Introduction to Python: Getting Started

Ubuntu

Ubuntu 22.04

Running Python

Ubuntu 22.04 LTS (Jammy Jellyfish) comes with Python 3.10.6 pre-installed. To get started, open a terminal and check that this is indeed true by running the following:

$ python3 --version

This should return Python 3.10.6 or similar. It’s worth noting that it’s possible to have multiple copies and versions of Python installed at the same time on your machine so to check which instance of Python you are using you can run the following:

$ which python3

This should return /usr/bin/python3 or similar. Note that it’s possible to specify exactly which copy and/or version (up to the second version number) of Python you want to use. This means that, on a fresh install of Ubuntu 22.04, the following are all equivalent because there is only one copy of Python installed and it happens to be Python 3.10:

python3
python3.10
/usr/bin/python3
/usr/bin/python3.10

For the rest of this section we will just use python3, but any of the above could be substituted in.

Now that you’ve got that admin out of the way you can start using Python in the terminal in one of a number of ways:

Open Python in the terminal in interactive mode:
```
$ python3
```
In interactive mode you can write individual Python commands directly in at the >>> prompt and then run them immediately by pressing Enter. This is clearly not a user-friendly way to programme because it doesn’t save the commands you are using to a script file that you can then edit, but it’s useful for quickly checking something small.

Exit Python interactive mode and return to the normal terminal by running exit().
Run a Python script file:
```
$ python3 filename.py
```
This command will run Python on a script called filename.py that is in the same folder as the one your terminal is currently pointing at. Obviously, if no filename.py file exists in that folder then it won’t work (you’ll get a No such file or directory message). Less obviously, your terminal might not be pointing at the same folder as the one your script is in, in which case you can…
…run a Python script in a different folder:
```
$ python3 path/to/folder/filename.py
```
Two dots (..) means ‘one folder up’, for example:
```
$ python3 ../path/to/folder/filename.py
```
Alternatively, you can change into the directory where the file is located using the cd command (change directory) in your terminal:
```
$ cd path/to/folder/
$ python3 filename.py
```

If there is a space in a file or folder name you can either use quotation marks or back slashes to escape the space characters:

$ python3 "Python File.py"
$ python3 Python\ File.py
$ python3 "../Path To/Python File.py"
$ python3 ../Path\ To/Python\ File.py

Note that the .py extension (which tells you that it’s a Python file) must be included in the command you use - running the following will give you an error:

# Oops...
$ python3 filename

Note also that running python2 or python will not work on a fresh install of Ubuntu 22.04. Previously, both of these commands referred to Python 2 but this version is no longer supported and it doesn’t come pre-installed anymore. You can, if you want, install Python 2 yourself and/or make the python command refer to Python 3 (or Python 2), but that’s up to you.

Updating Python

To update the pre-installed version of Python (3.10) to the latest version (3.12) two common options are:

Option 1: Installing from the terminal:
- Run the following:
```
$ sudo apt-get install python3.12
```
- Note that the terminal command python3 will still run Python 3.10 even after you’ve installed 3.12. However, the command python3.12 will now be available and will run 3.12, so you can use that from now on.
Option 2: Downloading from the Python website and building from source:
- Go to https://www.python.org/
- Hover your cursor over “Downloads” then click the big grey “Python 3.12.0” button under “Python Source”. A .tar.xz file will be downloaded to your Downloads folder.
- Open a terminal and change directory into your Downloads folder:
```
$ cd Downloads/
```
- Extract the folder containing the programme:
```
$ tar -xf Python-3.12.0.tar.xz
```
- Change directory into this new folder:
```
$ cd Python-3.12.0/
```
- Run the following to complete the installation:
```
$ ./configure
$ make
$ sudo make install
```
- Check that it’s worked:
```
$ python3.12 --version
```
- The following should also return a 3.12.x version number:
```
$ python3 --version
```
- You can now delete the .tar.xz file and the corresponding folder it unzipped to from your Downloads folder

Note that Option 1 will download Python to /usr/bin/python3.12 whereas Option 2 will download it to /usr/local/bin/python3.12.

Configuring Python

Most users will not need to configure Python but, for the record, if you followed Option 2 above and downloaded and installed Python ‘manually’ (ie from the Python website) then you had the option to configure the installation when you ran configure:

$ ./configure <options>

If you used Option 1 (ie if you used apt-get) then you bypassed this opportunity. As mentioned, for many users this won’t matter. However, there are a couple of use cases where Python needs to be configured so as to have a shared library - one example is if you want to use Python in R Markdown using R’s “reticulate” package. A shared library can be enabled via the following while installing Python:

$ ./configure --enable-shared

If you have already finished installing Python/have installed it via apt-get and are using version 3.10 (the default version on Ubuntu 22.04) then you can run the following:

$ sudo apt-get install libpython3.10

This will download the libpython3.10 Ubuntu package which is the shared Python runtime library for Python 3.10 (for the record, this package’s homepage is over here).

Unfortunately, there is no libpython3.12 for Ubuntu 22.04, only for 23.10+ (see the homepage for this over here).

Installing Python Packages

The best option is to use the standard Python package manager “pip” (aka “pip3” for Python 3) for installing packages. The name “pip” is a recursive acronym for “Pip Installs Packages”.

Install pip from the terminal with:
```
$ sudo apt-get install python3-pip
```
Check that it’s worked from the terminal by running:
```
$ python3.12 -m pip --version
```

This should return the version number and install location. Note that running pip --version will probably return the details of the version of pip that was installed for Python 3.10 (if one was installed) and running pip3 --version might do this as well if you followed Option 1 above when updating Python. In general, it’s better to use the python3.12 -m pip ... format when using pip because this guarantees that you are using the version associated with Python 3.12.

