Address CRAN comments, update documentation

.gitignore

@@ -3,6 +3,7 @@
 archive/
 docs/
 .virtual_documents/
+cran_package/
 
 # History files
 .Rhistory

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: ComplexUpset
 Type: Package
 Title: Create Complex UpSet Plots Using 'ggplot2' Components
-Version: 0.7.2
+Version: 0.7.3
 Authors@R: person(
   "Michał", "Krassowski", email = "[email protected]", role = c("aut", "cre"),
   comment = c(ORCID = "0000-0002-9638-7785"))
@@ -10,7 +10,7 @@ Description: UpSet plots are an improvement over Venn Diagram for set overlap vi
     complex overlap visualisations, using simple and familiar tools, i.e. geoms of 'ggplot2'.
 License: MIT + file LICENSE
 Encoding: UTF-8
-URL: https://github.com/krassowski/complex-upset
+URL: https://github.com/krassowski/complex-upset, https://krassowski.github.io/complex-upset/
 BugReports: https://github.com/krassowski/complex-upset/issues
 LazyData: true
 Suggests: 

inst/CITATION

@@ -0,0 +1,35 @@
+citHeader("To cite ComplexUpset in publications use:")
+
+citEntry(
+  entry    = "Misc",
+  title    = "ComplexUpset",
+  author   = c(
+    person("Michał", "Krassowski")
+  ),
+  year     = 2020,
+  url      = "https://doi.org/10.5281/zenodo.3700590",
+  doi      = "10.5281/zenodo.3700590",
+  textVersion = paste(
+    "Michał Krassowski. (2020). krassowski/complex-upset.",
+    "Zenodo. http://doi.org/10.5281/zenodo.3700590"
+  )
+)
+
+
+citEntry(
+  entry    = "Article",
+  title    = "UpSet: Visualization of Intersecting Sets,",
+  author   = as.person("Alexander Lex, Nils Gehlenborg, Hendrik Strobelt, Romain Vuillemot, Hanspeter Pfister"),
+  journal  = "IEEE Transactions on Visualization and Computer Graphics",
+  year     = 2014,
+  volume   = 20,
+  number   = 12,
+  pages    = "1983–1992",
+  url      = "https://doi.org/10.1109/TVCG.2014.2346248",
+  doi      = "10.1109/TVCG.2014.2346248",
+  textVersion = paste(
+    "Alexander Lex, Nils Gehlenborg, Hendrik Strobelt, Romain Vuillemot, Hanspeter Pfister,",
+    "UpSet: Visualization of Intersecting Sets,",
+    "IEEE Transactions on Visualization and Computer Graphics (InfoVis '14), vol. 20, no. 12, pp. 1983–1992, 2014."
+  )
+)

inst/WORDLIST

@@ -11,3 +11,4 @@ UpSetR
 vdiffr
 Lex
 ComplexHeatmap
+geoms

scripts/document.sh

@@ -6,6 +6,7 @@ cd vignettes
 cd ..
 for v in Examples_Python Examples_R
 do
+    rm -r "vignettes/${v}_files"
     jupyter nbconvert  --to markdown "vignettes/${v}.ipynb" 
     mv "vignettes/${v}.md" "vignettes/${v}.Rmd"
     sed 's/```r/```{r eval=FALSE}/g' "vignettes/${v}.Rmd" -i
@@ -16,3 +17,8 @@ do
 done
 rm -rf docs/articles
 Rscript -e 'pkgdown::build_site()'
+echo "Compressing images"
+for v in Examples_Python Examples_R
+do
+    trimage -q -d "vignettes/${v}_files"
+done

scripts/package_for_cran.sh

@@ -4,17 +4,22 @@ for folder in R man;
     do cp -r ${folder} cran_package/;
 done;
 mkdir cran_package/vignettes
+mkdir cran_package/inst
 cp -r vignettes/Examples_R_files cran_package/vignettes/
 cp -r vignettes/Examples_R.Rmd cran_package/vignettes/
-for file in DESCRIPTION LICENSE NAMESPACE README.md .Rbuildignore;
+cp inst/CITATION cran_package/inst/
+cp inst/WORDLIST cran_package/inst/
+for file in DESCRIPTION NAMESPACE README.md .Rbuildignore;
     do cp ${file} cran_package/;
 done;
+# so CRAN requires a different "template" for MIT license...
+# see: https://stackoverflow.com/questions/43550479/how-to-satisfy-both-cran-and-github-license-file-naming-requirements
+# and: https://github.com/tidyverse/tidyr/issues/262
+# and: https://r-pkgs.org/description.html#description-license
+echo "YEAR: 2020
+COPYRIGHT HOLDER: Michał Krassowski" > LICENSE
 cd cran_package
 ../scripts/cmd_check.sh
 ../scripts/spell_check.sh
-cd vignettes
-echo "Compressing images"
-trimage -q -d Examples_R_files
-cd ..
 R CMD build .
 R CMD check --as-cran ComplexUpset_*.tar.gz