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Allow package version designation for CRAN packages w/ estimator #310

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merged 13 commits into from
Apr 9, 2020
Merged

Allow package version designation for CRAN packages w/ estimator #310

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7e5769c
add package version handling
diondrapeck Apr 4, 2020
16fe489
add example of cran version
diondrapeck Apr 4, 2020
bcf8b9c
remove whitespace
diondrapeck Apr 6, 2020
7aa0852
refactor
diondrapeck Apr 6, 2020
d954ed9
update tests
diondrapeck Apr 6, 2020
faf8d94
add cran_package object constructor
diondrapeck Apr 8, 2020
0907680
add cran_package object
diondrapeck Apr 9, 2020
13019d2
update estimator example to include cran_package
diondrapeck Apr 9, 2020
106ec36
update tests
diondrapeck Apr 9, 2020
526d2ab
update estimators in vignettes
diondrapeck Apr 9, 2020
f29d4de
update man files
diondrapeck Apr 9, 2020
2ab51f0
update estimator test
diondrapeck Apr 9, 2020
6e32e4d
add cran_package to ref page
diondrapeck Apr 9, 2020
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19 changes: 16 additions & 3 deletions R/environment.R
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Original file line number Diff line number Diff line change
Expand Up @@ -256,10 +256,23 @@ generate_docker_file <- function(custom_docker_image = NULL,

if (!is.null(cran_packages)) {
for (package in cran_packages) {

# parse to split package name from version, if version provided
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package_info <- strsplit(package, "==")[[1]]
package_name <- package_info[1]
version <- NULL

if (length(package_info) == 2) {
version <- sprintf(" version = \'%s\',", package_info[2])
}

base_dockerfile <- paste0(
base_dockerfile,
sprintf("RUN R -e \"install.packages(\'%s\', ", package),
"repos = \'https://cloud.r-project.org/\')\"\n")
base_dockerfile,
paste0(sprintf("RUN R -e \"remotes::install_version(\'%s\',",
package_name),
version,
" repos = \'https://cloud.r-project.org/\')\"\n")
)
}
}

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7 changes: 7 additions & 0 deletions R/estimator.R
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Expand Up @@ -71,6 +71,13 @@
#' objects to use as input.
#' @return The `Estimator` object.
#' @export
#' @section Examples:
#' ```
#' est <- estimator(source_directory = ".",
#' entry_script = "train.R",
#' cran_packages = c("ggplot2==3.3.0", "stringr"),
#' compute_target = compute_target)
#' ```
#' @seealso
#' \code{\link{r_environment}}
#' \code{\link{container_registry}}
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12 changes: 12 additions & 0 deletions man/estimator.Rd
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16 changes: 12 additions & 4 deletions tests/testthat/test_environment.R
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Expand Up @@ -50,14 +50,22 @@ test_that("create dockerfile", {
", repos = 'https://cloud.r-project.org/', ",
"upgrade = FALSE)\"\n"))

# cran packages
# cran packages w/o version
dockerfile <- generate_docker_file(custom_docker_image = "ubuntu-18.04",
cran_packages = c("ggplot2"),
install_system_packages = FALSE)
expect_equal(dockerfile, paste0("FROM ubuntu-18.04\nRUN R -e \"install.",
"packages('ggplot2', repos = \'https://",
expect_equal(dockerfile, paste0("FROM ubuntu-18.04\nRUN R -e \"remotes::install_version",
"('ggplot2', repos = \'https://",
"cloud.r-project.org/\')\"\n"))


# cran packages w/ version
dockerfile <- generate_docker_file(custom_docker_image = "ubuntu-18.04",
cran_packages = c("ggplot2==0.0.0"),
install_system_packages = FALSE)
expect_equal(dockerfile, paste0("FROM ubuntu-18.04\nRUN R -e \"remotes::install_version",
"('ggplot2', version = '0.0.0', repos = \'https://",
"cloud.r-project.org/\')\"\n"))

# github packages
dockerfile <- generate_docker_file(github_packages = c(
"https://github/user/repo1",
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