Merge pull request #120 from UrbanAnalyst/fs

fs for #119

.pre-commit-config.yaml

@@ -8,7 +8,7 @@ repos:
         args: [--style_pkg=spaceout, --style_fun=spaceout_style]    
         additional_dependencies:
         - ropensci-review-tools/spaceout
-    -   id: roxygenize
+      # -   id: roxygenize
     # codemeta must be above use-tidy-description when both are used
     # -   id: codemeta-description-updated
     -   id: use-tidy-description

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: gtfsrouter
 Title: Routing with 'GTFS' (General Transit Feed Specification) Data
-Version: 0.1.2.014
+Version: 0.1.2.018
 Authors@R: c(
     person("Mark", "Padgham", , "[email protected]", role = c("aut", "cre")),
     person("Marcin", "Stepniak", , "[email protected]", role = "aut",
@@ -18,6 +18,7 @@ Depends:
 Imports:
     cli,
     data.table,
+    fs,
     geodist,
     methods,
     Rcpp (>= 0.12.6)

NEWS.md

@@ -3,6 +3,7 @@
 ## Minor changes:
 
 - Fix bug with return values of traveltimes (#116; thanks to @FlxPo)
+- Use 'fs' package for all file path manipulations.
 
 ---
 

R/extract-gtfs.R

@@ -89,7 +89,7 @@ unzip_gtfs <- function (filename, quiet = FALSE) {
         )
     }
 
-    flist <- utils::unzip (filename, exdir = tempdir ())
+    flist <- utils::unzip (filename, exdir = fs::path_temp ())
 
     if (!quiet) {
         message ("\r", cli::col_green (
@@ -106,7 +106,7 @@ check_extract_pars <- function (filename, stn_suffixes) {
     if (is.null (filename)) {
         stop ("filename must be given")
     }
-    if (!file.exists (filename)) {
+    if (!fs::file_exists (filename)) {
         stop ("filename ", filename, " does not exist")
     }
     if (!(is.null (stn_suffixes) || is.character (stn_suffixes))) {
@@ -191,7 +191,7 @@ extract_objs_into_env <- function (flist, quiet = FALSE) {
             value = fout,
             envir = e
         )
-        chk <- file.remove (flist [f]) # nolint
+        chk <- fs::file_delete (flist [f]) # nolint
     }
 
     if (!quiet) {

R/go_home_work.R

@@ -104,7 +104,7 @@ go_home_work <- function (home = TRUE, wait, start_time) {
 
     vars <- get_envvars ()
     fname <- get_rds_name (vars$file)
-    if (!file.exists (fname)) {
+    if (!fs::file_exists (fname)) {
         stop (
             "This function requires the GTFS data to be pre-processed ",
             "with 'process_gtfs_local'."
@@ -145,7 +145,7 @@ get_envvars <- function () {
     }
 
     f <- (Sys.getenv ("gtfs_data"))
-    if (!file.exists (f)) {
+    if (!fs::file_exists (f)) {
         stop (
             "File ", f, " specified by environmental variable ",
             "'gtfs_data' does not exist"

R/transfers.R

@@ -130,9 +130,9 @@ dl_net <- function (gtfs) {
     stops <- gtfs$stops [, c ("stop_lon", "stop_lat")]
     requireNamespace ("digest")
     hash <- digest::digest (stops)
-    net_name <- file.path (tempdir (), paste0 ("net", hash, ".Rds"))
+    net_name <- fs::path (fs::path_temp (), paste0 ("net", hash, ".Rds"))
 
-    if (!file.exists (net_name)) {
+    if (!fs::file_exists (net_name)) {
         requireNamespace ("dodgr")
         net <- dodgr::dodgr_streetnet_sc (pts = stops)
         saveRDS (net, file = net_name)

R/utils.R

@@ -21,7 +21,7 @@ berlin_gtfs_to_zip <- function () {
         si <- strsplit (i, ".txt") [[1]]
         res <- tryCatch (
             data.table::fwrite (f [[si]],
-                file.path (tempdir (), i),
+                fs::path (fs::path_temp (), i),
                 quote = TRUE
             ),
             error = function (e) e
@@ -33,10 +33,10 @@ berlin_gtfs_to_zip <- function () {
         stop ("Unable to write files to tempdir()")
     } # nocov
 
