Scientific Programming with Python

Procedure 1: Setting Up a Biopython Environment

Recall that working with Conda requires using a shell, a command-line interpreter that is available on both Macs and Windows; each statement must end with the key return (Macs) or Enter (Windows) to submit them for execution.

1. Launch a shell:
• On Windows: Menu Start> Anaconda3 > Anaconda PowerShell Prompt.
• On Macs: Navigate to the folder Applications and then the folder Utilities, and open the application Terminal.

A window will appear with a text prompt that looks something like:

(base) [username@hostname ~]$

If (base) appears, it represents the conda default environment; ~ is an abbreviation for your home folder.

2. Create a conda environment by typing, for example:

conda create -n biopython

Conda will provide some setup information and then ask if you want to Proceed ([y]/n)?; type y.

3. Activate this environment, for example:

conda activate biopython

Your prompt will now show this environment at its beginning, for example:

(biopython) [username@hostname ~]$

4. Install other packages into this environment, for example:

conda install biopython

Again, Conda will provide some setup information and then ask if you want to Proceed ([y]/n)?; type y.

5. Test that the package is available by running Python and loading one of its modules, for example:

python
import Bio

If the package is properly installed, there will be no response. Type exit() or ctrl-D to leave Python.

6. Also any other packages you might need, e.g. matplotlib: 

conda install matplotlib

7. To use a new environment with Spyder:
1. Install Spyder components in the environment:
   

conda install spyder-kernels=2.5

The version assignment seen here will install the appropriate version of this package for version 5 of Spyder, which is provided with the 2025 version of Anaconda.

2. Quit Spyder if it’s open.
3. Open Spyder.
4. Menu python > Preferences….
5. In the dialog Preferences, in the left-side list, choose Python interpretor:
   
   
6. In the section Python Interpreter, click on the button Use the following Python interpreter:.
7. In the menu of possible interpreters, all of your environments will be listed (note they will all be in a subfolder named envs). Select the option for your new environment, e.g. /opt/anaconda3/envs/biopython/bin/python.
8. Click on the button OK to both apply these changes and close the dialog.
9. In the pane iPython Console, in the upper right corner, menu ꠵ Options > Restart kernel.
10. Test that the environment and package(s) you just installed are available in Spyder by loading one of its modules, e.g.:

import Bio

If the environment and package(s) are properly installed, there will be no response.