Virtual Environments

We highly recommend installing SEISMIC-RNA into a virtual environment. Doing so will likely spare you much frustration well into the future. If you are not familiar with creating and managing virtual environments, then we recommend that you read this brief primer.

Why a virtual environment is worth the effort of setting it up

Virtually every piece of software that you use requires other pieces of software to be installed. Why? Because software developers want to focus on implementing their own ideas, rather than “re-inventing the wheel” by implementing algorithms that have already been written.

Suppose that you are developing a piece of software that requires linear algebra routines (e.g. matrix multiplication), as does SEISMIC-RNA. Because these routines are needed ubiquitously, algorithms that perform them have been distributed in many excellent software packages, such as NumPy for Python. Using a pre-made, well-tested package would save you all the time you would need to plan, code, test, debug, and optimize your own algorithms (which would take a lot of time). Thus, it would expedite the development of your project to borrow routine tasks from pre-existing software packages. This borrowing of code is called a “dependency”, and SEISMIC-RNA has dozens.

While dependencies alleviate issues of re-inventing the wheel, they can also cause problems if dependencies conflict with each other. Suppose you use two pieces of software regularly at work: call them software A version 1 (Av1) and software B version 1 (Bv1). Both are dependent on software C version 1 (Cv1). All goes well until Bv1 becomes deprecated and you need to update it to Bv2. Bv2 is incompatible with Cv1 and needs Cv2. But Av1 is incompatible with Cv2, and no upgrade is available that is compatible with Cv2. So you need to have two versions of software C installed simultaneously: Cv1 for Av1, and Cv2 for Bv2. How can you accomplish this feat without mixing up the two versions?

How a virtual environment lets conflicting sofware versions coexist

Virtual environments let you keep more than one version of a piece of software on one computer system, without uninstalling and reinstalling the software every time you needed to use a different version (which would, of course, be a pain). Instead, you can “activate” a “virtual environment” that contains the specific version you need. When finished using that version, you can “deactivate” the virtual environment, which hides that version of the software.

A virtual environment is simply a collection of software in which each piece of software has a specific version that you can control, as well as a list of its dependencies and their versions. The aforementioned example incompatibility among software A, B, and C could be solved by installing Av1 and Bv2 into separate virtual environments; call them venv1 and venv2, respectively. Into venv1, you would install Av1 and Cv1; and into venv2, you would install Bv2 and Cv2. If you needed to use softwareA, you would activate venv1 so that you could run Av1 and Av1 could see Cv1 (but not Cv2). Conversely, when you needed to use software B, you would activate venv2 so that you could run Bv2 and Bv2 could see Cv2 (but not Cv1).

Creating, activating, and deactivating virtual environments

Creation, deletion, activation, and deactivation of virtual environments is performed by a piece of software called an “environment manager”. Two popular environment managers for Python are venv (Python’s built-in virtual environment manager) and conda (the package manager for the Anaconda distribution of Python). If you are unsure of which to use, then we recommend conda because it is also a package manager (see Managing software in a virtual environment).

For example, to create a new virtual environment named seismic for SEISMIC-RNA using conda, you would enter the following command:

conda create -n seismic python=3.10

Note that Python 3.10 is currently the only version of Python that is compatible with SEISMIC-RNA and all of its dependencies.

To activate the environment seismic, enter the following command:

conda activate seismic

Note that it is advisable to give your virtual environments short names because you will need to type their names every time you activate them.

To deactivate the active virtual environment when you are finished, enter the following command:

conda deactivate

Note that you do not need to type the name of the environment after deactivate because this command simply deactivates the environment that is currently active.

Managing software in a virtual environment

It would be tedious (and risky) to install, uninstall, upgrade, and downgrade, and all of your software manually. Every time you changed a piece of software, you would need to install a compatible version of every one of its dependencies. Fortunately, these tasks can be automated using another piece of software called a “package manager”. (A “package” is just a specific version of a piece of software and all its code that you can download.) Two popular package managers for Python are pip (short for “Package Installer for Python”, Python’s official package manager) and conda, which is also an environment manager (see Creating, activating, and deactivating virtual environments).