[Biopython] [PATCH] Use https:// instead of git:// in examples

[Adam Sjøgren]

Peter writes:

> A pull request via GitHub would be easiest for us, but if you have
> philosophical issues with their new ownership, I can understand that.

I can provide a publicly available git repository to pull from instead,
if that is easier than "git am".

> As to the issue at hand, I've had problems both ways round depending
> on the network, but still lean to the git protocol by default.

Ok, I've never seen git:// being open and https:// being closed, but I
don't doubt that all permutations exist. My intention was just to remove
a stumbling block for newcomers.

Speaking of stumbling blocks: I cloned the biopython repo to try and
make a small change (the .fetch() thing we talked about earlier).

What I would usually do is to use "PYTHONPATH=path/to/checkout/of/library python"
while experimenting/developing, but this failed with a warning and an
error about something that couldn't be linked¹.

How do you do development - do you make your changes and go through
"python setup.py install" before trying them out?


  Best regards,

    Adam


¹ The warning:

    /home/adsj/work/biopython/Bio/__init__.py:128: BiopythonWarning: You may be importing Biopython from inside the source tree. This is bad practice and might lead to downstream issues. In particular, you might encounter ImportErrors due to missing compiled C extensions. We recommend that you try running your code from outside the source tree. If you are outside the source tree then you have a setup.py file in an unexpected directory: /home/adsj/work/biopython.
      format(_parent_dir), BiopythonWarning)

  The error:

    ...
        from Bio.SeqIO import write
      File "/home/adsj/work/biopython/Bio/SeqIO/__init__.py", line 390, in <module>
        from Bio.Align import MultipleSeqAlignment
      File "/home/adsj/work/biopython/Bio/Align/__init__.py", line 22, in <module>
        from Bio.Align import _aligners
    ImportError: cannot import name '_aligners'

-- 
 "I trust my family jewels only to Linux"                     Adam Sjøgren
                                                         asjo at koldfront.dk