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Merge pull request #43 from Merck/housekeeping
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Housekeeping
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@nanxstats
nanxstats committed Jul 9, 2023
2 parents 6f094f9 + 41386e9 commit cf4e265
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Showing 3 changed files with 39 additions and 60 deletions.
2 changes: 2 additions & 0 deletions .github/workflows/pkgdown.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,8 @@ jobs:
group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
permissions:
contents: write
steps:
- uses: actions/checkout@v3

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2 changes: 1 addition & 1 deletion _pkgdown.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@ footer:
left: [developed_by, built_with, legal]
right: [blank]
components:
legal: "<br>Copyright &copy; 2022 Merck & Co., Inc., Rahway, NJ, USA and its affiliates. All rights reserved."
legal: "<br>Copyright &copy; 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates. All rights reserved."
blank: "<span></span>"

code:
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95 changes: 36 additions & 59 deletions tests/testthat/test-independent-test_templates.R
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Original file line number Diff line number Diff line change
Expand Up @@ -13,13 +13,13 @@ file_spec_func_valid <- function() {
)

return(
fs_source$path == path
& fs_source$pattern == pattern
& fs_source$format == format
& fs_source$recursive == recursive
& fs_source$ignore_case == ignore_case
& fs_source$all_files == all_files
& class(fs_source) == "file_spec"
fs_source$path == path &
fs_source$pattern == pattern &
fs_source$format == format &
fs_source$recursive == recursive &
fs_source$ignore_case == ignore_case &
fs_source$all_files == all_files &
class(fs_source) == "file_spec"
)
}

Expand All @@ -35,8 +35,7 @@ fs_unlist <- function(fs) {
if (class(x) == "file_spec") {
ls_cnt <- ls_cnt + 1
ls[[ls_cnt]] <- x
}
else if (class(x) == "list") {
} else if (class(x) == "list") {
ls_tmp <- fs_unlist(x)
for (j in seq_len(length(ls_tmp))) {
ls_cnt <- ls_cnt + 1
Expand All @@ -50,13 +49,13 @@ fs_unlist <- function(fs) {

# check if a file_spec object has all of the parameters as specified
is_file_spec_type <- function(fs_source, path, pattern, format, recursive, ignore_case, all_files) {
return(fs_source$path == path
& fs_source$pattern == pattern
& fs_source$format == format
& fs_source$recursive == recursive
& fs_source$ignore_case == ignore_case
& fs_source$all_files == all_files
& class(fs_source) == "file_spec")
return(fs_source$path == path &
fs_source$pattern == pattern &
fs_source$format == format &
fs_source$recursive == recursive &
fs_source$ignore_case == ignore_case &
fs_source$all_files == all_files &
class(fs_source) == "file_spec")
}

testthat::test_that("file_root_core() creates the correct 'file_spec' object", {
Expand Down Expand Up @@ -110,8 +109,7 @@ testthat::test_that("file_r() creates the correct 'file_spec' objects", {
)
) {
is_spec_code <- TRUE
}
else if
} else if
(!is_spec_data & is_file_spec_type(
fs_source = fs,
path = "R/",
Expand Down Expand Up @@ -155,8 +153,7 @@ testthat::test_that("file_man() creates the correct 'file_spec' objects", {
)
) {
is_spec_rd <- TRUE
}
else if
} else if
(!is_spec_fig_binary & is_file_spec_type(
fs_source = fs,
path = "man/figures/",
Expand All @@ -168,8 +165,7 @@ testthat::test_that("file_man() creates the correct 'file_spec' objects", {
)
) {
is_spec_fig_binary <- TRUE
}
else if
} else if
(!is_spec_fig_text & is_file_spec_type(
fs_source = fs,
path = "man/figures/",
Expand Down Expand Up @@ -242,8 +238,7 @@ testthat::test_that("file_vignettes() creates the correct 'file_spec' objects",
)
) {
is_spec_text <- TRUE
}
else if
} else if
(!is_spec_binary & is_file_spec_type(
fs_source = fs,
path = "vignettes/",
Expand Down Expand Up @@ -295,8 +290,7 @@ testthat::test_that("file_default() creates the correct 'file_spec' objects", {
)
) {
is_root_core <- TRUE
}
else if (!is_spec_code & is_file_spec_type(
} else if (!is_spec_code & is_file_spec_type(
fs_source = fs,
path = "R/",
pattern = "\\.R$|\\.r$|\\.s$|\\.q$",
Expand All @@ -307,8 +301,7 @@ testthat::test_that("file_default() creates the correct 'file_spec' objects", {
)
) {
is_spec_code <- TRUE
}
else if
} else if
(!is_spec_data & is_file_spec_type(
fs_source = fs,
path = "R/",
Expand All @@ -320,8 +313,7 @@ testthat::test_that("file_default() creates the correct 'file_spec' objects", {
)
) {
is_spec_data <- TRUE
}
else if (!is_spec_rd & is_file_spec_type(
} else if (!is_spec_rd & is_file_spec_type(
fs_source = fs,
path = "man/",
pattern = "\\.Rd$|\\.rd$",
Expand All @@ -332,8 +324,7 @@ testthat::test_that("file_default() creates the correct 'file_spec' objects", {
)
) {
is_spec_rd <- TRUE
}
else if
} else if
(!is_spec_fig_binary & is_file_spec_type(
fs_source = fs,
path = "man/figures/",
Expand All @@ -345,8 +336,7 @@ testthat::test_that("file_default() creates the correct 'file_spec' objects", {
)
) {
is_spec_fig_binary <- TRUE
}
else if
} else if
(!is_spec_fig_text & is_file_spec_type(
fs_source = fs,
path = "man/figures/",
Expand All @@ -358,8 +348,7 @@ testthat::test_that("file_default() creates the correct 'file_spec' objects", {
)
) {
is_spec_fig_text <- TRUE
}
else if
} else if
(!is_src & is_file_spec_type(
fs_source = fs,
path = "src/",
Expand All @@ -371,9 +360,7 @@ testthat::test_that("file_default() creates the correct 'file_spec' objects", {
)
) {
is_src <- TRUE
}

