Adapt to changed error message. Closes #1385.

* Use PEP 517 pyproject.toml (taking proper care of dependencies of setup.py itself)
* Use setup.cfg
* NOTE: creating a source distribution now requires https://github.com/pypa/build (or manual installation of the build requirements)

Allows specifying e.g. `-fno-openmp` via AMICI_CXXFLAGS

Fixes CMake deprecation warning

Petablint previously failed if observableFormula or noiseFormula contained pysb observables or expressions

and support paths containing spaces

* Upgrade to sundials 5.7.0

* Disable shared libs

* No __attribute__ ((__deprecated__)) for msvc

* Revert "No __attribute__ ((__deprecated__)) for msvc"

This reverts commit 8dfac2b.

* No __attribute__ ((__deprecated__)) for msvc

* Fix error C2059: syntax error: 'constant'?

* DBG

* d'oh

* ..

* SUNDIALS_DEPRECATED

* SUNDIALS_DEPRECATED for __GNUC__

* update error code for singular jacobian and add static assert

Co-authored-by: Fabian Fröhlich <[email protected]>
Co-authored-by: FFroehlich <[email protected]>

* Extract ModelDimensions from Model

update code generation and templates

* Regenerate test models

* update tests

* Update serialization

* Extract ModelDimensions from ReturnData

* Update operator==

* Swig: order matters

* const&

* static cast const&

Missed updating this one in d7392e2

* account for heaviside functions in expressions

* fix adjoint events if event coincides with datapoint

* fixup

* fix cassert

* enable starting in an event

* change assert to exception

* fixup adjoint

* fixup heaviside implementation

* fix xdot backsubstitutions

* reinit heaviside after pre-simulation/equilibration

* fix heaviside initialization

* add documentation, fix cpp Heaviside implementation

* disable Chen because that model is just awesome

* update unittest

Re-apply #1351 to updated sundials

* Refactor Model: Extract ModelStateDerived

* Remove unused my_ and mz_

* Use swig 4.0.2 for docs

…initial value (#1397)

* unspecified initial states in PEtab conditions table default to SBML initial value

* review, fix f-string

* review

* review

Co-authored-by: Fabian Fröhlich <[email protected]>
Co-authored-by: Daniel Weindl <[email protected]>

Should prevent errors like

```
RuntimeError: module compiled against API version 0xe but this version of numpy is 0xd
[...]
ImportError: numpy.core.multiarray failed to import
```

…1407)

This allows using Model without ExpData unless there really are measurements. Also avoids having to add any new member of ExpData also to Model and slims down Model a bit. Getters and setters for SimulationParameters members are still in Model, which is to preserve backwards compatibility for ExpData, which allowed unchecked access to the respective members. Further refactoring to follow.

Partially addresses #931 (moving ID / name functions is still missing).

In some places it was already written that we require python>=3.7.
This removes any Python3.6 leftovers.

(previously, only README.md was updated)

as the GitHub action workers don't have too much disk space and those files should be removed anyways.

... because thousands of line per file are a pain

* CI: Allow tests on unstable python version to fail

* Disable 3.10.0-alpha.5 for now

* Doc: Add table with AMICI C++/Python/Matlab feature comparison
* Link and update details on SBML support

Co-authored-by: Fabian Fröhlich <[email protected]>

fixes #1217

* slim model/abstract model

* ignore context managers

* add ignores for solver

* try again to get rid of context managers

* fixup?

* fixup

* add more model ignores

* Update swig/amici.i

Co-authored-by: Daniel Weindl <[email protected]>

Co-authored-by: Daniel Weindl <[email protected]>

fixes #1421

* test

* test

* test

* fix

* fixup

* fixup?

* try autolink?

* fixup?

* fixup?

* fix fixup

fixes #1415

* fix notebook?

* fix notebook formatting?

Include supported tags (i.e. at least 1 passed test with the given tag) in sbml semantic test suite summary.
Description of the tags is available at https://github.com/sbmlteam/sbml-test-suite/blob/master/docs/tags-documentation/all-tags.txt

…fixes (#1417)

Adds possibility to provide state indices for selective reinitialization based on fixed parameters.

The previous `ExpData::reinitializeFixedParameterInitialStates` is still there, but will be removed in an upcoming version.


Addresses #1345, #1396, #1319

Supersedes #1344 

Include new test cases from PEtab-dev/petab_test_suite#35

Co-authored-by: Fabian Fröhlich <[email protected]>

* add pysb benchmarking script

* add file description

Co-authored-by: Daniel Weindl <[email protected]>