Merge pull request #2597 from dweindl/release_0.29.0

Release 0.29.0

Author: dweindl

.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

.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

.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

.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

.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_*/
 

.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

.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

.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/*

.readthedocs.yml

@@ -21,6 +21,7 @@ build:
   os: "ubuntu-22.04"
   apt_packages:
     - libatlas-base-dev
+    - libhdf5-serial-dev
     - swig
   tools:
     python: "3.11"

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**