The -m flag stands for “module” and causes a specific module of a specific installation of Python to be run, hence why it’s useful for ensuring that you are using the correct versions of everything.

Once pip is installed and working you can install most packages from the terminal as follows:

$ python3.12 -m pip install <package_name>

Note that you install Python packages from the terminal, not from within Python itself (unlike some other languages, eg R).

To install a bunch of the most useful packages in one go, run the following in the terminal to download all these packages one after the other:

# NumPy is the fundamental package for scientific computing with Python
python3.12 -m pip install numpy
# SciPy ("Sigh Pie") is software for mathematics, science and engineering
python3.12 -m pip install scipy
# Statsmodels provides a complement to SciPy for statistical computations
python3.12 -m pip install statsmodels
# scikit-learn is a module for machine learning built on top of SciPy
python3.12 -m pip install scikit-learn
# Pandas is a powerful data analysis toolkit
python3.12 -m pip install pandas
# Matplotlib is for creating static, animated and interactive visualizations
python3.12 -m pip install matplotlib
# Seaborn allows for statistical data visualization based on Matplotlib
python3.12 -m pip install seaborn
# end

Check that this has worked by opening Python in the terminal with python3.12 then running:

import numpy
import scipy
import statsmodels
import sklearn
import pandas
import matplotlib
import seaborn

There should be no errors.

Upgrading Packages

To upgrade (update) a package called “<package_name>” simply run:

$ python3.12 -m pip install <package_name> --upgrade

To upgrade pip itself:

$ python3.12 -m pip install pip --upgrade

Remember that using pip install will probably install packages to the pre-installed version of Python and/or upgrade that version’s copy of pip. Using python3.12 -m pip install will explicitly install packages for Python 3.12 and/or upgrade Python 3.12’s copy of pip.

See What Version of Each Package You Have

Run the following:

$ python3.12 -m pip freeze

The below variation will check what version of a specific package you have (it searches through the results of the python3.12 -m pip freeze command):

$ python3.12 -m pip freeze | grep <package_name>

If we want to save the package version numbers to a file then we can ‘pipe’ the output of python3.12 -m pip freeze into a text document. By convention, this kind of file gets called requirements.txt because it contains the packages and versions that are required to run your project:

$ python3.12 -m pip freeze >> requirements.txt

A better option is to install and use the pipreqs package (see here for more info):

$ python3.12 -m pip install pipreqs
$ pipreqs '.' --force

This creates the requirements.txt file using only the packages that are actually used by whatever Python files are in the folder your terminal is pointing at.

Fixing pipreqs if it doesn’t work:

If pipreqs doesn’t work immediately, ie if you get the following message when you run pipreqs '.' --force in the terminal:

bash: pipreqs: command not found

Locate the pipreqs.py file on your computer (try looking in /usr/local/lib/python3.12/dist-packages/pipreqs). Try to run that with Python. If it gives you the following error:

ImportError: cannot import name '__version__' from partially initialized module 'pipreqs' (most likely due to a circular import)

It means it is trying to import a package with the same name as the file itself (ie ‘pipreqs’). Get around this by re-naming the file to python_pipreqs.py after which it should work from the terminal with:

/usr/local/lib/python3.12/dist-packages/pipreqs/python_pipreqs.py '.' --force

⇦ Back

Ubuntu 20.04

Installing and Setting Up

There is no need to install Python on Ubuntu 20.04 because it comes with Python 3.8.2 automatically (and 2.7.18 as well, although that version - and, indeed, any version of Python 2 as opposed to Python 3 - is outdated and shouldn’t be used). Note, however, that:

The default version of Python on Ubuntu is still Python 2 (version 2.7.18, as mentioned) so if you open the terminal and run python then this is the version that will open. To avoid this, you specifically need to use python3 to use the most recent version of Python 3 you have installed.
There are more recent versions of Python 3 available than 3.8.2. See the “Updating Python” section below to read how to get those.

Using Python from the Terminal

If you open a terminal and run python3 you will open Python in that terminal.

This is known as ‘interactive mode’
You can enter individual Python commands directly in at the >>> prompt and run them immediately by pressing enter
This is obviously not a user-friendly way to programme because it doesn’t save the commands you are using to a script file that you can edit, but it’s useful for quickly checking something small
Exit by running exit()

If you have a script file (one with the “.py” extension) you can run it from the terminal by:

Opening your terminal
Changing into the directory where the file is located (using the cd command to change directory in your terminal)
Running python3 <filename> with the “.py” extension included in the filename

In fact, you don’t actually need to change directory into the one where the script is located, you can just run python3 <path_to_folder>/<filename> (with the “.py” extension included in the filename) and it will work.

