[Biopython-dev] PEP8 lower case module names?

[João Rodrigues]

Hi everyone,

A bit late for the party but my two cents.

I agree with Eric in that we should take the opportunity to review some
"dark corners" of the code. Regarding what I can contribute to, there are a
lot of changes planned for Bio.PDB that could benefit from a "cleaner
start".

However, and also in line with Michiel, splitting the distribution in
core/extras would be more cumbersome for new users. However, what about
having in the setup file a part where the user can turn on/off installation
of particular parts of the package. This way you can control if you need
the dependencies or not. By default you would install everything as it is
now, but it would give you a larger degree of control.

As for the namespace and lowercase, I don't really have strong arguments,
but I like 'bio'.

Cheers,

João

João [...] Rodrigues
http://nmr.chem.uu.nl/~joao



2012/11/2 Michiel de Hoon <mjldehoon at yahoo.com>

> Hi everybody,
>
> --- On Thu, 11/1/12, Eric Talevich <eric.talevich at gmail.com> wrote:
> > 1. If we're going to change the API substantially, we might
> > as well "do it right". Besides our PEP8 non-compliance, there
> > are some dark, dusty corners of Biopython that we ought to clean
> > up while we're at it -- reorganize the little historical fiefdoms
> > into a coherent structure. We'd call it Biopython 2.
>
> +1.
>
> > 2. Observing BioPerl and BioRuby, it could make sense to
> > split the distribution into multiple, with a sequence- and
> > data-oriented "biopython-core" package and separate packages
> > for, say, 3D structures ("biopython-struct") and perhaps other
> > existing components that have ready
> > maintainers and which the "core" of Biopython doesn't rely
> > on. I don't think we need to fragment the code base much,
> > primarily just extract PDB, SCOP and the other parts that
> > depend on NumPy.
>
> This goes against the "coherent structure" in point 1. What is the
> advantage of splitting the distribution according to whether a module needs
> NumPy or not? I don't see an advantage to the user, and I don't see an
> advantage to the developers either. Already I feel that we need to install
> too many packages to get going with Python in bioinformatics (Python
> itself, NumPy, Matplotlib and its dependencies, Pysam, Cython (needed to
> compile Pysam), ezsetup, perhaps SciPy, Biopython). I find this hard to
> explain to people new to bioinformatics or new to Python. So I would prefer
> to keep one distribution.
>
> We can be more lenient in terms of dependencies, especially those that
> don't occur at compile time.
>
> > 4. Naming: "bio" is clean but might cause problems on
> > Windows? (I wouldn't know, nyah); "bio2" is nearly as clean;
> > "biopy" follows the numpy/scipy convention.
>
> Any problems on Windows will only occur during a transition period, so I
> wouldn't worry about that too much. Perhaps we should check if there would
> be any problems; if they are severe, we could check for an existing
> Biopython installation in setup.py.
>
> bio2 would stay with us forever (well at least until bio3) and is just
> plain ugly, especially to new users who are not aware of the transition.
> Then there is the issue that "bio2" would not be for Python 2 but for
> Python 3.
>
> The "py" is needed in numpy and scipy because otherwise it would be "num"
> and "sci", which is too short. On the other hand, "bio" is used as a prefix
> in lots of words, and can stand on its own. Therefore, hurray for "bio".
>
> > 5. Porting: I, personally, would keep using the old Biopython for
> > everything that's meant to run on Python 2, which is, currently,
> > everything. Biopython2 running on Python 3 would give me an
> > excuse to start using Python 3 for new code. Keeping these
> > separate would be more difficult if the lowercasing were done
> > under the same "Bio" namespace.
>
> Yes that makes sense.
>
> Best,
> -Michiel.
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