A multi-language overview on how to handle dependencies within a research project

Your future self and others should be able to recreate the minimal environment to run the scripts in your research project. This is best achieved using package managers and virtual environments.

This post is part of a series of posts on best practices for managing research project code. Much of this material was developed in collaboration with Mauro Werder as part of the Course On Reproducible Research, Data Pipelines, and Scientific Computing (CORDS). If you have experiences to share or spot any errors, please reach out!

Content

• Content
• Some definitions
  • What is a dependency?
  • What is a package manager?
  • What is a virtual environment?
• Package managers
  • Multilanguage overview
    • conda
    • renv
    • Pkg
  • Environment files
    • Julia
    • Python
    • R
  • Working with interactive environments
  • Caveats of virtual environments
• Advanced topic: package development
• Take-home messages

Some definitions

What is a dependency?

A dependency is an external package that a project requires to run.

What is a package manager?

A package manager like conda, Pkg or renv automates the process of installing, upgrading, configuring, and managing dependencies. It usually relies on a package repository, which is a central location that stores in one place the source code of packages or where to find it.

What is a virtual environment?

A virtual environment is an isolated environment where you can install and manage dependencies separately from the system-wide installation. This isolation ensures that different projects can have different dependencies and versions of packages without causing conflicts. Why use a virtual environment?

• For yourself, to best deal with multiple projects and to prevent your code from breaking down overtime.
  • Without specifying a virtual environment, you install packages in your base environment, which is shared across all your projects.
  • Imagine you are working with Project A and Project B, which both depend on Package1 (currently @v1.1).
  • You leave aside Project A for a few months, and focus on Project B.
  • A new feature in Package1 motivate you to upgrade to v1.2, which modifies the API or the behavior of one function used in both projects.
  • You then want to come back to Project A, but now everything is broken! Because your code has been formatted to work with Package1@v1.1.
  • Hence, you want to make sure to compartmentalize environments.
• To share your environment with others individuals and machines.
  • A virtual environement tracks the minimum dependencies, which can easily be shared and installed on other machines (e.g., a HPC).

Package managers

Multilanguage overview

This table is very much inspired by The Scientific Coder article on package managers.

Julia or R have built-in package managers which can be called within the REPL but Python package managers are called from outside the language.

conda

conda is a very appropriate package manager for scientific projects in Python. Over its older concurrent pip, it can handle python versions and all sorts non-python dependencies artifacts. With two lines of code, it allows someone to quickly install the virtual environment, without any pre-requiste python installation.

Here are some essential conda commands.

conda create --name myenv # creates new virtual environment
conda activate myenv # activate the environment
conda install numpy -c conda-forge # install a package
conda deactivate

Note that not using -c conda-forge will do just fine, but what is it? conda-forge is a community-driven channel (repository in the python jargon) that often has more up-to-date packages and a broader selection than the default Anaconda repository. You should use for several reasons, but mostly because conda-forge generally has the largest volume of packages and the most up-to-date versions

Note that some packages are only available through PyPi (pip). But you are covered for that: You can install pip packages within a conda env, by first activating the conda env and then normally using pip. pip should be part of your dependencies though. Always try to install packages using conda first.

We highly recommend using mamba as a drop-in replacement for conda, for much faster use.

Some useful resources

• A good resource for better understanding difference between mamba and conda, and their lightweights alternatives

• Advanced tutorial on using conda environments for a scientific project

• Tutorial on how to install a package directly from github repository

renv

Here are some basics on how to use renv, but see the renv vignette and documentation for more advanced usage.

