[BioPython] biopython-epydoc

[Frederic.Sohm at iaf.cnrs-gif.fr]

Hi,

Sorry, I have no idea about what the problem is, but I have an advice if you do 
use epydoc, because I have had the problem before. 

To avoid getting a lot of useless output and a very long documentation you 
should comment out the following lines in Bio.Restriction.Restriction.py 
which are at the bottom end of the file.

This code create the class for the restriction enzymes (and there is about 600 
of them). Epydoc will create the documentation for each enzyme. It is always 
more or less the same. The processing is very long and the doc quite useless.

If you comment these lines before running epydoc you will still get the 
documentation once (for the super class) 

Here are the line to comment out.
Don't forget to uncomment them after :-)

Sorry for not being to helping you with your problem, I have had a look and it 
doesn't ring a bell.

Fred

"""
CommOnly    = RestrictionBatch()    # commercial enzymes
NonComm     = RestrictionBatch()    # not available commercially
for TYPE, (bases, enzymes) in typedict.iteritems() :
    #
    #   The keys are the pseudo-types TYPE (stored as type1, type2...)
    #   The names are not important and are only present to differentiate
    #   the keys in the dict. All the pseudo-types are in fact 
RestrictionType.
    #   These names will not be used after and the pseudo-types are not
    #   kept in the locals() dictionary. It is therefore impossible to
    #   import them.
    #   Now, if you have look at the dictionary, you will see that not all the
    #   types are present as those without corresponding enzymes have been
    #   removed by Dictionary_Builder().
    #
    #   The values are tuples which contain
    #   as first element a tuple of bases (as string) and
    #   as second element the names of the enzymes.
    #
    #   First eval the bases.
    #
    bases = tuple([eval(x) for x in bases])
    #
    #   now create the particular value of RestrictionType for the classes
    #   in enzymes.
    #
    T = type.__new__(RestrictionType, 'RestrictionType', bases, {})
    for k in enzymes :
        #
        #   Now, we go through all the enzymes and assign them their type.
        #   enzymedict[k] contains the values of the attributes for this
        #   particular class (self.site, self.ovhg,....).
        #
        newenz = T(k, bases, enzymedict[k])
        #
        #   we add the enzymes to the corresponding batch.
        #
        #   No need to verify the enzyme is a RestrictionType -> add_nocheck
        #
        if newenz.is_comm() : CommOnly.add_nocheck(newenz)
        else : NonComm.add_nocheck(newenz)
#
#   AllEnzymes is a RestrictionBatch with all the enzymes from Rebase.
#
AllEnzymes = CommOnly | NonComm
#
#   Now, place the enzymes in locals so they can be imported.
#
names = [str(x) for x in AllEnzymes]
locals().update(dict(map(None, names, AllEnzymes)))
__all__=['FormattedSeq', 'Analysis', 
'RestrictionBatch','AllEnzymes','CommOnly','NonComm']+names
del k, x, enzymes, TYPE, bases, names
""


Le vendredi 8 Avril 2005 10:53, Rafael C. Jimenez a écrit :
> I am trying to get html help pages of biopython through epydoc. Epydoc
> generate the html files but there is not information inside about the
> modules, classes, and/or functions. Any idea of how to do this?
>
> My input/output:
> ----------------------------------------------------------------------
> nbn213:/System/Library/Frameworks/Python.framework/Versions/2.3/bin rc$
> ls
> epydoc          epydocgui       idle            pydoc           python
>          python2.3
>
> nbn213:/System/Library/Frameworks/Python.framework/Versions/2.3/bin rc$
> ./epydoc -o /Users/rc/Desktop/epydoc/biopython  --css blue
> --private-css green -v -n biopython -u http://biopython.org
> --inheritance listed Bio
>
> Importing 1 modules.
>    [1/1] Importing Bio
> Building API documentation for 1 modules.
>    [1/1] Building docs for Bio
> Writing HTML docs (10 files) to '/Users/rc/Desktop/epydoc/biopython'.
>    [ 1/10] Writing epydoc.css
>    [ 2/10] Writing Bio-module.html
>    [ 3/10] Writing indices.html
>    [ 4/10] Writing trees.html
>    [ 5/10] Writing help.html
>    [ 6/10] Writing frames.html
>    [ 7/10] Writing toc.html
>    [ 8/10] Writing toc-everything.html
>    [ 9/10] Writing toc-Bio-module.html
>    [10/10] Writing index.html
>
> _______________________________________________
> BioPython mailing list  -  BioPython at biopython.org
> http://biopython.org/mailman/listinfo/biopython

-- 
Frédéric Sohm
Equipe INRA U1126 "Morphogenèse du système nerveux des Chordés"
UPR 2197 DEPSN, CNRS
Institut de Neurosciences A. Fessard
1 Avenue de la Terrasse
91 198 GIF-SUR-YVETTE
FRANCE
Phone: +33 (0) 1 69 82 34 12
Fax:+33 (0) 1 69 82 34 47