Getting started with `manifesto`

The manifesto package provides tools for managing project environments in R using standardized TOML manifest files. These manifest files make project metadata, dependencies, and environment settings explicit and portable. This vignette introduces the core features of manifesto and demonstrates how to use it in typical R workflows.

library(manifesto)

Installation

You can install the stable version of manifesto from CRAN:

pak::pak('manifesto')

To install the development version from GitHub:

pak::pak('christopherkenny/manifesto')

Installing from a Manifest

For example purposes, we’ll use a manifest file included with the manifesto package. This file is located in the inst/examples directory of the package.

manifest_path <- system.file('complex.toml', package = 'manifesto')

To install all dependencies listed in a TOML manifest:

manifest_install(manifest_path)

To install with optional groups:

manifest_install(manifest_path, groups = 'dev')
manifest_install(manifest_path, groups = c('dev', 'ci'))

To preview what would be installed:

manifest_install(manifest_path, dry_run = TRUE)
#> 
#> ── Dry run: would install the following 3 packages ──
#> 
#> • dplyr@>=1.0.10
#> • BiocManager@>=1.30.10
#> • readr@2.1.4

Creating and Using a Manifest

Creating a Minimal Manifest

path <- manifest_create()
path
#> [1] "/tmp/RtmpUtD65y/file1f7846d608db.toml"

#> [manifesto]
#> version = "0.0.1"
#> 
#> [project]
#> name = "Project"
#> version = "0.0.1"
#> 
#> [environment]
#> r_version = "*"
#> 
#> [dependencies]

This creates a file with default sections:

• [manifesto] with the current package version
• [project] with name and version placeholders
• [environment] with a default R version
• [dependencies], initialized as an empty table

Example Manifest Files

Basic project manifest

In general, this structure is only useful when there are dependencies to specify. Suppose we want to list dplyr and ggplot2 as dependencies for our project. Here, we specify that we need dplyr version >= 1.0.0 and any version of ggplot2. (Practically, “any” version will be limited to versions that meet the R version requirement and match with other dependencies.)

Then run:

manifest_create(
  path = tempfile(fileext = '.toml'),
  name = 'myproject',
  r_version = '>= 4.2.0',
  dependencies = list(
    dplyr = '>= 1.0.0',
    ggplot2 = '*'
  )
)

This creates a manifest file with the following content:

[manifesto]
version = "0.0.1"

[project]
name = "myproject"
version = "0.1.0"

[environment]
r_version = ">= 4.2.0"

[dependencies]
dplyr = ">= 1.0.0"
ggplot2 = "*"

Adding optional dependency groups

Often, we need to specify optional dependencies for development, testing, or CI. We can do this by passing additional named arguments to manifest_create().

manifest_create(
  path = tempfile(fileext = '.toml'),
  name = 'myproject',
  r_version = '>= 4.2.0',
  dependencies = list(
    dplyr = '>= 1.0.0',
    ggplot2 = '*'
  ),
  'dev-dependencies' = list(
    testthat = '>= 3.1.0',
    lintr = '*'
  ),
  'ci-dependencies' = list(
    pkgdown = '*'
  )
)

[manifesto]
version = "0.0.1"

[project]
name = "myproject"
version = "0.1.0"

[environment]
r_version = ">= 4.2.0"

[dependencies]
dplyr = ">= 1.0.0"
ggplot2 = "*"

[suggests-dependencies]
testthat = ">= 3.0.0"
devtools = "*"

[ci-dependencies]
pkgdown = "*"

Including a package from GitHub

Not all packages are available on CRAN. You can include packages from GitHub or other sources by specifying additional details. Note that manifesto uses the pak package to handle these dependencies, so any source that pak supports can be used.

