Running your Code as a Python Script

Overview

Teaching: 15 min
Exercises: 25 min

Questions

• How can I export my Jupyter notebook as a Python script?

• How do I run a Python script?

• How can I pass an argument to my script?

Objectives

• Export a Jupyter notebook to a Python script

• Run a Python script using the terminal

• Write a Python script which takes a command line argument

In the previous lessons we wrote some code for plotting the average, maximum and mean of the absorption. If you wanted to share this script with other researchers you may want to export this code cell as a plain text file. You can then send the file in an email or - even better - publish it on a website like Github or Gitlab. Plain text can be easier to version control than Jupyter Notebooks, although there are a growing number of tools (example nbdime) which are designed to make the version control of Jupyter Notebooks easier.

To convert the code in your Jupyter Notebook cell into a plain text .py file there are two options:

• Option one:
  • copy the code cell
  • open a text editor
  • paste the code into your text editor
  • save with a .py extension
• Option two:
  • Use the Jupyter Magic command %%writefile myfile.py in your code block

Let’s use option two.

%%writefile transmittance_plots.py

import numpy
import matplotlib.pyplot as plt

numpy.loadtxt("./data/transmittance_cleaned.csv")
wavelengths = data[:,0]
ITO_transmittance = data[:,1]
CdS_transmittance = data[:,2]
Si_transmittance = data[:,3]
GaAs_transmittance = data[:,4]

fig = plt.figure(figsize=(10.0, 10.0))

axes1 = fig.add_subplot(2, 2, 1)
axes2 = fig.add_subplot(2, 2, 2)
axes3 = fig.add_subplot(2, 2, 3)
axes4 = fig.add_subplot(2, 2, 4)

axes1.plot(wavelengths,ITO_transmittance)
axes1.set_ylabel("Transmittance (%)")
axes1.set_title("ITO")

axes2.plot(wavelengths,CdS_transmittance)
axes2.set_title("CdS")
axes2.sharey(axes1)

axes3 .plot(wavelengths,Si_transmittance)
axes3.set_xlabel("wavelength (nm) ")
axes3.set_ylabel("Transmittance (%)")
axes3.set_title("Si")

axes4.plot(wavelengths,GaAs_transmittance)
axes4.set_xlabel("wavelength (nm) ")
axes4.set_title("GaAs")
axes4.sharey(axes3)

fig.tight_layout()

plt.savefig('./group_transmittance.png')

plt.show()

Exporting a complete Notebook

If you want to export all the code in a Jupyter Notebook you’ll need to execute the following command from the terminal.

jupyter nbconvert --to script my_notebook.ipynb

This uses the nbconvert tool.

We can now run the script in a terminal to generate the plot. Note that the transmittance data file will need to be in a sub-folder called data.

python3 transmittance_plots.py

The data file that is read in by the script are currently hard coded - they cannot be changed without changing the code itself. Instead, we can import the sys library which allows us to provide command line arguments specifying the filenames for our data. The first command line argument is accessed with the variable sys.argv[1] , the second command line argument is accessed with the sys.argv[2] argument and so on. We can adapt the transmittance_plots.py script as follows:

import sys
import numpy
import matplotlib.pyplot as plt

numpy.loadtxt(sys.argv[1])
wavelengths = data[:,0]
ITO_transmittance = data[:,1]
CdS_transmittance = data[:,2]
Si_transmittance = data[:,3]
GaAs_transmittance = data[:,4]

fig = plt.figure(figsize=(10.0, 10.0))

axes1 = fig.add_subplot(2, 2, 1)
axes2 = fig.add_subplot(2, 2, 2)
axes3 = fig.add_subplot(2, 2, 3)
axes4 = fig.add_subplot(2, 2, 4)

axes1.plot(wavelengths,ITO_transmittance)
axes1.set_ylabel("Transmittance (%)")
axes1.set_title("ITO")

axes2.plot(wavelengths,CdS_transmittance)
axes2.set_title("CdS")
axes2.sharey(axes1)

axes3 .plot(wavelengths,Si_transmittance)
axes3.set_xlabel("wavelength (nm) ")
axes3.set_ylabel("Transmittance (%)")
axes3.set_title("Si")

axes4.plot(wavelengths,GaAs_transmittance)
axes4.set_xlabel("wavelength (nm) ")
axes4.set_title("GaAs")
axes4.sharey(axes3)

fig.tight_layout()

plt.savefig(sys.argv[2])

plt.show()

In this example sys.argv[1] should correspond to the cleaned data file, and sys.argv[2] should correspond to the name you would like to give the resulting plot.

python3 absorption_plots.py ./data/transmittance_cleaned.csv ./transmittance_plot_scr.png

Key Points

• Copy/paste or use the %%writefile myfile.py notebook magic to export a single cell

• Use jupyter nbconvert --to script my_notebook.ipynb to export a complete notebook

• Use python3 script_name.py to run a script from the terminal

• Import the sys module and use sys.argv to take a command line argument