Python Snippets

Using pass

pass is the “no-op” statement in Python. It can be used in blocks where no action is to be taken; it is only required because Python uses whitespace to delimit blocks:

if x < 0:
    print 'negative!'
elif x == 0:
    # TODO: put something
    pass
else:
	print 'positive!'

It’s common to use pass as a place-holder in code while working on a new piece of functionality:

def f(x, y, z):
    # TODO: implement this function!
    pass

Exceptions handling

Handling Python errors or exceptions gracefully is an important part of building robust programs. In data analysis applications, many functions only work on certain kinds of input.

Example: Python’s float function is capable of casting a string to a floating point number, but fails with ValueError on improper inputs:

In [343]: float('1.2345')
Out[343]: 1.2345
In [344]: float('something')

ValueError                                Traceback (most recent call last)
<ipython-input-344-439904410854> in <module>()
----> 1 float('something')
ValueError: could not convert string to float: something

Using try and except

Suppose we wanted a version of float that fails gracefully, returning the input argument. We can do this by writing a function that encloses the call to float in a try/except block:

def attempt_float(x):
    try:
        return float(x)
    except:
        return x

The code in the except part of the block will only be executed if float(x) raises an exception:

In [346]: attempt_float('1.2345')
Out[346]: 1.2345

In [347]: attempt_float('something')
In [348]: 'something'

In [350]: attempt_float((1, 2))

TypeError                                 Traceback (most recent call last)
<ipython-input-350-9bdfd730cead> in <module>()
----> 1 attempt_float((1, 2))
TypeError: float() argument must be a string or a number

You can catch multiple exception types by writing a tuple of exception types:

def attempt_float(x):
    try:
        return float(x)
    except (TypeError, ValueError):
        return x

Using else and finally

f = open(path, 'w')


try:
    write_to_file(f)
except:
    # executes only if the 'try' block fails
    print 'Failed'
else:
    # executes only if the 'try' block succeeds
    print 'Succeeded'
finally:
    # executes always
    f.close()

Use a dict to replace values in a Series

df = DataFrame({
    'grade': list('ABC' * 4),
    'val': np.random.randn(12)}
)

lookup = {
    'A': 'Excellent',
    'B': 'Satisfactory',
    'C': 'Improve'
}

df['grade_desc'] = df['grade'].map(lookup)

Export a dict as a json

with open('dest.json', 'w') as f:
	f.write(json.dumps(my-dictionary))

Check dir() for objects in the environment

[x for x in dir() if '<pattern>' in x]

Flatten a list of lists

# using Comprehensions
list_flat = [item for sublist in list_nested for item in sublist]

# using a function
from more_itertools import flatten
flatten(list_nested)

Read UNIX timestamps (and convert them to IST)

• The choice of unit= below depends on the granularity of the UNIX timestamp.
• Check here for details

df['pandas_ts'] = \
(pd
 .to_datetime(df['unix_ts'], unit='ms')
 .map(lambda x: x.tz_localize('UTC').tz_convert('Asia/Kolkata'))
)

Cartesian Product of two or more lists.

X = list('xyz')
A = list('abc')
P = ...
[(x, a) for x in X for a in A for p in ...]

Useful pd.Series() methods

method	syntax	action
between	s.between(left, right, inclusive=True)	Return boolean Series equivalent to left <= series <= right. NA values will be treated as False
corr	s.corr(other, method='pearson', min_periods=None)	Compute correlation with other Series, excluding missing values. Method is one of 'kendall', 'spearman', 'pearson'
kurt	s.kurt()	kurtosis over requested axis
skew	s.skew()	skewness over requested axis
nlargest	s.nlargest(10)	Return the largest n elements.
nsmallest	s.nsmallest(10)	Return the smallest n elements.
quantile	s.quantile([.25, .5, .75])	Return value at the given quantile
nunique	s.nunique()	Return number of unique elements in the object.
sample	s.sample(n or frac, replace, random_state)	Return n or frac% of items, with or without replacement using a seed for the random number generator
where	s.where(cond, else)	Return an object of same shape as self, whose entries are from self where cond is True and from other where cond is False.
interpolate	s.interpolate(method, axis)	Interpolate values according to different methods (such as 'nearest', 'linear', 'quadratic', 'polynomial')
idxmax		Find the index of the largest value

Copy/Paste/Move Files & Folders

import shutil

# copy a file
shutil.copy(src, dst) 

# copy a directory
shutil.copytree(src, dst)

# move file or directory
shutil.move(src, dst)

Today's date to use in filenames

import datetime
str(datetime.datetime.now().date())

# or
pd.Timestamp.today()

To avoid unalignable indexes before join/merge

• Find a UNION of all the indexes in the objects that need to be merged.
• Reindex all the objects with this UNIONd index
• NaNs will be introduced whereever there are missing rows/columns based on that index
• Handle missings as required.

Sort DataFrame by multiple columns

df = df.sort(['col1','col2','col3'], ascending = [1,1,0])

Display an image/Video in Jupyter

from IPython.display import Image, display, SVG, YouTubeVideo

# To display an image
display(Image(url='http://history.nasa.gov/ap11ann/kippsphotos/5903.jpg'))

# To display an SVG
SVG(url='http://upload.wikimedia.org/wikipedia/en/a/a4/Flag_of_the_United_States.svg')

# To display a YouTube Video
YouTubeVideo('link-to-video')

Replace multiple whitespaces with single

' '.join(mystring.split())

Conditional Formatting on DataFrame

# by columns
df.style.background_gradient(cmap='Greens')

# by rows
df.style.background_gradient(cmap='Greens', axis=1)

Remove a file

import os
os.remove('path/to/file')

JavaScript PivotTables in Jupyter

from pivottablejs import pivot_ui
pivot_ui(df)

