Re: [Rdkit-devel] Beta of Q2 2011 Release Available

[Greg L. <gre...@gm...>]

Hi Gianluca,

On Fri, Jul 8, 2011 at 12:14 AM, Gianluca Sforna <gi...@gm...> wrote:
> On Thu, Jul 7, 2011 at 3:35 PM, Greg Landrum <gre...@gm...> wrote:
>> On Thu, Jul 7, 2011 at 9:53 AM, Gianluca Sforna <gi...@gm...> wrote:
>>> I just tried to build the beta into RPM packages; I've read that inchi
>>> support is optional, so I guess there is a new cmake switch to trigger
>>> it. However, all py* tests are now failing because "from inchi import
>>> *" gives an ImportError.
>>
>> That's defniitely not what's supposed to happen (and isn't what
>> happens for me when doing the standard in-tree install).
>
> Now I see. The problem is that I'd need some help from your side to
> also support some alternate standards, otherwise building proper
> packages for end users is increasingly painful.

Sorry that we created the problem, we will get it fixed. The packaging
work that you're doing is really valuable and I certainly don't want
to make it either more difficult or complex. I will start to make a
habit of doing an out-of-source build to make sure things like this
are less likely to happen again.

>>> Probably I'm missing something obvious here, but given that import
>>> line is in rdkit/Chem/__init__.py  that means python bindings are
>>> basically unusable right now unless you also activate Inchi support.
>>
>> If you don't do the inchi installation cmake should create a file
>> $RDBASE/rdkit/Chem/inchi.py that is basically empty.
>
> So, examined this part a bit more and unfortunately, the feature as is
> makes packaging harder: the main issue is that we will need to use the
> system's provided inchi library but right now the build lacks any
> support for that. In practice, I think I'd suggest:
>
> 1. add an option to build or not inchi support
> 2. add an option to use system's provided inchi
> 3. ensure tests works also before the in-tree install
> 4. skip inchi feature tests if disabled

I agree with all of these.

> For reference, I found OpenBabel is doing something very similar:
> https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/trunk/CMakeLists.txt
> https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/trunk/cmake/modules/FindInchi.cmake
>
> Of course, if you are ok with the plan, I am willing to provide
> patches for the above.

It would be great if you could do that; otherwise Eddie and I will get
something put together today.

Best,
-greg