-
Notifications
You must be signed in to change notification settings - Fork 19
/
processData.R
810 lines (785 loc) · 24.9 KB
/
processData.R
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
.validate_render_root <- function(x) {
# catch an error if it doesn't exist, otherwise return normalized path
# important for handling relative paths in a rmarkdown::render() context
if (! dir.exists(x)){
.multilog_error(paste0("render_root = ", x, " doesn't exist"))
stop(paste0("render_root = ", x, " doesn't exist"))
}
normalizePath(x, winslash = "/")
# old comments below have been retained:
# try creating, even if it's an old temp dir.
# This isn't ideal. Would like to rather say it's a temporary
# directory and use the current one..
}
#' Process data generation code in 'data-raw'
#'
#' Assumes .R files in 'data-raw' generate rda files to be stored in 'data'.
#' Sources datasets.R which can source other R files.
#' R files sourced by datasets.R must invoke \code{sys.source('myRfile.R',env=topenv())}.
#' Meant to be called before R CMD build.
#' @name DataPackageR
#' @param arg \code{character} name of the package to build.
#' @param deps \code{logical} should scripts pass data objects to each other (default=TRUE)
#' @return logical TRUE if successful, FALSE, if not.
#' @importFrom desc desc
#' @importFrom rmarkdown render
#' @importFrom usethis proj_set proj_get
#' @noRd
DataPackageR <- function(arg = NULL, deps = TRUE) {
if (! getOption('DataPackageR_verbose', TRUE)){
old_usethis_quiet <- getOption('usethis.quiet')
on.exit(options(usethis.quiet = old_usethis_quiet))
options(usethis.quiet = TRUE)
}
pkg_dir <- arg
if (getOption('DataPackageR_verbose', TRUE)) cat("\n")
usethis::proj_set(path = pkg_dir)
#set the option that DataPackageR is building the package. On exit ensures when it leaves, it will set it back to false
options("DataPackageR_packagebuilding" = TRUE)
on.exit(options("DataPackageR_packagebuilding" = FALSE), add = TRUE)
# validate that render_root exists.
# if it's an old temp dir, what then?
logpath <- file.path(pkg_dir, "inst", "extdata", "Logfiles")
dir.create(logpath, recursive = TRUE, showWarnings = FALSE)
# open a log file
LOGFILE <- file.path(logpath, "processing.log")
.multilog_setup(LOGFILE)
.multilog_thresold(console = INFO, logfile = TRACE)
.multilog_trace(paste0("Logging to ", LOGFILE))
# validate package
validate_package_skeleton(pkg_dir)
.multilog_trace("Processing data")
# validate datapackager.yml
ymlconf <- validate_yml(pkg_dir)
# get vector of R and Rmd files from validated YAML
r_files <- file.path(pkg_dir, 'data-raw', get_yml_r_files(ymlconf))
objects_to_keep <- get_yml_objects(ymlconf)
render_root <- .validate_render_root(.get_render_root(ymlconf))
# The test for a valid DESCRIPTION here is no longer needed since
# we use proj_set().
# TODO Can we configure documentation in yaml?
do_documentation <- FALSE
# This flag indicates success
can_write <- FALSE
# environment for the data
ENVS <- new.env(hash = TRUE, parent = .GlobalEnv)
object_tally <- 0
already_built <- NULL
building <- NULL
r_dir <- normalizePath(file.path(pkg_dir, "R" ), winslash = "/")
r_dir_files <- list.files( r_dir )
r_dir_files <- r_dir_files[ !grepl( validate_pkg_name(pkg_dir),
r_dir_files ) ]
for (i in seq_along(r_files)) {
dataenv <- new.env(hash = TRUE, parent = .GlobalEnv)
for( j in seq_along( r_dir_files ) ){
curr_path <- normalizePath(file.path(pkg_dir,
"R",
r_dir_files[j] ),
winslash = "/")
source( curr_path,
local = dataenv )
}
# assign ENVS into dataenv.
# provide functions in the package to read from it (if deps = TRUE)
if (deps) assign(x = "ENVS", value = ENVS, dataenv)
.multilog_trace(paste0(
"Processing ", i, " of ",
length(r_files), ": ", r_files[i]
))
# config file goes in the root render the r and rmd files
## First we spin then render if it's an R file
flag <- FALSE
.isRfile <- function(f) {
grepl("\\.r$", tolower(f))
}
if (flag <- .isRfile(r_files[i])) {
knitr::spin(r_files[i],
precious = TRUE,
knit = FALSE
)
r_files[i] <- paste0(tools::file_path_sans_ext(r_files[i]), ".Rmd")
if (! file.exists(r_files[i])){
stop(paste0("File: ", r_files[i], " does not exist!"))
