Menu
▾
▴
[Cdk-commits] CVS: cdk/doc/devel-guide docs.xml,1.6,1.7 library-development.xml,1.12,1.13 library-release.xml,1.3,1.4
|
From: Egon W. <eg...@us...> - 2005-04-24 12:55:20
|
Update of /cvsroot/cdk/cdk/doc/devel-guide In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv13588 Modified Files: docs.xml library-development.xml library-release.xml Log Message: More updates of the devel docs Index: docs.xml =================================================================== RCS file: /cvsroot/cdk/cdk/doc/devel-guide/docs.xml,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- docs.xml 4 Apr 2005 14:52:50 -0000 1.6 +++ docs.xml 24 Apr 2005 12:55:10 -0000 1.7 @@ -52,7 +52,7 @@ <para> Indicates a keyword for this class allowing users to find the class more easily. More than one tag may be used. The index is found -<ulink url="http://almost.cubic.uni-koeln.de/cdk/docu/featurefolder/">online</ulink>. +<ulink url="http://almost.cubic.uni-koeln.de/cdk/cdk_top/docu/featurefolder/">online</ulink>. </para> </listitem> </varlistentry> Index: library-development.xml =================================================================== RCS file: /cvsroot/cdk/cdk/doc/devel-guide/library-development.xml,v retrieving revision 1.12 retrieving revision 1.13 diff -u -r1.12 -r1.13 --- library-development.xml 10 Apr 2005 14:54:34 -0000 1.12 +++ library-development.xml 24 Apr 2005 12:55:10 -0000 1.13 @@ -11,65 +11,40 @@ <title>CDK Modules</title> <para> All CDK classes are categorized into classes. Currently, these classes - are defined: cdk-core, cdk-standard, cdk-io, cdk-render, - cdk-libio and cdk-extra. + are defined: cdk-data, cdk-core, cdk-standard, cdk-io, cdk-render, + cdk-libio, cdk-extra, cdk-experimental, cdk-orphaned, and several more. + </para> + <para> + The data module contains the data classes of the CDK library. Nothing + more, nothing less. + The core module contains several of the more central algorithms in CDK, + i.e. algorithms that are used by many other algorithms. Both these classes + are now stable. + </para> + <para> + Many of these modules have dependencies on other modules. An overview + is available on the CDK website: <ulink url="http://almost.cubic.uni-koeln.de/cdk/cdk_top/devel/modules/">module + dependencies</ulink>. </para> <section> - <title>Core classes</title> - <para> - In the cdk-core module the core classes represent chemical entities, like - bonds, atoms, molecules, and - more abstract entities, like connectivity tables, used for in common - computational and information chemistry. - </para> - </section> - <section> - <title>Standard classes</title> - <para> - The standard classes found in the cdk-standard module are those classes that - do not store chemical data, but that are used by two or more of the modules - below, and that are considered basic. - </para> - </section> - <section> - <title>IO classes</title> - <para> - The cdk-io module contains classes for file, internet and database input and - output. - </para> - </section> - <section> - <title>Rendering classes</title> - <para> - The cdk-render module provides classes for displaying 2D and 3D chemical - information, and classes that provide ways to have users interact with these - graphical representations. - </para> - </section> - <section> - <title>LibIO classes</title> - <para> - These classes interface to other (Java) libraries, like JOELib and CMLDOM. - </para> - </section> - <section> - <title>Extra classes</title> + <title>Library IO modules</title> <para> - These are classes that do not belong to either of the other two categories. + CDK contains three modules that allow interaction with other libraries: + libio-cml for CMLDOM, libio-joelib for + <ulink url="http://joelib.sf.net/">JOELib</ulink>, and io-jmol for the + IO classes in <ulink url="http://www.jmol.org/">Jmol</ulink>. </para> </section> <section> - <title>Experimental classes</title> + <title>Special modules</title> <para> - This package