The corresponding call to manifest_create() would look like this:

manifest_create(
  path = tempfile(fileext = '.toml'),
  name = 'myproject',
  r_version = '>= 4.2.0',
  dependencies = list(
    dplyr = '>= 1.0.0',
    ggplot2 = '*',
    cli = '*'
  ),
  'dev-dependencies' = list(
    gh = list(source = 'github', repo = 'r-lib/gh', ref = 'v1.4.0')
  )
)

[manifesto]
version = "0.0.1"

[project]
name = "myproject"
version = "0.1.0"

[environment]
r_version = ">= 4.2.0"

[dependencies]
dplyr = ">= 1.0.0"
ggplot2 = "*"
cli = "*"

[dev-dependencies]
gh = { source = "github", repo = "r-lib/gh", ref = "v1.4.0" }

Using a local package path

You can also specify a local package path for development or testing purposes.

manifest_create(
  path = tempfile(fileext = '.toml'),
  name = 'myproject',
  r_version = '>= 4.2.0',
  dependencies = list(
    dplyr = '>= 1.0.0'
  ),
  'dev-dependencies' = list(
    mydevpkg = list(source = 'local', path = '../mydevpkg')
  )
)

[manifesto]
version = "0.0.1"

[project]
name = "myproject"
version = "0.1.0"

[environment]
r_version = ">= 4.2.0"

[dependencies]
dplyr = ">= 1.0.0"

[dev-dependencies]
mydevpkg = { source = "local", path = "../mydevpkg" }

These examples reflect common patterns for specifying runtime, development, CI, and local dependencies.

Validating a Manifest

You can validate the structure and content of a manifest with:

manifest_validate(path = manifest_path)

This checks for required sections, valid dependency specifications, and correct field usage.

Example Workflow

In general, you only have to create and share a file. You can use the manifest_create() function to create a manifest file. Then anyone with the file can use manifest_install() to install the dependencies. manifesto is a generally lightweight package, so it should not add much overhead to your workflow.

The use of groups allows you to specify different sets of dependencies for different purposes, such as development, testing, or for workshops. The original motivation was as a workshop tool, but has expanded a bit to allow for more general use.

1. Creating a new manifest with common dependencies

manifest <- manifest_create(
  path = tempfile(fileext = '.toml'),
  name = 'myproject',
  version = '0.1.0',
  r_version = '>= 4.2.0',
  dependencies = list(
    dplyr = '>= 1.0.0',
    ggplot2 = '*',
    glue = '*'
  ),
  'dev-dependencies' = list(
    testthat = '>= 3.1.0',
    lintr = '*'
  )
)

This creates a manifest for an R project that uses dplyr and ggplot2, with development tools like testthat grouped separately.

2. Installing core and dev dependencies

manifest_install(manifest, groups = 'dev', dry_run = TRUE)
#> 
#> ── Dry run: would install the following 5 packages ──
#> 
#> • dplyr@>=1.0.0
#> • ggplot2
#> • glue
#> • testthat@>=3.1.0
#> • lintr

This installs everything from [dependencies] and [dev-dependencies]. Here, for CRAN purposes, dry_run = TRUE means no packages are installed, but the output shows what would be installed.

The general idea then is that dependencies must always be installed. Groups like dev would be used for development or testing.

3. Installing all dependencies

The special group name all is reserved to allow a user to install everything in the manifest.

manifest_install(manifest, groups = 'all', dry_run = TRUE)
#> 
#> ── Dry run: would install the following 5 packages ──
#> 
#> • dplyr@>=1.0.0
#> • ggplot2
#> • glue
#> • testthat@>=3.1.0
#> • lintr

By default, only [dependencies] is installed, whereas all installs everything.

Manifest File Structure

A valid TOML manifest must contain the following top-level sections:

• [manifesto] (required)
  • version: (required) should match the version of the manifesto package used to generate it.
• [project] (required)
  • name: (required) the name of the project.
  • version: (required) the version of the project.
  • authors: (optional) an array of tables with fields such as name, email, and roles.
• [environment] (required)
  • r_version: (required) a valid R version requirement string (e.g., “>= 4.2.0”).
• [dependencies] (required)
  • List of core package dependencies (name = version).

Optional groups:

• [<group>-dependencies] (optional)
  • Named groups such as dev, suggests, ci, enhances, workshop, etc.
  • Each contains its own set of package references.