}
lines <- readLines(r_files[i])
# do we likely have a yaml header? If not, add one.
if (lines[1] != "---") {
lines <- c(
"---",
paste0("title: ", basename(r_files[i])),
paste0("author: ", Sys.info()["user"]),
paste0("date: ", Sys.Date()),
"---",
"",
lines
)
con <- file(r_files[i])
writeLines(lines, con = con, sep = "\n")
close(con)
}
}
rmarkdown::render(
input = r_files[i], envir = dataenv,
output_dir = logpath, clean = TRUE, knit_root_dir = render_root,
quiet = TRUE
)
# The created objects
object_names <- setdiff(ls(dataenv),
c("ENVS", already_built)) # ENVS is removed
object_tally <- object_tally | objects_to_keep %in% object_names
already_built <- unique(c(already_built,
objects_to_keep[objects_to_keep %in% object_names]))
.multilog_trace(paste0(
sum(objects_to_keep %in% object_names),
" data set(s) created by ",
basename(r_files[i])
))
.done(paste0(
sum(objects_to_keep %in% object_names),
" data set(s) created by ",
basename(r_files[i])
))
if (sum(objects_to_keep %in% object_names) > 0) {
.add_newlines_to_vector <- function(x) {
x <- paste0(x, sep = "\n")
x[length(x)] <- gsub("\n", "", x[length(x)])
x
}
.bullet(
.add_newlines_to_vector(
objects_to_keep[which(objects_to_keep %in% object_names)]),
cli::col_red("\u2022")
)
}
.bullet(
paste0(
"Built ",
ifelse(
sum(object_tally) == length(object_tally),
"all datasets!",
paste0(sum(object_tally), " of ",
length(object_tally), " data sets.")
)
),
ifelse(
sum(object_tally) == length(object_tally),
cli::col_green("\u2618"),
cli::col_green("\u2605")
)
)
if (sum(objects_to_keep %in% object_names) > 0) {
for (o in objects_to_keep[objects_to_keep %in% object_names]) {
assign(o, get(o, dataenv), ENVS)
# write the object to render_root
o_instance <- get(o,dataenv)
saveRDS(o_instance, file = paste0(file.path(render_root,o),".rds"),
version = 2)
}
}
}
# currently environments for each file are independent.
dataenv <- ENVS
do_digests(pkg_dir, dataenv)
do_doc(pkg_dir, dataenv)
# copy html files to vignettes
.ppfiles_mkvignettes(dir = pkg_dir)
.multilog_trace("Done")
return(TRUE)
}
#' Get R and Rmd files from YAML configuration
#'
#' @param ymlconf YAML configuration list produced by validate_yml()
#'
#' @return Character vector of enabled R and Rmd files specified in YAML file
#' @noRd
get_yml_r_files <- function(ymlconf) {
r_files <- names(
Filter(
x = ymlconf[["configuration"]][["files"]],
f = function(x) x$enabled
)
)
}
#' Get data objects from YAML configuration
#'
#' @param ymlconf YAML configuration list produced by validate_yml()
#'
#' @return Character vector of object names
#' @noRd
get_yml_objects <- function(ymlconf){
ymlconf$configuration$objects
}
#' Validate YAML file, extracted out from big DataPackageR function
#'
#' @param pkg_dir Path of top level of data package
#'
#' @return List object from read_yaml(ymlfile)
#' @noRd
validate_yml <- function(pkg_dir){
# read YAML
ymlfile <- list.files(
path = pkg_dir, pattern = "^datapackager.yml$",
full.names = TRUE
)
if (length(ymlfile) == 0) {
.multilog_fatal(paste0("Yaml configuration file not found at ", pkg_dir))
stop("exiting", call. = FALSE)
}
ymlconf <- read_yaml(ymlfile)
