On Mon, Dec 10, 2012 at 4:51 PM, Andrew Dalke wrote:
> On Dec 8, 2012, at 7:01 AM, Greg Landrum wrote:
> > It's a pretty small API change, but there's a huge amount of code that
> needs to be changed in the back and lots and lots of testing that has to be
> done, so this is going to take a while.
On Dec 8, 2012, at 7:01 AM, Greg Landrum wrote:
> It's a pretty small API change, but there's a huge amount of code that needs
> to be changed in the back and lots and lots of testing that has to be done,
> so this is going to take a while.
Speaking of hydrogens, I came across a strange query (p
On Dec 9, 2012, at 8:06 PM, Gianluca Sforna wrote:
> I believe a commonly accepted approach to this kind of issues is something
> like:
>
> 1. add warnings about the deprecated or changed methods, but keep the
> current behavior so code do not break, but becomes verbose when called
...
That p
On Dec 8, 2012, at 7:01 AM, Greg Landrum wrote:
> Please let me know if this sounds reasonable or if you have suggestions on
> how to handle the logistics more cleanly.
It looks quite reasonable to me.
Only a bit of my code will be affected by the change, and that's code
which is just at the beg
Gianluca 's plan is better.
I think step 5 can be the step where depreciated methods exist but they
are redirecting to the new methods if this is possible, otherwise there
have to be removed.
The key point to the whole plan is to give users the time to update their
code.
Regards,
Christos
Sent f
On Sat, Dec 8, 2012 at 7:01 AM, Greg Landrum wrote:
> My current plan is to keep this branch in sync with the trunk through (at
> least) the Q4 2012 release and then consider moving it onto the trunk and
> creating a v1 API branch in Q1 of next year. I guess I should be able to
> keep the v1 API b
Hi,
This is an unusually long email for me, so here's the TL;DR version:
The RDKit handling of implicit hydrogens is confusing. This leads to
needlessly complicated code and, almost certainly, bugs. I'm proposing to
fix it, but doing so requires an API change. This work will be done on a
branch un
