Pandashells
Introduction
For decades, system administrators, dev-ops engineers and data analysts have been piping textual data between unix tools like grep, awk, sed, etc. Chaining these tools together provides an extremely powerful workflow.
The more recent emergence of the "data-scientist" has resulted in the increasing popularity of tools like R, Pandas, IPython, etc. These tools have amazing power for transforming, analyzing and visualizing data-sets in ways that grep, awk, sed, and even the dreaded perl-one-liner could never accomplish.
Pandashells is an attempt to marry the expressive, concise workflow of the shell pipeline with the statistical and visualization tools of the python data-stack.
What is Pandashells?
- A set of command-line tools for working with tabular data
- Easily read/write data in CSV, or space delimited formats
- Quickly aggregate, join, and summarize tabular data
- Compute descriptive statistics
- Perform spectral decomposition and linear regression
- Create data visualizations that can be saved to images or rendered interactively using either a native backend or html.
- Easily integrate with unix tools like curl, awk, grep, sed, etc.
If you work with data using Python, you have almost certainly encountered Pandas, SciPy, Matplotlib, Statsmodels and Seaborn. Pandashells opens up a bash API into the python data stack with command syntax closely mirroring the underlying libraries on which it is built. This should allow those familiar with the python data stack to be immediately productive.
I would also like to call your attention to a related tool by Saul Pwanson: visidata.
Visidata is an interactive terminal-based app that excels at loading/transforming/summarizing tabular data
from the command line.
Installation
Install with pip
Pandashells can be installed with pip, but a few words of caution are in order. First,
you should really use a recent version of pip so you can access wheels on pypi
pip install -U pip. Secondly, if your setup requires building from source rather
than using wheels, you may run into problems with systems libraries being either out of
date or missing. If you encounter these problems, you may want to use conda to install those
dependencies.
Pandashells, no dependencies
Use this option if you want to completely manage your own dependencies. (See requirements section below).
[~]$ pip install pandashells Pandashells console tools
Use this option to install Pandashells and only the console tools dependencies. This will not install the graphics dependencies (matplotlib and friends)
[~]$ pip install pandashells[console]Pandashells full install
Use this option to install Pandashells and all dependencies
[~]$ pip install pandashells[full]Requirements
Pandashells is both Python2 and Python3 compatible. There are no default requirements because some of the tools only require the standard library, and there's no sense installing unnecessary packages if you only want to use that subset of tools. If a particular tool encounters a missing dependency, it will fail with an error message indicating the missing dependency. Below is a list of all imports used across the Pandashells toolkit, and ordered according to install option.
[console]numpy, scipy, pandas, statsmodels, gatspy, supersmoother[full]numpy, scipy, pandas, statsmodels, gatspy, supersmoother, matplotlib, mpld3, seaborn
Important: If you want to use pandashells without interactive visualizations (e. g. on a VM without X-forwarding), but would like to retain the ability to create static-image or html-based visualizations, you may need to configure pandashells to use the Agg backend as follows:
p.config --plot_backend AggOverview
All Pandashells executables begin with a "p." This is designed to work nicely with the bash-completion feature. If you can't remember the exact name of a command, simply typing p.[tab] will show you a complete list of all Pandashells commands.
Every command can be run with a -h option to view help. Each of these help messages will contain multiple examples of how to properly use the tool.
Pandashells is equipped with a tool to generate sample csv files. This tool provides standardized inputs for use in the tool help sections as well as this documentation.
[~]$ p.example_data -hTool Descriptions
| Tool | pip install | Purpose |
|---|---|---|
| p.config | pandashells |
Set default Pandashells configuration options |
| p.crypt | pandashells |
Encrypt/decrypt files using open-ssl |
| p.format | pandashells |
Render python string templates using input data |
| p.gui | pandashells |
Open dataframe in pandasgui interactive environment |
| p.parallel | pandashells |
Read shell commands from stdin and run them in parallel |
| p.example_data | pandashells |
Create sample csv files for training/testing |
| p.df | pandashells[console] |
Pandas dataframe manipulation of text files |
| p.linspace | pandashells[console] |
Generate a linearly spaced series of numbers |
| p.lomb_scargle | pandashells[console] |
Generate Lomb-Scarge spectrogram of input time series |
| p.merge | pandashells[console] |
Merge two data files by specifying join keys |
| p.rand | pandashells[console] |
Generate random numbers |
| p.regress | pandashells[console] |
Perform (multi-variate) linear regression with R-like patsy syntax |
| p.sig_edit | pandashells[console] |
Remove outliers using iterative sigma-editing |
| p.smooth | pandashells[console] |
Smooth data |
| p.cdf | pandashells[full] |
Plot emperical distribution function |
| p.facet_grid | pandashells[full] |
Create faceted plots for data exploration |
| p.hist | pandashells[full] |
Plot histograms |
| p.plot | pandashells[full] |
Create xy plot visualizations |
| p.regplot | pandashells[full] |
Quickly plot linear regression of data to a polynomial |
DataFrame Manipulations
Pandashells allows you to specify multiple dataframe operations in a single command.