Creating Pipelines in sklearn

• Usual method of building a classification model using SVM involves
  • Standardization
  • Dimensionality Reduction
  • Model Fitting
  • Scoring

from sklearn.preprocessing import StandardScaler
from sklearn.decomposition import RandomizedPCA
from sklearn.svm import SVC

scaler = StandardScaler()
X_train_scaled = scaler.fit_transform(X_train)
pca = RandomizedPCA(n_components=10)

X_train_pca = pca.fit_transform(X_train_scaled)
svm = SVC(C=0.1, gamma=1e-3)
svm.fit(X_train_pca, y_train)

X_test_scaled = scaler.transform(X_test)
X_test_pca = pca.transform(X_test_scaled)

y_pred = svm.predict(X_test_pca)
accuracy_score(y_test, y_pred)

• Using Pipelines, this can be reduced to ...

from sklearn.preprocessing import StandardScaler
from sklearn.decomposition import RandomizedPCA
from sklearn.svm import SVC
from sklearn.pipeline import make_pipeline

pipeline = make_pipeline(
 StandardScaler(),
 RandomizedPCA(n_components=10),
 SVC(C=0.1, gamma=1e-3),
)

pipeline.fit(X_train, y_train)

y_pred = pipeline.predict(X_test)
accuracy_score(y_test, y_pred)

Grid Search on Pipeline

import numpy as np
from sklearn.grid_search import RandomizedSearchCV

params = {
 'randomizedpca__n_components': [5, 10, 20],
 'svc__C': np.logspace(-3, 3, 7),
 'svc__gamma': np.logspace(-6, 0, 7),
}

search = RandomizedSearchCV(pipeline, params, n_iter=30, cv=5)
search.fit(X_train, y_train)

print search.best_params_
print search.grid_scores_

Fixing Locale Errors

This happens because bash loads locale settings automatically and they might conflict with Pandas' defaults (which change on upgrading)

• Open up the Terminal

• Run open ~/.bash_profile

• On the TextEdit file that opens up, append

  export LC_ALL=en_US.UTF-8
  export LANG=en_US.UTF-8

• Save and quit.

• Run source ~/.bash_profile

Extract all numbers from a string

import re
str_ = '25 is greater than -4'

re.findall(r'\d+', str_)

Month as Text from Number

df.my_date.dt.strftime('%b')

Scatterplot with a Regression Line

sns.regplot(x="X", y = "Y", data=df)

Objects and Memory Locations

x = 'hello'
memloc_1 = id(x)
print memloc_1
print x

x += 'world'
memloc_2 = id(x)
print memloc_2
print x

import ctypes
print ctypes.cast(memloc_1, ctypes.py_object).value
print ctypes.cast(memloc_2, ctypes.py_object).value

Convert TimeDelta to int

# taking the difference of two pd.datetime objects gives a timeDelta object
x_td = x['ts1'] - x['ts2'] 			

x_td_int = x_td/np.timedelta64(1, 'D')

See: np.allclose()

Running t-tests

from scipy.stats import ttest_ind

# Find all booleans/cateogorical variables with 2 levels
catg_and_bools = [x for x in df.columns if df[x].value_counts().count() == 2 and 'target' not in x]

# Test the catg_and_bools against the target
def runTtestAgainstTarget(df=DataFrame(), col='', numr=''):
    """
    Splits a numeric variable into 2 parts based on the values of a categorical
    Performs a ttest on the 2 parts
    """
    a = df.loc[df[col] == df[col].unique()[0], numr]
    b = df.loc[df[col] == df[col].unique()[1], numr]

    tstat, pval = ttest_ind(a, b)

    return {'Variable': col, 'T-statistic': tstat, 'P-value': pval}

DataFrame(map(lambda x: runTtestAgainstTarget(df=df, col=x, numr='target'), catg_and_bools))

Running ANOVA

from scipy.stats import f_oneway

# Find all categorical columns with >2 levels
catg_3 = [x for x in df.dtypes[df.dtypes == object].index.tolist() \
          if df[x].value_counts().count() > 2 and 'target' not in x]

def runANOVA(df=DataFrame(), catg='', numr=''):
    """
    Run ANOVA on a Categorical IV and Numeric DV
    """
    grpd = df.groupby(catg)

    dict_anova_input = {k:grpd.get_group(k).loc[:, numr] for k in grpd.groups.keys()}
    anova_res = f_oneway(*dict_anova_input.values())

    return {'Variable': catg, 'F-value': anova_res[0], 'P-value': anova_res[1]}

DataFrame(map(lambda x: runANOVA(df=df, catg=x, numr='target'), catg_3))

Using where to filter a series

The lambda function returns the value of the series where condition == True, and returns NaNs where False. We chain a dropna() so that the output contains only those values in the Series that satisfy the condition.

pd.Series.where(lambda x: condition).dropna()

bisect_left to find the insertion point in a sorted array

from bisect import bisect_left
import numpy as np

x = np.random.randint(0, 50, 15)
# array([29, 10, 18, 27,  3, 32, 22, 32, 41, 34, 30, 30, 24, 24, 20])

x.sort()
# array([ 3, 10, 18, 20, 22, 24, 24, 27, 29, 30, 30, 32, 32, 34, 41])

# The number fifteen would be inserted between
x[bisect_left(x, 15)] # 18
# and
x[bisect_left(x, 15) - 1] # 10

# Can also be used for quickly searching a number in an array

ParseError when importing large files into Pandas

• Cause 1: too many columns in a particular row

• Remedies

  • Extract a portion of the file (say 250 rows) and find the number of columns and specify usecols= with read_csv
  • Use error_bad_lines=False to skip lines with too many fields

• Cause 2: an EOF character encountererd in a row

• Remedy

  • Use quoting=csv.QUOTE_NONE when calling read_csv

Run bash commands on Python, receive output in a DataFrame

import subprocess as sbp
from io import StringIO
import pandas as pd

run_on_bash = \
lambda i: sbp.check_output("{}".format(i), shell=True).decode('utf-8').strip()

result_ = run_on_bash("""
seq 1 20 | awk 'BEGIN{OFS=","}{print rand(),rand(),rand()}'
""")

pd.read_csv(StringIO(result_), header=None)

Using Python-env with Hydrogen on Atom

# create env, activate
conda create -n py3-env python=3.6 pandas scikit-learn seaborn 
source activate py3-env

# pass it to ipython
python -m ipykernel install --user --name py3-env

After you run these two lines and restart Atom, you will be prompted to choose which environment you use when evaluating code using Hydrogen.

