[Biopython-dev] Small Typo in PDBParser

[Peter]

On Thu, Mar 18, 2010 at 11:33 AM, João Rodrigues <anaryin at gmail.com> wrote:
> Hello All,
>
> There's a small typo in the Bio.PDB PDBParser module. Line 159:
>
> "PDBContructionError" should be "PDBConstructionError"
>
> So that I learn, how do I submit a bug and a patch to the project, such as
> in this case?
>
> Best!

Hi João,

I've you've found a bug in a release, and worked out how to fix it, one
of the first steps would be to try the latest code from the repository to
see if the bug is still there (and if you fix would need changing). In this
case the problem has already been fixed (February 23, 2010), see:

http://github.com/biopython/biopython/commits/master/Bio/PDB/PDBParser.py

For a simple change like this, you can use the command line tool diff
to generate a patch file (see "man diff" for details), which you can then
attach to a bug report on our bugzilla. The basic diff usage would be:

diff original_file.py fixed_file.py > bug_fix.patch

For more complex changes, I would suggest you look at learning git.
If you make a change locally you can get a patch file with this:

git diff > bug_fix.patch

Or, publish the fix to a public copy of the repository (e.g. on github).

See also http://biopython.org/wiki/GitUsage

I hope that helps, and that you'll have more patches for us in future :)

Peter