From fa238899a722fcc8d9d7af47471ea7cd9732a454 Mon Sep 17 00:00:00 2001 From: Kelly Sovacool Date: Mon, 25 Oct 2021 13:21:33 -0400 Subject: [PATCH 1/2] Only test the options we modify --- tests/testthat/test-rmd_helpers.R | 22 ++++++---------------- 1 file changed, 6 insertions(+), 16 deletions(-) diff --git a/tests/testthat/test-rmd_helpers.R b/tests/testthat/test-rmd_helpers.R index 7efd5cd..ed394ee 100644 --- a/tests/testthat/test-rmd_helpers.R +++ b/tests/testthat/test-rmd_helpers.R @@ -33,23 +33,13 @@ test_that("inline_hook() uses paste_oxford_list() and format_number() correctly" test_that("set_knitr_opts() works", { chunk <- list( - eval = TRUE, echo = FALSE, results = "markup", tidy = TRUE, - tidy.opts = NULL, collapse = FALSE, prompt = FALSE, comment = "##", - highlight = TRUE, strip.white = TRUE, size = "normalsize", - background = "#F7F7F7", cache = FALSE, cache.path = "cache/", - cache.vars = NULL, cache.lazy = TRUE, dependson = NULL, autodep = FALSE, - cache.rebuild = FALSE, fig.keep = "high", fig.show = "asis", - fig.align = "default", fig.path = "figure/", dev = NULL, - dev.args = NULL, dpi = 72, fig.ext = NULL, fig.width = 7, - fig.height = 7, fig.env = "figure", fig.cap = NULL, fig.scap = NULL, - fig.lp = "fig:", fig.subcap = NULL, fig.pos = "", out.width = NULL, - out.height = NULL, out.extra = NULL, fig.retina = 1, external = TRUE, - sanitize = FALSE, interval = 1, aniopts = "controls,loop", - warning = FALSE, error = TRUE, message = TRUE, render = NULL, - ref.label = NULL, child = NULL, engine = "R", split = FALSE, - include = TRUE, purl = TRUE + tidy = TRUE, + echo = FALSE, + eval = TRUE, + warning = FALSE, + cache = FALSE ) set_knitr_opts() - expect_equal(knitr::opts_chunk$get(), chunk) + expect_equal(knitr::opts_chunk$get()[names(chunk)], chunk) expect_equal(knitr::knit_hooks$get("inline"), inline_hook) }) From a9c6a75365766ff04eba470708aa09a284627aa1 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Mon, 25 Oct 2021 17:27:42 +0000 Subject: [PATCH 2/2] =?UTF-8?q?=F0=9F=93=91=20Build=20docs=20site?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- docs/articles/introduction.html | 2 +- docs/pkgdown.yml | 2 +- docs/reference/read_dist.html | 16 ++++++++-------- docs/reference/read_tax.html | 18 +++++++++--------- 4 files changed, 19 insertions(+), 19 deletions(-) diff --git a/docs/articles/introduction.html b/docs/articles/introduction.html index 359b496..3dedd65 100644 --- a/docs/articles/introduction.html +++ b/docs/articles/introduction.html @@ -99,7 +99,7 @@

package = "schtools") dist_tbl <- read_dist(dist_filepath) head(dist_tbl) -#> # A tibble: 6 x 3 +#> # A tibble: 6 × 3 #> rows columns distances #> <chr> <chr> <dbl> #> 1 104_1_D1 104_1_D0 0.893 diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index e5e720a..785e1ce 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -3,5 +3,5 @@ pkgdown: 1.6.1 pkgdown_sha: ~ articles: introduction: introduction.html -last_built: 2021-05-19T19:53Z +last_built: 2021-10-25T17:27Z diff --git a/docs/reference/read_dist.html b/docs/reference/read_dist.html index 3b50b2e..7aa61e2 100644 --- a/docs/reference/read_dist.html +++ b/docs/reference/read_dist.html @@ -152,15 +152,15 @@

Examp ) dist_tbl <- read_dist(dist_filepath) head(dist_tbl) -
#> # A tibble: 6 x 3 +
#> # A tibble: 6 × 3 #> rows columns distances -#> <chr> <chr> <dbl> -#> 1 104_1_D1 104_1_D0 0.893 -#> 2 104_1_D10 104_1_D0 0.254 -#> 3 104_1_D10 104_1_D1 0.922 -#> 4 104_1_D2 104_1_D0 0.874 -#> 5 104_1_D2 104_1_D1 0.109 -#> 6 104_1_D2 104_1_D10 0.904
+#> <chr> <chr> <dbl> +#> 1 104_1_D1 104_1_D0 0.893 +#> 2 104_1_D10 104_1_D0 0.254 +#> 3 104_1_D10 104_1_D1 0.922 +#> 4 104_1_D2 104_1_D0 0.874 +#> 5 104_1_D2 104_1_D1 0.109 +#> 6 104_1_D2 104_1_D10 0.904
#> # A tibble: 6 x 9 -#> OTU Kingdom Phylum Class Order Family Genus tax_otu_label otu_label -#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> -#> 1 Otu00… Bacteria Bacter… Bacte… Bacte… Bacter… Bacter… Bacteroides (… OTU 1 -#> 2 Otu00… Bacteria Bacter… Bacte… Bacte… Porphy… Porphy… Porphyromonad… OTU 3 -#> 3 Otu00… Bacteria Bacter… Bacte… Bacte… Porphy… Porphy… Porphyromonad… OTU 4 -#> 4 Otu00… Bacteria Proteo… Gamma… Enter… Entero… Entero… Enterobacteri… OTU 8 -#> 5 Otu00… Bacteria Bacter… Bacte… Bacte… Bacter… Bacter… Bacteria (OTU… OTU 44 -#> 6 Otu00… Bacteria Bacter… Bacte… Bacte… Bacter… Bacter… Bacteria (OTU… OTU 56
+
#> # A tibble: 6 × 9 +#> OTU Kingdom Phylum Class Order Family Genus tax_otu_label otu_label +#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> +#> 1 Otu0001 Bacteria Bacter… Bacte… Bacte… Bacter… Bacte… Bacteroides … OTU 1 +#> 2 Otu0003 Bacteria Bacter… Bacte… Bacte… Porphy… Porph… Porphyromona… OTU 3 +#> 3 Otu0004 Bacteria Bacter… Bacte… Bacte… Porphy… Porph… Porphyromona… OTU 4 +#> 4 Otu00008 Bacteria Proteo… Gamma… Enter… Entero… Enter… Enterobacter… OTU 8 +#> 5 Otu0044 Bacteria Bacter… Bacte… Bacte… Bacter… Bacte… Bacteria (OT… OTU 44 +#> 6 Otu0056 Bacteria Bacter… Bacte… Bacte… Bacter… Bacte… Bacteria (OT… OTU 56