diff --git a/.github/workflows/check-old-tinytest.yaml b/.github/workflows/check-old-tinytest.yaml
index 192d544bd..8aebca4cb 100644
--- a/.github/workflows/check-old-tinytest.yaml
+++ b/.github/workflows/check-old-tinytest.yaml
@@ -76,9 +76,14 @@ jobs:
- uses: r-lib/actions/setup-pandoc@v2
- - name: Install tinytest from CRAN
+ - name: Install suggested pkgs (and tinytest) from CRAN
run: |
- install.packages("tinytest", repos = "https://cran.r-project.org")
+ desc_lines <- readLines('DESCRIPTION')
+ suggests <- readLines('DESCRIPTION')[grepl("^(Suggests:| )", readLines('DESCRIPTION'))]
+ suggests <- suggests[(which(grepl("^Suggests", suggests)) + 1):length(suggests)]
+ suggests <- gsub("[ ,]", "", suggests)
+ pkgs <- unique(c(suggests, "tinytest"))
+ for (p in pkgs) try(install.packages(p, repos = "https://cran.r-project.org"), silent = TRUE)
shell: Rscript {0}
- name: Show session info
diff --git a/.github/workflows/lintr.yaml b/.github/workflows/lintr.yaml
deleted file mode 100644
index 81bc107f9..000000000
--- a/.github/workflows/lintr.yaml
+++ /dev/null
@@ -1,85 +0,0 @@
-# ==================================================================== #
-# TITLE: #
-# AMR: An R Package for Working with Antimicrobial Resistance Data #
-# #
-# SOURCE CODE: #
-# https://github.com/msberends/AMR #
-# #
-# PLEASE CITE THIS SOFTWARE AS: #
-# Berends MS, Luz CF, Friedrich AW, et al. (2022). #
-# AMR: An R Package for Working with Antimicrobial Resistance Data. #
-# Journal of Statistical Software, 104(3), 1-31. #
-# https://doi.org/10.18637/jss.v104.i03 #
-# #
-# Developed at the University of Groningen and the University Medical #
-# Center Groningen in The Netherlands, in collaboration with many #
-# colleagues from around the world, see our website. #
-# #
-# This R package is free software; you can freely use and distribute #
-# it for both personal and commercial purposes under the terms of the #
-# GNU General Public License version 2.0 (GNU GPL-2), as published by #
-# the Free Software Foundation.
-# We created this package for both routine data analysis and academic #
-# research and it was publicly released in the hope that it will be #
-# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
-# #
-# Visit our website for the full manual and a complete tutorial about #
-# how to conduct AMR data analysis: https://amr-for-r.org #
-# ==================================================================== #
-
-on:
- push:
- branches: '**'
- pull_request:
- branches: '**'
-
-name: lintr
-
-jobs:
- lintr:
- runs-on: ubuntu-latest
- env:
- GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
- steps:
- - uses: actions/checkout@v4
-
- - uses: r-lib/actions/setup-pandoc@v2
-
- - uses: r-lib/actions/setup-r@v2
- with:
- r-version: release
- # use RStudio Package Manager to quickly install packages
- use-public-rspm: true
-
- - uses: r-lib/actions/setup-r-dependencies@v2
- with:
- extra-packages: |
- any::lintr
- any::cyclocomp
- any::roxygen2
- any::devtools
- any::usethis
-
- - name: Remove unneeded folders
- run: |
- # do not check these folders
- rm -rf data-raw
- rm -rf tests
- rm -rf vignettes
-
- - name: Lint
- run: |
- # get ALL linters, not just default ones
- linters <- getNamespaceExports(asNamespace("lintr"))
- linters <- sort(linters[grepl("_linter$", linters)])
- # lose deprecated
- linters <- linters[!grepl("^(closed_curly|open_curly|paren_brace|semicolon_terminator|consecutive_stopifnot|no_tab|single_quotes|unnecessary_nested_if|unneeded_concatenation)_linter$", linters)]
- linters <- linters[linters != "linter"]
- # and the ones we find unnnecessary
- linters <- linters[!grepl("^(commented_code|extraction_operator|implicit_integer|indentation|line_length|namespace|nonportable_path|object_length|object_name|object_usage|is)_linter$", linters)]
- # put the functions in a list
- linters_list <- lapply(linters, function(l) eval(parse(text = paste0("lintr::", l, "()")), envir = asNamespace("lintr")))
- names(linters_list) <- linters
- # run them all!
- lintr::lint_package(linters = linters_list, exclusions = list("R/aa_helper_pm_functions.R"))
- shell: Rscript {0}
diff --git a/pkgdown/assets/logo_umcg.svg b/pkgdown/assets/logo_umcg.svg
old mode 100644
new mode 100755
index 2488a4b21..d418b1f81
--- a/pkgdown/assets/logo_umcg.svg
+++ b/pkgdown/assets/logo_umcg.svg
@@ -1,3890 +1,17 @@
-
-
-
+
+
\ No newline at end of file