-Models-PEtab/Benchmark-Models/" \
-          && pip3 install -e $BENCHMARK_COLLECTION/../src/python \
-          && AMICI_PARALLEL_COMPILE="" tests/benchmark-models/test_benchmark_collection.sh
+          && python3 -m pip install -e Benchmark-Models-PEtab/src/python
+
+    - name: Run tests
+      env:
+        AMICI_PARALLEL_COMPILE: ""
+      run: |
+          cd tests/benchmark-models && pytest --durations=10
 
-    # run gradient checks
-    - name: Run Gradient Checks
+    # collect & upload results
+    - name: Aggregate results
       run: |
-        pip install git+https://github.com/ICB-DCM/fiddy.git \
-          && cd tests/benchmark-models && pytest --durations=10 ./test_petab_benchmark.py
+          cd tests/benchmark-models && python3 evaluate_benchmark.py
 
-    # upload results
     - uses: actions/upload-artifact@v4
       with:
         name: computation-times-${{ matrix.python-version }}-${{ matrix.extract_subexpressions }}

diff --git a/deps/AMICI/.github/workflows/test_python_cplusplus.yml b/deps/AMICI/.github/workflows/test_python_cplusplus.yml
@@ -247,6 +247,8 @@ jobs:
   macos_cpp_py:
     name: Tests MacOS C++/Python
     runs-on: macos-latest
+    env:
+      PYTHONFAULTHANDLER: "1"
 
     steps:
     - name: Set up Python
@@ -291,7 +293,8 @@ jobs:
 
     - name: Python tests
       run: |
-        scripts/run-python-tests.sh \
+        # ignore warnings until https://github.com/swig/swig/issues/3061 is resolved
+        scripts/run-python-tests.sh -W ignore:: \
           test_pregenerated_models.py \
           test_splines_short.py \
           test_misc.py
@@ -300,6 +303,8 @@ jobs:
   macos_python:
     name: Tests MacOS Python
     runs-on: macos-latest
+    env:
+      PYTHONFAULTHANDLER: "1"
 
     steps:
     - name: Cache
@@ -351,7 +356,8 @@ jobs:
 
     - name: Python tests
       run: |
-        scripts/run-python-tests.sh \
+        # ignore warnings until https://github.com/swig/swig/issues/3061 is resolved
+        scripts/run-python-tests.sh -W ignore:: \
           --ignore=test_pregenerated_models.py \
           --ignore=test_splines_short.py \
           --ignore=test_misc.py
diff --git a/deps/AMICI/.github/workflows/test_python_ver_matrix.yml b/deps/AMICI/.github/workflows/test_python_ver_matrix.yml
@@ -33,7 +33,7 @@ jobs:
           - python-version: '3.12'
             experimental: false
           - python-version: '3.13'
-            experimental: true
+            experimental: false
 
     steps:
     - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV

diff --git a/deps/AMICI/.gitrepo b/deps/AMICI/.gitrepo
@@ -5,8 +5,8 @@
 ;
 [subrepo]
 	remote = [email protected]:ICB-DCM/AMICI.git
-	branch = v0.27.0
-	commit = 638c3eef18261f82192ac250f4ef3cef5a0359e4
-	parent = df42a8926e9cb6aa46c4f225aa279d7742ddab09
+	branch = v0.28.0
+	commit = c3bbdd9e7261da247ef5e2a648901fd07c2f52fa
+	parent = db859ddeba0094b964aaba66e3aab70746e1eb80
 	cmdver = 0.4.8
 	method = merge
diff --git a/deps/AMICI/CHANGELOG.md b/deps/AMICI/CHANGELOG.md
@@ -4,6 +4,63 @@ See also our [versioning policy](https://amici.readthedocs.io/en/latest/versioni
 
 ## v0.X Series
 
+### v0.28.0 (2024-11-11)
+
+**Breaking changes**
+
+* Changed the default steady-state method to `integrationOnly`
+  (by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2574)
+
+  The default mode for computing steady states and sensitivities at steady
+  state was changed to `integrationOnly`
+  (from previously `integrateIfNewtonFails`).
+
+  This was done for a more robust default behavior. For example, the evaluation
+  in https://doi.org/10.1371/journal.pone.0312148 shows that - at least for
+  some models - Newton's method may easily lead to physically impossible
+  solutions.
+
+  To keep the previous behavior, use:
+  ```python
+  amici_model.setSteadyStateComputationMode(amici.SteadyStateComputationMode.integrateIfNewtonFails)
+  amici_model.setSteadyStateSensitivityMode(amici.SteadyStateSensitivityMode.integrateIfNewtonFails)
+  ```
+
+**Fixes**
+
+* PEtab import: **Fixed potentially incorrect sensitivities** with
+  observable/state-dependent sigmas.
+  This was fixed for all cases amici can handle, others cases will now result
+  in `ValueError`s (https://github.com/AMICI-dev/AMICI/pull/2563).
+
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2562
+
+* Fixed potentially incorrect disabling of Newton's method
+
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2576
+
+* Fixed `ModelStateDerived` copy ctor, where previously dangling pointers
+  could lead to crashes in some situations
+
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2583
+
+* Added missing simulation status codes
+
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2560
+
+* Check for unsupported observable IDs in sigma expressions
+
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2563
+
+
+**Features**
+
+* Optional warning in `fill_in_parameters`
+
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2578
+
+**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.27.0...v0.28.0
+
 ### 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).