Each operation assumes data is in a dataframe named df. Operations
performed on this dataframe will overwrite the df variable with
the results of that operation. Special consideration is taken for
assignments such as df['a'] = df.b + 1. These are understood
to make column assignments on df. By way of example, this command at the bash prompt:
p.df 'df["c"] = 2 * df.b' 'df.groupby(by="a").c.count()' 'df.reset_index()'is equivalent to the following python snippet:
import pandas as pd
df = pd.read_csv(sys.stdin)
df["c"] = 2 * df.b
df = df.groupby(by="a").c.count()
df = df.reset_index()
df.to_csv(sys.stdout, index=False)Shown below are several examples of how to use the p.df tool. You are encourage
to copy/paste these commands to your bash prompt to see Pandashells in action.
-
Show a few rows of an example data set.
[~]$ p.example_data -d tips | head "total_bill","tip","sex","smoker","day","time","size" 16.99,1.01,"Female","No","Sun","Dinner",2 10.34,1.66,"Male","No","Sun","Dinner",3 21.01,3.5,"Male","No","Sun","Dinner",3 23.68,3.31,"Male","No","Sun","Dinner",2 -
Transform the sample data from csv format to table format
[~]$ p.example_data -d tips | p.df 'df.head()' -o table total_bill tip sex smoker day time size 16.99 1.01 Female No Sun Dinner 2 10.34 1.66 Male No Sun Dinner 3 21.01 3.50 Male No Sun Dinner 3 23.68 3.31 Male No Sun Dinner 2 24.59 3.61 Female No Sun Dinner 4
-
Compute statistics for numerical fields in the data set.
[~]$ p.example_data -d tips | p.df 'df.describe().T' -o table index count mean std min 25% 50% 75% max total_bill 244 19.785943 8.902412 3.07 13.3475 17.795 24.1275 50.81 tip 244 2.998279 1.383638 1.00 2.0000 2.900 3.5625 10.00 size 244 2.569672 0.951100 1.00 2.0000 2.000 3.0000 6.00 -
Find the mean tip broken down by gender and day
[~]$ p.example_data -d tips | p.df 'df.groupby(by=["sex","day"]).tip.mean()' -o table index tip sex day Female Fri 2.781111 Sat 2.801786 Sun 3.367222 Thur 2.575625 Male Fri 2.693000 Sat 3.083898 Sun 3.220345 Thur 2.980333
Join files on key fields
Pandashells can join files based on a set of key fields. This example uses only one field as a key, but like the pandas merge function on which it is based, multiple key fields can be used for the join.
-
Show poll resultes for the 2008 US presidential election
[~]$ p.example_data -d election | p.df -o table | head days state obama mccain poll -305 OH 43 50 SurveyUSA -303 PA 38 46 Rasmussen -298 OR 47 47 SurveyUSA -298 WA 52 43 SurveyUSA -294 AL 29 63 SurveyUSA -294 NY 44 42 Siena Coll. -294 VA 40 52 SurveyUSA -290 NM 41 50 SurveyUSA -290 NY 49 43 SurveyUSA -
Show population and electoral college numbers for states
[~]$ p.example_data -d electoral_college | p.df -o table | head state name electors population AK Alaska 3 710000 AL Alabama 9 4780000 AR Arkansas 6 2916000 AZ Arizona 11 6392000 CA California 55 37254000 CO Colorado 9 5029000 CT Connecticut 7 3574000 DC Dist. of Col. 3 602000 DE Delaware 3 898000 -
Join poll and electoral-college data (Note the use of bash process substitution to specify files to join.)
[~]$ p.merge <(p.example_data -d election) <(p.example_data -d electoral_college) --how left --on state | p.df -o table | head days state obama mccain poll name electors population -252 AK 43 48 SurveyUSA Alaska 3 710000 -213 AK 43 48 Rasmussen Alaska 3 710000 -176 AK 41 50 Rasmussen Alaska 3 710000 -143 AK 41 45 Rasmussen Alaska 3 710000 -112 AK 40 45 Rasmussen Alaska 3 710000 -99 AK 39 44 Rasmussen Alaska 3 710000 -65 AK 35 54 Ivan Moore Research Alaska 3 710000 -58 AK 33 64 Rasmussen Alaska 3 710000 -56 AK 39 55 ARG Alaska 3 710000
Visualization Tools
Pandashells provides a number of visualization tools to help you quickly explore your data. All visualizations are automatically configured to show an interactive plot using the configured backend (default is TkAgg, but can be configured with the p.config tool).
As of version 0.2.0 pandashells supports the WebAgg backend for matplotlib. This enables interactive plots to be shown in a browser. To run with this option, set configuration with
p.config --plot_backend WebAggNote that WebAgg requires that Tornado be installed. This installation is left up to the user.
The visualizations can also be saved to image files (e.g. .png) or rendered to html. The html generated can either be opened directly in the browser to show an interactive plot (using mpld3), or can be embedded in an existing html file. The examples below show Pandashells-created png images along with the command used to generate them.