# test that the structure of the yaml file is correct!
if (!"configuration" %in% names(ymlconf)) {
.multilog_fatal("YAML is missing 'configuration:' entry")
stop("exiting", call. = FALSE)
}
if (!all(c("files", "objects") %in% names(ymlconf$configuration))) {
.multilog_fatal("YAML is missing files: and objects: entries")
stop("exiting", call. = FALSE)
}
.multilog_trace("Reading yaml configuration")
# files that have enable: TRUE
stopifnot("configuration" %in% names(ymlconf))
stopifnot("files" %in% names(ymlconf[["configuration"]]))
stopifnot(!is.null(names(ymlconf[["configuration"]][["files"]])))
# object with same name as package causes problems with
# overwriting documentation files
if (basename(pkg_dir) %in% ymlconf$configuration$objects){
err_msg <- "Data object not allowed to have same name as data package"
flog.fatal(err_msg, name = "console")
stop(err_msg, call. = FALSE)
}
render_root <- .get_render_root(ymlconf)
.validate_render_root(render_root)
if (length(get_yml_objects(ymlconf)) == 0) {
.multilog_fatal("You must specify at least one data object.")
stop("exiting", call. = FALSE)
}
r_files <- get_yml_r_files(ymlconf)
if (length(r_files) == 0) {
.multilog_fatal("No files enabled for processing!")
stop("error", call. = FALSE)
}
if (any(duplicated(r_files))){
err_msg <- "Duplicate R files specified in YAML."
.multilog_fatal(err_msg)
stop(err_msg, call. = FALSE)
}
for (file in r_files){
if (! file.exists(file.path(pkg_dir, 'data-raw', file))){
err_msg <- paste("Missing R file specified in YAML:", file)
.multilog_fatal(err_msg)
stop(err_msg, call. = FALSE)
}
}
.multilog_trace(paste0("Found ", r_files))
return(ymlconf)
}
#' Validate data package skeleton, extracted out from big DataPackageR function
#'
#' @param pkg_dir Path of top level of data package
#'
#' @return Silently returns pkg_dir if no errors thrown
#' @noRd
validate_package_skeleton <- function(pkg_dir){
# we know it's a proper package root, but we want to test if we have the
# necessary subdirectories
dirs <- file.path(pkg_dir, c("R", "inst", "data", "data-raw"))
for (dir in dirs){
if (! utils::file_test(dir, op = "-d")){
err_msg <- paste("Missing required subdirectory", dir)
.multilog_fatal(err_msg)
stop(err_msg)
}
}
# check we can read a DESCRIPTION file
d <- desc::desc(pkg_dir)
invisible(pkg_dir)
}
#' Validate data package description
#'
#' @param pkg_dir The top-level directory path for the data package
#'
#' @returns validated description object, cf. [desc::desc()]
#' @noRd
validate_description <- function(pkg_dir){
d <- desc::desc(pkg_dir)
dv <- d$get('DataVersion')
if (is.na(dv)) {
err_msg <- paste0(
"DESCRIPTION file must have a DataVersion",
" line. i.e. DataVersion: 0.2.0"
)
.multilog_fatal(err_msg)
stop(err_msg, call. = FALSE)
}
validate_DataVersion(dv)
d
}
#' Validate and return DataVersion
#'
#' @param DataVersion Character, e.g. '0.1.1', or a valid base R object of class 'package_version'
#'
#' @returns Class 'character', the validated DataVersion, e.g. '0.1.1'
#' @noRd
validate_DataVersion <- function(DataVersion){
# allow input as package_version
if (inherits(DataVersion, 'package_version')){
DataVersion <- as.character(DataVersion)
}
stopifnot(! is.null(DataVersion),
is.character(DataVersion),
length(DataVersion) == 1,
! is.na(DataVersion)
)
# base::R_system_version enforces valid 3-number version (major, minor, patch)
as.character(R_system_version(DataVersion))
}
#' do_digests() function extracted out from DataPackageR
#'
#' @param pkg_dir The top level file path of the data package
#' @param dataenv The data environment, from DataPackageR
#'
#' @returns TRUE if success
#' @noRd
do_digests <- function(pkg_dir, dataenv) {
# Digest each object
old_data_digest <- .parse_data_digest(pkg_dir = pkg_dir)
pkg_desc <- validate_description(pkg_dir)
new_data_digest <- .digest_data_env(
ls(dataenv),
dataenv,
pkg_desc$get('DataVersion'))
.newsfile()
if (is.null(old_data_digest)){
# first time data digest & early return
.update_news_md(new_data_digest[["DataVersion"]],
interact = getOption(
"DataPackageR_interact",
interactive()))
# this will write list of first time added objects to NEWS
changed_objects <- .qualify_changes(new_data_digest, list())
.update_news_changed_objects(changed_objects)
.save_data(new_data_digest,
pkg_desc$get('DataVersion'),
ls(dataenv),
dataenv,
old_data_digest = NULL,
pkg_path = pkg_dir)
return(TRUE)
}
check_new_DataVersion <- .check_dataversion_string(
new_data_digest,
old_data_digest
)
can_write <- FALSE
same_digests <- .compare_digests(old_data_digest, new_data_digest)
if ((! same_digests) && check_new_DataVersion == "higher"){
# not sure how this would actually happen
err_msg <- 'Digest(s) differ but DataVersion had already been incremented'
.multilog_fatal(err_msg)
stop(err_msg, call. = FALSE)
}
if (same_digests && check_new_DataVersion == "equal") {
can_write <- TRUE
.multilog_trace(paste0(
"Processed data sets match ",
"existing data sets at version ",
new_data_digest[["DataVersion"]]
))
} else if ((! same_digests) && check_new_DataVersion == "equal") {
updated_version <- .increment_data_version(
pkg_desc,
new_data_digest
)
#TODO what objects have changed?