Updating Python

Although it’s possible to update Python entirely from within the terminal my personal preference is to do it manually. Every time there’s a new version I go to the Python website and download it directly as a tar.xz file (you can use this shortcut to download Python 3.12.0 immediately). It can then be installed alongside any existing versions via the following steps:

Unzip the tar.xz file that gets downloaded. If, for example, you have downloaded Python 3.12.0 then this file will be called Python-3.12.0.tar.xz.
Open your terminal and cd into the folder that was created during the unzipping process: cd Downloads/Python-3.12.0/

You now have two options:

Follow the Build Instructions found in the README.rst file within this Python-3.12.0 folder exactly. This involves running the following commands (the last of which prompts you to enter your computer password):
```
$ ./configure
$ make
$ make test
$ sudo make install
```
Personally, I use the --enable-shared option instead:
```
$ ./configure --enable-shared
$ make
$ make test
$ sudo make install
```
- This --enable-shared option creates a shared library. This is needed by the Reticulate package and R Markdown. Specifically, Reticulate and R Markdown require that the /usr/local/lib/libpython3.12.a file exists (or whatever libpython file corresponds to the version of Python you have).
- If you use this option, you now need to tell Python where this shared library file is by opening ~/.basrc and adding the following:
```
# Manually set where a Python module looks when it uses shared object files or
# static libraries
$ export LD_LIBRARY_PATH=/usr/local/lib
```

Running python3.12 --version in the terminal should now return Python 3.12.0 and running python3.12 should open Python 3.12.0 in the terminal (in ‘interactive mode’). The same should also be true for python3, although python will still correspond to Python 2.7.18 (unless you’ve manually changed this at some point).

Installing Packages

The best option is to use the standard Python package manager, “pip” (aka pip3 for Python 3):

# Install pip
$ sudo apt-get install python3-pip

Once this is done you can install most packages as follows:

# Install a package
$ sudo pip3 install <package_name>

However, I recommend that you use the following instead:

# Run pip as a module (which is what is meant by "-m") of a specific Python
# version (in this case 3.12) in order to install a package
$ python3.12 -m pip install <package_name>

This will guarantee that you are installing the package to the correct version of Python. If you have multiple versions of Python and pip installed on your computer at the same time (and seeing as Ubuntu comes with two versions of Python already pre-installed this will almost always be true!) it can get confusing as to what packages are being installed where.

To install a bunch of the most common packages in one go, switch into ‘permanent’ sudo mode with sudo su and run the following in the terminal to download all these packages one after the other (this assumes you are using Python 3.12; change the version number in the python3.12 commands if not):

# Mathematics & arrays
python3.12 -m pip install numpy
# Scientific & technical computing
python3.12 -m pip install scipy
# Plotting
python3.12 -m pip install matplotlib
# Data manipulation and analysis
python3.12 -m pip install pandas
# Symbolic computation
python3.12 -m pip install sympy
# Testing
python3.12 -m pip install nose
# Spreadsheet integration
python3.12 -m pip install xlwt
python3.12 -m pip install xlrd
python3.12 -m pip install openpyxl
# Using serial ports for microprocessors
python3.12 -m pip install pyserial
# Image processing
python3.12 -m pip install scikit-image
# Pass arguments from the terminal
python3.12 -m pip install argparse
# Linux distribution information
python3.12 -m pip install distro
# Print to terminal in colour
# print(colored('hello', 'red'), colored('world', 'green'))
python3.12 -m pip install termcolor
# end

Check that it has worked by opening Python in the terminal with python3.12 then running:

import numpy
import scipy
import matplotlib
import pandas
import sympy
import nose
import xlwt
import xlrd
import openpyxl
import serial
import skimage
import argparse
import distro
import termcolor

There should be no errors.

Upgrading Packages

To upgrade (update) a package called “<package_name>” simply run:

$ python3.12 -m pip install <package_name> --upgrade

To upgrade pip itself:

$ python3.12 -m pip install --upgrade pip

See What Version of Each Package You Have

To check what version of each package you have, you can run:

$ pip freeze

…and to check what version of a specific package you have, you can search the results of pip freeze like so:

$ pip freeze | grep <package_name>

To store the package version numbers we can ‘pipe’ the output of pip freeze into a text file. By convention, this kind of file gets called ‘requirements.txt’ because it contains the packages and versions that are required to run your project:

$ pip freeze >> requirements.txt

An even better option, however, is to install and use the pipreqs package (see here for more info on pipreqs):

# Install pipreqs. The "python3.12" command should be changed to match the version of Python you have installed.
$ python3.12 -m pip install pipreqs
# Use pipreqs to create requirements.txt
$ pipreqs '.' --force

This creates the requirements.txt file using only the packages that are actually used by whatever Python files are in the folder your terminal is pointing at.

Fixing pipreqs if it doesn’t work

If pipreqs doesn’t work immediately, ie if you get the following message when you run pipreqs '.' --force in the terminal:

bash: pipreqs: command not found

then locate the pipreqs.py file on your computer (try looking in /usr/local/lib/python3.12/dist-packages/pipreqs). Try to run that with Python. If it gives you the following error:

ImportError: cannot import name '__version__' from partially initialized module 'pipreqs' (most likely due to a circular import)

$ /usr/local/lib/python3.12/dist-packages/pipreqs/python_pipreqs.py '.' --force

⇦ Back

Ubuntu 16.04 to 18.04

Installing and Setting Up

There is no need to install Python on Ubuntu 16.04 to 18.04: it comes already installed. In fact, multiple versions of Python come pre-installed (these multiple installations can be found in the /usr/bin/ folder)
However, the version of Python that Ubuntu uses by default is version 2 (usually 2.7) even though it has Python 3 installed. This is not good; Python 2 is no longer supported so everyone should be using Python 3. Check which version you are using from the terminal with:
```
python --version
```
If this tells you that you are using Python 2 you should change this by running the following from a terminal*:
```
sudo update-alternatives --install /usr/bin/python python /usr/bin/python3 30
```
- You will be prompted to enter your computer password. This is needed because you are using the sudo (super doer) command which allows you to change your computer’s settings
- The update-alternatives command changes the symbolic links that determine what your commands do. In this case you are changing python to link to python3 instead of the default (which is python2).
- The 30 at the end means that you are giving python3 a priority of 30 over python2
Check that this has worked by running python --version again and seeing if this returns a Python 3 version number

*Elsewhere on the internet you will see advice saying to solve this exact same problem by editing your “.bashrc” file and adding an alias. That solution will work for most but not all situations, eg it will not work if you run Python using sudo or from within R Markdown. The reason for this is that these bypass the .bashrc file, hence why I recommend the solution above. Test that you’ve done it correctly by running bash -c "python --version" - this invokes bash directly (and thus bypasses the .bashrc file) and should print a version 3 version number.