Add/Remove Kernels to IPython/Jupyter (also for use with Atom)

# see installed kernels
jupyter kernelspec list

# remove a kernel
jupyter kernelspec remove <kernel-to-drop>

Installing packages from a running Notebook

import sys

# Conda Packages
!conda install --yes --prefix {sys.prefix} numpy

# pip Packages
!{sys.executable} -m pip install numpy

Aside // Even when installing packages with pip inside an environment, it is better to write python -m pip install <package> than pip install <package>.

.translate() in Python3

The translate method now requires a table mapping ordinals to be replaced to the replacements. This table could be a dictionary mapping Unicode ordinals (to be replaced) to Unicode ordinals, strings, or None (replacements). The following code can be used to remove all punctuation:

import string
remove_ = str.maketrans(dict.fromkeys(string.punctuation))
cleaned_str = dirty_str.translate(remove_)

ModuleNotFoundError when running scripts that use local modules

Python tries to look for modules on the system path and raises this error when it doesn't find it. To solve this, update the path as:

import os
import sys

if __name__ == '__main__':
	# Set project root to the path where the local module exists
	PROJECT_ROOT = os.getcwd()
	
	# Add it to the system path
	sys.path.append(PROJECT_ROOT)
	
	# Now you can import anything from the local module
	from foo.bar import baz

Setting Formats for Charts

import seaborn as sns
import matplotlib.pyplot as plt
from matplotlib.pylab import rcParams

plt.style.use('seaborn-white')
sns.set_context("talk")

rcParams['figure.figsize'] = 12, 5 
rcParams['font.family'] = 'sans-serif'

font_title = {
    'size': 18, 
    'weight': 200, 
    'name': 'Georgia'
}

font_axes = {
    'size': 16, 
    'weight': 200, 
    'name': 'Verdana'
}

font_text = {
    'size': 14, 
    'weight': 200, 
    'name': 'Verdana'
}

%pylab inline

Making Publication Quality Charts

# set up the canvas, draw the plot
fig, ax = plt.subplots(figsize=(10, 5))
df_.plot.barh(ax=ax)

TITLE_ = "Lorem Ipsum"
XLABEL_ = "Lorem Ipsum"
YLABEL_ = "Lorem Ipsum"
VLINE_AT = 0
VLINE_X_LOW = 
VLINE_X_HIGH = 
INSIGHT_X = 
INSIGHT_Y =


# Title, Labels
# Can also use ax.set(title=, ...)
ax.set_title("{}\n".format(TITLE_), fontdict=font_title);
ax.set_xlabel("\n {}".format(XLABEL_), fontdict=font_axes)
ax.set_ylabel("{}\n".format(YLABEL_), fontdict=font_axes)

# Draw a vertical line, annotate it
ax.vlines(VLINE_AT, VLINE_X_LOW, VLINE_X_HIGH, color='green', linestyle='dashed', alpha=0.4)
ax.annotate(s="Avg. Survival %", xy=(VLINE_AT - 0.095 , XHIGH-2), color='darkgreen', fontsize=12)

# Add grid, remove spines
ax.grid(True, linestyle=":", alpha=0.6)
ax.spines['top'].set_visible(False)
ax.spines['left'].set_visible(False)
ax.spines['right'].set_visible(False)
ax.legend(bbox_to_anchor=(1.05, 1))

ax.text(INSIGHT_X, INSIGHT_Y, 
        """Almost half the people on the ship were \nin the 20-29 age group.
        \nApparently, this group was the least fortunate
        """, 
        fontdict=font_text)

plt.savefig("reports/figures/{}.png".format("-".join(TITLE_.split(" "))), bbox_inches='tight', pad_inches=0.5)

Directory Sizes in UNIX

du -h -d 1 [PATH]

• the -h switch returns human-readable file sizes (in MB)
• the -d switch limits the depth of directories to 1

Check available (free) RAM in Unix

free -m

Run Jupyter in the background

jupyter lab --allow-root --ip 0.0.0.0 --port 8008 &> /dev/null &

# get the token
jupyter notebook list

# stop a kernel (using the port number)
jupyter notebook stop --NbserverStopApp.port=8008

Copy a file into a running docker container

# get the container id
docker ps -a

# copy file 
docker cp [SRC] container_id:[DEST]

Format floats for print()

print("Dataset has {:.2f}% duplicate records.".format(100*(df_.shape[0] - df_.drop_duplicates().shape[0])/df_.shape[0]))

Parallelize for-loops

import multiprocessing
from sklearn.externals.joblib import delayed, Parallel

CPUs = multiprocessing.cpu_count()

result = \
Parallel(n_jobs=CPUs, verbose=3)(
    delayed(my_function)
    (*args, **kwargs) for i in iterable
)

# example
# Parallel(n_jobs=2)(
# 	delayed(sqrt)
#	(i) for i in [4, 9, 16, 25, 36, 49]
# )

Download a Youtube Playlist as MP3 files

# brew install ffmpeg
# brew link ffmepg
youtube-dl --extract-audio --audio-format mp3 -o "%(title)s.%(ext)s" [youtube-playlist-tag]

