lint + don't skip test

.github/workflows/test-coverage.yaml

@@ -13,7 +13,6 @@ jobs:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      ON_CI: "TRUE"
 
     steps:
       - uses: actions/checkout@v3

R/util_assert.R

@@ -80,7 +80,8 @@ assert_file_exists <- function(files, name = "File", call = NULL, arg = NULL) {
 }
 
 
-deprecate_old_orderly_name <- function(src, reportname, suppress_errors = FALSE) {
+deprecate_old_orderly_name <- function(src, reportname,
+                                       suppress_errors = FALSE) {
   names <- c(sprintf("%s.R", reportname), "orderly.R")
   files_exist <- file.exists(file.path(src, names))
   if (sum(files_exist) > 1 && !suppress_errors) {

tests/testthat/test-orderly.R

@@ -75,10 +75,10 @@ test_that("error if a non-directory file is found in the src dir", {
 })
 
 
-test_that("allow creation of <reportname>.R in existing dir if force is given", {
+test_that("allow creation of foo.R in existing src/foo if force is given", {
   path <- test_prepare_orderly_example(character())
   fs::dir_create(file.path(path, "src", "foo"))
-  file.create(file.path(path, "src", "foo", "bar"))
+  file.create(file.path(path, "src", "foo", "deprebar"))
   err <- expect_error(
     orderly_new("foo", root = path),
     "'src/foo/' already exists and contains files")

tests/testthat/test-run.R

@@ -83,12 +83,9 @@ test_that("error if declared artefacts are not produced", {
 
 
 test_that("raises deprecation warning for orderly.R", {
-  skip_if(!identical(Sys.getenv("ON_CI"), "TRUE"),
-          message = paste("Skipping as deprecation warning",
-                          "only appears every 8 hours per R",
-                          "session. Will be tested on CI."))
   path <- test_prepare_orderly_example("deprecated-orderly-name")
   envir <- new.env()
+  rlang::reset_message_verbosity("deprecate_orderly_file_name")
   suppressMessages(
     expect_message(
       orderly_run("deprecated-orderly-name", root = path,
@@ -451,7 +448,8 @@ test_that("can copy resource from directory, implicitly", {
 test_that("fail to copy resource from directory, implicitly, strictly", {
   path <- test_prepare_orderly_example("resource-in-directory")
   envir <- new.env()
-  path_src <- file.path(path, "src", "resource-in-directory", "resource-in-directory.R")
+  path_src <- file.path(path, "src", "resource-in-directory",
+                        "resource-in-directory.R")
   prepend_lines(path_src, "orderly2::orderly_strict_mode()")
   err <- suppressWarnings(tryCatch(read.csv("data/a.csv"), error = identity))
   expect_error(suppressWarnings(
@@ -464,7 +462,8 @@ test_that("fail to copy resource from directory, implicitly, strictly", {
 test_that("can copy resource from directory, included by file", {
   path <- test_prepare_orderly_example("resource-in-directory")
   envir <- new.env()
-  path_src <- file.path(path, "src", "resource-in-directory", "resource-in-directory.R")
+  path_src <- file.path(path, "src", "resource-in-directory",
+                        "resource-in-directory.R")
   prepend_lines(path_src,
                 c('orderly2::orderly_resource("data/a.csv")',
                   'orderly2::orderly_resource("data/b.csv")'))
@@ -482,7 +481,8 @@ test_that("can copy resource from directory, included by file", {
 test_that("can copy resource from directory, included by file, strict mode", {
   path <- test_prepare_orderly_example("resource-in-directory")
   envir <- new.env()
-  path_src <- file.path(path, "src", "resource-in-directory", "resource-in-directory.R")
+  path_src <- file.path(path, "src", "resource-in-directory",
+                        "resource-in-directory.R")
   prepend_lines(path_src,
                 c("orderly2::orderly_strict_mode()",
                   'orderly2::orderly_resource("data/a.csv")',
@@ -501,7 +501,8 @@ test_that("can copy resource from directory, included by file, strict mode", {
 test_that("can copy resource from directory, included by directory", {
   path <- test_prepare_orderly_example("resource-in-directory")
   envir <- new.env()
-  path_src <- file.path(path, "src", "resource-in-directory", "resource-in-directory.R")
+  path_src <- file.path(path, "src", "resource-in-directory",
+                        "resource-in-directory.R")
   prepend_lines(path_src, 'orderly2::orderly_resource("data")')
   id <- orderly_run_quietly("resource-in-directory", root = path, envir = envir)
 
