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spaceout R/function-params.R
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@mpadge
mpadge committed Oct 18, 2023
1 parent a721bb1 commit 65d4607
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
Package: autotest
Title: Automatic Package Testing
Version: 0.0.2.202
Version: 0.0.2.203
Authors@R: c(
person("Mark", "Padgham", , "[email protected]", role = c("aut", "cre"),
comment = c(ORCID = "0000-0003-2172-5265")),
Expand Down
206 changes: 129 additions & 77 deletions R/function-params.R
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Original file line number Diff line number Diff line change
@@ -1,4 +1,3 @@

# extracts the i-th list of complete parameters from the result of a parsed yaml
get_params <- function (res, i, this_fn) {

Expand All @@ -8,9 +7,9 @@ get_params <- function (res, i, this_fn) {
p_vals <- lapply (p, function (i) i [[1]])

# remove any with NULL values
#index <- which (vapply (p_vals, function (i) !is.null (i), logical (1)))
#p_keys <- p_keys [index]
#p_vals <- p_vals [index]
# index <- which (vapply (p_vals, function (i) !is.null (i), logical (1)))
# p_keys <- p_keys [index]
# p_vals <- p_vals [index]

. <- NULL # suppress no visible binding note # nolint
pre <- res$preprocess [[i]]
Expand All @@ -23,23 +22,28 @@ get_params <- function (res, i, this_fn) {

for (p in pre) {
# remove "`" except if they name list items
if (!grepl ("\\$`", p))
if (!grepl ("\\$`", p)) {
p <- gsub ("`", "", p)
}
expr <- parse (text = p)
suppressMessages (
tmp <- tryCatch (utils::capture.output (eval (expr,
envir = pkg_env)),
error = function (e) NULL)
tmp <- tryCatch (
utils::capture.output (eval (expr,
envir = pkg_env
)),
error = function (e) NULL
)
)
}

params <- fill_param_vals (p_keys, p_vals, pkg_env, res$package)

# Parse fn definition to get list of all parameters:
if (!res$package %in% search ())
if (!res$package %in% search ()) {
suppressMessages (
library (res$package, character.only = TRUE)
)
)
}
if (grepl (":::", this_fn)) { # internal fn, so attach to pkg_env
this_fn <- rm_internal_namespace (this_fn)
tmp_fn <- utils::getFromNamespace (this_fn, res$package)
Expand Down Expand Up @@ -76,8 +80,10 @@ get_params <- function (res, i, this_fn) {
# finally, remove any params that are if conditionals, since evaluting these
# requires parsing and evaluating all other parameters, and if conditions
# can not be mutated anyway
index <- which (vapply (params, function (i) !methods::is (i, "if"),
logical (1)))
index <- which (vapply (
params, function (i) !methods::is (i, "if"),
logical (1)
))
params <- params [index]

return (params)
Expand All @@ -91,23 +97,26 @@ get_Rd_value <- function (package, fn_name) { # nolint
f <- file.path (package, "man", paste0 (fn_name, ".Rd"))
suppressWarnings (
rd <- tools::parse_Rd (f)
)
)
} else {
if (basename (package) == package) {
x <- tools::Rd_db (package = package)
} else {
# packages installed into local tempdir via covr:
x <- tools::Rd_db (package = basename (package),
dir = package)
x <- tools::Rd_db (
package = basename (package),
dir = package
)
}
rd <- x [[paste0 (fn_name, ".Rd")]]
}


# just to check whether there is a return value:
val <- get_Rd_metadata (rd, "value")
if (length (val) == 0)
if (length (val) == 0) {
return (NULL)
}

# Then get actual value by converting to text:
f <- tempfile (fileext = ".txt")
Expand All @@ -132,12 +141,14 @@ get_Rd_param <- function (package, fn_name, param_name) { # nolint

if (pkg_is_source (package)) {

f <- file.path (package,
"man",
a$name [a$alias == fn_name])
f <- file.path (
package,
"man",
a$name [a$alias == fn_name]
)
suppressWarnings (
rd <- tools::parse_Rd (f)
)
)
} else {

if (basename (package) == package) {
Expand All @@ -146,16 +157,21 @@ get_Rd_param <- function (package, fn_name, param_name) { # nolint
} else {