Suppress Warnings

import warnings
warnings.simplefilter('ignore', category=FutureWarning)

Read SPSS files (.sav) into Python via R

# Dependencies
!conda install -y -c r rpy2 r-foreign

sav_file = "path/to/sav"
csv_file = "path/to/csv"

from rpy2.robjects.packages import importr
pkg_foreign = importr('foreign')

r_df = pkg_foreign.read_spss(sav_file, to_data_frame=True, reencode=True)
r_df.to_csvfile(csv_file)

Round integers to nearest 10 (useful with Binning) with round(x, -1)

numeric_col = 'foo'
num_bins = 5
LL = 0
UL = round(df.loc[: 'numeric_col'].max(), -1)


BINS = np.linspace(LL, UL, num_bins)
LBLS = [f"{str(i).zfill(2)}-to-{str(j).zfill(2)}" for i, j in zip(BINS[:-1], BINS[1:])]

srs_binned = df.loc[:, numeric_col].pipe(pd.cut, bins=BINS, labels=LBLS)
srs_binned.value_counts(normalize=True)

Chart Formatting v1.0

import matplotlib.pyplot as plt
import seaborn as sns
import altair as alt

from ipywidgets import interactive, Dropdown

sns.set_style("whitegrid")
sns.set_context("talk")

plt.rcParams['figure.figsize'] = 12, 5 
plt.rcParams['font.family'] = 'monospace'

%matplotlib inline

def format_plot(ax):
    """
    Modify the font dicts for the design language you're following
    
    Titles and axes labels 
    - should be set before calling this function
    - here they will be spaced away from the chart
    
    Text, annotations etc. should also be set before 
    See: ax.annotate, ax.text, ax.vlines, ax.hlines ...
    """
    font_title = {
        'size': 20, 
        'weight': 600, 
        'name': 'monospace'
    }

    font_axes = {
        'size': 14, 
        'weight': 'bold', 
        'name': 'monospace'
    }

    ax.grid(True, linestyle=":", alpha=0.6)
    sns.despine(ax=ax, left=True)

    if ax.get_legend():
        ax.legend(bbox_to_anchor=(1.1, 1))
    
    ax.set_title(f"\n\n{ax.get_title().title()}\n", fontdict=font_title)
    ax.set_xlabel(f"\n{ax.get_xlabel().title()} ➞", fontdict=font_axes)
    ax.set_ylabel(f"{ax.get_ylabel().title()} ➞\n", fontdict=font_axes)

Change number format for plot axes

# Get thousands separator 
ax.set_yticklabels([f'{x:,}' for x in ax.get_yticks().tolist()])

# Format as %
ax.set_xticklabels([f'{x:.0%}' for x in ax.get_xticks().tolist()])

Store pwd as hidden file, get it on clipboard

cat ~/.pwds/.gw | tr -d '\n' | pbcopy

Make seaborn annot text larger

sns.set(font_scale=1)
sns.heatmap(df_, annot=True)

Limit output to a few rows when printing a DataFrame

pd.set_option("display.max_rows", 20)

Handy Aliases

• Put these in your .bashrc or .zshrc

alias cel='conda env list'

alias cact='function _f0(){conda activate $1;};_f0'
# usage: cact dataviz

alias cdeac='conda deactivate'

alias jlab='function _f1(){nohup jupyter lab --no-browser --allow-root --ip "*" --port $1 &;};_f1'
# usage: jlab 8800

alias jnl='jupyter notebook list'

alias jstop='function _f2(){jupyter notebook stop --NbserverStopApp.port=$1;};_f2'
# usage jstop 8800

Setting up ZSH + iTerm2

• Follow https://medium.freecodecamp.org/jazz-up-your-zsh-terminal-in-seven-steps-a-visual-guide-e81a8fd59a38
• Customize Agnoster https://github.com/agnoster/agnoster-zsh-theme
• Remove machine name from prompt https://stackoverflow.com/questions/28491458/zsh-agnoster-theme-showing-machine-name

Remove redundant (and annoying) files

find . -name '*.pyc' -delete
find . -name '__pycache__' -delete

Using Hydrogen with Atom to run Python code in-line like Jupyter

conda activate my-env
conda install ipykernel
python -m ipykernel install --user

Using DataClasses

• code generator that removes boilerplate from Class definitions
• essentially still a flexible data and methods holder
• use the @dataclass decorator with params
• by default, it is
  • mutable (and hence unhashable)
  • unordered
  • but, these defaults can be overridden using the frozen and order params
• Read more here

# Example 1
from dataclasses import dataclass, asdict, astuple, replace, field
@dataclass
class Color:
	hue: int
	saturation: float
	lightness: float = 0.5
	
c = Color(120, 4.2)
c
c.lightness
replace(c, hue=120)
asdict(c)

# Example 2
@dataclass(frozen=True, order=True)
class Color:
	hue: int
	saturation: float
	lightness: float = 0.5

list_colors = [Color(10, 2.0), Color(1, 90.5), Color(120, 45.2), Color(45, 77.8), Color(45, 77.8)]
sorted(list_colors)
set(list_colors) # will ignore dups

Using Jinja2 Templates

• Templating language
• In a nutshell, fills placeholders with text
• Templates are text files with {{a-variable}}
• We fill or render the template by passing data to variables
• Basic Usage

mkdir templates
touch templates/namaste.txt
echo 'Namaste, {{name}}!' > namaste.txt

from jinja2 import Environment, FileSystemLoader, Template
fsl = FileSystemLoader('./templates')
env = Environment(loader=fsl)
template_1 = env.get_template('namaste.txt')
template_1.render(name='Dushyant')