Note: you can still run Python 2 should you need it. This is done by explicitly using the python2 command, or the python2.7 command if you specifically need version 2.7. In general, you can run a specific version of Python by running pythonx.x from the terminal.

Using Python from the Terminal

If you open a terminal and run python3 you will open Python in that terminal.

This is known as ‘interactive mode’
You can enter individual Python commands directly in at the >>> prompt and run them immediately by pressing enter
This is obviously not a user-friendly way to programme because it doesn’t save the commands you are using to a script file that you can edit, but it’s useful for quickly checking something small
Exit by running exit()

If you have a script file (one with the “.py” extension) you can run it from the terminal by:

Opening your terminal
Changing into the directory where the file is located (using the cd command to change directory in your terminal)
Running python3 <filename> with the “.py” extension included in the filename

Updating Python

Although it’s possible to update Python entirely from within the terminal my personal preference is to do it manually. Every time there’s a new version I go to the Python website and download it directly as a tar.xz file (you can use this shortcut to download Python 3.11.0 immediately). It can then be installed alongside any existing versions via the following steps:

Unzip the tar.xz file that gets downloaded. If, for example, you have downloaded Python 3.11.0 then this file will be called Python-3.11.0.tar.xz.
Open your terminal and cd into the folder that was created during the unzipping process: cd Downloads/Python-3.11.0/

You now have two options:

Follow the Build Instructions found in the README.rst file within this Python-3.11.0 folder exactly. This involves running the following commands (the last of which prompts you to enter your computer password):
```
./configure
make
make test
sudo make install
```
Personally, I use the --enable-shared option instead:
```
./configure --enable-shared
make
make test
sudo make install
```
- This --enable-shared option creates a shared library. This is needed by the Reticulate package and R Markdown. Specifically, Reticulate and R Markdown require that the /usr/local/lib/libpython3.10.so.1.0 file exists (or whatever .so file corresponds to the version of Python you have).
- If you use this option, you now need to tell Python where this shared library file is by opening ~/.basrc and adding the following:
```
# Manually set where a Python module looks when it uses shared object files or
# static libraries
export LD_LIBRARY_PATH=/usr/local/lib
```

Running python3.11 --version in the terminal should now return Python 3.11.0 and running python3.11 should open Python 3.11.0 in the terminal (in ‘interactive mode’).

Installing Packages

The best option is to use the standard Python package manager, “pip” (aka pip3 for Python 3):

# Install pip
sudo apt-get install python3-pip

Once this is done you can install most packages as follows:

# Install a package
sudo pip3 install <package_name>

However, I recommend that you use the following instead:

# Run pip as a module (which is what is meant by "-m") of a specific Python
# version (in this case 3.11) in order to install a package
python3.11 -m pip install <package_name>

To install a bunch of the most common packages in one go, switch into ‘permanent’ sudo mode with sudo su and run the following in the terminal to download all these packages one after the other (this assumes you are using Python 3.11, change the version number in the python3.11 commands if not):

# Mathematics & arrays
python3.11 -m pip install numpy
# Scientific & technical computing
python3.11 -m pip install scipy
# Plotting
python3.11 -m pip install matplotlib
# Data manipulation and analysis
python3.11 -m pip install pandas
# Symbolic computation
python3.11 -m pip install sympy
# Testing
python3.11 -m pip install nose
# Spreadsheet integration
python3.11 -m pip install xlwt
python3.11 -m pip install xlrd
python3.11 -m pip install openpyxl
# Using serial ports for microprocessors
python3.11 -m pip install pyserial
# Image processing
python3.11 -m pip install scikit-image
# Pass arguments from the terminal
python3.11 -m pip install argparse
# Linux distribution information
python3.11 -m pip install distro
# Print to terminal in colour
# print(colored('hello', 'red'), colored('world', 'green'))
python3.11 -m pip install termcolor
# end

Check that it has worked by opening Python in the terminal with python3.11 then running:

import numpy
import scipy
import matplotlib
import pandas
import sympy
import nose
import xlwt
import xlrd
import serial
import skimage
import argparse
import termcolor

There should be no errors.

Upgrading Packages

To upgrade (update) a package called “<package_name>” simply run:

python3.11 -m pip install <package_name> --upgrade

To upgrade pip itself:

python3.11 -m pip install --upgrade pip

See What Version of Each Package You Have

To check what version of each package you have, you can run:

pip freeze

…and to check what version of a specific package you have, you can search the results of pip freeze like so:

pip freeze | grep <package_name>

pip freeze >> requirements.txt

An even better option, however, is to install and use the pipreqs package (see here for more info on pipreqs):

# Install pipreqs. The "python3.11" command should be changed to match the version of Python you have installed.
python3.11 -m pip install pipreqs
# Use pipreqs to create requirements.txt
pipreqs '.' --force

This creates the requirements.txt file using only the packages that are actually used by whatever Python files are in the folder your terminal is pointing at.

