Package 'repro'

Automate the use of Docker & Make

Description

automate() & friends use yaml metadata from RMarkdowns to create Dockerfile's and Makefile's. It should be clear which is created by automate_docker() & which by automate_make().

Usage

automate(path = ".")

automate_make(path = ".")

automate_publish(path = ".")

automate_docker(path = ".")

Arguments

path	Where should we look for RMarkdowns?

See Also

automate_load_packages(), automate_load_data(), automate_load_scripts()

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Access repro YAML Metadata from within the document

Description

• automate_load_packages() loads all packages listed in YAML via library()

• automate_load_scripts() registeres external scripts via knitr::read_chunk()

• automate_load_data() reads in the data from the yaml with abitrary functions

Usage

automate_load_packages()

automate_load_scripts()

automate_load_data(data, func, ...)

Arguments

data	How is the entry in the YAML called? It will be the name of the object.
func	Which function should be used to read in the data? Its first argument must be the path to the file.
...	Further arguments supplied to func.

Value

automate_load_packages() & automate_load_scripts() do not return anything. automate_load_data() returns the data.

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Check System Dependencies

Description

Check if a dependency is installed and if not it recommends how to install it depending on the operating system. Most importantly it checks for git, make & docker. And just for convenience of the installation it checks on OS X for Homebrew and on Windows for Chocolately.

Usage

check_docker()

check_make()

check_git()

check_brew()

check_choco()

check_ssh(install = getOption("repro.install"))

check_github_token(install = getOption("repro.install"))

check_github_token_access()

check_github_ssh()

check_github(auth_method = "token")

check_renv(install = getOption("repro.install"))

check_targets(install = getOption("repro.install"))

check_worcs(install = getOption("repro.install"))

Arguments

install	Should something be installed? Defaults to "ask", but can be TRUE/FALSE.
auth_method	How do you want to authenticate with GitHub? Either "token" (default) or "ssh".

See Also

Other checkers: check_package(), has_package(), has, uses

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Check if package exists

Description

Check if package exists

Usage

check_package(pkg, install = getOption("repro.install"), github = NULL)

Arguments

pkg	Which package are we talking about?
install	Should we install the package in case its missing?
github	A github username/package from which the package is installed. If NULL (the default) CRAN (or whatever repo) you have set is used.

See Also

Other checkers: check, has_package(), has, uses

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Report Current Hash

Description

Find out what the currently checked out commit is and report its respective hash.

Usage

current_hash(length = 7L, backend = NULL)

Arguments

length	The length to which the hash is cut.
backend	Can be either of NULL, "gert", or "git". If NULL Git is used with preference and gert as a fallback.

---

Use Docker

Description

Add or modify the Dockerfile in the current project.

Usage

use_docker(
  rver = NULL,
  stack = "verse",
  date = Sys.Date(),
  file = "Dockerfile",
  open = TRUE
)

use_dockerignore(file, open = TRUE)

Arguments

rver	Which r version to use, defaults to current version.
stack	Which stack to use, possible values are c("r-ver", "rstudio", "tidyverse", "verse", "geospatial").
date	Which date should be used for package instalation, defaults to today.
file	Which file to save to
open	Open the newly created file for editing? Happens in RStudio, if applicable, or via utils::file.edit() otherwise.

---

Generate the weird format for docker on windows.

Description

Generate the weird format for docker on windows.

Usage

docker_windows_path(path = NULL, todo = interactive())

Arguments

path	Some windows path. If NULL the current directory.
todo	Should an actionable advice be given. Defaults to TRUE.

---

Check System Dependencies

Description

Corresponding functions to check, but intended for programatic use.

Usage

has_make(silent = TRUE, force_logical = TRUE)

has_git(silent = TRUE, force_logical = TRUE)

has_docker(silent = TRUE, force_logical = TRUE)

has_docker_running(silent = TRUE, force_logical = TRUE)

has_choco(silent = TRUE, force_logical = TRUE)

has_brew(silent = TRUE, force_logical = TRUE)

has_ssh(silent = TRUE, force_logical = TRUE)

has_github_token(silent = TRUE, force_logical = TRUE)

has_github_token_access(silent = TRUE, force_logical = TRUE)

has_github_ssh(silent = TRUE, force_logical = TRUE)

has_github(silent = TRUE, force_logical = TRUE)

has_renv(silent = TRUE, force_logical = TRUE)

has_targets(silent = TRUE, force_logical = TRUE)

has_worcs(silent = TRUE, force_logical = TRUE)

has_gert(silent = TRUE, force_logical = TRUE)

Arguments

silent	Should a message be printed that informs the user?
force_logical	Should the return value be passed through isTRUE?

See Also

Other checkers: check_package(), check, has_package(), uses

---

Check if package exists

Description

Check if package exists

Usage

has_package(pkg, silent = TRUE, force_logical = TRUE)

Arguments

pkg	Which package are we talking about?
silent	Should a message be printed that informs the user?
force_logical	Should the return value be passed through isTRUE?

See Also

Other checkers: check_package(), check, has, uses

---

Use Make

Description

Add a (GNU-)Makefile(s) with special emphasis on the use of containers.