# or 
template_2 = Template("Hello {{name}}!")
template_2.render(name='Dushyant')

• Conditionals and Loops

# Conditionals
{% if x > 0 %}
	X is positive
{% else %}
	X is Negative
{% endif %}

# Looping
{% for color in colors %}
	{{ color }}
{% endfor %}	

• Templates can be combined
  • If you have header.html, body.html, you can call them in an index.html with include

<HTML>
	{% include 'header.html' %}
	<BODY>
	{% include 'body.html' %}
	</BODY>
</HTML>

Create combinations with itertools

• useful to generate search grids or test-cases

from itertools import product, permutations, combinations

for t in product('ABC', 'DE', 'xyz'):
	print(t)
	
# Generate nPm
for t in permutations('HELLO', 2):
	print(t)

# Generate nCm
for t in combinations('HELLO', 2):
	print(t)

Writing robust Python code

• Write docstrings with examples, check with doctest
• Detect common errors with pyflakes
• Add type checking with mypy
• Run unit tests with pytest and hypothesis

python3 -m pyflakes my-module.py
mypy my-module.py
pytest my-module.py

Convert 1D numpy array to 2D

x = np.linspace(start=0, stop=1, num=10**3)
X = x[:, np.newaxis]
print(x.ndim, X.ndim)

Jupyter Widgets: Passing fixed arguments to function under interact

• An interactive viz. is created as interact(func, par_1=widget_1, ...)
• Here, func usually takes values from the widgets like Dropdowns or Sliders
• Sometimes, we want to pass values not taken from widgets (ex. a dataframe or a sqlite connection)
• Then, we use the fixed pseudo-widget

from ipywidgets import Dropdown, Slider, interactive, fixed

def f(x, y, kwargs):
    '''
    '''
    result = ... kwargs['a'] ...
    return result
    
interactive(f,
	    x=Dropdown(...),
	    y=Slider(...),
	    kwargs=fixed({'a': a, 'b': b}))

Using scp to transfer data between local machine and remote

scp -r path-to-source path-to-destination

• path to a remote directory will be built as USERNAME@REMOTE-MACHINE-IP:path/to/directory

Exiting a program during execution

import os
import sys

if not os.path.exists('config.ini'):
    print('Could not find config file.\nPlease ensure config.ini exists and try again.')
    sys.exit()

Find files and perform actions

• Use the bash find command
• Syntax: find DIRECTORY -type xxx -size xxx -iname "xxx" -exec xxx {} \;

find ./src -type f -name "*.pyc" -exec rm -f {} \; 

Start Jupyter Lab, direct output to file

• works for any command (syntax: nohup <command> &)
• output is redirected to a file nohup.out

nohup jupyter lab --no-browser --allow-root --ip "*" --port 1508 &

Regex over pd.Series

• The following pattern will keep only alphabets and numbers
• Removes all other/special characters

pd.Series(['abcd-1234-##$', 'wxyz-7890-@@&']).replace('[^a-z|0-9]', '', regex=True)

Flatten column names in a Pandas MultiIndex

df.columns = ['_'.join(col).strip() for col in df.columns.values]

Multiprocessing

import multiprocessing

def my_func():
    pass
    
pool = multiprocessing.Pool()
pool.map(my_func, list_of_inputs)

Run a function over a Pandas GroupBy object in parallel using Multiprocessing

from multiprocessing import Pool

def aggregate():
    '''
    Reduces a GroupBy group into a row
    '''
    pass
    
## list(df.groupby('KEY')) returns a list of tuples like (key, group)
## pool.map() --> returns a list 
    
with Pool() as pool:
    list_result = \
    pool.map(func=aggregate,
             iterable=[x[1] for x in list(df.groupby("KEY"))])

df_aggregated = pd.concat(list_result, axis=1).T

Postgres + Pandas

• First, from the Terminal

# Get image
docker pull postgres

# Start a container
# see: https://docs.docker.com/samples/library/postgres/
# options: POSTGRES_USER (default: postgres), POSTGRES_DB (default: postgres), PGDATA (to defined a directory for database files)
docker run --rm -d --name psql \
		   -e POSTGRES_USER=dkhosla \
                   -e POSTGRES_PASSWORD=xxxxxxxx \
		   -e POSTGRES_DB=default \
		   -p 5432:5432 \
		   -v $(PWD):/var/lib/postgresql/data \
		   postgres

# Requirements
pip install pandas==0.24.2
pip install psycopg2-binary
pip install sqlalchemy sqlalchemy-utils

• Then, in Python

from sqlalchemy import create_engine
from sqlalchemy_utils import create_database, database_exists

config = {
    'POSTGRES_USER': 'dkhosla',
    'POSTGRES_PASSWORD': 'xxxxxxxx',
    'HOST': 'localhost',
    'PORT': 5432,
    'POSTGRES_DB': 'default',
}

# Connect to the default DB 
str_connection_1 = "postgresql://{POSTGRES_USER}:{POSTGRES_PASSWORD}@{HOST}:{PORT}/{POSTGRES_DB}".format(**config)
engine = create_engine(str_connection_1)

# Create more databases if needed
str_connection_2 = "postgresql://{POSTGRES_USER}:{POSTGRES_PASSWORD}@{HOST}:{PORT}/data_raw".format(**config)

if not database_exists(str_connection_2):
    create_database(str_connection_2)
    engine_2 = create_engine(str_connection_2)

# Read data from text files, load into DB
df = pd.read_csv(...)
df.to_sql(
    'table_name', 
    con=engine, 
    if_exists='replace', 
    index=False, 
    method='multi', 
    chunksize=10**5
)

# PS: This should work for DataFrames under 10M rows.
# For larger dataframes (More than 10**7 rows,) try:

def psql_insert_copy(table, conn, keys, data_iter):
    """
    """
    dbapi_conn = conn.connection
    with dbapi_conn.cursor() as cur:
        s_buf = StringIO()
        writer = csv.writer(s_buf)
        writer.writerows(data_iter)
        s_buf.seek(0)

        columns = ', '.join('"{}"'.format(k) for k in keys)
        if table.schema:
            table_name = '{}.{}'.format(table.schema, table.name)
        else:
            table_name = table.name

        sql = f'COPY {table_name} ({columns}) FROM STDIN WITH CSV'
        cur.copy_expert(sql=sql, file=s_buf)

(df
 .rename(columns=lambda x: x.lower())
 .to_sql(
    'table_name',
    con=engine, 
    if_exists='replace', 
    index=False, 
    method=psql_insert_copy,
    chunksize=10**6))
    
# This took ~10mins to load a 3GB+ file (10**8 rows) into the DB.

# PS: 
# Postgres works with lowercase database and table names only.
# Ensure that you don't use uppercase or special characters.

