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

[Peter Cock]

On Fri, Oct 4, 2019 at 10:31 AM Adam Sjøgren <asjo at koldfront.dk> wrote:
>
> 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".

I personally could work with that - probably easier as I've never
needed "git am" before.

> > 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.

Probably that would only work with pure Python code, compiled C
extensions are more fragile.

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

Using pip for a development installation (where if you change a Python file,
it is live next time something imports the library):

$ pip install -e .

There was an equivalent with $ python setup.py install ... but I forget
the switch right now.

Peter