else if (!is_spec_text & is_file_spec_type(
} else if (!is_spec_text & is_file_spec_type(
fs_source = fs,
path = "vignettes/",
pattern = "\\.R$|\\.r$|\\.s$|\\.q$|\\.Rd$|\\.rd$|\\.svg$|\\.c$|\\.h$|\\.cpp$|\\.cc$|\\.hpp$|\\.hxx$|\\.hh$|\\.f$|\\.f90$|\\.f95$|\\.f03$|\\.win$|\\.in$|\\.ucrt$|\\.ac$|\\.Rmd$|\\.md$|\\.csl$|\\.Rnw$|\\.tex$|\\.ltx$|\\.rsp$|\\.cls$|\\.sty$|\\.bib$|\\.bst$|\\.asis$|\\.el$|\\.Rproj$|\\.dcf$|\\.yml$|\\.yaml$|\\.note$|\\.csv$|\\.tsv$|\\.txt$|\\.html$|\\.htm$|\\.shtml$|\\.css$|\\.js$|\\.json$|\\.xml$|\\.scss$|\\.less$|\\.rtf$|\\.save$|\\.Rout$|\\.stan$|\\.bug$|\\.jags$|\\.py$|\\.ipynb$|\\.sh$|\\.java$|\\.bat$|\\.m4$|\\.cmake$|\\.sql$|\\.lua$|\\.rs$|\\.jl$|\\.pl$|\\.pm$|\\.brew$|\\.po$|\\.pot$|\\.geojson$|\\.kml$|\\.prj$|\\.cpg$|\\.qpj$|\\.fasta$|\\.fastq$|\\.vcf$|\\.ped$|\\.bim$|\\.fam$|\\.gff$|\\.gtf$",
Expand All @@ -384,8 +371,7 @@ testthat::test_that("file_default() creates the correct 'file_spec' objects", {
)
) {
is_spec_text <- TRUE
}
else if
} else if
(!is_spec_binary & is_file_spec_type(
fs_source = fs,
path = "vignettes/",
Expand All @@ -397,8 +383,7 @@ testthat::test_that("file_default() creates the correct 'file_spec' objects", {
)
) {
is_spec_binary <- TRUE
}
else if
} else if
(!is_data & is_file_spec_type(
fs_source = fs,
path = "data/",
Expand Down Expand Up @@ -457,8 +442,7 @@ testthat::test_that("file_ectd() creates the correct 'file_spec' objects", {
)
) {
is_root_core <- TRUE
}
else if (!is_spec_code & is_file_spec_type(
} else if (!is_spec_code & is_file_spec_type(
fs_source = fs,
path = "R/",
pattern = "\\.R$|\\.r$|\\.s$|\\.q$",
Expand All @@ -469,8 +453,7 @@ testthat::test_that("file_ectd() creates the correct 'file_spec' objects", {
)
) {
is_spec_code <- TRUE
}
else if
} else if
(!is_spec_data & is_file_spec_type(
fs_source = fs,
path = "R/",
Expand All @@ -482,8 +465,7 @@ testthat::test_that("file_ectd() creates the correct 'file_spec' objects", {
)
) {
is_spec_data <- TRUE
}
else if (!is_spec_rd & is_file_spec_type(
} else if (!is_spec_rd & is_file_spec_type(
fs_source = fs,
path = "man/",
pattern = "\\.Rd$|\\.rd$",
Expand All @@ -494,8 +476,7 @@ testthat::test_that("file_ectd() creates the correct 'file_spec' objects", {
)
) {
is_spec_rd <- TRUE
}
else if
} else if
(!is_spec_fig_binary & is_file_spec_type(
fs_source = fs,
path = "man/figures/",
Expand All @@ -507,8 +488,7 @@ testthat::test_that("file_ectd() creates the correct 'file_spec' objects", {
)
) {
is_spec_fig_binary <- TRUE
}
else if
} else if
(!is_spec_fig_text & is_file_spec_type(
fs_source = fs,
path = "man/figures/",
Expand All @@ -520,8 +500,7 @@ testthat::test_that("file_ectd() creates the correct 'file_spec' objects", {
)
) {
is_spec_fig_text <- TRUE
}
else if
} else if
(!is_src & is_file_spec_type(
fs_source = fs,
path = "src/",
Expand All @@ -533,8 +512,7 @@ testthat::test_that("file_ectd() creates the correct 'file_spec' objects", {
)
) {
is_src <- TRUE
}
else if
} else if
(!is_data & is_file_spec_type(
fs_source = fs,
path = "data/",
Expand Down Expand Up @@ -581,8 +559,7 @@ testthat::test_that("file_auto() creates the correct 'file_spec' objects", {
)
) {
is_spec_text <- TRUE
}
else if
} else if
(!is_spec_binary & is_file_spec_type(
fs_source = fs,
path = "inst/",
Expand Down

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