Python snippets

argparse.py

"""
  test docstring
  https://docs.python.org/3/library/argparse.html#nargs
"""

import argparse, textwrap

if __name__ == '__main__':
    linebreaks=argparse.RawTextHelpFormatter
    descrip=textwrap.dedent(globals()['__doc__'])
    parser = argparse.ArgumentParser(formatter_class=linebreaks,description=descrip)
    parser.add_argument('files',nargs='*',type=str,help='filelist')
    #parser.add_argument('outdir', nargs=1,type=str,help='output directory')
    parser.add_argument("--verbose", help="increase output verbosity",
                    action="store_true")
    #--verbose will set args.verbose=True
    parser.add_argument("-y", "--year", type=str, choices=['2013','2014'],
                    help="fiscal year in database name")
    args=parser.parse_args()
    print('args.files: ',args.files)
    print('args.year ',args.year)

basemap.py

import numpy as np
from mpl_toolkits.basemap import Basemap
from matplotlib import cm
from matplotlib.colors import Normalize
import numpy.ma as ma

context_timer.py

# useful Python snippet
import contextlib,time
@contextlib.contextmanager
def timeit():
    t=time.time()
    yield
    print(time.time()-t,"sec")
    

convert_ascii.py

    comment=''.join([i if ord(i) < 128 else ' ' for i in comment])

datetime.py

import datetime
end=dt.datetime(end_year-1,12,31) + dt.timedelta(days=end_day)
start_date=start.strftime('%Y-%m-%d')
end_date=end.strftime('%Y-%m-%d')
f.attrs['created_on']=time.strftime("%c")

exceptions.py

import traceback

        except TypeError as ex:
            ex_type, ex_val, tb = sys.exc_info()
            print('bummer: ',ex_val)
            print('\nhere is the traceback:\n')
            traceback.print_tb(tb)
            print("python3 reads band_names as bytes, won't split on comma")



using loggin

#https://realpython.com/blog/python/the-most-diabolical-python-antipattern/
#!/usr/bin/env python3
from __future__ import division,print_function
import traceback,sys,logging
logging.basicConfig(filename='example.log',level=logging.DEBUG)

def get_number():
    return int('foo')

def log_traceback2(ex, ex_traceback=None):
    #works under 2.7 and 3.4
    ## if ex_traceback is None:
    ##     ex_traceback = ex.__traceback__
    ## tb_lines = [ line.rstrip('\n') for line in
    ##              traceback.format_exception(ex.__class__, ex, ex_traceback)]
    #print('here is exception: 2.7 -- ',tb_lines)
    logging.exception(ex)

def log_traceback3(ex):
    #3.4 only
    tb_lines = traceback.format_exception(ex.__class__, ex, ex.__traceback__)
    tb_text = ''.join(tb_lines)
    # I'll let you implement the ExceptionLogger class,
    # and the timestamping.
    ## print('here is the exception: 3.4 -- ',tb_text)
    ## print('now with logger')
    logging.exception(ex)

try:
    x = get_number()
except Exception as ex:
    if sys.version > '3':
        log_traceback3(ex)
    else:
        log_traceback2(ex)


and

pdb.set_trace()

ipython_notebook

from IPython.display import Image
EmbedNorth = Image('http://oceancolor.gsfc.nasa.gov/cmsdocs/product_definitions/L3Bins/L3Bins.north.png',width=500)
prob6_9 = Image('figures/prob6_9.png',width=500)
prob6_28 = Image('figures/prob6_28.png',width=500)

cp  ~/Documents/Snagit/prob6_28.png $ecode/notebooks/figures/.

line_profile.py

#http://stackoverflow.com/questions/16074376/how-do-you-get-the-python-profiler-to-work
import cProfile, pstats
pr = cProfile.Profile()
pr.enable()
...
pr.disable()

f = open('x.prof', 'a')
sortby = 'cumulative'
pstats.Stats(pr, stream=f).strip_dirs().sort_stats(sortby).print_stats()
f.close()


#using a contextlib
#http://yt-project.org/doc/_modules/yt/funcs.html

@contextlib.contextmanager
def parallel_profile(prefix):
    r"""A context manager for profiling parallel code execution using cProfile

    This is a simple context manager that automatically profiles the execution
    of a snippet of code.

    Parameters
    ----------
    prefix : string
        A string name to prefix outputs with.

    Examples
    --------

    >>> with parallel_profile('my_profile'):
    ...     yt.PhasePlot(ds.all_data(), 'density', 'temperature', 'cell_mass')
    """
    import cProfile
    from yt.config import ytcfg
    fn = "%s_%04i_%04i.cprof" % (prefix,
                ytcfg.getint("yt", "__topcomm_parallel_size"),
                ytcfg.getint("yt", "__topcomm_parallel_rank"))
    p = cProfile.Profile()
    p.enable()
    yield fn
    p.disable()
    p.dump_stats(fn)

makedirs

import errno

try:
    os.makedirs(the_dir)
except OSError, e:
    if e.errno == errno.EEXIST:
        pass  #not a problem if file exists


or

    if not os.path.exists('output'):
        os.mkdir('output')
    if not os.path.exists('hdf5'):
        os.mkdir('hdf5')

matplotlib.py

import numpy as np
from matplotlib import pyplot as plt
from mpl_toolkits.basemap import Basemap
import numpy.ma as ma

plotdir='{}/{}'.format(os.getcwd(),'plots')
if not os.path.exists(plotdir):
    os.makedirs(plotdir)

fig, ax = plt.subplots(1, 1, figsize = (12, 12) )
out = ax.plot(small_lons, small_lats, 'b+')
ax.set_title()

from matplotlib import cm
from matplotlib.colors import Normalize
import seaborn as sns

    cmap=cm.YlGn  #see http://wiki.scipy.org/Cookbook/Matplotlib/Show_colormaps
    cmap.set_over('r')
    cmap.set_under('b')
    cmap.set_bad('0.75') #75% grey
    vmin= -1.5
    vmax= 1.5
    #
    # tell the colormap what the maximum and minimum
    # values are
    #
    the_norm=Normalize(vmin=vmin,vmax=vmax,clip=False)
    chlor=ma.array(chlor,mask=np.isnan(chlor))

pandas.py

import h5py
import pandas as pd
import pandas as pd

    with  h5py.File(binned_file,'r') as infile:
        root_key=infile.keys()[0]

time_conv.py

from datetime import timedelta

def days_hours_minutes(td):
    days, hours, minutes = td.days, td.seconds // 3600, td.seconds // 60 % 60
    return days,hours,minutes

hours=timedelta(hours=3.4512)
print(days_hours_minutes(hours))

timer.py

from contexttimer import Timer

        with Timer() as t:

toc.rst

• Here is a list
  • Context timer timer.py

unicode.py

#python3 remove all non-ascii characters and replace with _
>>> text=text + 'αβγιορ'
>>> text
'a star is bornαβγιορ'
>>> ''.join([i if ord(i) < 128 else '_' for i in text])
'a star is born______'