[Ifeffit] Larch as python library

[Matt Newville]

Hi Sean,

On Tue, Nov 1, 2016 at 1:39 PM, Sean Fackler <swfackler at lbl.gov> wrote:

> Dear Matt,
>
> I’ve been working to implement Larch functions as a Python library. During
> the implementation I found a number of things I needed to do including:
>
>
You can use Larch functions from Python, of course.   Normally, you'd do
something like

    import larch
    from larch_plugins.xafs import pre_edge, mback



> 1. Identifiying a functions’ python callable name, i.e. _group as a python
> callable function instead of group as the larch function.
>

I'm not sure I understand.  You shouldn't need "a function's python
callable name", you should just need the function.  Maybe I misunderstand.

If you need a larch Group, you should be able to do
    import larch
    agroup = larch.Group(name='mygroupname', xdata = range(100),
label='hello')




>
> 2. The need to pass '_larch = mylarch’ in the said function or I get the
> 'AttributeError: 'NoneType' object has no attribute ‘symtable’ ‘
>
>
Yes, many of the larch plugin functions either require or are much happier
with an instance of a larch session passed in as the '_larch' argument.
It's kind of a feature ;).


> 3. The need to run the script through the Python console as oppose to
> running as a script.
>
>
I'm not sure I understand what this means.  You should be able to run a
python program from any environment.


> You can see my sample script with data attached. Keep in mind I am a
> Python novice. So for point 3 in particular *I don’t understand the
> difference between running some selected code in the Python console and
> running the whole script in the shell *(I am using PyCharm CE). I checked
> my Python interpreter with sys.executable (path) and sys.version_info
> (version) which are the same between the console and interpreter which were
> initial issues I found online. Is the interpreter somehow not seeing the
> xraylarch library?
>

Hmm, that doesn't make a lot of sense to me either.  What errors do you get
when you run your script?

I don't use PyCharm, so maybe that's not seeing all of the modules from
anaconda?   Is PyCharm seeing your  anaconda distribution?

A few comments on your script:
   a) there should be no need to do a os.chdir() to any folder, especially
not to source code folders.
   b) doing   from xxx import *  is bound to lead to confusion.  Import
what you need, and don't import what you don't need.


Finally: 1. Is there an easier way to use the larch functions as a python
> library?
>

Is the above suggestion better?


> 2. Is a larch group basically a python dictionary?
>

Actually, it's basically an empty class:

    class Group:
        def __init__(self, **kws):
             ....

    mygroup = Group()
    mygroup.x = 1
    mygroup.y = 'a string'

even in more detail, it's an empty class.  In most cases it would probably
be OK to substitute almost any class instance as a Group.

In Larch, I tend to make as many things as possible "group-like" so that
accessing elements is easy.


> If so, this could be made clearer in the documentation. I am interested to
> contribute to the documentation if that’s of interest/help.
>
>
Sure!  The docs are definitely in need of some serious work.



> I am running MacOS Sierra 10.12.1 on a mid-2015 15" MacBook Pro with
> Python 2.7.
>
> Ron and Alpha: Maybe you have some ideas to the above points?
>
> Thanks everyone for any help.
>
> Sean
>
>
The attached modified version of your script works for me from a Terminal
(The fit's not very good, yet, but it did run).   On Mac OSX with anaconda,
you probably have to run this as "pythonw import_fit.py"  (note: pythonw,
not python).

Hope that helps,

--Matt
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20161101/107d9f68/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: import_fitMN.py
Type: text/x-python
Size: 2468 bytes
Desc: not available
URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20161101/107d9f68/attachment.py>