Re: [Cdk-devel] Patches

[<ste...@eb...>]

Hi Egon
> does the order in which they should be applied matter?
As long as those from email from 31.7. are used first and those from
yesterday sesond, it should be ok.
> Right now, they
> are almost all called 0001-foo.patch, and I have no clue about the
> order...
I did them module-wise, as requested (which is the reason for the number
of patches). The 0001 is generated by git - sorry for that. I try to work
with git, but I may have missed something. Forgive my for git trouble.
>
> I also very much appreciate if you could discuss what each patch is
> doing, so that I have a clue where what is supposed to go.
The idea is as follows:

0001-added-more-stereo-bond-types.patch
Adds new types to CDKConstants, namely for the wedged criss cross (which
has a direction, so two needed) and the wiggly bond

0001-comments-in-BasicBondGenerator.patch
changes the BasicBond generator to take into account the new types and
adds comments

0001-added-everything-needed-for-drawing-wiggle-and-criss.patch
Alters the AlterBondStereoModule to take into account the new types

0001-added-wiggly-line-to-elements-comments-for-wedge-li.patch
This is about render elements, added a wiggly line and extending the wedge
bonds to include the criss cross one

0001-AWTVisitor-visits-wiggly-bonds.patch
The AWTVisitor visits=draws the new elements

0001-svg-visitor-visits-crisscrossbonds.patch
Same for the svg visitor

0002-added-everything-needed-for-drawing-wiggle-and-criss.patch
Changes the controller hub to handle new types

0001-added-a-reference-to-iupac-recommendations-on-drawin.patch
Adds the IUPAC reference

0001-added-reference-to-reference-to-iupac-recommendation.patch
Adds reference to comments

0001-tests-for-mdl-readers-writers-stereo-properties-3-an.patch
0001-mdl-readers-or-now-reading-stereo-types-3-and-4.-Bot.patch
MDLReader/Writer uses the new types (mdl spec has to stereo undefined
fields, but only one was handled till  now)
> The above
> suggests a patch to the MDL reader, which should go up for review for
> CDK master directly, or cdk-1.2.x...
It's all done agains jcp-primary. I think it's up to you to decide what to
put where - I don't feel in a position to decide. But only using the mdl
stuff is not possible, you need at least the CDKConstants as well.
>
> In particular, keeping patches of the same nature together and
> separate, it makes things easier to review... two patches against CDK
> master for the MDL reader as much easier to review then a whole set of
> 8 patches...
>
> BTW, I also strongly suggest to use the patch tracker for patches
> against CDK master and cdk-1.2.x...
As I said, I found that myself. It was once said that we can use mailing
list or tracker, but I convinced myself the list is not good. Sorry for
realizing late.
I hope this clarifies things a bit.
Stefan

-- 
Stefan Kuhn B. Sc. M. A.
Software Engineer in the Chemoinformatics and Metabolism Team
European Bioinformatics Institute (EBI)
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD UK
Phone +44 1223 49 2657
Fax +44 (0)1223 494 468