# Initialize renv in your project
renv::init(project = "path/to/environment")

# Install a package and snapshot the environment
install.packages("dplyr")
renv::snapshot()

# Load the renv environment for the project
renv::activate()

# Restore the project's dependencies
renv::restore()

renv::update()

renv::history()
renv::revert()

Pkg

using Pkg

# Create a new project environment
Pkg.activate("path/to/MyProject")

# Add packages to the project environment
Pkg.add("DataFrames")

You can also use the Julia REPL by typing ]

(@v1.10) pkg> add DataFrames

or string macros pkg"add DataFrames"

Not that in Julia, the global shared environment is inherited in custom environment. This can be useful! It is a good idea to install utility packages that you will use for development but that are not mandatory to run your code in the global environment. For instance, the macro @btime from BenchmarkTools is very handy to profile code. But you may not want to have BenchmarkTools in your dependencies. Just install it in base, and then you will be able to call julia using BenchmarkTools within your custom environment. Other utility packages to consider having in your global environments are

• Test,
• TestEnv,
• Revise
• LocalRegistry

Environment files

Environment files specify the exact versions of the dependencies in your virtual environment, and are used by package managers to instantiate the environment. They are usually .txt, .toml or .yml files.

Always version control your environment files!

Julia

In Julia, the environment is defined using two files: the Project.toml and Manifest.toml. The Project.toml file lists the direct dependencies, while the Manifest.toml file captures the full dependency graph, including all transitive dependencies. The Manifest.toml file may not be tracked in a project, and will be reconstructed if missing. It specifies the exact version of the environment. For reproducibility, you want to include Manifest.toml in your git repo. Artifacts.toml is used to handle non-Julia package dependencies.

authors = ["Some One ",
           "Foo Bar "]
name = "MyEnv"
uuid = "7876af07-990d-54b4-ab0e-23690620f79a" # mandatory for packages
version = "1.2.5"
[deps]
DataFrames = “7876af07-990d-54b4-ab0e-23690620f79a”
Plots = “8dfed614-e22c-5e08-85e1-65c5234f0b40”
[compat]
CUDA = “4.4, 5”
julia = “1.10”

When you are located within the project root folder containing the .toml file, start julia with

$ julia --project=.

This will load the environment. If it is the first time that you use it, you need to instantiate it with

(Example) pkg> instantiate

Some useful resources

• see here for more info on Julia .toml files here

Python

conda env reads .yml, which can take any names. .yml files are not created automatically! Create environment.yml with

conda env export --name machine-learning-env --from-history --file environment.yml

This creates an environment.yml file

name: machine-learning-env
channels:

pytorch
conda-forge

dependencies:

pytorch=1.1

Not using --from-history will result in listing all dependencies, those installed explicitly AND implicitly. This may be a bit messier.

To specify pip packages, just insert in the .toml

  - pip=19.1
  - pip:
    - kaggle==1.5
    - yellowbrick==0.9

Note the double ‘==’ instead of ‘=’ for the pip installation and that you should include pip itself as a dependency and then a subsection denoting those packages to be installed via pip. Also, note that --from-history won’t catch the pip dependencies. So the best way to proceed is to specify the dependencies by hand.

Installing from environment.yml

mamba env create --prefix ./.env --file environment.yml

Some additional resources

• Good resource on managing packages with pip

R

Environments with renv are specified in a renv.lock and DESCRIPTION files. It is a JSON file that has two main components: R and Packages. The R component specifies the R version used and the list of repositories where packages were installed. The Packages component includes a record for each package used in the project, with all necessary details for reinstalling that exact version. These details are derived from the installed package’s DESCRIPTION file and cover installations from any source, including CRAN, Bioconductor, GitHub, Gitlab, and Bitbucket. For more information on supported sources, refer to vignette(“package-sources”).

