Merge branch 'develop' into jax_sciml

AMICI-dev · Dec 13, 2024 · 731b925 · 731b925
2 parents 1349ddb + 2d58f54
commit 731b925
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diff --git 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
@@ -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**

diff --git 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
@@ -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
@@ -1 +1 @@
-0.29.0
+0.30.0