diff --git a/deps/AMICI/codecov.yml b/deps/AMICI/codecov.yml
@@ -1,8 +1,10 @@
-fixes:
-  - "build/venv/lib/python3.9/site-packages/::python/"
-  - "build/venv/lib/python3.10/site-packages/::python/"
-  - "build/venv/lib/python3.11/site-packages/::python/"
+# see https://docs.codecov.com/docs/codecovyml-reference
 
+fixes:
+  # https://docs.codecov.com/docs/fixing-paths
+  - "build/venv/lib/python[0-9.]+/site-packages/::python/"
+  - "python/sdist/build/temp_amici/CMakeFiles/amici.dir/src/::src/"
+  - "build/CMakeFiles/amici.dir/src/::src/"
 codecov:
   require_ci_to_pass: yes
 
@@ -27,6 +29,8 @@ comment:
 ignore:
   - "tests/*"
   - "tests/**/*"
+  - "build/tests/**"
+  - "amici_models/**"
 
 flags:
   python:

diff --git a/deps/AMICI/include/amici/defines.h b/deps/AMICI/include/amici/defines.h
@@ -74,7 +74,13 @@ constexpr int AMICI_CONSTR_FAIL=             -15;
 constexpr int AMICI_CVODES_CONSTR_FAIL=      -15;
 constexpr int AMICI_IDAS_CONSTR_FAIL=        -11;
 constexpr int AMICI_ILL_INPUT=               -22;
+constexpr int AMICI_BAD_T=                   -25;
+constexpr int AMICI_BAD_DKY=                 -26;
 constexpr int AMICI_FIRST_QRHSFUNC_ERR=      -32;
+constexpr int AMICI_SRHSFUNC_FAIL=           -41;
+constexpr int AMICI_FIRST_SRHSFUNC_ERR=      -42;
+constexpr int AMICI_REPTD_SRHSFUNC_ERR=      -43;
+constexpr int AMICI_UNREC_SRHSFUNC_ERR=      -44;
 constexpr int AMICI_ERROR=                   -99;
 constexpr int AMICI_NO_STEADY_STATE=         -81;
 constexpr int AMICI_DAMPING_FACTOR_ERROR=    -86;

diff --git a/deps/AMICI/include/amici/model.h b/deps/AMICI/include/amici/model.h
@@ -2063,12 +2063,12 @@ class Model : public AbstractModel, public ModelDimensions {
 
     /** method for steady-state computation */
     SteadyStateComputationMode steadystate_computation_mode_{
-        SteadyStateComputationMode::integrateIfNewtonFails
+        SteadyStateComputationMode::integrationOnly
     };
 
     /** method for steadystate sensitivities computation */
     SteadyStateSensitivityMode steadystate_sensitivity_mode_{
-        SteadyStateSensitivityMode::integrateIfNewtonFails
+        SteadyStateSensitivityMode::integrationOnly
     };
 