changed_objects <- .qualify_changes(new_data_digest,old_data_digest)
.update_news_md(updated_version$new_data_digest[["DataVersion"]],
interact = getOption("DataPackageR_interact", interactive())
)
.update_news_changed_objects(changed_objects)
pkg_desc <- updated_version$pkg_description
new_data_digest <- updated_version$new_data_digest
can_write <- TRUE
.multilog_trace(paste0(
"Data has been updated and DataVersion ",
"string incremented automatically to ",
new_data_digest[["DataVersion"]]
))
} else if (same_digests && check_new_DataVersion == "higher") {
# edge case that shouldn't happen
# but we test for it in the test suite
can_write <- TRUE
.multilog_trace(paste0(
"Data hasn't changed but the ",
"DataVersion has been bumped."
))
} else if (check_new_DataVersion == "lower" && same_digests) {
# edge case that shouldn't happen but
# we test for it in the test suite.
.multilog_trace(paste0(
"New DataVersion is less than ",
"old but data are unchanged"
))
new_data_digest <- old_data_digest
pkg_desc$set('DataVersion',
validate_DataVersion(new_data_digest[["DataVersion"]])
)
can_write <- TRUE
} else if (check_new_DataVersion == "lower" && ! same_digests) {
updated_version <- .increment_data_version(
pkg_desc,
new_data_digest
)
# TODO what objects have changed?
changed_objects <- .qualify_changes(new_data_digest,old_data_digest)
.update_news_md(updated_version$new_data_digest[["DataVersion"]],
interact = getOption("DataPackageR_interact", interactive())
)
.update_news_changed_objects(changed_objects)
pkg_desc <- updated_version$pkg_description
new_data_digest <- updated_version$new_data_digest
can_write <- TRUE
}
if (can_write) {
.save_data(new_data_digest,
pkg_desc$get('DataVersion'),
ls(dataenv),
dataenv,
old_data_digest = old_data_digest,
pkg_path = pkg_dir
)
}
return(TRUE)
}
#' do_doc() function extracted out from end of DataPackageR
#'
#' @param pkg_dir The top level file path of the data package
#' @param dataenv The data environment, from DataPackageR
#' @returns TRUE if success
#' @noRd
do_doc <- function(pkg_dir, dataenv) {
# Run .doc_autogen #needs to be run when we have a partial build..
if (!file.exists(file.path(pkg_dir, 'data-raw', "documentation.R"))) {
.doc_autogen(basename(pkg_dir),
ds2kp = ls(dataenv),
env = dataenv,
path = file.path(pkg_dir, 'data-raw')
)
}
# parse documentation
doc_parsed <- .doc_parse(file.path(pkg_dir, 'data-raw', "documentation.R"))
# case where we add an object,
# ensures we combine the documentation properly
pkg_name <- validate_pkg_name(pkg_dir)
missing_doc_for_autodoc <- setdiff(
ls(dataenv),
setdiff(names(doc_parsed), pkg_name)
)
if (length(missing_doc_for_autodoc) != 0) {
tmptarget <- tempdir()
file.info("Writing missing docs.")