Fixing pipreqs if it doesn’t work

If pipreqs doesn’t work immediately, ie if you get the following message when you run pipreqs '.' --force in the terminal:

bash: pipreqs: command not found

then locate the pipreqs.py file on your computer (try looking in /usr/local/lib/python3.11/dist-packages/pipreqs). Try to run that with Python. If it gives you the following error:

ImportError: cannot import name '__version__' from partially initialized module 'pipreqs' (most likely due to a circular import)

/usr/local/lib/python3.11/dist-packages/pipreqs/python_pipreqs.py '.' --force

⇦ Back

macOS

macOS 14 (Sonoma)

**What Not To Do**

While it is true that macOS comes with Python pre-installed on it (located in /usr/bin/) it is not recommended to use this pre-installed version. This is because it is out-of-date and, because some background macOS programmes rely on this out-of-date version in order to work, it is not recommended to update it.

A common solution to the above problem is to use aliases inserted into your terminal’s settings files (eg ~/.bash_profile, ~/.zshrc or ~/.zprofile). This is no longer recommended either: these run commands are specific to a terminal instance and do not apply in situations where these setting folders are bypassed (eg when running Python from R Markdown which invokes bash -c python, not python)

Using pyenv (a Python version manager from Homebrew) is another option. However, you still need to download Python and add configuration steps to your terminal’s settings files, meaning you run into the same problem mentioned above.

Downloading and Installing Python

The best option is to download and install Python manually from the Python website:

Go to https://www.python.org/
Hover your cursor over “Downloads” then click the big grey button under “Python Source” to download the latest version of Python. At the time of writing this is version 3.12.0 but the following instructions should work for any version if you swap in the relevant numbers.
Double-click the file that gets downloaded and follow the installation process
- If you downloaded version 3.12.0 the file will be python-3.12.0-macos11.pkg
- macOS finishes the installation by opening the folder where Python was installed for you: /Applications/Python 3.12. You can just ignore that and close it.
Check that it has worked by opening a terminal (press Cmd+Space to open Spotlight Search then search for “Terminal”) and running:
```
$ python3.12 --version
```
If this returns Python 3.12.0 or similar then you’re all good.
You can check where this version of Python is installed by running:
```
$ which python3.12
```
Usually it will be /Library/Frameworks/Python.framework/Versions/3.12/bin/python3.12
- This is a useful thing to remember if and when you have multiple instances of Python installed - while it’s ok to have multiple versions of Python installed (eg versions 3.10, 3.11, 3.12, etc) you generally want to avoid have multiple copies installed (eg one in /Library/Frameworks and another in /usr/local/bin). Using the which command can help you keep track of which one you are using.

Aside: Python vs Python 3 vs Python 3.12

Note that using python3 instead of python3.12 should give identical results because this command’s intended behaviour is to default to using the latest installed version of Python 3:

$ python3 --version
$ which python3

If the above two commands give unexpected results then it is a sign that your computer is getting confused between multiple copies of Python; see the “Troubleshooting” section at the bottom of this page.

On the other hand, using just python with no numbers at the end will give errors on a fresh install of macOS Sonoma:

$ python --version
$ which python

The above will return zsh: command not found: python and python not found respectively. This marks a change from previous versions of macOS where these commands would have worked. Note that it’s possible to “alias” the python command to something else and thus to make it work, it’s just that it will fail by default on a fresh install of Sonoma.

Using Python with a Command-Line Interface (CLI)

Run the following in a terminal to open Python in interactive mode in that terminal:

$ python3.12

You can enter individual Python commands directly in at the >>> prompt and run them immediately by pressing enter. This is obviously not a user-friendly way to programme because it doesn’t save the commands you are using to a script file that you can then edit, but it’s useful for quickly checking something small. Exit by running exit().

If you do have a script file (one with the “.py” extension) you can run Python directly on it from the terminal:

Change into the directory where the file is located (using the “cd” command to change directory) and run the following (with the “.py” extension included):
```
$ python3.12 <filename>.py
```
As a matter of fact, you don’t actually need to change directory into the one where the script is located, you can just include the path to the file and it will work:
```
$ python3.12 <path_to_folder>/<filename>.py
```

If there is a space in the path or filename, you can surround them with quotation marks: "path to folder/file name.py".

Updating Python

When a new version of Python is released you can repeat the process of downloading it from the Python website and installing it. There will now be multiple copies of Python on your computer, which is fine. Make sure you always use a command like python3.12 as opposed to python3 or python to ensure you’re always using the version you intend to.

Note that, although it’s possible to update Python from the terminal, it doesn’t always work.

Installing Packages

The best option is to use the standard Python package manager: “pip”. The name “pip” is short for “Pip Installs Packages” - it’s an example of a recursive acronym. It means that we will never actually know what the first “p” in pip stands for.

Pip enables you to install packages with:

$ pip install <package_name>

…but it is recommended that you use the following format instead:

$ python3.12 -m pip install <package_name>

The -m flag stands for “module” and it means that Python 3.12 is running its pip module. This is useful because, as mentioned above, almost all macOS users will have multiple copies of Python - and multiple versions thereof - installed on their computers. This means that it’s important to explicitly say which version you are using. You want to guarantee that you are using the right instance of pip to install packages to the right instance of Python.

