Merge pull request #326 from vimc/vimc-7040

add orderly_packages method

Author: richfitz

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: orderly
 Title: Lightweight Reproducible Reporting
-Version: 1.5.1
+Version: 1.6.0
 Description: Order, create and store reports from R.  By defining a
     lightweight interface around the inputs and outputs of an
     analysis, a lot of the repetitive work for reproducible research
@@ -46,7 +46,7 @@ Suggests:
     rmarkdown,
     testthat,
     vaultr (>= 1.0.4)
-RoxygenNote: 7.2.0
+RoxygenNote: 7.2.3
 Roxygen: list(markdown = TRUE)
 VignetteBuilder: knitr
 Language: en-GB

NAMESPACE

@@ -35,6 +35,7 @@ export(orderly_log_off)
 export(orderly_log_on)
 export(orderly_migrate)
 export(orderly_new)
+export(orderly_packages)
 export(orderly_pull_archive)
 export(orderly_pull_dependencies)
 export(orderly_push_archive)

R/info.R

@@ -71,3 +71,21 @@ orderly_info <- function(id, name, root = NULL, locate = TRUE) {
     error = error
   )
 }
+
+##' Return details of packages required by all src reports in this orderly repo
+##'
+##' @inheritParams orderly_list
+##'
+##' @return List of packages required by all src reports
+##' @export
+##'
+##' @examples
+##' path <- orderly::orderly_example("minimal")
+##' orderly::orderly_packages(root = path)
+orderly_packages <- function(root = NULL, locate = TRUE) {
+  cfg <- orderly_config(root, locate)
+  names <- basename(list_dirs(path_src(cfg$root)))
+  packages <- lapply(names,
+                     function(name) orderly_recipe$new(name, cfg)$packages)
+  unique(as.list(unlist(packages)))
+}

_pkgdown.yml

@@ -99,6 +99,7 @@ reference:
     contents:
       - orderly_example
       - orderly_run_info
+      - orderly_packages
       - orderly_log
       - orderly_log_off
       - orderly_log_on

inst/examples/minimal/src/example/orderly.yml

@@ -6,3 +6,4 @@ artefacts:
   staticgraph:
     description: A graph of things
     filenames: mygraph.png
+

inst/examples/minimal/src/example2/orderly.yml

@@ -0,0 +1,10 @@
+data:
+  dat:
+    query: SELECT name, number FROM thing
+script: script.R
+artefacts:
+  staticgraph:
+    description: A graph of things
+    filenames: mygraph.png
+packages:
+  - withr

inst/examples/minimal/src/example2/script.R

@@ -0,0 +1,4 @@
+png("mygraph.png")
+par(mar = c(15, 4, .5, .5))
+barplot(setNames(dat$number, dat$name), las = 2)
+dev.off()

man/orderly_config.Rd

@@ -0,0 +1,9 @@
+packages:
+  - dplyr
+  - readr
+  - stringr
+script: script.R
+artefacts:
+  staticgraph:
+    description: A graph of things
+    filenames: mygraph.png

man/orderly_log.Rd

@@ -0,0 +1,6 @@
+packages: stringr
+script: script.R
+artefacts:
+  staticgraph:
+    description: A graph of things
+    filenames: mygraph.png

man/orderly_packages.Rd

@@ -4,7 +4,7 @@ test_that("cleanup nothing", {
   path <- test_prepare_orderly_example("minimal")
   out <- capture_logs(orderly_cleanup(root = path))
   expect_null(out$result)
-  expect_equal(orderly_list(root = path), "example")
+  expect_equal(orderly_list(root = path), c("example", "example2"))
   expect_match(out$messages, "Found 0 draft reports", all = FALSE)
   expect_match(out$messages, "Found 0 csv files", all = FALSE)
   expect_match(out$messages, "Found 0 rds files", all = FALSE)

man/orderly_run.Rd

@@ -74,3 +74,20 @@ test_that("info errors if fails to find report rds", {
       id),
     fixed = TRUE)
 })
+
+test_that("can retrieve package info", {
+  path <- test_prepare_orderly_example("packages", testing = TRUE)
+  packages <- orderly_packages(path)
+  expect_length(packages, 3)
+  expect_equal(class(packages), "list")
+  expect_equal(packages[[1]], "dplyr")
+  expect_equal(packages[[2]], "readr")
+  expect_equal(packages[[3]], "stringr")
+})
+
+test_that("can retrieve empty package info", {
+  path <- test_prepare_orderly_example("changelog", testing = TRUE)
+  packages <- orderly_packages(path)
+  expect_length(packages, 0)
+  expect_equal(class(packages), "list")
+})

man/orderly_search.Rd

@@ -15,7 +15,7 @@ test_that("run", {
   expect_identical(res$target, main_do_run)
 
   capture.output(res$target(res))
-  expect_equal(orderly_list(path), "example")
+  expect_equal(orderly_list(path), c("example", "example2"))
   expect_equal(nrow(orderly_list_archive(path)), 1)
 })
 
@@ -36,7 +36,7 @@ test_that("run: id-file", {
   expect_identical(res$target, main_do_run)
 
   capture.output(res$target(res))
-  expect_equal(orderly_list(path), "example")
+  expect_equal(orderly_list(path), c("example", "example2"))
 
   expect_true(file.exists(id_file))
   id <- readLines(id_file)
@@ -302,7 +302,7 @@ test_that("list", {
   args <- c("--root", path, "list")
   res <- cli_args_process(args)
 
-  expect_output(res$target(res), "^example$")
+  expect_output(res$target(res), "^example\\nexample2$")
 
   for (i in c("names", "drafts", "archive")) {
     expect_equal(
@@ -420,7 +420,7 @@ test_that("list", {
   orderly_commit(id2, root = path)
 
   res <- cli_args_process(c("--root", path, "list", "names"))
-  expect_equal(capture.output(res$target(res)), "example")
+  expect_equal(capture.output(res$target(res)), c("example", "example2"))
 
   res <- cli_args_process(c("--root", path, "list", "drafts"))
   out1 <- capture.output(res$target(res))
@@ -697,7 +697,7 @@ test_that("run can save workflow metadata", {
   expect_equal(res$options$workflow_id, "123")
 
   capture.output(res$target(res))
-  expect_equal(orderly_list(path), "example")
+  expect_equal(orderly_list(path), c("example", "example2"))
   expect_equal(nrow(orderly_list_archive(path)), 1)
   id <- orderly_list_archive(path)$id
   rds <- path_orderly_run_rds(file.path(path, "archive", "example", id))

tests/testthat/examples/packages/orderly_config.yml

@@ -15,13 +15,13 @@ test_that("empty", {
 
 test_that("non-empty", {
   path <- test_prepare_orderly_example("minimal")
-  expect_equal(orderly_list(path), "example")
+  expect_equal(orderly_list(path), c("example", "example2"))
 })
 
 test_that("query through lifecycle", {
   skip_on_cran_windows()
   path <- test_prepare_orderly_example("minimal")
-  expect_equal(orderly_list(root = path), "example")
+  expect_equal(orderly_list(root = path), c("example", "example2"))
 
   empty <- data.frame(name = character(0), id = character(0),
                       stringsAsFactors = FALSE)