Release 0.16.1 - #2019
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According to [CVODES docs](https://sundials.readthedocs.io/en/latest/cvodes/Mathematics_link.html#checkpointing-scheme), polynomial should be the better choice: > The variable-degree polynomial is more memory-efficient (it requires only half of the memory storage of the cubic Hermite interpolation) and is more accurate.
Adapt to new default homebrew version. Should fix current failures in, e.g., https://github.com/AMICI-dev/AMICI/actions/runs/4022709019/jobs/6912732658
to skip PEtab validation
* how to create a container * make Dockerfile compatible with spython/singularity * mv docker/ container/
Fixup for #1932 This fixes importing the swig wrapper for a model directly (not via the package).
….py (#1968) Fixes ``` C:\hostedtoolcache\windows\Python\3.8.10\x64\lib\site-packages\_pytest\python.py:199: PytestReturnNotNoneWarning: Expected None, but python/tests/test_conserved_quantities_demartino.py::test_compute_moiety_conservation_laws_demartino2014 returned 7.324800299999993, which will be an error in a future version of pytest. Did you mean to use `assert` instead of `return`? ```
* Update edata.i * fixup
Removes `-W` compiler flags on Windows, which aren't understood by MSVC. Fixes `cl : Command line error D8021 : invalid numeric argument '/Werror'` (which for some reason currently only occurs on branch `adjoint_event` 🤷♂️) See also https://learn.microsoft.com/en-us/cpp/build/reference/wx-treat-linker-warnings-as-errors?view=msvc-170
Ensures they are gone after running tests.
…1973) The filter function should only be called on AssignmentRule targets. Currently it's called on all parameters.
* fix typos * fix typos in example_errors
* Move different interfaces one level up * Add top-level link to Python examples [before](https://amici.readthedocs.io/en/develop/) / [after](https://amici--1978.org.readthedocs.build/en/1978/)
Events are meanwhile supported via Python
Bumps [ipython](https://github.com/ipython/ipython) from 8.4.0 to 8.10.0. - [Release notes](https://github.com/ipython/ipython/releases) - [Commits](ipython/ipython@8.4.0...8.10.0) --- updated-dependencies: - dependency-name: ipython dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
So far, the value of `Solver::getMaxTime()` was checked against `std::chrono::system_clock`, which measures wall time. This is probably not what we want and can cause issues if a program is paused or the cpu is oversubscribed. Now changed to CPU time. Closes #1913
* module-level variables to sphinx * add/update docstrings * typos, cross-reference * ... see also #1950
…1987) Allows specifying default parameter values for output parameters introduced in the PEtab observables table. This is convenient for placeholder parameters, for which the current value of 0.0 is not good choice (e.g. scaling parameters). Allows for meaningful model outputs if the model is just simulated with default parameters.
* Change default ReturnData::status to AMICI_NOT_RUN So far, if a simulation with `runAmiciSimulations(...., failfast=True)` failed, an empty `ReturnData` with `status=AMICI_SUCCESS` was returned for the skipped conditions. This was rather confusing. This adds a new status: `AMICI_NOT_RUN`. Fixes #1949
* Don't check `clock()` on every rhs evaluation, but only every 500. * Avoid `clock()` completely, if there is no max time specified. Co-authored-by: Fabian Fröhlich <fabian_froehlich@hms.harvard.edu>
* fix equilibraton status discrepancy * Update src/steadystateproblem.cpp Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com> --------- Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com>
Fix SuiteSparse Makefiles for compiler-paths containing blanks, parentheses, ... which is the case for default MSVC installations.
`find ThirdParty/SuiteSparse/ -name Makefile -exec sed -ri 's/([ \t])(\$\(CC\)) /\1"\2" /' {} \;`
By default, if HDF5 is available, use it.
Seems fair to require a CMake version not older than 3 years+ Simplifies CMake files, and some newer features will be required for #1992.
* fix indentation for INFO level messages * add logging for SBML loading * fixup
* make errors for equilibration more transparent * add test for SteadyStateStatus::failed_too_long_simulation * fix testcase * fix & check message * fix logger for steadystate solver * remove magic numbers, add error code * fix fallthrough
For all mex calls, catch exception, print mex invocation, rethrow. Will make bug reports way more informative and simplify debugging. Resolves #913
* Use cmake-install instead of funny manual copying * Build parallel * Upload build artifacts for debugging * Silence stupid MSVC copyright messages
Helps to avoid issues with too long paths on Windows 💩
* Updates SuiteSparse to v7.0.1 * Removes heaps of unused SuiteSparse files * SuiteSparse_config requires `-fPIC`, `CMakeLists.txt` modified. Closes #1879
Codecov Report
Additional details and impacted files@@ Coverage Diff @@
## master #2019 +/- ##
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+ Coverage 76.03% 76.18% +0.14%
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Files 76 76
Lines 12982 13004 +22
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+ Hits 9871 9907 +36
+ Misses 3111 3097 -14
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