To install a bunch of the most useful packages in one go, run the following in the terminal to download all of these packages one after the other:

# NumPy is the fundamental package for scientific computing with Python
python3.12 -m pip install numpy
# SciPy ("Sigh Pie") is software for mathematics, science and engineering
python3.12 -m pip install scipy
# Statsmodels provides a complement to SciPy for statistical computations
python3.12 -m pip install statsmodels
# scikit-learn is a module for machine learning built on top of SciPy
python3.12 -m pip install scikit-learn
# Pandas is a powerful data analysis toolkit
python3.12 -m pip install pandas
# Matplotlib is for creating static, animated and interactive visualizations
python3.12 -m pip install matplotlib
# Seaborn allows for statistical data visualization based on Matplotlib
python3.12 -m pip install seaborn
# end

Check that this has worked by opening Python in the terminal with python3.12 and running:

import numpy
import scipy
import statsmodels
import sklearn
import pandas
import matplotlib
import seaborn

There should be no errors.

Upgrading Packages

To upgrade (update) a package called “<package_name>” simply run:

$ python3.12 -m pip install --upgrade <package_name>

To upgrade pip itself, run:

$ python3.12 -m pip install --upgrade pip

See What Version of Each Package You Have

To check what version of each package you have you can run:

$ pip freeze

…and to check what version of a specific package you have you can search the results of pip freeze like so:

$ pip freeze | grep <package_name>

To save the package version numbers to a file we can ‘pipe’ the output of pip freeze into a text file. By convention, this kind of file gets called requirements.txt because it contains the packages and versions that are required to run your project:

$ pip freeze >> requirements.txt

An even better option, however, is to install and use the pipreqs package (see here for more info):

$ python3.12 -m pip install pipreqs
$ pipreqs '.' --force

This creates the requirements.txt file using only the packages that are actually used by whatever Python files are in the folder your terminal is pointing at.

Troubleshooting: I’m suddenly getting a `ModuleNotFoundError` when it previously worked

If you previously installed packages and imported them into scripts with no problems but now suddenly find yourself getting ModuleNotFoundError messages it’s implying that it can no longer find those packages. It’s probably because you have multiple copies of Python installed on your computer - possibly not all with the same version number - and you installed those packages using one copy but are now running another copy. Check which you are using from the terminal by running:

$ which python3.12

If you are using Python via an IDE there should be some way to check which copy it is using. Make sure it is using the one you want. Alternatively, you could just re-download all the packages you need using the new copy of Python, or try to fix it:

Check your PATH:

Possibly the mix-up was caused by your PATH environment variable changing - maybe you installed a programme that prepended a new path at which a different instance of Python was found and this instance is now being given priority? Check your PATH variable via:

$ echo $PATH

If the location of your preferred instance of Python is not there - or does not appear at the start and hence does not have top priority - you can change this by editing your terminal’s environment variables. The best place to do this is in one of two hidden files in your home directory - either .zprofile or .zshrc. The terminal on macOS Sonoma uses “Z shell” and .zprofile and .zshrc are startup files that can be used to set the Z shell profile and the Z shell run commands, respectively. Generally, it is considered better practice to edit your PATH variable in .zprofile so as to reserve .zshrc for setting run commands in, but bear in mind that .zshrc is sourced after .zprofile and hence it has the potential to overwrite (or out-prioritise) anything that was set before it.

While it is true that there is potentially a third startup file - .zshenv - this is not a good place for editing the PATH variable because the order of the paths in PATH might change from what this file sets. The reason for this is that there is a utility called path_helper which gets run after .zshenv is sourced which might have the effect of re-ordering your PATH.

Let’s assume you’ve chosen to edit your PATH in .zprofile:

Open .zprofile in an editor (the below command will open it in the nano editor):
```
$ nano ~/.zprofile
```
Even if the file doesn’t exist (not all of the Z Shell startup files have to exist) the above will work because nano can create and open files in one step.
Add the following to the bottom of the file (this assumes you’ve downloaded Python 3.12 from the Python website and built it from source):
```
# Prepend a location for Python 3.12 to PATH
export PATH=/Library/Frameworks/Python.framework/Versions/3.12/bin:$PATH
```

You can also add the following (it removes duplicates from PATH):

# Remove duplicates from PATH (-U makes it *U*nique)
typeset -U PATH

Save and exit (in nano, this is done via Ctrl+O then Enter to save, then Ctrl+X to exit)
Close and re-open the terminal (or run source ~/.zprofile). Check the Python version via which python3.12 again and it should correspond to the one in the location you just added to .zprofile.

Create an alias:

Alternatively, it could be that the Python command you are running has been aliased to the wrong copy. Another option would be to add the following to .zshrc (as this is a run command):

# Create an alias for Python 3.12
alias python3.12=/Library/Frameworks/Python.framework/Versions/3.12/bin/python3.12

This will explicitly make python3.12 refer to the version of Python at this location. Again, save and exit .zshrc, close and re-open the terminal (or run source ~/.zshrc) and re-check which python3.12.