.doc_autogen(basename(pkg_dir),
ds2kp = missing_doc_for_autodoc,
env = dataenv,
path = tmptarget,
name = "missing_doc.R"
)
missing_doc <- .doc_parse(file.path(tmptarget, "missing_doc.R"))
doc_parsed <- .doc_merge(
old = doc_parsed,
new = missing_doc
)
file.info("Writing merged docs.")
writeLines(Reduce(c, doc_parsed),
file.path(pkg_dir, 'data-raw', "documentation.R")
)
}
# Partial build if enabled=FALSE for
# any file We've disabled an object but don't
# want to overwrite its documentation
# or remove it The new approach just builds
# all the docs independent of what's enabled.
writeLines(Reduce(c, doc_parsed),
file.path(pkg_dir, "R", paste0(pkg_name, ".R"))
)
.multilog_trace(
paste0(
"Copied documentation to ",
file.path(pkg_dir, "R", paste0(pkg_name, ".R"))
)
)
# TODO test that we have documented
# everything successfully and that all files
# have been parsed successfully
return(TRUE)
}
.ppfiles_mkvignettes <- function(dir = NULL) {
if (proj_get() != dir) {
usethis::proj_set(dir) #nocov
}
pkg <- desc::desc(dir)
pkg$set_dep("knitr", "Suggests")
pkg$set_dep("rmarkdown", "Suggests")
pkg$set("VignetteBuilder" = "knitr")
pkg$write()
usethis::use_directory("vignettes")
usethis::use_directory("inst/doc")
# TODO maybe copy only the files that have both html and Rmd.
rmdfiles_for_vignettes <-
list.files(
path = file.path(dir, "data-raw"),
pattern = "Rmd$",
full.names = TRUE,
recursive = FALSE
)
htmlfiles_for_vignettes <-
list.files(
path = file.path(dir, "inst/extdata/Logfiles"),
pattern = "html$",
full.names = TRUE,
recursive = FALSE
)
pdffiles_for_vignettes <-
list.files(
path = file.path(dir, "inst/extdata/Logfiles"),
pattern = "pdf$",
full.names = TRUE,
recursive = FALSE
)
lapply(htmlfiles_for_vignettes,
function(x) {
file.copy(x,
file.path(
dir,
"inst/doc",
basename(x)
),
overwrite = TRUE
)
}
)
lapply(
pdffiles_for_vignettes,
function(x) {
file.copy(x,
file.path(
dir,
"inst/doc",
basename(x)
),
overwrite = TRUE
)
}
)
lapply(
rmdfiles_for_vignettes,
function(x) {
file.copy(x,
file.path(
dir,
"vignettes",
basename(x)
),
overwrite = TRUE
)
}
)
vignettes_to_process <- list.files(
path = file.path(dir, "vignettes"),
pattern = "Rmd$",
full.names = TRUE,
recursive = FALSE
)
write_me_out <- lapply(vignettes_to_process, function(x) {
title <- "Default Vignette Title. Add yaml title: to your document"
thisfile <- read_file(x)
stripped_yaml <- gsub("---\\s*\n.*\n---\\s*\n", "", thisfile)
frontmatter <- gsub("(---\\s*\n.*\n---\\s*\n).*", "\\1", thisfile)
con <- textConnection(frontmatter)
fm <- rmarkdown::yaml_front_matter(con)
if (is.null(fm[["vignette"]])) {
# add boilerplate vignette yaml
if (!is.null(fm$title)) {
title <- fm$title
}
fm$vignette <- paste0("%\\VignetteIndexEntry{", title, "}
%\\VignetteEngine{knitr::rmarkdown}
\\usepackage[utf8]{inputenc}")
} else {
# otherwise leave it as is.
}
tmp <- fm$vignette
tmp <- gsub(
" $",
"",
paste0(
"vignette: >\n ",
gsub(
"\\}\\s*",
"\\}\n ",
tmp
)
)
)
fm$vignette <- NULL
write_me_out <- paste0(
"---\n",
paste0(yaml::as.yaml(fm), tmp),
"---\n\n",
stripped_yaml
)
write_me_out
})
names(write_me_out) <- vignettes_to_process
for (i in vignettes_to_process) {
writeLines(write_me_out[[i]], con = i)
writeLines(write_me_out[[i]],
con = file.path(
dir,
"inst/doc",
basename(i)
)
)
}
}
#' Get DataPackageR Project Root Path
#'
#' @details Returns the path to the data package project root, or
#' constructs a path to a file in the project root from the
#' file argument.