-    flist <- file.path (tempdir (), flist)
-    zipname <- file.path (tempdir (), "vbb.zip")
+    flist <- fs::path (fs::path_temp (), flist)
+    zipname <- fs::path (fs::path_temp (), "vbb.zip")
     utils::zip (zipname, files = flist, flags = "-q")
-    chk <- file.remove (flist)
+    chk <- fs::file_delete (flist)
 
     return (zipname)
 }

codemeta.json

@@ -7,7 +7,7 @@
   "codeRepository": "https://github.com/UrbanAnalyst/gtfsrouter",
   "issueTracker": "https://github.com/UrbanAnalyst/gtfsrouter/issues",
   "license": "https://spdx.org/licenses/GPL-3.0",
-  "version": "0.1.2.014",
+  "version": "0.1.2.018",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",

tests/testthat/test-extract.R

@@ -6,41 +6,41 @@ test_all <- (identical (Sys.getenv ("MPADGE_LOCAL"), "true") |
 nthr <- data.table::setDTthreads (1L)
 
 test_that ("extract non gtfs", {
-    f <- file.path (tempdir (), "junk.txt")
+    f <- fs::path (fs::path_temp (), "junk.txt")
     con <- file (f)
     writeLines ("blah", con)
     close (con)
-    fz <- file.path (tempdir (), "vbb.zip")
-    if (file.exists (fz)) {
-        chk <- file.remove (fz)
+    fz <- fs::path (fs::path_temp (), "vbb.zip")
+    if (fs::file_exists (fz)) {
+        chk <- fs::file_delete (fz)
     }
     chk <- zip (fz, file = f)
 
     msg <- paste0 (fz, " does not appear to be a GTFS file")
     if (test_all) { # windows paths get mucked up
         expect_error (g <- extract_gtfs (fz), msg)
     }
-    invisible (file.remove (fz))
+    invisible (fs::file_delete (fz))
 })
 
 test_that ("extract", {
     berlin_gtfs_to_zip ()
-    f <- file.path (tempdir (), "vbb.zip")
-    expect_true (file.exists (f))
+    f <- fs::path (fs::path_temp (), "vbb.zip")
+    expect_true (fs::file_exists (f))
     expect_message (g <- extract_gtfs (f, quiet = FALSE))
 
     # remove calendar and transfers from feed:
-    unzip (file.path (tempdir (), "vbb.zip"),
-        exdir = tempdir (),
+    unzip (fs::path (fs::path_temp (), "vbb.zip"),
+        exdir = fs::path_temp (),
         junkpaths = TRUE
     )
-    froutes <- file.path (tempdir (), "routes.txt")
-    ftrips <- file.path (tempdir (), "trips.txt")
-    fstop_times <- file.path (tempdir (), "stop_times.txt")
-    fstops <- file.path (tempdir (), "stops.txt")
-    ftransfers <- file.path (tempdir (), "transfers.txt")
-    fcalendar <- file.path (tempdir (), "calendar.txt")
-    f_cut <- file.path (tempdir (), "vbb_cut.zip")
+    froutes <- fs::path (fs::path_temp (), "routes.txt")
+    ftrips <- fs::path (fs::path_temp (), "trips.txt")
+    fstop_times <- fs::path (fs::path_temp (), "stop_times.txt")
+    fstops <- fs::path (fs::path_temp (), "stops.txt")
+    ftransfers <- fs::path (fs::path_temp (), "transfers.txt")
+    fcalendar <- fs::path (fs::path_temp (), "calendar.txt")
+    f_cut <- fs::path (fs::path_temp (), "vbb_cut.zip")
 
     chk <- zip (f_cut,
         file = c (
@@ -62,7 +62,7 @@ test_that ("extract", {
     names (vals) <- nms
     expect_identical (vals, vapply (g, nrow, numeric (1)))
     expect_true (!"transfers" %in% names (vals))
-    invisible (file.remove (f_cut))
+    invisible (fs::file_delete (f_cut))
 
     chk <- zip (f_cut,
         file = c (
@@ -82,13 +82,13 @@ test_that ("extract", {
     names (vals) <- nms
     expect_identical (vals, vapply (g, nrow, numeric (1)))
     expect_true (!"calendar" %in% names (vals))
-    invisible (file.remove (f_cut))
+    invisible (fs::file_delete (f_cut))
 })
 
 test_that ("summary", {
     berlin_gtfs_to_zip ()
-    f <- file.path (tempdir (), "vbb.zip")
-    expect_true (file.exists (f))
+    f <- fs::path (fs::path_temp (), "vbb.zip")
+    expect_true (fs::file_exists (f))
     expect_silent (g <- extract_gtfs (f, quiet = TRUE))
 
     x <- capture.output (summary (g))
@@ -103,8 +103,8 @@ test_that ("summary", {
 
 test_that ("timetable summary", {
     berlin_gtfs_to_zip ()
-    f <- file.path (tempdir (), "vbb.zip")
-    expect_true (file.exists (f))
+    f <- fs::path (fs::path_temp (), "vbb.zip")
+    expect_true (fs::file_exists (f))
     expect_silent (g <- extract_gtfs (f, quiet = TRUE))
     gt <- gtfs_timetable (g, day = 3)
 