Useful functions -

# Check if database exists
database_exists(str_connection)

# List tables in a database
engine.table_names()

# Create table
engine.execute("""
CREATE TABLE test_1 (
    col_1 SERIAL PRIMARY KEY, 
    col_2 VARCHAR(255)
)
""")

# Insert values from a DataFrame in a table
my_df.to_sql('table_name', con=engine, if_exists='append', index=False)

# Drop a table
engine.execute("DROP TABLE <table_name>")

Print numbers as f-strings with thousands separators

num = 10000000
print(f"{num:,d}")
# 10,000,000

Get Project Root Directory path from any Python file

import os
import sys

# Location of file being executed
absFilePath = os.path.abspath(__file__)
print(absFilePath)

# Go up one level with os.path.dirname
fileDir = os.path.dirname(os.path.abspath(__file__))
print(fileDir)

# Two levels up 
parentDir = os.path.dirname(fileDir)
print(parentDir)

# Now, add the module you need to PYTHONPATH for easy imports
sys.path.append(parentDir)

Number Formats for DataFrames

df['amount'].style.format('${0:,.2f}')

# Different styles for each column
format_dict = {'sum':'${0:,.0f}', 
	       'date': '{:%m-%Y}', 
	       'pct_of_total': '{:.2%}'}
	       
df.style.format(format_dict).hide_index()

# Highlight numbers
(df
 .style
 .format(format_dict)
 .hide_index()
 .highlight_max(color='lightgreen')
 .highlight_min(color='#cd4f39'))
 
 # Excel-like Conditional Formats
 (df
 .style
 .format(format_dict)
 .background_gradient(subset=['sum'], cmap='BuGn'))

Install 3rd Party Software on Mac OS

sudo spctl --master-disable

List of tables in a Sqlite DB as pandas Series

import sqlite3
import pandas as pd

conn = sqlite3.connect("my.db")

srs_tables = \
pd.Series([i[0] for i in 
           (conn
            .cursor()
            .execute("SELECT name FROM sqlite_master WHERE type='table';")
            .fetchall())
          ])

Translate all special characters to underscores

• Useful when cleaning up column names

import string

# create translation table
tr_punctuation_to_underscores = str.maketrans(string.punctuation, "_" * len(string.punctuation))

# apply to column names
pd.Series(df.columns).map(lambda i: i.translate(tr_punctuation_to_underscores))

Visualize data in 2-dimensions using PCA, TSNE, Isomap

• Useful especially in classification problems
• Helps in understanding
  • if the classes are separable
  • what the decision boundary would look like (and hence whether a linear or non-linear kernel is appropriate)
• In the examples below,
  • X_scaled is the array of independent variables (with outliers removed and standardization done.)
  • y is the dependent variable (category labels)

from sklearn.decomposition import PCA
from sklearn.manifold import Isomap, TSNE

# 1. Principal Components Analysis

pca = PCA(n_components=2)
pca.fit(X_scaled)
evr = pca.explained_variance_ratio_.sum().round(2)

(pd.DataFrame(
    data=pca.transform(X_scaled), 
    columns=['Comp_1', 'Comp_2'])
 .plot.scatter(x='Comp_1', 
               y='Comp_2', 
               c=[i for i in y],
               title=f'\nExplained Variance: {evr:.0%}\n'));

# 2 - Isomap

iso = Isomap(n_components=2)
(pd.DataFrame(data=iso.fit_transform(X_scaled), 
           columns=['Comp_1', 'Comp_2'])
 .plot
 .scatter(x='Comp_1', 
          y='Comp_2', 
          c=[i for i in y]))

# 3 - TSNE

tsne = TSNE(n_components=2)
(pd.DataFrame(tsne.fit_transform(X_scaled), 
              columns=['Comp_1', 'Comp_2'])
 .plot
 .scatter(x='Comp_1', 
          y='Comp_2', 
          c=[i for i in y]));

Write DataFrames as Excel Files

# create the xlsx
df_1.to_excel(f"{path_to_data}/Output/Predictions.xlsx", sheet_name='input')

# adding sheets
with pd.ExcelWriter(f"{path_to_data}/Output/Predictions.xlsx", mode='a') as writer:
        df_2.to_excel(writer, sheet_name='intermediate')
	df_3.to_excel(writer, sheet_name='output')

• Browse https://xlsxwriter.readthedocs.io/examples.html for conditional formatting, inserting images etc.