⇦ Back

macOS 10.12 (Sierra) to 13 (Ventura)

Installing and Setting up

While it is true that macOS comes with Python pre-installed on it (located in /usr/bin/) it is not recommended to use this pre-installed version. This is because it is out-of-date and, because some background macOS programmes rely on this out-of-date version in order to work, it is not recommended to update it.
A common solution to the above problem is to use “aliases” inserted into your terminal’s ‘settings’ files (eg ~/.bash_profile, ~/.zshrc or ~/.zprofile). This is no longer recommended either: these run commands are specific to a terminal instance and do not apply in situations where these setting folders are bypassed (eg when running Python from R Markdown which invokes bash -c python, not python)
The best option is to just download and install Python from scratch (so it will be installed multiple times on your computer, which is fine)
- Go to the Python website and download the latest version of Python (here’s a shortcut to immediately download Python 3.11)
- Double-click on the file that gets downloaded (if you downloaded version 3.11.0, for example, the file will be python-3.11.0-macos11.pkg) and follow the installation process
- macOS finishes the installation by opening the folder where Python was installed for you (/Applications/Python 3.11). You can just ignore that and close it
Check that it has worked by opening a terminal (press Cmd+Space to open Spotlight Search then search for “Terminal”) and running python3.11 --version. If it returns Python 3.11.0 (or whatever version you installed) then it’s all good.
You can check where this version of Python is installed by running which python3.11
- Usually it will be /Library/Frameworks/Python.framework/Versions/3.11/bin/python3.11
- This is a useful thing to remember if and when you have multiple instances of Python installed - while it’s ok to have multiple versions of Python installed (eg version 3.10 and 3.11) you generally want to avoid have multiple copies installed (eg one in /Library/Frameworks and another in /usr/local/bin). Using the which command can help you keep track of which one you’re using.

Using Python with a Command-Line Interface (CLI)

If you run python3.11 in a terminal you will open Python in interactive mode in that terminal. You can enter individual Python commands directly in at the >>> prompt and run them immediately by pressing enter. This is obviously not a user-friendly way to programme because it doesn’t save the commands you are using to a script file that you can edit, but it’s useful for quickly checking something small. Exit by running exit().
If you have a script file (one with the “.py” extension) you can run Python directly on it from the terminal:
- Change into the directory where the file is located (using the “cd” command to change directory) and run python <filename>.py (with the “.py” extension included)
- As a matter of fact, you don’t actually need to change directory into the one where the script is located, you can just run python <path_to_file>/<filename>.py and it will work

Updating Python

Although it’s possible to update Python from the terminal it doesn’t always work. Instead, every time there’s a new version available just download it from the Python website as described above and install it alongside your existing versions.

Installing Packages

The best option is to use the standard Python package manager, “pip”.

The name “pip” is short for “Pip Installs Packages”. It’s an example of a recursive acronym and it means that we will never actually know what the first “p” in pip stands for.

Pip enables you to install packages with:

# Install a package
pip install <package_name>

…but I recommend that you use this method instead:

# Run pip as a module (which is what is meant by "-m") of a specific Python
# version (in this case 3.11) in order to install a package
python3.11 -m pip install <package_name>

This will guarantee that you are installing the package to the correct version of Python. If you have multiple versions of Python and pip installed on your computer at the same time (and seeing as macOS comes with two versions of Python already pre-installed this will almost always be true!) it can get confusing as to what packages are being installed where.

To install a bunch of the most common packages in one go, run the following in the terminal:

# Mathematics & arrays
python3.11 -m pip install numpy
# Scientific & technical computing
python3.11 -m pip install scipy
# Plotting
python3.11 -m pip install matplotlib
# Data manipulation and analysis
python3.11 -m pip install pandas
# Symbolic computation
python3.11 -m pip install sympy
# Spreadsheet integration
python3.11 -m pip install xlwt
python3.11 -m pip install xlrd
python3.11 -m pip install openpyxl
# Pass arguments from the terminal
python3.11 -m pip install argparse
# Print to terminal in colour
# print(colored('hello', 'red'), colored('world', 'green'))
python3.11 -m pip install termcolor
# end

Check that it has worked by opening Python in the terminal with python3.11 then running:

import numpy
import scipy
import matplotlib
import pandas
import sympy
import xlwt
import xlrd
import openpyxl
import argparse
import termcolor

There should be no errors.

Upgrading Packages

To upgrade (update) a package called “<package_name>” simply run:

python3.11 -m pip install --upgrade <package_name>

To upgrade pip itself, run:

python3.11 -m pip install --upgrade pip

See What Version of Each Package You Have

To check what version of each package you have, you can run:

pip freeze

…and to check what version of a specific package you have, you can search the results of pip freeze like so:

pip freeze | grep <package_name>

pip freeze >> requirements.txt

An even better option, however, is to install and use the pipreqs package (see here for more info on pipreqs):

# Install pipreqs. The "python3.11" command should be changed to match the version of Python you have installed.
python3.11 -m pip install pipreqs
# Use pipreqs to create requirements.txt
pipreqs '.' --force

This creates the requirements.txt file using only the packages that are actually used by whatever Python files are in the folder your terminal is pointing at.

⇦ Back

Windows

The following works for Windows 7, 8 and 10.

Installing and Setting up

Download Python from the Python website
During installation, select “add Python to PATH”

Updating Python

The easiest way to update is just to install the latest version (again, from the Python website). You can have multiple versions of Python installed side-by-side without them interfering with each other.

Using Python from the Command-Line

Check that you have your “PATH” variable correct:
- Windows 7: Start > right-click on “Computer” > Properties > Advanced system settings > Environment Variables > edit the top one (path)
- Windows 10: Control Panel > System and Security > System - Advanced stystem settings > Environment Variables > edit the top one (path)
Append the following (with your username in place of “<username>”)

;C:/Users/<username>/AppData/Local/Programs/Python/Python36-32/

Open Command Prompt (if it is already open, close it and open it again) and run:

python

Python should open in the Command Prompt, showing you version and help information
- Exit Python with exit()
Run a Python script (a file with the “.py” extension) using python <filename> if the file is in the same folder as the one your Command Prompt is currently in or python <path_to_file>/<filename> if it is in a different folder.

