Merge pull request #2622 from dweindl/release

Release 0.30.0

Author: dweindl

.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 \

.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

CHANGELOG.md

@@ -4,6 +4,48 @@ See also our [versioning policy](https://amici.readthedocs.io/en/latest/versioni
 
 ## v0.X Series
 
+### 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**

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
 +++++++++++++++++++++
 

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_);
     }

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