IPywidets "Play" for animation

import numpy as np
import pandas as pd
from ipywidgets import interactive, Play

df = pd.concat([
    pd.Series(np.random.random(size=1000), name=str(i)) 
    for i in range(1965, 2011)
], axis=1)

play = Play(
    interval=700,
    value=1965,
    min=1965,
    max=2010,
    step=1,
    description="Press play",
    disabled=False
)

def f(year):
    """
    Plot histogram of data for `year`
    """
    (df
     .loc[:, str(year)]
     .plot
     .hist(bins=20, title=f"For {year}", figsize=(8, 5), ylim=(0, 100)))

interactive(f, year=play)

Setting up Atom for DS Development

1. Install Atom from https://atom.io/ (Unzip, move app to Applications, run it once)
2. Run which atom to confirm you have apm installed (Atom Package Manager)
3. Create a conda environment
4. Activate ipykernel
5. Launch Atom

# Create conda env, install dependencies
conda update -n base -c defaults conda
conda create -y -n atom-pyds python=3.6
conda activate atom-pyds
conda install -y -c conda-forge jupyterlab seaborn altair statsmodels scikit-learn ipywidgets xlrd graphviz
conda install -y -c conda-forge ipykernel flake8 autopep8

# Install Atom packages
apm install hydrogen platformio-ide-terminal atom-file-icons minimap autocomplete-python-jedi linter linter-flake8 python-autopep8

# Activate ipykernel
python -m ipykernel install --user

# Launch Atom (from activated env)
atom .

Note: Jedi works with python=3.6 by default. If your env has 3.7 or 3.8, check this for a fix.

Remove Atom

Put the following commands in a bash script and run it.

rm -rf ~/.atom
rm -rf /usr/local/bin/atom
rm -rf /usr/local/bin/apm
rm -rf /Applications/Atom.app
rm -rf ~/Library/Preferences/com.github.atom.plist
rm -rf "~/Library/Application Support/com.github.atom.ShipIt"
rm -rf "~/Library/Application Support/Atom"
rm -rf "~/Library/Saved Application State/com.github.atom.savedState"
rm -rf ~/Library/Caches/com.github.atom
rm -rf ~/Library/Caches/Atom

UnicodeDecodeError in Pandas' read_csv

• Errors s.a. 'utf-8' codec can't decode byte xxxx in position yy,
• Cause: non-Latin characters in file
• Solution:
  • Use engine='python' instead of the default engine='c'
  • Use appropriate encoding from https://docs.python.org/2.4/lib/standard-encodings.html
  • For example, encoding="iso8859_7" for Greek
  • Finally, use transliterate.translit(str, reversed=True)

ModuleNotFound errors in Jupyter

• You've installed a new package from within the notebook, and from the terminal
• It shows up in pip list and conda list
• Yet, inside the notebook, module cannot be found?
• CAUSE: Notebook started with the wrong kernel.
• TEST: Run sys.executable and check if you're using the right environment.
• FIX: Run

conda activate my-env
python -m ipykernel install --name my-new-kernel

• Select my-new-kernel from the dropdown in Jupyter

Correlation between categoricals

# 1. Chi-squared
# --------------
from itertools import product
from scipy.stats import chi2_contingency
import pandas as pd

list_categoricals = df.select_dtypes(include=object).columns.tolist()

def get_chi2(a, b, df):
    """
    """
    obs = pd.crosstab(df.loc[:, a], df.loc[:, b])
    chi2, pval, _, _ = chi2_contingency(observed=obs)
    return chi2, pval

df_chi2 = \
pd.DataFrame([
    (i,j, *run_chi2(i,j)) 
    for i, j in product(list_categoricals, 
                        list_categoricals)
    if i != j
], columns=['col_1', 'col_2', 'chi2', 'pvals'])

# 2. Cramer's V
# --------------
def get_cramers_v(a, b, df):
    """
    Returns Cramer's V for given pd.Series
    """
    x, y = df.loc[:, a], df.loc[:, b] 
    confusion_matrix = pd.crosstab(x,y)
    
    chi2 = chi2_contingency(confusion_matrix)[0]
    n = confusion_matrix.sum().sum()
    phi2 = chi2/n
    r,k = confusion_matrix.shape
    phi2corr = max(0, phi2-((k-1)*(r-1))/(n-1))
    rcorr = r-((r-1)**2)/(n-1)
    kcorr = k-((k-1)**2)/(n-1)
    
    cramers_v = np.sqrt(phi2corr/min((kcorr-1),(rcorr-1)))
    
    return cramers_v

df_cramers_v = \
pd.DataFrame([
    (i,j, get_cramers_v(i,j, df=df))
    for i, j in product(list_categoricals, 
                        list_categoricals)
    if i != j
], columns=['col_1', 'col_2', 'cramers_v'])

Read all sheets of an Excel workbook into a dict of DataFrames

import pandas as pd
import xlrd

str_path_to_excel_file = 'home/dir/data/workbook.xlsx'

# Read all sheets using sheet_name=None, and capture their names
list_sheet_names = list(pd.read_excel(str_path_to_excel_file, sheet_name=None).keys())

# Read the sheets you want into a dict of dfs
dict_dfs = pd.read_excel(str_path_to_excel_file, sheet_name=list_sheet_names[1:])

Password-less SSH access to remote machines

# If you don't already have a public key, create it
ssh-keygen -t rsa -C "USER@EMAIL"

# Copy it to the remote machine 
cat ~/.ssh/id_rsa.pub | ssh USER@REMOTE.MACHINE 'cat >> ~/.ssh/authorized_keys'

# SSH into the remote machine without needing to use a password
ssh USER@REMOTE.MACHINE

Sample docker-compose script for DS

• Contents of docker-compose.yml

---
version: '3'
services:
  ds-dev:
    container_name: dev-x
    image: dushyantkhosla/py38-ds-dev:latest
    ports:
      - "9000:9000"
    restart: on-failure
    network_mode: "host"
    tty: true
    volumes:
      - /dir-on-host-0:/dir-in-container-0
      - /dir-on-host-1:/dir-in-container-1

Then,

• Start the container with docker-compose up -d
• Attach to the running container docker exec -it dev-x /bin/zsh
• Start Jupyter nohup jupyter lab --no-browser --allow-root --ip "*" --port 9000 &
• Get the token jupyter notebook list