Installing Packages

For most packages, use Python’s standard package manager “pip”. pip should come already installed with Python; double check this by running the following two separate commands from Command Prompt:
```
python
import pip
```
- If nothing happens (no errors appear), then all is good
- ‘pip2’ is the version of pip for Python 2, ‘pip3’ is for Python 3 and ‘pip’ uses whichever version of Python is installed
- Now that you are sure you have pip, you can use it directly from a new Command Prompt (or from the same Command Prompt after exiting Python with exit()) to install packages with:
```
python -m pip install --user <package_name>
```
When installing packages, rather install them one-by-one as opposed to all at once. This is because pip sometimes installs multiple packages at once but not sequentially, and so if something fails you don’t know what caused what.
Install most of the common packages with the following commands:

python -m pip install --user numpy
python -m pip install --user scipy
python -m pip install --user setuptools
python -m pip install --user python-dateutil
python -m pip install --user matplotlib
python -m pip install --user ipython
python -m pip install --user jupyter
python -m pip install --user pandas
python -m pip install --user sympy
python -m pip install --user nose
python -m pip install --user opencv-python
python -m pip install --user openpyxl
python -m pip install --user xlwt
python -m pip install --user xlrd
python -m pip install --user odfpy
python -m pip install --user Pillow
python -m pip install --user pygame
python -m pip install --user pyglet
python -m pip install --user moviepy
python -m pip install --user unidecode
python -m pip install --user httplib2
python -m pip install --user apiclient
python -m pip install --user sklearn

You can upgrade pip with:

python -m pip install --upgrade pip

⇦ Back

Fedora

This works for Fedora 22.

Installing and Setting up

There is no need to install Python on Fedora: it comes already installed. In fact, multiple versions of Python come pre-installed (these multiple installations can be found in the /usr/bin/ folder)
However, the version of Python that Fedora uses by default is version 2 (usually 2.7) even though it has Python 3 installed. This is not good; Python 2 is no longer supported so everyone should be using Python 3. Check which version you are using from the terminal with:
```
python --version
```
If this tells you that you are using Python 2 you should change this by running the following from a terminal*:
```
sudo update-alternatives --install /usr/bin/python python /usr/bin/python3 30
```
- You will be prompted to enter your computer password. This is needed because you are using the sudo (super doer) command which allows you to change your computer’s settings
- The update-alternatives command changes the symbolic links that determine what your commands do. In this case you are changing python to link to python3 instead of the default (which is python2).
- The 30 at the end means that you are giving python3 a priority of 30 over python2
Check that this has worked by running python --version again and seeing if this returns a Python 3 version number

Using Python from the Command-Line

If you open a terminal and run python you will open Python in that terminal. You can enter individual Python commands directly in at the >>> prompt and run them immediately by pressing enter. This is obviously not a user-friendly way to programme because it doesn’t save the commands you are using to a script file that you can edit, but it’s possible. Exit by running exit().
If you have a script file (one with the “.py” extension) you can run it from the terminal by changing into the directory where the folder is located (using the “cd” command to change directory) and running python <filename> with the “.py” extension included. In fact, you don’t actually need to change directory into the one where the script is located, you can just run python <path_to_file>/<filename> and it will work.

Installing Packages

The best option is to use the standard Python package manager, “pip” (aka pip3 for Python 3):

sudo dnf install python3-pip

Update pip with:

sudo pip3 install --update pip

Most of the common packages can be installed with:

sudo pip3 install numpy
sudo pip3 install scipy
sudo pip3 install matplotlib
sudo pip3 install ipython
sudo pip3 install jupyter
sudo pip3 install pandas
sudo pip3 install sympy
sudo pip3 install nose
sudo pip3 install xlwt
sudo pip3 install xlrd
sudo pip3 install pygame
sudo pip3 install pyyaml
sudo pip3 install pyserial
sudo pip3 install scikit-image
sudo pip3 install gpxpy
sudo pip3 install argparse
sudo pip3 install imageio
sudo pip3 install sklearn

If it says that pip3 is not a recognised command, reinstalling it might work:

sudo dnf reinstall python3-pip

⇦ Back

Introduction to Python:Getting Started

Choose your OS:

Ubuntu

Ubuntu 22.04

Running Python

Updating Python

Configuring Python

Installing Python Packages

Upgrading Packages

See What Version of Each Package You Have

Ubuntu 20.04

Installing and Setting Up

Using Python from the Terminal

Updating Python

Installing Packages

Upgrading Packages

See What Version of Each Package You Have

Ubuntu 16.04 to 18.04

macOS

macOS 14 (Sonoma)

What Not To Do

Downloading and Installing Python

Using Python with a Command-Line Interface (CLI)

Updating Python

Installing Packages

Upgrading Packages

See What Version of Each Package You Have

Troubleshooting: I’m suddenly getting a ModuleNotFoundError when it previously worked

macOS 10.12 (Sierra) to 13 (Ventura)

Installing and Setting up

Using Python with a Command-Line Interface (CLI)

Updating Python

Installing Packages

Upgrading Packages

See What Version of Each Package You Have

Windows

Installing and Setting up

Updating Python

Using Python from the Command-Line

Installing Packages

Fedora

Installing and Setting up

Using Python from the Command-Line

Installing Packages

Introduction to Python:
Getting Started

**What Not To Do**

Troubleshooting: I’m suddenly getting a `ModuleNotFoundError` when it previously worked