diff --git a/.github/workflows/test_benchmark_collection_models.yml b/.github/workflows/test_benchmark_collection_models.yml index e68ec1518b..77470367d7 100644 --- a/.github/workflows/test_benchmark_collection_models.yml +++ b/.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 \ diff --git a/CHANGELOG.md b/CHANGELOG.md index 3a46670e10..cba09d146c 100644 --- a/CHANGELOG.md +++ b/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÷ 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** diff --git a/documentation/python_installation.rst b/documentation/python_installation.rst index eb4d87d59c..54acbddce1 100644 --- a/documentation/python_installation.rst +++ b/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 +++++++++++++++++++++ diff --git a/tests/benchmark-models/test_petab_benchmark.py b/tests/benchmark-models/test_petab_benchmark.py index 7c70015a8c..4a63d8bfda 100644 --- a/tests/benchmark-models/test_petab_benchmark.py +++ b/tests/benchmark-models/test_petab_benchmark.py @@ -123,7 +123,9 @@ "Elowitz_Nature2000", "Fiedler_BMCSystBiol2016", "Fujita_SciSignal2010", - "Isensee_JCB2018", + # Excluded until https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab/pull/253 + # is sorted out + # "Isensee_JCB2018", "Lucarelli_CellSystems2018", "Schwen_PONE2014", "Smith_BMCSystBiol2013", diff --git a/version.txt b/version.txt index ae6dd4e203..c25c8e5b74 100644 --- a/version.txt +++ b/version.txt @@ -1 +1 @@ -0.29.0 +0.30.0