Daniel Weindl

Hi, I stumbled across a problem in `CVode` which seems to yield a wrong `yout` if `h` becomes zero. After `CVode`: `Internal t = 0 and h = 0 are...

State mapping in reaction rules?

8

Hi, BNGL supports state mapping using "%" in reaction rules, e.g. `A(a%x) -> B(a%x)`, to indicate that the state of `A` is transferred to `B`. I was wondering if there...

Since https://github.com/ICB-DCM/pyPESTO/pull/909 it's not possible to load History from write protected hdf5 files, because `Hdf5History._maybe_generate_hdf5_group` in `Hdf5History.__init__` always tries to open the file for appending.

Flaky test `test/sample/test_sample.py::test_samples_cis`

5

See https://github.com/ICB-DCM/pyPESTO/runs/7522438577?check_suite_focus=true ``` _______________________________ test_samples_cis _______________________________ def test_samples_cis(): """ Test whether :py:func:`pypesto.sample.calculate_ci_mcmc_sample` produces percentile-based credibility intervals correctly. """ # load problem problem = gaussian_problem() # set a sampler sampler =...

Start collecting references

3

We should keep track of papers for which pypesto was used. Relevant for any potential applications for funding.

Python version support policy

1

Shall we use (and reference) https://numpy.org/neps/nep-0029-deprecation_policy.html as pypesto's python version support policy?

Can this be handled more gracefully, or can we add some random seed, so this does not happen in the test? https://github.com/ICB-DCM/pyPESTO/runs/5881283280?check_suite_focus=true ``` _____________________ test_pipeline[Metropolis-rosenbrock] _____________________ sampler = problem =...

Importing pypesto.sample imports tons of packages

2

... do we really want/need that? https://github.com/ICB-DCM/pyPESTO/blob/a4ce1d219774b265b9825eca827e7e18d57f37ef/pypesto/sample/__init__.py#L9-L18 (with all their dependencies)

Flaky test_result_from_hdf5_history?

7

Fails here https://github.com/ICB-DCM/pyPESTO/runs/3893112578?check_suite_focus=true I don't think that's related to that commit. ``` ________________________ test_result_from_hdf5_history _________________________ def test_result_from_hdf5_history(): problem = create_petab_problem() with tempfile.TemporaryDirectory(dir=".") as tmpdirname: _, fn = tempfile.mkstemp(".hdf5", dir=f"{tmpdirname}") history_options_hdf5...

Interface additional optimizers: pygmo?

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https://esa.github.io/pagmo2/index.html