{
  "R": {
    "Version": "4.3.3",
    "Repositories": [
      {
        "Name": "CRAN",
        "URL": "https://cloud.r-project.org"
      }
    ]
  },
  "Packages": {
    "markdown": {
      "Package": "markdown",
      "Version": "1.0",
      "Source": "Repository",
      "Repository": "CRAN",
      "Hash": "4584a57f565dd7987d59dda3a02cfb41"
    },
    "mime": {
      "Package": "mime",
      "Version": "0.12.1",
      "Source": "GitHub",
      "RemoteType": "github",
      "RemoteHost": "api.github.com",
      "RemoteUsername": "yihui",
      "RemoteRepo": "mime",
      "RemoteRef": "main",
      "RemoteSha": "1763e0dcb72fb58d97bab97bb834fc71f1e012bc",
      "Requirements": [
        "tools"
      ],
      "Hash": "c2772b6269924dad6784aaa1d99dbb86"
    }
  }
}

Working with interactive environments

Jupyter notebooks can use Pkg, conda and renv environments, but you may need some extra steps (see how to make Jupyter aware of your Conda environments here and there. You do not need to follow these steps if you are using Visual Studio Code.

Other interactive notebooks solutions store directly the environemnts in the files, which is great for reproducibility purposes. This is the case of Pluto notebooks, which are designed to be reproducible. Under the hood they contain the package environment inside them Binder notebooks also ship with a virtual environment, but using Docker (see below and a tutorial here).

I personally do not like notebooks, and prefer using scripts in Visual Studio Code, executing them line by line for development with whether the Julia extension or the Jupyter extension with "jupyter.interactiveWindow.textEditor.executeSelection": true. With such an approach, you can specify which virtual environment should be used at login, and never worry again with that later.

Caveats of virtual environments

Some packages/libraries rely on system libraries and utilities; for instance pytorch relies on CUDA drivers, which are specific to a certain machine (see how you can deal with CUDA drivers with conda here), or the behavior of the packages my be dependent on system environmental variables. As such, by replicating a virtual environment, you won’t necessarily reproduce the same exact computing environment. To reproduce more closely a computing environment, containers may be used. Containers virtualize layers of the operating system, replicating to a deeper lever your environment and making it more reproducible. Docker or Singularity are popular solutions. Unfortunately, building containers may be difficult, and the virtualization may add a layer of complexity to your pipeline… But see Using singularity as a development environment and How to remote dev with vscode and singularity. Note that you could use both a container and a virtual environment… See here a tutorial with renv.

Some additional resources For more information, check Reproducible Computational Environments Using Containers: Introduction to Docker.

Advanced topic: package development

It can make sense for research projects to distinguish between scripts placed in scripts/ and reused functions, models, etc., placed in src. We’ll cover that more broadly in another post. In such case, it is best to compartmentalize dependencies so as to have a minimal working environment for the src/ functions and classes, independent of that for your scripts. One practical approach for this is to specify the src folder as a package. This has a few advantages, including

• not having to deal with relative position of files to call the functions in src/
• maximizing your productivity by creating a generic package additionally to your main research project.

You can achieve this easily with development tools.

For Python, tools like setuptools and poetry facilitate package development. If you’re working in R, devtools is the go-to tool for developing packages. In Julia, the Pkg tool serves a similar purpose.

Package templates can be useful to simplify the creation of packages by generating package skeletons. In Python, checkout out cookiecutter. In R, check usethis. For Julia, use the Pkg.generate() built-in functionality, or the more advanced PkgTemplates.jl package.

Note that you may want at some point to locate your src/ (and associated tests, docs, etc…) in a separate git repo.

Some additional resources

• goodresearch tutorial on how to install a project package
• the Python Packages book offers comprehensive guidance using poetry.
• the R Packages book covers all aspects of package development.
• the Pkg documentation and this how-to guide for detailed instructions.

Take-home messages

• Make sure you understand what are package managers, virtual environments, and dependencies both within your project scripts and at the system level.
• Clearly document all dependencies and environment setup instructions in project repositories.
• Provide instructions in an Installation section in the readme.md on how to set up the virtual environment.
• Check out these toy research repositories in Julia (which uses relative paths for importing the src functions), Python (which has src as package), and R (which has src as package) that implement what I believe good examples of research projects!