     /**

diff --git a/deps/AMICI/include/amici/model_state.h b/deps/AMICI/include/amici/model_state.h
@@ -146,71 +146,37 @@ struct ModelStateDerived {
         , dwdw_(other.dwdw_)
         , dwdx_hierarchical_(other.dwdx_hierarchical_)
         , dJydy_dense_(other.dJydy_dense_) {
-        // Update the SUNContext of all matrices
-        if (J_.data()) {
-            J_.get()->sunctx = sunctx_;
+        // Update the SUNContext of all SUNDIALS objects
+        J_.set_ctx(sunctx_);
+        JB_.set_ctx(sunctx_);
+        dxdotdw_.set_ctx(sunctx_);
+        dwdx_.set_ctx(sunctx_);
+        dwdp_.set_ctx(sunctx_);
+        M_.set_ctx(sunctx_);
+        MSparse_.set_ctx(sunctx_);
+        dfdx_.set_ctx(sunctx_);
+        dxdotdp_full.set_ctx(sunctx_);
+        dxdotdp_explicit.set_ctx(sunctx_);
+        dxdotdp_implicit.set_ctx(sunctx_);
+        dxdotdx_explicit.set_ctx(sunctx_);
+        dxdotdx_implicit.set_ctx(sunctx_);
+        dx_rdatadx_solver.set_ctx(sunctx_);
+        dx_rdatadtcl.set_ctx(sunctx_);
+        dtotal_cldx_rdata.set_ctx(sunctx_);
+        dxdotdp.set_ctx(sunctx_);
+
+        for (auto& dJydy : dJydy_) {
+            dJydy.set_ctx(sunctx_);
         }
-        if (JB_.data()) {
-            JB_.get()->sunctx = sunctx_;
+        for (auto& dwdp : dwdp_hierarchical_) {
+            dwdp.set_ctx(sunctx_);
         }
-        if (dxdotdw_.data()) {
-            dxdotdw_.get()->sunctx = sunctx_;
-        }
-        if (dwdx_.data()) {
-            dwdx_.get()->sunctx = sunctx_;
-        }
-        if (dwdp_.data()) {
-            dwdp_.get()->sunctx = sunctx_;
-        }
-        if (M_.data()) {
-            M_.get()->sunctx = sunctx_;
-        }
-        if (MSparse_.data()) {
-            MSparse_.get()->sunctx = sunctx_;
-        }
-        if (dfdx_.data()) {
-            dfdx_.get()->sunctx = sunctx_;
-        }
-        if (dxdotdp_full.data()) {
-            dxdotdp_full.get()->sunctx = sunctx_;
-        }
-        if (dxdotdp_explicit.data()) {
-            dxdotdp_explicit.get()->sunctx = sunctx_;
-        }
-        if (dxdotdp_implicit.data()) {
-            dxdotdp_implicit.get()->sunctx = sunctx_;
-        }
-        if (dxdotdx_explicit.data()) {
-            dxdotdx_explicit.get()->sunctx = sunctx_;
-        }
-        if (dxdotdx_implicit.data()) {
-            dxdotdx_implicit.get()->sunctx = sunctx_;
-        }
-        if (dx_rdatadx_solver.data()) {
-            dx_rdatadx_solver.get()->sunctx = sunctx_;
-        }
-        if (dx_rdatadtcl.data()) {
-            dx_rdatadtcl.get()->sunctx = sunctx_;
-        }
-        if (dtotal_cldx_rdata.data()) {
-            dtotal_cldx_rdata.get()->sunctx = sunctx_;
-        }
-        for (auto const& dwdp : dwdp_hierarchical_) {
-            if (dwdp.data()) {
-                dwdp.get()->sunctx = sunctx_;
-            }
-        }
-        for (auto const& dwdx : dwdx_hierarchical_) {
-            if (dwdx.data()) {
-                dwdx.get()->sunctx = sunctx_;
-            }
-        }
-        if (dwdw_.data()) {
-            dwdw_.get()->sunctx = sunctx_;
-        }
-        if (dJydy_dense_.data()) {
-            dJydy_dense_.get()->sunctx = sunctx_;
+        for (auto& dwdx : dwdx_hierarchical_) {
+            dwdx.set_ctx(sunctx_);
         }
+        sspl_.set_ctx(sunctx_);
+        dwdw_.set_ctx(sunctx_);
+        dJydy_dense_.set_ctx(sunctx_);
     }
 
     /**

diff --git a/deps/AMICI/include/amici/sundials_matrix_wrapper.h b/deps/AMICI/include/amici/sundials_matrix_wrapper.h
@@ -506,6 +506,19 @@ class SUNMatrixWrapper {
      */
     SUNContext get_ctx() const;
 
+    /**
+     * @brief Set SUNContext
+     *
+     * Update the SUNContext of the wrapped SUNMatrix.
+     *
+     * @param ctx SUNDIALS context to set
+     */
+    void set_ctx(SUNContext ctx) {
+        if (matrix_) {
+            matrix_->sunctx = ctx;
+        }
+    }
+
   private:
     /**
      * @brief SUNMatrix to which all methods are applied

diff --git a/deps/AMICI/include/amici/vector.h b/deps/AMICI/include/amici/vector.h
@@ -413,6 +413,20 @@ class AmiVectorArray {
      */
     void copy(AmiVectorArray const& other);
 
+    /**
+     * @brief Set SUNContext
+     *
+     * If any AmiVector is non-empty, this changes the current SUNContext of the
+     * associated N_Vector. If empty, do nothing.
+     *
+     * @param ctx SUNDIALS context to set
+     */
+    void set_ctx(SUNContext ctx) {
+        for (auto& vec : vec_array_) {
+            vec.set_ctx(ctx);
+        }
+    }
+
   private:
     /** main data storage */
     std::vector<AmiVector> vec_array_;