Release 0.20.0 #2210
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Release 0.20.0 #2210
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Relevant changes are only in .pre-commit-config.yaml * run black on notebooks via pre-commit * set proper line width (pyproject.toml is not used if we are running things from the repo root) * compatible line width for black + isort * fix json error in binder/overview.ipynb * re-blacken everything
New title + some minor updates Closes #1990 Mark notebook to always execute it under nbsphinx
Fixes ``` CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument <min> value or use a ...<max> suffix to tell CMake that the project does not need compatibility with older versions. ```
When preequilibration (or finding a steadystate in general) fails, `SteadystateProblem::handleSteadyStateFailure` produced `AMICI simulation failed: Steady state computation failed. First run of Newton solver failed. Simulation to steady state failed: No convergence was achieved. Second run of Newton solver failed.`, even in cases where no Newton solve or no simulation was attempted. This is confusing and is changed here, so that the message now reflects what has actually happened. Closes #2178
…2152) Adds functions `amici.numpy.evaluate` and `amici.plotting.plot_expressions` to evaluate or directly plot symbolic expressions of model quantities, respectively. Demo: see end of this section https://amici--2152.org.readthedocs.build/en/2152/ExampleSteadystate.html#Plotting-trajectories
We had to require setuptools<64 because it change its temporary build directory from a known path to a randomly named temporary directory. However, setuptools<64 doesn't work with for Python3.12 (#2179). Therefore, this adds an option to change the setuptools temporary build directory via the `AMICI_BUILD_TEMP` environment variable, so we have those temp files in a known path for coverage analysis. Not meant to be used by users.
ExpDataView provides convenient access to measurements and the like as numpy arrays. However, accessing the associated timepoints is currently only possible via `ExpDataView(...)._swigptr.ts_` which returns an amici.amici.DoubleVector. That's awkward. Now: ```python amici.ExpDataView(amici.ExpData(1, 2, 3, [4, 5, 6])).ts Out[3]: array([4., 5., 6.]) ``` Resolves #2191
Previously: ``` <ReturnDataView(<amici.amici.ReturnData; proxy of <Swig Object of type 'amici::ReturnData *' at 0x7f794a9ef8d0> >)> ``` Now: ``` <ReturnDataView(id='ctrl+basal_preeq', status=AMICI_SUCCESS)> ```
Wasn't automatically handled by swig for unclear reasons. Works now. Fixes #2190.
Fixes a bug in `SwigPtrView.__deepcopy__` which did not produce a deep copy. Add `SwigPtrView.__eq__` to allow for comparison. The view objects are considered equal if the underlying viewed objects are equal. Fixes #2189.
simulate_petab was mainly intended to simulate all conditions at once, but the `simulation_conditions` argument provides also an easy way to simulate only a subset of conditions. However, this currently fails, because the full parameter mapping is used an then wrong conditions are assigned. This is fixed here. Also it saved a minuscule amount of time.
* GHA: Test composite actions * .. * sonar
Handle installation and dependencies in one single place.
* GHA: Cleanup custom swig usage * Previously the newest swig was downloaded and built, but not used because of a wrong path. Fixed here. * Make scripts/downloadAndBuildSwig.sh accept a version number argument * Use composite action to make it more maintainable and avoid issues as fixed above * ..
Replacing redundant sections and some reformatting.
... instead of twice on 3.9
* HasenauerMer2023 * RaimundezFed2023 * Add Mendes2023 * HuckBal2023
* Ensure cmake can find OpenMP * Assert that amici was compiled with OpenMP support * Update installation guide Fixes #2182
Codecov Report
Additional details and impacted files@@ Coverage Diff @@
## master #2210 +/- ##
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+ Coverage 76.62% 76.78% +0.16%
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Files 82 82
Lines 14939 15012 +73
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+ Hits 11447 11527 +80
+ Misses 3492 3485 -7
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FFroehlich
approved these changes
Nov 21, 2023
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