#' @return \code{character}
#' @param file \code{character} or \code{NULL} (default).
#' @export
#'
#' @examples
#' if(rmarkdown::pandoc_available()){
#' project_path( file = "DESCRIPTION" )
#' }
project_path <- function(file = NULL) {
if (is.null(file)) {
return(usethis::proj_get())
} else {
return(normalizePath(file.path(usethis::proj_get(), file), winslash = "/",
mustWork = FALSE))
}
}
#' Get DataPackageR extdata path
#'
#' @details Returns the path to the data package extdata subdirectory, or
#' constructs a path to a file in the extdata subdirectory from the
#' file argument.
#' @return \code{character}
#' @param file \code{character} or \code{NULL} (default).
#' @export
#'
#' @examples
#' if(rmarkdown::pandoc_available()){
#' project_extdata_path(file = "mydata.csv")
#' }
project_extdata_path <- function(file = NULL) {
if (is.null(file)) {
return(file.path(usethis::proj_get(), "inst", "extdata"))
} else {
return(normalizePath(
file.path(
usethis::proj_get(),
"inst", "extdata", file
),
winslash = "/",
mustWork = FALSE
))
}
}
#' Get DataPackageR data path
#'
#' @details Returns the path to the data package data subdirectory, or
#' constructs a path to a file in the data subdirectory from the
#' file argument.
#' @return \code{character}
#' @param file \code{character} or \code{NULL} (default).
#' @export
#'
#' @examples
#' if(rmarkdown::pandoc_available()){
#' project_data_path( file = "data.rda" )
#' }
project_data_path <- function(file = NULL) {
if (is.null(file)) {
return(file.path(usethis::proj_get(), "data"))
} else {
return(normalizePath(
file.path(
usethis::proj_get(),
"data", file
),
winslash = "/",
mustWork = FALSE
))
}
}
#' @name document
#' @rdname document
#' @title Build documentation for a data package using DataPackageR.
#' @param path \code{character} the path to the data package source root.
#' @param install \code{logical} install the package. (default FALSE)
#' @param ... additional arguments to \code{install}
#' @returns Called for side effects. Returns TRUE on successful exit.
#' @export
#' @examples
#' # A simple Rmd file that creates one data object
#' # named "tbl".
#' if(rmarkdown::pandoc_available()){
#' f <- tempdir()
#' f <- file.path(f,"foo.Rmd")
#' con <- file(f)
#' writeLines("```{r}\n tbl = data.frame(1:10) \n```\n",con=con)
#' close(con)
#' \donttest{
#' # construct a data package skeleton named "MyDataPackage" and pass
#' # in the Rmd file name with full path, and the name of the object(s) it
#' # creates.
#'
#' pname <- basename(tempfile())
#' datapackage_skeleton(name=pname,
#' path=tempdir(),
#' force = TRUE,
#' r_object_names = "tbl",
#' code_files = f)
#'
#' # call package_build to run the "foo.Rmd" processing and
#' # build a data package.
#' package_build(file.path(tempdir(), pname), install = FALSE)
#' document(path = file.path(tempdir(), pname), install = FALSE)
#' }
#' }
document <- function(path = ".", install = FALSE, ...) {
if (getOption('DataPackageR_verbose', TRUE)) cat("\n")
usethis::proj_set(path = path)
path <- usethis::proj_get()
stopifnot(file.exists(file.path(path, "data-raw", "documentation.R")))
desc <- desc::desc(file.path(path, "DESCRIPTION"))
docfile <- paste0(desc$get("Package"), ".R")
file.copy(
from = file.path(path, "data-raw", "documentation.R"),
to = file.path(path, "R", docfile),
overwrite = TRUE
)
.multilog_trace("Rebuilding data package documentation.")
local({
on.exit({
if (basename(path) %in% names(utils::sessionInfo()$otherPkgs)){
pkgload::unload(basename(path))
}
})
roxygen2::roxygenize(package.dir = path)
})
location <- pkgbuild::build(
path = path, dest_path = dirname(path),
vignettes = FALSE, quiet = TRUE
)
# try to install and then reload the package in the current session
if (install) {
utils::install.packages(location, repos = NULL, type = "source", ...)
}
return(TRUE)
}