[Biophp-dev] Standards

[biophp-dev@bioinformatics.org]

>  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