-
Simple xy scatter plots
[~]$ p.example_data -d tips | p.plot -x total_bill -y tip -s 'o' --title 'Tip Vs Bill'
-
Faceted plots
[~]$ p.example_data -d tips | p.facet_grid --row smoker --col sex --hue day --map pl.scatter --args total_bill tip --kwargs 'alpha=.2' 's=100'
-
Histograms plots (Note the use of bash process substitution to paste two outputs together.)
[~]$ paste <(p.rand -t normal -n 10000 | p.df --names normal) <(p.rand -t gamma -n 10000 | p.df --names gamma) | p.hist -i table -c normal gamma
-
Empirical cumulative distribution plots
[~]$ p.rand -t normal -n 500 | p.cdf -c value --names value
Spectral Estimation
-
Plot a time series over which to compute a spectrum
[~]$ p.example_data -d sealevel | p.plot -x year -y sealevel_mm
-
Plot the spectrum
[~]$ p.example_data -d sealevel | p.lomb_scargle -t year -y sealevel_mm --interp_exp 3 | p.plot -x period -y amp --xlim 0 1.5 --ylim 0 6.5 --xlabel 'Period years' --ylabel 'Amplitude (mm)' --title 'Global Sea Surface Height Spectrum'
Linear Regression
Pandashells leverages the excellent Seaborn and Statsmodels libraries to handle linear regression.
-
Quick and dirty fit to a line
[~]$ p.linspace 0 10 20 | p.df 'df["y_true"] = .2 * df.x' 'df["noise"] = np.random.randn(20)' 'df["y"] = df.y_true + df.noise' --names x | p.regplot -x x -y y
-
Multi-variable linear regression
[~]$p.example_data -d sealevel | p.df 'df["sin"]=np.sin(2*np.pi*df.year)' 'df["cos"]=np.cos(2*np.pi*df.year)' | p.regress -m 'sealevel_mm ~ year + sin + cos' OLS Regression Results ============================================================================== Dep. Variable: sealevel_mm R-squared: 0.961 Model: OLS Adj. R-squared: 0.961 Method: Least Squares F-statistic: 6442. Date: Mon, 27 Jul 2015 Prob (F-statistic): 0.00 Time: 23:28:11 Log-Likelihood: -2234.0 No. Observations: 780 AIC: 4476. Df Residuals: 776 BIC: 4495. Df Model: 3 Covariance Type: nonrobust ============================================================================== coef std err t P>|t| [95.0% Conf. Int.] ------------------------------------------------------------------------------ Intercept -6500.1722 47.829 -135.903 0.000 -6594.063 -6406.282 year 3.2577 0.024 136.513 0.000 3.211 3.305 sin -4.6933 0.217 -21.650 0.000 -5.119 -4.268 cos 1.4061 0.214 6.566 0.000 0.986 1.826 ============================================================================== Omnibus: 5.332 Durbin-Watson: 0.709 Prob(Omnibus): 0.070 Jarque-Bera (JB): 5.401 Skew: -0.189 Prob(JB): 0.0672 Kurtosis: 2.846 Cond. No. 6.29e+05 ============================================================================== Warnings: [1] Standard Errors assume that the covariance matrix of the errors is correctly specified. [2] The condition number is large, 6.29e+05. This might indicate that there are strong multicollinearity or other numerical problems.
Further examples of each tool can be seen by calling it with the -h switch. You are encouraged to fully explore these examples. They highlight how Pandashells can be used to significantly improve your efficiency.
Simple Profiling Utility
In addition to command-line tools, Pandashells exposes a useful profiling tool that can be imported into your python code. The tools is just a simple context manager that sends timing information to stdout. The csv-like format of this output makes it easy to pipe through Pandashells pipelines. Here are a couple examples.
Profiling different parts of your code
Code
import time
from pandashells import Timer
with Timer('entire script'):
for nn in range(3):
with Timer('loop {}'.format(nn + 1)):
time.sleep(.1 * nn)
# Will generate the following output on stdout
# col1: a string that is easily found with grep
# col2: the time in seconds (or in hh:mm:ss if pretty=True)
# col3: the value passed to the 'name' argument of TimerOutput
__time__,2.6e-05,loop 1
__time__,0.105134,loop 2
__time__,0.204489,loop 3
__time__,0.310102,entire script
Profiling how code scales (measuring "big-O")
Code
import time
from pandashells import Timer
# initialize a list to hold results
results = []
# run a piece of code with different values of the var you want to scale
for nn in range(3):
# time each iteration
with Timer('loop {}'.format(nn + 1), silent=True) as timer:
time.sleep(.1 * nn)
# add results
results.append((nn, timer))
# print csv compatible text for further pandashells processing/plotting
print 'nn,seconds'
for nn, timer in results:
print '{},{}'.format(nn,timer.seconds)Projects by robdmc.
- Pandashells Pandas at the bash command line
- Consecution Pipeline abstraction for Python
- Behold Helping debug large Python projects
- Crontabs Simple scheduling library for Python scripts
- Switchenv Manager for bash environments
- Gistfinder Fuzzy-search your gists