# packages installed into local tempdir via covr:
x <- tools::Rd_db (package = basename (package),
dir = package)
x <- tools::Rd_db (
package = basename (package),
dir = package
)
}

rd <- x [[a$name [a$alias == fn_name]]]
}

index <- vapply (rd, function (i)
attr (i, "Rd_tag") == "\\arguments",
logical (1))
index <- vapply (
rd, function (i) {
attr (i, "Rd_tag") == "\\arguments"
},
logical (1)
)
index <- which (index)
if (length (index) == 0) {
return (NULL)
Expand All @@ -170,12 +186,15 @@ get_Rd_param <- function (package, fn_name, param_name) { # nolint
rd <- rd [which (len > 1)]
rd <- lapply (rd, unlist)
params <- vapply (rd, function (i) i [1], character (1))
rd <- vapply (rd, function (i) paste0 (i [-1], collapse = ""),
character (1))
rd <- vapply (
rd, function (i) paste0 (i [-1], collapse = ""),
character (1)
)

ret <- NA_character_
if (param_name %in% params)
if (param_name %in% params) {
ret <- rd [which (params == param_name)]
}
return (ret)
}

Expand All @@ -190,19 +209,25 @@ get_param_descs_source <- function (package, fn) {

index <- grep ("^\\\\item\\{", x)
index <- rep (seq (index),
times = c (diff (index), length (x) - max (index) + 1))
times = c (diff (index), length (x) - max (index) + 1)
)
xs <- split (x, f = as.factor (index))

items <- vapply (xs, function (i) {
i <- gsub ("^\\\\item\\{|\\}$", "", i)
return (strsplit (i, "\\}") [[1]] [1]) },
character (1), USE.NAMES = FALSE)
i <- gsub ("^\\\\item\\{|\\}$", "", i)
return (strsplit (i, "\\}") [[1]] [1]) },
character (1),
USE.NAMES = FALSE
)
descs <- vapply (xs, function (i) {
i <- paste0 (gsub ("^\\\\item\\{|\\}$", "", i),
collapse = " ")
return (substr (i, regexpr ("\\{", i) + 1, nchar (i)))
},
character (1), USE.NAMES = FALSE)
i <- paste0 (gsub ("^\\\\item\\{|\\}$", "", i),
collapse = " "
)
return (substr (i, regexpr ("\\{", i) + 1, nchar (i)))
},
character (1),
USE.NAMES = FALSE
)

names (descs) <- items

Expand All @@ -216,17 +241,21 @@ fill_param_vals <- function (p_keys, p_vals, pkg_env, package) {
for (p in seq_along (p_keys)) {

this_val <- p_vals [[p]]
if (is.null (this_val))
if (is.null (this_val)) {
next
}

this_val <- get_non_formula_val (this_val,
pkg_env,
package,
p_vals,
p)
this_val <- get_non_formula_val (
this_val,
pkg_env,
package,
p_vals,
p
)
# leave formulae as strings:
if (methods::is (this_val, "formula"))
if (methods::is (this_val, "formula")) {
this_val <- p_vals [[p]]
}

params [[length (params) + 1]] <- this_val
names (params) [length (params)] <- p_keys [p]
Expand All @@ -244,34 +273,47 @@ get_non_formula_val <- function (this_val, pkg_env, package, p_vals, p) {
temp_val <- paste0 (this_val)

temp_val_get <- tryCatch (get (temp_val, envir = pkg_env),
error = function (e) NULL)
temp_val_eval <- tryCatch (eval (parse (text = this_val),
envir = pkg_env),
error = function (err) NULL)
error = function (e) NULL
)
temp_val_eval <- tryCatch (
eval (parse (text = this_val),
envir = pkg_env
),
error = function (err) NULL
)

can_get <- !is.null (tryCatch (get (temp_val),
error = function (e) NULL))
can_eval <- !is.null (tryCatch (eval (parse (text = this_val),
envir = pkg_env),
error = function (err) NULL))
error = function (e) NULL
))
can_eval <- !is.null (tryCatch (
eval (parse (text = this_val),
envir = pkg_env
),
error = function (err) NULL
))

