Info on build stuff below...
Begin forwarded message:
> From: John May <[email protected]>
> Subject: Re: [Cdk-user] ant dist-large after adding custom classes to cdk?
> Date: 24 July 2013 21:15:16 BST
> To: Nick Vandewiele <[email protected]>
>
> Hi Nick,
>
> Would you be willing to submit these as patches - sounds like useful stuff?
>
> The CDK build is… complicated.
>
> Each file needs a module tag in the javadoc, e.g you SMILES one would go have
> '@cdk.module smiles'
>
> /**
> * @cdk.module smiles
> */
> final class SMILESParser {
>
> }
>
> With that you need to make sure you declare your (jar) dependencies in
> 'src/meta-inf/*': see how each module declares it's dependencies,
> (internal,external and devel)
> https://github.com/egonw/cdk/tree/master/src/META-INF
>
> Introducing new dependancies will likely require a change in the build order
> which needs to manually set in
> 'https://github.com/egonw/cdk/blob/master/build.xml#L522-L576'
>
> I do have a maven/gradle build (https://github.com/johnmay/cdk/tree/cdk-mvn)
> which explicitly makes the modules a lot clear an the IDE will actually build
> it correctly. I did hope to have this as the default build system by now… and
> also be on a 1.6 release but I don't think either of those will be happening
> anytime soon.
>
> As a side note I'm currently writing a separate library for handling
> OpenSMILES. I may well add radical support but this isn't currently defined
> in the spec - would be interesting to see how you handle it.
>
> J
>
> On 24 Jul 2013, at 16:44, Nick Vandewiele <[email protected]> wrote:
>
>> Hi Joos,
>>
>> Thanks for your answer.
>> I understand the use of cdk as a dependency to other projects. But assume
>> that I created classes whose function should be part of CDK and not of a
>> custom project.
>> One example is the SMILES parser that is notoriously bad at keeping track of
>> unpaired electrons. I created a custom class that took of care of this and
>> is called from SMILESParser. Or think of adding new atom types in
>> CDKAtomTypeMatcher. Or adding isotope info to atomcontainers parsed using
>> the InchIParser, etc…
>>
>> These aforementioned pieces of code run fine from within my development
>> environment (ic: Eclipse). But once I decide I want to have my project as a
>> production release, I want to call cdk from a single jar, thus my calling
>> “ant dist-large”. That’s where the shit hits the fan. Any thoughts on this?
>>
>> Regards,
>>
>> Nick
>>
>>
>> From: Joos Kiener [mailto:[email protected]]
>> Sent: Wednesday, July 24, 2013 4:40 PM
>> To: Nick Vandewiele
>> Cc: [email protected]
>> Subject: Re: [Cdk-user] ant dist-large after adding custom classes to cdk?
>>
>> Hi Nick,
>>
>> no you don't need to do that. I suggest you remove everything you put into
>> the cdk folder again and just build it normally. You then use CDK as a
>> dependency in your own project. There is no need to only have one jar. You
>> can have as many as you want but the must all be on the classpath:
>>
>> http://en.wikipedia.org/wiki/Classpath_%28Java%29
>>
>> Your jar file then must only have a classpath entry in its manifest file
>> pointing to the cdk dependency (usually in folder lib):
>>
>> http://en.wikipedia.org/wiki/Classpath_%28Java%29#Setting_the_path_in_a_Manifest_file
>>
>> I suggest you use an IDE like netbeans as it makes this stuff a lot easier.
>>
>> Best Regards,
>>
>> Joos
>>
>> Am 24.07.2013 14:51, schrieb Nick Vandewiele:
>> Hi,
>>
>> I wanted to build a single jar file of the CDK using “ant dist-large”
>> defined in build.xml. It fails with messages such as
>>
>> …/cdk/build/src/extra/org/openscience/cdk/qsar/descriptors/molecular/DoubleBondsDescriptor.java:11:
>> cannot find symbol: class IMolecularDescriptor
>>
>> I think the reason why it failed is because I created some classes (eg
>> custom made molecular descriptors, vide supra) and just put them in the cdk
>> folder structure where I thought they belonged to. However, the build file
>> apparently looks into the build folder and then runs into trouble.
>>
>> Any thoughts on how to make sure that custom made classes don’t result in
>> build fails? The documentation wasn’t that helpful for this matter.
>>
>> Thanks in advance,
>> Nick
>>
>>
>>
>>
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