Usage

use_make(
  docker = FALSE,
  publish = FALSE,
  singularity = FALSE,
  torque = FALSE,
  open = TRUE
)

use_make_docker(file, use_docker = TRUE, dockerignore = TRUE, open = FALSE)

use_make_singularity(file, use_singularity = TRUE, open = FALSE)

use_make_publish(file, open = FALSE)

Arguments

docker	If true or a path a setup is created that can partially send make commands to a Docker container.
publish	Should the Makefile_publish also be created?
singularity	If true or a path a setup is created that can partially send make commands to a Singularity container (which requires the Dockerimage)
torque	If true a or a path setup is created that can partially send make comands to a TORQUE job scheduler. Especially usefull in combination with a Singularity container.
open	Open the newly created file for editing? Happens in RStudio, if applicable, or via utils::file.edit() otherwise.
file	Path to the file that is to be created.
use_docker	If true use_docker() is called.
dockerignore	If true a .dockerignore file is created.
use_singularity	If true use_singularity() is called.

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Find entrypoint for analysis and suggest how to reproduce it.

Description

reproduce() inspects the files of a project and suggest a way to reproduce the project.

Usage

reproduce(fun, ..., path = ".", cache = FALSE, silent = FALSE)

reproduce_make(path, cache = FALSE, silent = FALSE)

Arguments

fun	a function that inspects dir and advises on how to reproduce the analysis. Defaults to reproduce_funs.
...	more functions like fun.
path	Were should I look for entrypoints?
cache	Default is FALSE. Some entrypoints have a cache, which you probably do not want to use in a reproduction.
silent	Should a message be presented?

Details

reproduce() walks through a list of functions that check for a specific entrypoint. As soon as a function returns a possible entrypoint the search stops. If no function is supplied the standard list of reproduce_funs is used.

Value

Returns invisibly the command users should use to reproduce.

See Also

reproduce_funs

---

A list of functions to detect entrypoints.

Description

At the moment only reproduce_make is available.

Usage

reproduce_funs

Format

An object of class list of length 1.

Details

reproduce_make detects make as an entrypoint if there is a Makefile at top level. If it does also encounter a Makefile_Docker somewhere it recognizes the different make instructions.

See Also

reproduce

---

Find entrypoint for analysis and suggest how to reproduce it.

Description

rerun() was renamed to reproduce(). rerun() is deprecated.

Usage

rerun(...)

Arguments

...	passed to reproduce().

See Also

reproduce_funs

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Create repro template

Description

Fills a newly created folder with examples of RMarkdown, scripts, and data, which work well with automate().

Usage

repro_template(path, ...)

use_repro_template(path, ...)

Arguments

path	character specifieng target folder. Will be created if it doesn't exist.
...	Passed down to the markdown template.

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Add dependencies to Dockerfile

Description

Adds package dependencies as a new RUN statement to Dockerfile. Sorts packages first into source (cran & github) and then alphabetically.

Usage

use_docker_packages(
  packages,
  github = NULL,
  strict = TRUE,
  file = "Dockerfile",
  write = TRUE,
  open = write,
  append = TRUE
)

Arguments

packages	Which packages to add.
github	Are there github packages?
strict	Defaults to TRUE, force a specific version for github packages.
file	Where is the 'Dockerfile'?
write	Should the 'Dockerfile' be modified?
open	Should the file be opened?
append	Should the return value be appended to the 'Dockerfile'?

---

Use GitHub Action to Build Dockerimage

Description

Add an standard actions that builds and publishes an Dockerimage from the Dockerfile.

Usage

use_gha_docker(file = getOption("repro.gha.docker"), open = TRUE)

Arguments

file	Which file to save to.
open	Open the newly created file for editing? Happens in RStudio, if applicable, or via utils::file.edit() otherwise.

---

Use GitHub Action to Publish Results

Description

Add an standard actions that builds the publish-target, and publishes the results on the gh-pages branch. Requires a Dockerimage published within the same GitHub repository. See use_gha_docker().

Usage

use_gha_publish(file = getOption("repro.gha.publish"), open = TRUE)

Arguments

file	Which file to save to.
open	Open the newly created file for editing? Happens in RStudio, if applicable, or via utils::file.edit() otherwise.

---

Deal with templates that are themselves whisker templates.

Description

If a template is itself used again as a whisker template, we need some other escape mechanism. The repro-template than uses ⁠[[]]⁠ instead of {{}} which are than later reinstated.

Usage

use_template_template(
  template,
  save_as = template,
  escape = c(`\\[\\[` = "{{", `\\]\\]` = "}}"),
  data = list(),
  ignore = FALSE,
  open = FALSE,
  package = "repro"
)

Arguments

template	usethis::use_template()
save_as	usethis::use_template()
escape	named vector, name is replacement (default curly), value is placeholder (default square)
data	usethis::use_template()
ignore	usethis::use_template()
open	usethis::use_template()
package	usethis::use_template()

---

Check Project Configuration

Description

Check if a project uses certain things, e.g. Make or Docker.

Usage

uses_make(silent = FALSE)

uses_docker(silent = FALSE)

uses_gha_docker(silent = FALSE)

uses_gha_publish(silent = FALSE)

uses_make_publish(silent = FALSE)

uses_make_rmds(silent = FALSE)

Arguments

silent

Defaults to false. Should a message be printed that informs the user?

See Also

Other checkers: check_package(), check, has_package(), has

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