Preserve your computing environment

Your analysis was done with specific versions of the program used (e.g. R 4.4.3) but also of all the packages involved, as well as the specifications of the Operating System (OS) that was used. The good use is that there are tools to let you systematically capture this information.

In R:

sessionInfo() or devtools::session_info() are great ways to capture this information. You should save it into a session_info.txt file to include in your GitHub repository

In Python:

pip freeze > requirements.txt will capture all the python modules installed in your current environment

Virtual environments

You can even go a step further and help others to recreate the same computing environment that you used independently of what versions you have installed on your machine.

Level up!

R

Here is a short introduction to renv, an R package that creates virtual environment to encapsulate your R work. source: https://rstudio.github.io/renv/articles/renv.html

We are going to add renv to our shorebird data cleaning project. Make sure you have the renv package installed:

install.packages("renv")

You may also choose Tools>Project Options>Environments and check “use renv for this project”

Or at the R console:

renv::init( )

Let’s check the new files that we have…

Look at the .gitignore
Look at the renv.lock file

Let’s say we reworked our script and suppose we would need the naniar R package to deal with the NAs. Let’s update or virtual environment:

renv::install("naniar")

Add some R code using this package, for example

library(naniar)

snowsurvey_csv %>% 
  miss_var_summary()

Alright, now that the installation is completed and we added this package to our code, we can save, and take a snapshot:

renv::snapshot()

This action will update the lock file, and we will see naniar and all its dependencies included.

Let’s check. If updated, you should be good to go. If your attempts to update packages introduced new problems, you may run renv::restore() to revert to the previous state as encoded in the lockfile.

Use .libPaths() to confirm where package installations are located!

Want to know more? here is a good resource to get started: https://rstudio.github.io/renv/articles/renv.html

Python

virtualenv is a tool to create Python virtual environments. In a nutsheel here are the steps to follow:

Create a new folder, your project folder. I will use first_example. Make sure you set the path to this folder.

Note: The environment will be created in the current version of Python that you are running (in Conda we can specify the version we want).

To create the environment: (second venv is the name of the environment)

python3 -m venv first_example

The -m flag makes sure you are creating a pip that is tied to the active Python executable

Time to activate it:

source first_example/bin/activate

You can tell it is activated because it shows (first_example) in the prompt.

Let’s check which packages are there with a new pip list

Nothing, right? Only setup tools, and pip). Nothing to worry about, it should be this way! Let’s proceed.

Install libraries:

We will be installing two packages for this example.

First:

pip install numpy

And then:

pip install pandas

This should take a little longer!

Another pip list

Alright, the packages and dependencies installed are right there!

Export and allow future replication of the environment:

Let’s save the packages and dependencies we have after the installs.

pip freeze

That should be stored in a `requirements.txt file

So let’s get it redirected to the required file:

pip freeze > requirements.txt

Question: This file won’t leave inside the venv folder, but rather in the project root folder any idea why?

Well, you only need that file to reproduce the environment. And the venv should be should throw away and be able to rebuild easily! So, do not include any project file in that folder and treat that as disposable after the pip freeze

To double-check if all is good, we can run the following command:

cat requirements.txt

This file should be included in your repository to let others reinstall your packages and dependencies as needed.

Deactivate

If you are done with that, you should deactivate that environment by typing:

deactivate

Then, you will see you no longer have the environment we created in our prompt.

If you are willing to delete the environment altogether, you should delete the directory for the virtual environment

Remove folder:

rm -rf first_example/

Reusing the Requirements

Create a new project folder to reuse the requirements

mkdir my_project

Create a virtual env for it

python3 -m venv my_project/venv

Activate it

source my_project/venv/bin/activate

Install required packages

pip install -r requirements.txt

Attention! Never include project files in the venv folder.
Do not commit your venv file to the environment itself to source control (git ignore)
You may install more packages and update the requirements.txt with the pip freeze command
You should commit /share only your requirements.txt file. That is all that others and your future self need to recreate the environment.
The environment should be something you should throw away and be able to rebuild easily.
Make sure to deactivate when done using it.

If you are using Conda

Checking what is in the system:

conda list

To create the environment:

conda create --name first_example

> proceed (\[y\]/n)? y

Time to activate it

conda activate first_example only work on conda 4.6 and later versions. For Conda versions prior to 4.6, run:

Windows: activate or Linux and macOS: source activate

You can tell it is activated because it shows (first_example) in the prompt.

Let’s check which packages are there with a new

conda list first_example

Empty, right? Nothing to worry about, it should be this way! Let’s proceed.

Install packages:

We will be installing two packages for this exercise.

First:

conda install numpy

> proceed (\[y\]/n)? y

And then, one more package:

conda install Pandas

> proceed (\[y\]/n)? y

Now check which packages are in the specific environment we are working on:

conda list

Alright, the packages and dependencies installed are right there!

Export and allow future replication of the environment:

Let’s save the packages and dependencies we have after the installs.

conda list --export

That should be stored in a environments.yml file

So let’s get it redirected to the required file:

conda list -e > environment.yml

This file should be included in your research compendium to let others reinstall your packages and dependencies as needed.

Deactivate it:

If you are done with that, you should deactivate that environment by typing:

conda deactivate

Note: only works on conda 4.6 and later versions. For conda versions before 4.6, run:

Windows: deactivate or Linux and macOS: source deactivate

Then, you will see you no longer have the environment we created in our prompt.

If you are willing to delete the environment altogether, you should delete the directory for the virtual environment

Back to base we can create a new environment based on the .yml packages and dependencies by running (this is noted on top of the yml file):

conda create --name my-env --file environment.yml

> proceed (\[y\]/n)? y

Activate it:

conda activate my-env (or see above if conda version \< 4.6)

proceed ([y]/n)? Y

Check if packages are there:

conda list

Remember to deactivate it when done:

conda deactivate (or see above if conda version \< 4.6)

Check all your environments conda env list

More info: https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html