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

[Markus Piotrowski]

Am 04.10.2019 um 11:28 schrieb Adam Sjøgren:
>
> 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 warning is mostly intended for end user who didn't properly 
installed their Biopython. As a developer you need to get used to it...

>
>    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'
>

Actually, the top-level import of _aligners, which should be a compiled 
C extension, is indeed a pain. We have this since a few versions and it 
makes testing of many modules, which actually do not use _aligners, more 
complicated. To get rid of it you need to compile Biopython.

Best,
Markus