[Biophp-dev] Standards

[Andrés Pinzón]

Sure niko, i agree, the core of this is "consensus"  so it would be ok if we
could talk to each other, and discuss this and other "features" about the
project. Do u know what's the thing with the IRC?

See u
Andres
PD: Could u please tell me what do u do and why r u involved in this project
(xcusme im a curious person)?
----- Original Message -----
From: <nicos@itsa.ucsf.edu>
To: <biophp-dev@bioinformatics.org>
Sent: Saturday, April 26, 2003 10:33 AM
Subject: Re: [Biophp-dev] Standards


> >  I've been thinking that maybe it would be OK if
> >  we stop for a moment and think about some "standards",i mean,
>
> Good point!
>
> >  1)why don't we try to give some parameters to the code?
> >  and...
>
> Ehmm, I am not sure what you mean with parameters in this context. Could
> you explain?
>
> >  2)Why don't we try to post the code at CVS under other parameters
> > (as someone else already said!)different from developer?
>
> Agreed.  I asked Sean for access to the biophp cvs.  I'll upload my
> modification of Serge's code once I have access.
>
> >  3) Why don't we try to choose what are we gonna develop based on the
> > classes  posted at the BIOPHP web page?
>
> Actually, it would be nice to compare the class structures of Sean (on
> the Biophp page) and Serge (in his code).  It would also be great if
> (another) class diagram was made.  Who is good at these kind of things?
> It will be worth putting some time into the organization and naming
> schemes (on the other hand, personally, I do these things best while
> coding).  As an example, I now came up with the 'parse' class.  Serge
> suggested this should be part of an 'IO' class which seems a very good
> idea (except that I would not what this class should contain).
>
> >
> >  How`s the deal?..............
> >
> >  Ok. As we are supossed to be watching at someone else code, it would
> > be easier to write the code
> >  in a way that everyone can easily interpret, for example:
> >
>
> Coding/layout rules are a good idea, but I would not want to dictate how
> someone else has to code.  Nevertheless, this is a good time to exchange
> ideas and for everyone to promise they will try...
>
> --------------------------------------------------------------------------
--------------
> >  "Rule 1"
> >        -All variables and properties must begin in capital letters as
> > follows:
> >             $Variable
>
> Disagree.  The '$' is perfect to indicate we have a variable. It looks
> rather ugly to me, and I don't remember ever having seen this in php code.
>
> >         ...if the variable or propertie has two or more words, each
> > one must begin the same way, as follows:
> >              $MyVariable
> >              $MySecondVariable
> >         ...and never like:
> >               $My_variable or
> >               $My_Second_Variable
> >         ...that will be the way to name classes and functions (I MEAN
> > WITH UNDERSCORE)!
>
> OK, but then:
>                 $myVariable
>                 $mySecondVariable
>
> >
> --------------------------------------------------------------------------
> ---------------
> >  "Rule 2"
> >        - All "{" or "}" in a loop or function must begin and end in a
> > new line,as follows:
> >
> >          for("whatever")
> >          {
> >                  CODE-HERE;
> >          }
> >
> >          ...and never like this:
> >
> >          for("whatever"){
> >          CODE-HERE;}
> >          ...OR OTHER VARIANT!
> >
>
> Partially diagree.  I like the Linux kernel rules.  Functions and classes
> follow your suggestion, but loops/ifs,etc.have the bracket on the same
line:
>
>             for ('whatever') {
>                   do something;
>             }
>
> Where I also tend to leave out the brackets if there is only a single
> statement.
>
> On a related note: Indentation!  I lately prefer single tabs (everyone
> can adjust their tab size).  Please no mixing of spaces and tabs....
>
> --------------------------------------------------------------------------
-----------------
> > "Rule 3"
> >       -All scripts must begin with a long comment at top as follows:
> >
> >       #######################
> >       #
> >       #  Description, version, author,  etc...
> >       #
> >       #
> >       #######################
> >
> >
>
>
> Lots of work (for the author and the parser).  Why not
> /*
> Description
> Version
> Author
> License
> */
>
>
> --------------------------------------------------------------------------
-----------------
> > I think this is a good idea and can be helpful in the near future! IF
> > U don't agree tell me why please!
> >
>
>
> Best,
>
> Nico
>
>
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