is for classes that provide experimental functionality. That is, - functions that are not fully implemented, or not for general use in any case. - Such classes may be used, however, in some programs to be able to be tested. - An example is the 'experimental' version of JChemPaint, which provides access - to the IUPAC name generator, which is only a proof of concept of a possible - design, and not really of production level quality. + There are a few special modules, which are normally not used by users. + The most obvious module is the test module. But others are: the experimental + module, which contains code not yet trusted or finished enough; and the + orphaned module with classes which can no longer be supported by the + CDK developers. </para> </section> - </chapter> <chapter id="sect:compiling"> @@ -81,36 +56,16 @@ </para> <para> - CDK can be compiled with and without support for Java3D. - How to compile these, is explained in the next two sections. + CDK can be compiled with and without support for a number of libraries: + Java3D, JOELib and Xerces. + The availability of those libraries is normally autodetected. An overview + is given with the command: + <programlisting> +cdk/$ ant info + </programlisting> </para> <section> - <title>Compiling without Java3D installed</title> - <para> - If not Java3D is installed or available for your platform, - you can compile CDK with: - <programlisting> -cdk/$ ant - </programlisting> - </para> - </section> - - <section> - <title>Compiling with Java3D installed</title> - <para> - The build procedure will automatically detect a Java3D installtion. - If, however, Java3D is not installed in the Java SDK directory, - you can define the path like this: - <programlisting> -cdk/$ ant -Dpathtojava3d=/some/path compile-with-java3d - </programlisting> - The parameter pathtojava3d can be used to tell Ant where - your Java3D installation (read: jar files) can be found. - </para> - </section> - - <section> <title>Debugging and Optimization</title> <para> It is useful to compile CDK with debugging information while @@ -200,21 +155,6 @@ Java versions. </para> - <para> - An alternative is to install the cdk-test package. - You can then do tests with - <programlisting> -$ cdk-test org.openscience.cdk.test.CDKTests - </programlisting> - </para> - - <para> - There are currently two major test suites: - <itemizedlist> - <listitem><para>org.openscience.cdk.test.CDKTests</para></listitem> - <listitem><para>org.openscience.cdk.test.io.cml.CMLIOTests</para></listitem> - </itemizedlist> - </para> </section> <section> @@ -286,7 +226,7 @@ return new TestSuite(RingSearchTest.class); } </programlisting> - </example> + </example> The nicest thing now is that JUnit automatically finds, by introspection, all methods in your @@ -304,7 +244,7 @@ assert(ringSet.size() == 2); } </programlisting> - </example> + </example> Interestingly, the method testAlphaPinene() does not return anything. Somehow they do the evaluation of the assert method in a different way, also by introspection, supposedly. @@ -332,7 +272,7 @@ assert(IsomorphismChecker.areIsomorphic(reference, testMol)); } </programlisting> - </example> + </example> Finally, the CDKTests class is supposed to be a host for all the single TestCases that we write: <example> @@ -360,7 +300,7 @@ } } </programlisting> - </example> + </example> It makes a TestSuite and then adds all the single tests and runs them, evaluating the result and printing a small summary. Index: library-release.xml =================================================================== RCS file: /cvsroot/cdk/cdk/doc/devel-guide/library-release.xml,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- library-release.xml 10 Apr 2005 14:54:34 -0000 1.3 +++ library-release.xml 24 Apr 2005 12:55:10 -0000 1.4 @@ -36,15 +36,15 @@ Update the website and add release notes to it. That is: <orderedlist> <listitem><para>update the API on <ulink