[SciPy-Dev] working on integrate.odeint

Juan Luis Cano juanlu001@gmail....
Fri Aug 23 04:00:43 CDT 2013


On 08/23/2013 09:32 AM, Benny Malengier wrote:
>
>
>
> 2013/8/23 Juan Luis Cano <juanlu001@gmail.com 
> <mailto:juanlu001@gmail.com>>
>
>     On 08/23/2013 08:42 AM, Juan Luis Cano wrote:
>     > On 08/23/2013 03:10 AM, Warren Weckesser wrote:
>     >> The other python file (test_lsoda.py) also needs the correction
>     to the
>     >> coefficient.
>     >>
>     >> Warren
>     >
>     > Warren, thank you so much for pointing that out - I should never
>     code
>     > at 2 AM. Now test_lsoda.py produces the correct output, which
>     suggests
>     > I have to tune the relative and absolute error in test_lsoda2.py.
>
>     Right, this was exactly the problem. Now the three tests produce the
>     same output and I understand much better the interface. In the
>     branch I
>     pointed out before I wrote some issues as a to-do list and I plan
>     working on fixing some integrate.odeint problems in the following
>     months, when time and circumstances allow for that.
>
>
> It is nice to clean up odeint or lsoda, but those are really 
> deprecated functions, replaced by sundials many years ago by Alan 
> Hindmarsh (http://history.siam.org/oralhistories/hindmarsh.htm). As I 
> mentioned before on this list, best would be to deprecate and replace 
> by the modern version which still sees bug fixes 
> (http://computation.llnl.gov/casc/sundials/main.html).
>
> There are 3 python interfaces to sundials, one of which by me and a 
> collaborator: https://github.com/bmcage/odes
> The other 2 are readily found on the internet, and expose even more of 
> the functionality.

Well, I am farily new to contributing to SciPy so I missed those past 
conversations, but I did some googling and found that you created 
scikits.odes. I don't know if there were some conclusions about 
ode/odeint in SciPy, and though I find value in replacing old code with 
new one, I cannot tell if odepack is deprecated or not (deprecated for 
who?) and at least with these little steps I can fix the existing 
problems without disturbing much while trying to find a new 
ground-breaking solution. Unless a new discussion raises and it's 
decided that we can, say, incorporate scikits.odes into SciPy, or any 
other Python interface to some modern DE solvers. I don't have a strong 
opinion on this, I just know that odeint has some flaws right now and 
want to scratch my itch.

Juan Luis
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