Convert FLAC to MP3 using ffmpeg and multiprocessing

from pathlib import Path
import subprocess
from multiprocessing import Pool, cpu_count


path_to_dirs = "/FLACs/"
path_to_dest = "/FLACs-to-MP3s/"

list_paths_flacs = [x for x in Path(f"{path_to_dirs}").glob(f"**/*.flac")]

def convert_flac_to_mp3(path_flac):
    """
    """
    path_dest_dir = Path(path_flac.parent.as_posix().replace(path_to_dirs, path_to_dest)) 
    try:
        if not path_dest_dir.exists():
            path_dest_dir.mkdir(parents=True)
        else:
            pass
        file_mp3 = path_flac.as_posix().replace(path_to_dirs, path_to_dest).replace(".flac", ".mp3")
        subprocess.call(['ffmpeg', '-i', path_flac.as_posix(), '-ab', '320k', '-id3v2_version', '3', file_mp3])
    except:
        print(f"Failed for {path_flac.as_posix()}")

with Pool(cpu_count()) as p:
    p.map(convert_flac_to_mp3,
          list_paths_flacs)

Sync files on local and remote machine with rsync

• Reference

# man rsync
# Syntax: rsync OPTIONS SOURCE DESTINATION
# -r = recursive
# -v = verbose
# -h = human-readable
# --progress
# --update = only transfer missing or newer files

# Example:
rsync -rvh --progress --update /home/user/path-to-local-dir ubuntu@192.168.1.5:/home/ubuntu/path-to-remote-dir

Add data labels to Matplotlib Barchart

ax = df[col].value_counts(normalize=True).plot.barh()

[ax.text(x=p.get_width() * 1.05, 
         y=p.get_y(), 
         s=f"{p.get_width():.0%}", 
         va='bottom', 
         ha='left', 
         fontdict={'size': 12, 'name': 'monospace', 'weight': 'bold'},) 
 for p 
 in ax.patches]

Easy pyspark on local using Docker, Parquet Files and SQL

First,

docker pull jupyter/pyspark-notebook
docker run -it -p 8010:8010 -v /path/to/projects/project_x:/home/jovyan/work/project_x jupyter/pyspark-notebook

Then,

from pyspark.sql import SparkSession

session = (SparkSession
           .builder
           .master("local")
           .appName("myapp")
           .getOrCreate())
	   
list_parquets = [x for x in os.listdir(path_data_raw) if x.endswith('parquet')]

print(f"Creating Temporary Views: ")

for pq in list_parquets:
    session.read.parquet(f"file:///{path_data_parquet}/{pq}").createOrReplaceTempView(f"table_{pq.split('.')[0]}")
    
df_1 = \
(session.sql(f"""
SELECT 
    TBL1.col_1,
    TBL1.col_2,
    TBL2.col_3,
    TBL2.col_4,
    TBL3.col_5,
    TBL4.col_6
FROM       table_1 TBL1    
LEFT JOIN  table_2 TBL2 ON (TBL1.pkey = TBL2.pkey)
LEFT JOIN  table_3 TBL3 ON (TBL1.pkey = TBL3.pkey) 
WHERE 1=1
AND clause_1
AND clause_2
""")
 .toPandas()
 .drop_duplicates())

Easy execute time in JupyterLab (without extensions)

try:
    %load_ext autotime
except:
    !pip install ipython-autotime
    %load_ext autotime

# To stop cell timing, use:
%unload_ext autotime

Make Publication Quality Barplots with Confidence Intervals

def make_barplot(data, x, y, ci, ylabel, title, fig_size=(15, 7), palette=None, hue=None, xlimit=1, srs_y=None, show_table=True, sort_order='values', single_color=None):
    """
    fig_size = tuple, controls the width, height of the chart
    kwargs   = dict,  optional for `hue` and `palette`
    srs_y    = pd.Series, to calculate population mean and plot vline
    show_table = bool, display or hide counts + percentages
    """
    srs_x = data.groupby(y)[x].mean()
    list_order = srs_x.sort_values().index.tolist()[::-1] if sort_order == 'values' else srs_x.sort_index().index.tolist()[::-1]
        
    if show_table:
        display(data
                .stb.freq([y])
                .assign(percent = lambda fr: fr['percent'].divide(100))
                .set_index(y)
                .loc[:, ['count', 'percent']]
                .rename(columns={'count': '# LAU', 'percent': '% LAU'})
                .join(data.groupby(y)[x].mean().rename('% Reached'))
                .applymap(lambda i: f"{i:.2%}" if i < 1 else f"{int(i):,d}"))
    
    _, ax = plt.subplots(figsize=fig_size)

    sns.barplot(data=data,
                x=x, 
                y=y, 
                palette=palette if palette is not None else None,
                color=single_color if single_color is not None else None,
                alpha=0.8,
                order=list_order,
                ax=ax,
                hue=hue if hue is not None else None,
                ci=ci if ci is not None else None
               )

    ax.set_xlim(0, xlimit)
    ax.set_xticklabels([f'{x:.0%}' for x in ax.get_xticks().tolist()])
    ax.set_xlabel("% Adoption Index")

    ax.set_ylabel(ylabel)

    ax.set_title(title)

    ax.vlines(x=srs_y.mean(), 
              ymin=data[y].nunique(), 
              ymax=-1, 
              colors='grey', 
              linestyles='dashed')

    [ax.text(
        x=p.get_width() * 1.02, 
        y=p.get_y() * 1.1, 
        s=f"{p.get_width():.1%}", 
        va='top', 
        ha='left', 
        fontdict={'size': 12, 'name': 'monospace', 'weight': 'bold'}) 
     for p 
     in ax.patches]
    
    ax.annotate(text=f'Mean\n{srs_y.mean():.1%}', xy=(1.02 * srs_y.mean(), -0.75), fontsize=10)

    format_plot(ax)