url="http://cdk.sf.net/api/">http://cdk.sf.net/api/</ulink></para></listitem> - <listitem><para>update the keyword list on <ulink url="http://almost.cubic.uni-koeln.de/cdk/docu/featurefolder/">http://almost.cubic.uni-koeln.de/cdk/docu/featurefolder/</ulink></para></listitem> - <listitem><para>update the ChangeLog list on <ulink url="http://almost.cubic.uni-koeln.de/cdk/docu/changelog/">http://almost.cubic.uni-koeln.de/cdk/docu/changelog/</ulink></para></listitem> - <listitem><para>update the library dependencies list on <ulink url="http://almost.cubic.uni-koeln.de/cdk/docu/dep/">http://almost.cubic.uni-koeln.de/cdk/docu/dep//</ulink></para></listitem> - <listitem><para>update the bibliography list on <ulink url="http://almost.cubic.uni-koeln.de/cdk/bib/base_view">http://almost.cubic.uni-koeln.de/cdk/bib/base_view</ulink></para></listitem> - <listitem><para>update the PMD results for the CDK modules on <ulink url="http://almost.cubic.uni-koeln.de/cdk/devel/quality/pmd/">http://almost.cubic.uni-koeln.de/cdk/devel/quality/pmd/</ulink></para></listitem> - <listitem><para>update the JavaDoc stats on <ulink url="http://almost.cubic.uni-koeln.de/cdk/devel/quality/javadoc_stats/">http://almost.cubic.uni-koeln.de/cdk/devel/quality/javadoc_stats/</ulink></para></listitem> - <listitem><para>update the source code stats on <ulink url="http://almost.cubic.uni-koeln.de/cdk/devel/quality/source_stats/">http://almost.cubic.uni-koeln.de/cdk/devel/quality/source_stats/</ulink></para></listitem> - <listitem><para>update the modules page on <ulink url="http://almost.cubic.uni-koeln.de/cdk/devel/modules/">http://almost.cubic.uni-koeln.de/cdk/devel/modules/</ulink></para></listitem> - <listitem><para>update all pages below the modules page on <ulink url="http://almost.cubic.uni-koeln.de/cdk/devel/modules/">http://almost.cubic.uni-koeln.de/cdk/devel/modules/</ulink></para></listitem> + <listitem><para>update the keyword list on <ulink url="http://almost.cubic.uni-koeln.de/cdk/cdk_top/docu/featurefolder/">http://almost.cubic.uni-koeln.de/cdk/cdk_top/docu/featurefolder/</ulink></para></listitem> + <listitem><para>update the ChangeLog list on <ulink url="http://almost.cubic.uni-koeln.de/cdk/cdk_top/docu/changelog/">http://almost.cubic.uni-koeln.de/cdk/cdk_top/docu/changelog/</ulink></para></listitem> + <listitem><para>update the library dependencies list on <ulink url="http://almost.cubic.uni-koeln.de/cdk/cdk_top/docu/dep/">http://almost.cubic.uni-koeln.de/cdk/cdk_top/docu/dep//</ulink></para></listitem> + <listitem><para>update the bibliography list on <ulink url="http://almost.cubic.uni-koeln.de/cdk/cdk_top/bib/base_view">http://almost.cubic.uni-koeln.de/cdk/cdk_top/bib/base_view</ulink></para></listitem> + <listitem><para>update the PMD results for the CDK modules on <ulink url="http://almost.cubic.uni-koeln.de/cdk/cdk_top/devel/quality/pmd/">http://almost.cubic.uni-koeln.de/cdk/cdk_top/devel/quality/pmd/</ulink></para></listitem> + <listitem><para>update the JavaDoc stats on <ulink url="http://almost.cubic.uni-koeln.de/cdk/cdk_top/devel/quality/javadoc_stats/">http://almost.cubic.uni-koeln.de/cdk/cdk_top/devel/quality/javadoc_stats/</ulink></para></listitem> + <listitem><para>update the source code stats on <ulink url="http://almost.cubic.uni-koeln.de/cdk/cdk_top/devel/quality/source_stats/">http://almost.cubic.uni-koeln.de/cdk/cdk_top/devel/quality/source_stats/</ulink></para></listitem> + <listitem><para>update the modules page on <ulink url="http://almost.cubic.uni-koeln.de/cdk/cdk_top/devel/modules/">http://almost.cubic.uni-koeln.de/cdk/cdk_top/devel/modules/</ulink></para></listitem> + <listitem><para>update all pages below the modules page on <ulink url="http://almost.cubic.uni-koeln.de/cdk/cdk_top/devel/modules/">http://almost.cubic.uni-koeln.de/cdk/cdk_top/devel/modules/</ulink></para></listitem> </orderedlist> Preferably, a large set of these things goes in a semi-automatic mechanism. Hence, my focus on the Plone FTP server! |