if (!is.null (temp_val_get)) {
this_val <- temp_val_get
} else if (!is.null (temp_val_eval)) {
this_val <- temp_val_eval
} else if (grepl ("::", temp_val)) {
this_pkg <- strsplit (temp_val, "::") [[1]] [1]
if (!this_pkg %in% search ())
if (!this_pkg %in% search ()) {
suppressMessages (
library (this_pkg,
character.only = TRUE)
library (this_pkg,
character.only = TRUE
)
)
}
this_val <- parse (text = temp_val) %>%
eval (envir = as.environment (paste0 ("package:",
this_pkg)))
eval (envir = as.environment (paste0 (
"package:",
this_pkg
)))
} else {
this_val <- tryCatch (eval (this_val, envir = pkg_env),
error = function (e) NULL)
error = function (e) NULL
)
}

} else if (is.character (this_val)) {
Expand All @@ -281,22 +323,28 @@ get_non_formula_val <- function (this_val, pkg_env, package, p_vals, p) {
eval (envir = pkg_env)
} else if (grepl ("::", this_val)) {
this_pkg <- strsplit (p_vals [[p]], "::") [[1]] [1]
if (!this_pkg %in% search ())
if (!this_pkg %in% search ()) {
suppressMessages (
library (this_pkg, character.only = TRUE)
library (this_pkg, character.only = TRUE)
)
}
this_val <- parse (text = this_val) %>%
eval (envir = as.environment (paste0 ("package:",
this_pkg)))
eval (envir = as.environment (paste0 (
"package:",
this_pkg
)))
} else {
tryeval <- tryCatch (eval (parse (text = this_val)),
error = function (e) NULL)
error = function (e) NULL
)
# Character values may also name functions, in which case these
# should NOT be assigned to the values. An example is ?var which has
# `method = "complete"`, where "complete" is also a function.
if (!is.null (tryeval))
if (!methods::is (tryeval, "function"))
if (!is.null (tryeval)) {
if (!methods::is (tryeval, "function")) {
this_val <- tryeval
}
}
}
}

Expand All @@ -315,13 +363,14 @@ clean_final_pars_list <- function (params, pars, nms) {
# parameters in formals with no default values are returned as empty
# 'symbol' expressions - this converts these to "MISSING":
pars <- lapply (pars, function (i) {
if (typeof (i) == "symbol" & all (deparse (i) == ""))
return ("MISSING")
else if (is.null (i))
return ("NULL")
else
return (i)
})
if (typeof (i) == "symbol" & all (deparse (i) == "")) {
return ("MISSING")
} else if (is.null (i)) {
return ("NULL")
} else {
return (i)
}
})
index <- pmatch (names (params), nms)
index <- index [which (!is.na (index))]
pars <- pars [-index]
Expand All @@ -331,11 +380,14 @@ clean_final_pars_list <- function (params, pars, nms) {
if (any (pars == "MISSING")) {
no_defaults <- nms [which (pars == "MISSING")]
no_defaults <- no_defaults [which (no_defaults %in% names (params))]
if (length (no_defaults) > 0)
stop ("function includes the following parameters which require ",
"non-default values:\n [",
paste0 (no_defaults, collapse = ", "),
"]")
if (length (no_defaults) > 0) {
stop (
"function includes the following parameters which require ",
"non-default values:\n [",
paste0 (no_defaults, collapse = ", "),
"]"
)
}
# The rest must be in params, so the default "MISSING" entries can be
# removed here:
pars <- pars [which (pars != "MISSING")]
Expand Down
2 changes: 1 addition & 1 deletion codemeta.json
View file
Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@
"codeRepository": "https://github.com/ropensci-review-tools/autotest",
"issueTracker": "https://github.com/ropensci-review-tools/autotest/issues",
"license": "https://spdx.org/licenses/GPL-3.0",
"version": "0.0.2.202",
"version": "0.0.2.203",
"programmingLanguage": {
"@type": "ComputerLanguage",
"name": "R",
Expand Down

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