Michael Clerx

Windows tests show unclosed file

1

``` sys:1: ResourceWarning: unclosed file ``` See very bottom of logs at e.g. https://ci.appveyor.com/project/martinjrobins/pints/builds/26014056/job/hdhmjs2jkj39tax2

New toy ODE models use undocumented property self._y0

1

Should either document this, or maybe add methods `set_initial_conditions` and `initial_conditions` to `ToyODEModel` class and use `initial_conditions()` inside `simulate` instead. Might also want to think about the case where we...

If you see it, please post the failed test output here :-)

Remove the LogLikelihood class

11

It doesn't add any functionality, just indicated that a certain LogPDF is intended as a LogLikelihood. In some cases, we test to see if something _is_ a LogLikelihood, but I'm...

Two parameters are missing a description: https://github.com/pints-team/pints/blob/9843b6402e4c2f0e8eb58f3f394b6d139212cbab/pints/_mcmc/_dual_averaging.py#L62-L65

@ben18785 looks like this is quite behind: https://pints-team.github.io/pints-methods-overview/ If we decide the maintenance burden outweighs the benefits we can just drop it too 😓

Wrong log_pdf evaluations returned?

2

@marcberliner wrote: > Calculating my objective function is expensive, so I’d like to store the `log_pdf` values alongside the samples to avoid recalculating them. > > As a side note,...

pip now complains if you try to install with ``` pip install -e . ``` > DEPRECATION: Legacy editable install of pints==0.5.1 from file:///home/michael/dev/pints (setup.py develop) is deprecated. pip 25.0...

System default browser not used, because serverapp started as "opening a local html file"

12

## Description On a fresh install of Fedora 41 (gnome 47) I suddenly found that the `jupyter notebook` command opened chrome, not my system default of firefox. This was really...

https://thomasnyberg.com/releasing_the_gil.html