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(v1.6.0.9060) unit tests

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dr. M.S. (Matthijs) Berends 2021-05-22 10:05:59 +02:00
parent adca43f8d9
commit fa2f5214b9
15 changed files with 22 additions and 21 deletions
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8
.github/workflows/codecovr.yaml vendored
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@ -60,7 +60,6 @@ jobs:
run: | run: |
tar -xf data-raw/AMR_latest.tar.gz tar -xf data-raw/AMR_latest.tar.gz
Rscript -e "source('data-raw/_install_deps.R')" Rscript -e "source('data-raw/_install_deps.R')"
Rscript -e "install.packages('covr')"
shell: bash shell: bash
- name: Show session info - name: Show session info
@ -76,10 +75,11 @@ jobs:
run: | run: |
library(AMR) library(AMR)
library(tinytest) library(tinytest)
library(covr)
source_files <- list.files("AMR/R", pattern = ".R$", full.names = TRUE) source_files <- list.files("AMR/R", pattern = ".R$", full.names = TRUE)
test_files <- list.files("AMR/inst/tinytest", full.names = TRUE) test_files <- list.files("AMR/inst/tinytest", full.names = TRUE)
cov <- covr::file_coverage(source_files = source_files, test_files = test_files, parent_env = asNamespace("AMR"), line_exclusions = list("R/atc_online.R", "R/mo_source.R", "R/translate.R", "R/resistance_predict.R", "R/aa_helper_functions.R", "R/aa_helper_pm_functions.R", "R/zzz.R")) cov <- file_coverage(source_files = source_files, test_files = test_files, parent_env = asNamespace("AMR"), line_exclusions = list("AMR/R/atc_online.R", "AMR/R/mo_source.R", "AMR/R/translate.R", "AMR/R/resistance_predict.R", "AMR/R/aa_helper_functions.R", "AMR/R/aa_helper_pm_functions.R", "AMR/R/zzz.R"))
print(cov) print(cov)
attr(cov, which = "package") <- list(path = "") # until https://github.com/r-lib/covr/issues/478 is solved attr(cov, which = "package") <- list(path = ".") # until https://github.com/r-lib/covr/issues/478 is solved
covr::codecov(cov, quiet = FALSE) codecov(coverage = cov, quiet = FALSE)
shell: Rscript {0} shell: Rscript {0}

3
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 1.6.0.9058 Version: 1.6.0.9060
Date: 2021-05-22 Date: 2021-05-22
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Authors@R: c( Authors@R: c(
@ -43,6 +43,7 @@ Depends:
R (>= 3.0.0) R (>= 3.0.0)
Suggests: Suggests:
cleaner, cleaner,
covr,
curl, curl,
dplyr, dplyr,
ggplot2, ggplot2,

2
NEWS.md
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@ -1,4 +1,4 @@
# `AMR` 1.6.0.9058 # `AMR` 1.6.0.9060
## <small>Last updated: 22 May 2021</small> ## <small>Last updated: 22 May 2021</small>
### Breaking change ### Breaking change

BIN
data-raw/AMR_latest.tar.gz
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4
data-raw/_install_deps.R
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@ -32,7 +32,7 @@ cat("Packages listed in Suggests:", paste(pkg_suggests, collapse = ", "), "\n")
to_install <- pkg_suggests[!pkg_suggests %in% rownames(utils::installed.packages())] to_install <- pkg_suggests[!pkg_suggests %in% rownames(utils::installed.packages())]
if (length(to_install) == 0) { if (length(to_install) == 0) {
message("Nothing to install") message("\nNothing to install\n")
} }
for (i in seq_len(length(to_install))) { for (i in seq_len(length(to_install))) {
cat("Installing package", to_install[i], "\n") cat("Installing package", to_install[i], "\n")
@ -45,7 +45,7 @@ for (i in seq_len(length(to_install))) {
to_update <- as.data.frame(utils::old.packages(repos = "https://cran.rstudio.com/"), stringsAsFactors = FALSE) to_update <- as.data.frame(utils::old.packages(repos = "https://cran.rstudio.com/"), stringsAsFactors = FALSE)
to_update <- to_update[which(to_update$Package %in% pkg_suggests), "Package", drop = TRUE] to_update <- to_update[which(to_update$Package %in% pkg_suggests), "Package", drop = TRUE]
if (length(to_update) == 0) { if (length(to_update) == 0) {
message("Nothing to update") message("\nNothing to update\n")
} }
for (i in seq_len(length(to_update))) { for (i in seq_len(length(to_update))) {
cat("Updating package", to_update[i], "\n") cat("Updating package", to_update[i], "\n")

2
docs/404.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a> <a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9058</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9060</span>
</span> </span>
</div> </div>

2
docs/LICENSE-text.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9058</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9060</span>
</span> </span>
</div> </div>

2
docs/articles/datasets.html
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@ -39,7 +39,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9058</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9060</span>
</span> </span>
</div> </div>

2
docs/articles/index.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9058</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9060</span>
</span> </span>
</div> </div>

2
docs/authors.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9058</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9060</span>
</span> </span>
</div> </div>

2
docs/index.html
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@ -42,7 +42,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9058</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9060</span>
</span> </span>
</div> </div>

8
docs/news/index.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9058</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9060</span>
</span> </span>
</div> </div>
@ -236,9 +236,9 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small> <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div> </div>
<div id="amr-1609058" class="section level1"> <div id="amr-1609060" class="section level1">
<h1 class="page-header" data-toc-text="1.6.0.9058"> <h1 class="page-header" data-toc-text="1.6.0.9060">
<a href="#amr-1609058" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9058</h1> <a href="#amr-1609060" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9060</h1>
<div id="last-updated-22-may-2021" class="section level2"> <div id="last-updated-22-may-2021" class="section level2">
<h2 class="hasAnchor"> <h2 class="hasAnchor">
<a href="#last-updated-22-may-2021" class="anchor"></a><small>Last updated: 22 May 2021</small> <a href="#last-updated-22-may-2021" class="anchor"></a><small>Last updated: 22 May 2021</small>

2
docs/pkgdown.yml
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@ -12,7 +12,7 @@ articles:
datasets: datasets.html datasets: datasets.html
resistance_predict: resistance_predict.html resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html welcome_to_AMR: welcome_to_AMR.html
last_built: 2021-05-22T06:56Z last_built: 2021-05-22T07:53Z
urls: urls:
reference: https://msberends.github.io/AMR//reference reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles article: https://msberends.github.io/AMR//articles

2
docs/reference/index.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9058</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9060</span>
</span> </span>
</div> </div>

2
docs/survey.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9058</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9060</span>
</span> </span>
</div> </div>