@@ -518,7 +519,8 @@ test_that("can copy resource from directory, included by directory", {
 test_that("can copy resource from directory, included by directory, strictly", {
   path <- test_prepare_orderly_example("resource-in-directory")
   envir <- new.env()
-  path_src <- file.path(path, "src", "resource-in-directory", "resource-in-directory.R")
+  path_src <- file.path(path, "src", "resource-in-directory",
+                        "resource-in-directory.R")
   prepend_lines(path_src,
                 c("orderly2::orderly_strict_mode()",
                   'orderly2::orderly_resource("data")'))
@@ -582,7 +584,8 @@ test_that("can pull resources programmatically", {
 
 test_that("can pull resources programmatically, strictly", {
   path <- test_prepare_orderly_example("programmatic-resource")
-  path_src <- file.path(path, "src", "programmatic-resource", "programmatic-resource.R")
+  path_src <- file.path(path, "src", "programmatic-resource",
+                        "programmatic-resource.R")
   prepend_lines(path_src, "orderly2::orderly_strict_mode()")
   id1 <- orderly_run_quietly("programmatic-resource", list(use = "a"),
                              root = path)

vignettes/dependencies.Rmd

@@ -28,7 +28,7 @@ Here, we show how to practically use dependencies in a few common scenarios of i
 
 ## Basic use
 
-The primary mechanism for using dependencies is to call `orderly2::orderly_dependency()` from within an `orderly.R` script; this finds a suitable completed packet and copies files that are found from within that packet into your current report.
+The primary mechanism for using dependencies is to call `orderly2::orderly_dependency()` from within a `<reportname>.R` script; this finds a suitable completed packet and copies files that are found from within that packet into your current report.
 
 ```{r, include = FALSE}
 path <- tempfile()
@@ -42,7 +42,7 @@ writeLines(c(
   'd <- read.csv("data.csv")',
   "d$z <- resid(lm(y ~ x, d))",
   'saveRDS(d, "data.rds")'),
-  file.path(path, "src", "data", "orderly.R"))
+  file.path(path, "src", "data", "data.R"))
 orderly2::orderly_run("data", root = path)
 
 fs::dir_create(file.path(path, "src", "analysis"))
@@ -52,18 +52,18 @@ writeLines(c(
   'png("analysis.png")',
   "plot(y ~ x, d)",
   "dev.off()"),
-  file.path(path, "src", "analysis", "orderly.R"))
+  file.path(path, "src", "analysis", "analysis.R"))
 ```
 
 ```{r, echo = FALSE}
 dir_tree(file.path(path), "src")
 ```
 
-and `src/analysis/orderly.R` contains:
+and `src/analysis/analysis.R` contains:
 
 
 ```{r, echo = FALSE, results = "asis"}
-r_output(readLines(file.path(path, "src/analysis/orderly.R")))
+r_output(readLines(file.path(path, "src/analysis/analysis.R")))
 ```
 
 Here, we've used `orderly2::orderly_dependency()` to pull in the file `data.rds` from the most recent version (`latest()`) of the `data` packet, then we've used that file as normal to make a plot, which we've saved as `analysis.png` (this is very similar to the example from `vignette("introduction")`, to get us started).
@@ -94,7 +94,7 @@ writeLines(c(
   "orderly2::orderly_parameters(cyl = NULL)",
   "d <- mtcars[mtcars$cyl == cyl, ]",
   'saveRDS(d, "data.rds")'),
-  file.path(path, "src", "data", "orderly.R"))
+  file.path(path, "src", "data", "data.R"))
 
 fs::dir_create(file.path(path, "src", "analysis"))
 writeLines(c(
@@ -107,17 +107,17 @@ writeLines(c(
   'png("analysis.png")',
   "plot(mpg ~ disp, d)",
   "dev.off()"),
-  file.path(path, "src", "analysis", "orderly.R"))
+  file.path(path, "src", "analysis", "analysis.R"))
 ```
 
 ```{r, echo = FALSE}
 dir_tree(file.path(path), "src")
 ```
 
-with `src/data/orderly.R` containing:
+with `src/data/data.R` containing:
 
 ```{r, echo = FALSE, results = "asis"}
-r_output(readLines(file.path(path, "src/data/orderly.R")))
+r_output(readLines(file.path(path, "src/data/data.R")))
 ```
 
 We can run this for several values of `cyl`:
@@ -131,7 +131,7 @@ orderly2::orderly_run("data", list(cyl = 8))
 Our follow-on analysis contains:
 
 ```{r, echo = FALSE, results = "asis"}
-r_output(readLines(file.path(path, "src/analysis/orderly.R")))
+r_output(readLines(file.path(path, "src/analysis/analysis.R")))
 ```
 
 Here the query `latest(parameter:cyl == this:cyl)` says "find the most recent packet where it's parameter "cyl" (`parameter:cyl`) is the same as the parameter in the currently running report (`this:cyl`).