@@ -131,7 +131,7 @@ test_that ("cpu time", {
 
     test <- function () {
         berlin_gtfs_to_zip ()
-        f <- file.path (tempdir (), "vbb.zip")
+        f <- fs::path (fs::path_temp (), "vbb.zip")
         gtfs <- extract_gtfs (f)
     }
     st <- system.time (test ())

tests/testthat/test-frequencies.R

@@ -10,7 +10,7 @@ test_that ("not gtfs", {
 
 test_that ("gtfs without frequencies", {
     berlin_gtfs_to_zip ()
-    tempfiles <- list.files (tempdir (), full.names = TRUE)
+    tempfiles <- list.files (fs::path_temp (), full.names = TRUE)
     filename <- tempfiles [grep ("vbb.zip", tempfiles)]
     gtfs <- extract_gtfs (filename)
 
@@ -21,7 +21,7 @@ test_that ("gtfs without frequencies", {
 
 test_that ("gtfs with empty frequencies", {
     berlin_gtfs_to_zip ()
-    tempfiles <- list.files (tempdir (), full.names = TRUE)
+    tempfiles <- list.files (fs::path_temp (), full.names = TRUE)
     filename <- tempfiles [grep ("vbb.zip", tempfiles)]
     gtfs <- extract_gtfs (filename)
 
@@ -41,7 +41,7 @@ test_that ("gtfs with empty frequencies", {
 
 test_that ("frequencies with missing columns", {
     berlin_gtfs_to_zip ()
-    tempfiles <- list.files (tempdir (), full.names = TRUE)
+    tempfiles <- list.files (fs::path_temp (), full.names = TRUE)
     filename <- tempfiles [grep ("vbb.zip", tempfiles)]
     gtfs <- extract_gtfs (filename)
 
@@ -63,7 +63,7 @@ test_that ("frequencies with missing columns", {
 
 test_that ("only routes with frequencies to stop_times", {
     f <- berlin_gtfs_to_zip ()
-    expect_true (file.exists (f))
+    expect_true (fs::file_exists (f))
     gtfs <- extract_gtfs (f)
 
     # filter only one route from gtfs
@@ -158,8 +158,8 @@ test_that ("only routes with frequencies to stop_times", {
 
 test_that ("gtfs with mixed frequencies", {
     berlin_gtfs_to_zip ()
-    f <- file.path (tempdir (), "vbb.zip")
-    expect_true (file.exists (f))
+    f <- fs::path (fs::path_temp (), "vbb.zip")
+    expect_true (fs::file_exists (f))
     gtfs <- extract_gtfs (f)
 
     # filter two routes: U1 - only one trip and U3 with all trips
@@ -215,7 +215,7 @@ test_that ("gtfs with mixed frequencies", {
 
 test_that ("gtfs frequencies in gtfs_route", {
     f <- berlin_gtfs_to_zip ()
-    expect_true (file.exists (f))
+    expect_true (fs::file_exists (f))
     gtfs <- extract_gtfs (f)
 
     gtfs$routes <- gtfs$routes [route_short_name %in% c ("U1", "U6")]

tests/testthat/test-go-home.R

@@ -14,7 +14,7 @@ test_that ("go home set up", {
             "This function requires environmental variables"
         )
     }
-    f <- file.path (tempdir (), "doesnotexist.zip")
+    f <- fs::path (fs::path_temp (), "doesnotexist.zip")
     Sys.setenv ("gtfs_home" = "Innsbrucker Platz")
     Sys.setenv ("gtfs_work" = "Alexanderplatz")
     Sys.setenv ("gtfs_data" = f)
@@ -29,7 +29,7 @@ test_that ("go home set up", {
         )
     }
     berlin_gtfs_to_zip ()
-    f <- file.path (tempdir (), "vbb.zip")
+    f <- fs::path (fs::path_temp (), "vbb.zip")
     Sys.setenv ("gtfs_data" = f)
 
     expect_error (