WIP: documentation updates

Dockerfile

@@ -22,6 +22,11 @@ RUN R_REMOTES_NO_ERRORS_FROM_WARNINGS=true \
                      'RcppEigen', \
                      'magrittr',  \
                      'rsvd',      \
+                     'ggpubr',      \
+                     'fpc',      \
+                     'reshape2',      \
+                     'cluster',      \
+                     'gridExtra',      \
                      'magic',     \
                      'psych'), dependencies = TRUE )"
 

Makefile

@@ -0,0 +1,38 @@
+VERSION = $(shell grep ^Version DESCRIPTION | sed s/Version:\ //)
+
+doc:
+	R --slave -e 'library(roxygen2); roxygenise()'
+	R --slave -e 'pkgdown::build_site()'
+	-git add --all man/*.Rd
+
+test:
+	R CMD INSTALL --install-tests .
+	R --slave -e 'Sys.setenv(NOT_CRAN="true"); library(testthat); setwd(file.path(.libPaths()[1], "subtyper", "tests")); system.time(test_check("subtyper", filter="${file}", reporter=ifelse(nchar("${r}"), "${r}", "summary")))'
+
+deps:
+	R --slave -e 'install.packages(c("codetools", "testthat", "devtools", "roxygen2", "knitr"), repo="http://cran.at.r-project.org", lib=ifelse(nchar(Sys.getenv("R_LIB")), Sys.getenv("R_LIB"), .libPaths()[1]))'
+
+build: doc
+	R CMD build .
+
+check: build
+	-export _R_CHECK_CRAN_INCOMING_REMOTE_=FALSE && R CMD check --as-cran subtyper_$(VERSION).tar.gz
+	rm -rf subtyper.Rcheck/
+
+man: doc
+	R CMD Rd2pdf man/ --force
+
+md:
+	R CMD INSTALL --install-tests .
+	mkdir -p inst/doc
+	R -e 'setwd("vignettes"); lapply(dir(pattern="Rmd"), knitr::knit, envir=globalenv())'
+	mv vignettes/*.md inst/doc/
+	-cd inst/doc && ls | grep .md | xargs -n 1 sed -i '' 's/.html)/.md)/g'
+	-cd inst/doc && ls | grep .md | xargs -n 1 egrep "^.. Error"
+
+build-vignettes: md
+	R -e 'setwd("inst/doc"); lapply(dir(pattern="md"), function(x) markdown::markdownToHTML(x, output=sub("\\\\.md", ".html", x)))'
+	cd inst/doc && ls | grep .html | xargs -n 1 sed -i '' 's/.md)/.html)/g'
+
+covr:
+	R --slave -e 'library(covr); cv <- package_coverage(); df <- covr:::to_shiny_data(cv)[["file_stats"]]; cat("Line coverage:", round(100*sum(df[["Covered"]])/sum(df[["Relevant"]]), 1), "percent\\n")'

docs/pkgdown.yml

@@ -2,6 +2,13 @@ pandoc: 3.2.1
 pkgdown: 2.0.7
 pkgdown_sha: ~
 articles:
+  ANTsR: ANTsR.html
+  MultiChannel: MultiChannel.html
+  RestingBOLD: RestingBOLD.html
+  antsrTransform: antsrTransform.html
+  deformationSimulation: deformationSimulation.html
+  iMath: iMath.html
+  multivarTemplateCoordinates: multivarTemplateCoordinates.html
   simlr_interpretation: simlr_interpretation.html
-last_built: 2024-08-11T14:40Z
+last_built: 2024-08-11T15:13Z