Each package reference may be: - A version string (e.g., “>= 1.0.0”) - A table with source, repo, ref, or url (e.g., for GitHub, GitLab, or custom sources)

Examples:

gh = { source = "github", repo = "r-lib/gh", ref = "v1.4.0" }
custompkg = { source = "url", url = "https://example.com/custompkg.tar.gz" }

Converting from DESCRIPTION to Manifest

manifest_desc <- tempfile(fileext = '.toml')
manifest_from_description(
  system.file(package = 'cli', 'DESCRIPTION'),
  path = manifest_desc
)

#> [manifesto]
#> version = "0.0.1"
#> 
#> [project]
#> name = "cli"
#> version = "3.6.5"
#> authors = [
#>     { name = "Gábor Csárdi", email = "gabor@posit.co", roles = ["aut", "cre"] },
#>     { name = "Hadley Wickham", roles = "ctb" },
#>     { name = "Kirill Müller", roles = "ctb" },
#>     { name = "Salim Brüggemann", email = "salim-b@pm.me", roles = "ctb" },
#>     { name = "Posit Software, PBC", roles = ["cph", "fnd"] }
#> ]
#> 
#> [environment]
#> r_version = ">= 3.4"
#> 
#> [dependencies]
#> utils = "*"
#> 
#> [suggests-dependencies]
#> callr = "*"
#> covr = "*"
#> crayon = "*"
#> digest = "*"
#> glue = ">= 1.6.0"
#> grDevices = "*"
#> htmltools = "*"
#> htmlwidgets = "*"
#> knitr = "*"
#> methods = "*"
#> processx = "*"
#> ps = """
#> >=
#> 1.3.4.9000"""
#> rlang = ">= 1.0.2.9003"
#> rmarkdown = "*"
#> rprojroot = "*"
#> rstudioapi = "*"
#> testthat = ">= 3.2.0"
#> tibble = "*"
#> whoami = "*"
#> withr = "*"

This uses fields from the DESCRIPTION file to populate:

• Project name and version
• Author information
• R version from Depends
• Dependency sections such as Imports, Suggests, LinkingTo, and Enhances

Converting from Manifest to DESCRIPTION

description_path <- tempfile(pattern = 'DESCRIPTION')
manifest_to_description(manifest_desc, out = description_path)

#> Package: cli
#> Version: 3.6.5
#> Title: TODO Title
#> Description: TODO Description
#> License: TODO License
#> Encoding: UTF-8
#> Authors@R: c( person("Gábor", "Csárdi", email = "gabor@posit.co", role
#>         = c("aut", "cre")), person("Hadley", "Wickham", role =
#>         c("ctb")), person("Kirill", "Müller", role = c("ctb")),
#>         person("Salim", "Brüggemann", email = "salim-b@pm.me", role =
#>         c("ctb")), person("Posit Software,", "PBC", role = c("cph",
#>         "fnd")) )
#> Depends: R (>= 3.4)
#> Imports: utils
#> Suggests: callr, covr, crayon, digest, glue (>= 1.6.0), grDevices,
#>         htmltools, htmlwidgets, knitr, methods, processx, ps (>=
#>         1.3.4.9000), rlang (>= 1.0.2.9003), rmarkdown, rprojroot,
#>         rstudioapi, testthat (>= 3.2.0), tibble, whoami, withr

Required DESCRIPTION fields such as Title, Description, and License are filled with placeholder TODO values if missing. Author information is translated into Authors@R format.

It’s very important to note that these types of files have different purposes. Not all fields in a DESCRIPTION file are required in a manifest file, so conversion can be lossy.

Learn More

For complete documentation, visit:

https://github.com/christopherkenny/manifesto

This package is intended to streamline environment specification and improve reproducibility in R projects.

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DISCLAIMER: This vignette has been written with help from ChatGPT 4o. It has been reviewed for correctness and edited for clarity by the package author. Please note any issues at https://github.com/christopherkenny/manifesto/issues.