Merge branch 'main' into fix-actions

.Rbuildignore

@@ -4,6 +4,10 @@
 ^.travis.yml$
 ^.git/.*$
 ^\.github$
+^.vscode$
+^src/*\.o$
+^src/*\.so$
+^src/RcppExports.cpp$
 ^_pkgdown\.yml$
 ^docs$
 ^pkgdown$
@@ -16,3 +20,7 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^\./RACES/\.git$
+^RACES$
+^_install$
+^_builds$
+^Makefile$

.github/workflows/R-CMD-check.yaml

@@ -19,7 +19,7 @@ jobs:
       matrix:
         config:
           - {os: macos-latest,   r: 'release'}
-          - {os: windows-latest, r: 'release'}
+#          - {os: windows-latest, r: 'release'}
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
           - {os: ubuntu-latest,   r: 'oldrel-1'}
@@ -47,3 +47,8 @@ jobs:
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
+
+      - uses: actions/upload-artifact@v3
+        with:
+          name: my-artifact
+          path: ./

.github/workflows/pkgdown.yaml

@@ -36,7 +36,7 @@ jobs:
           needs: website
 
       - name: Build site
-        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = TRUE)
         shell: Rscript {0}
 
       - name: Deploy to GitHub pages 🚀

.gitignore

@@ -14,3 +14,7 @@ _builds
 _install
 *.so
 *.o
+*.Rd
+*.log
+*.lock
+RACES

DESCRIPTION

@@ -1,33 +1,34 @@
 Package: rRACES
 Type: Package
-Title: rRACES: An R wrapper for RACES
+Title: rRACES: An R Wrapper for RACES
 Version: 0.0.1
 Date: 2023-10-25
-Authors@R: 
-  c(person(given = "Giulio",
-           family = "Caravagna",
-           role = c("aut", "cre"),
-           email = "[email protected]"),
-    person(given = "Alberto",
-           family = "Casagrande",
-           role = "aut"))
-Description: This is a wrapper for RACES. This package supports 
-        spacial evolution of different clones, different epigenetic 
-        clone states, timed-triggered driver mutations.
+Authors@R: c(
+    person("Giulio", "Caravagna", email = "[email protected]", role = c("aut", "cre")),
+    person("Alberto", "Casagrande", role = "aut"))
+Maintainer: Giulio Caravagna <[email protected]>
+Description: A wrapper for RACES. This package supports 
+        spacial evolution of different clones, different 
+        epigenetic clone states, timed-triggered driver 
+        mutations.
 License: GPL-3 + file LICENSE
 LinkingTo: Rcpp
 Encoding: UTF-8
-SystemRequirements: C++17
+SystemRequirements: C++17, GNU make
 Imports: 
-    methods,
-    magrittr,
     dplyr,
     Rcpp (>= 1.0.11),
     ggplot2,
     cli,
-    crayon
+    crayon,
+    RColorBrewer,
+    knitr,
+    rlang
 RoxygenNote: 7.2.3
 Suggests: 
-    knitr,
     rmarkdown
 VignetteBuilder: knitr
+Depends: 
+    methods,
+    R (>= 2.10)
+LazyData: true

Makefile

@@ -0,0 +1,31 @@
+# prepare the package for release
+PKGNAME := $(shell sed -n "s/Package: *\([^ ]*\)/\1/p" DESCRIPTION)
+PKGVERS := $(shell sed -n "s/Version: *\([^ ]*\)/\1/p" DESCRIPTION)
+PKGSRC  := $(shell basename `pwd`)
+
+.PHONY: all docs build build-cran install check travis clean
+
+docs:
+	R --vanilla --silent -e 'Rcpp::compileAttributes()'
+	R --vanilla --silent -e 'roxygen2::roxygenise(roclets=c("rd"))'
+
+build:
+	(cd .. && R CMD build --no-manual $(PKGSRC))
+
+build-cran:
+	(cd ..; && R CMD build $(PKGSRC))
+
+install: build
+	(cd .. && R CMD INSTALL $(PKGNAME)_$(PKGVERS).tar.gz)
+
+check: build-cran
+	(cd .. && R CMD check $(PKGNAME)_$(PKGVERS).tar.gz --as-cran)
+
+travis: build
+	(cd ..; && R CMD check $(PKGNAME)_$(PKGVERS).tar.gz --no-manual)
+
+clean:
+	rm -rf _install _builds RACES 
+	rm src/RcppExports.cpp src/*.o src/*.so R/RcppExports.R
+	rm -rf man/*.Rd
+	(cd .. && rm -rf $(PKGNAME).Rcheck)

NAMESPACE

@@ -1,9 +1,10 @@
 useDynLib(rRACES, .registration=TRUE)
+importFrom("dplyr", "pull", "row_number", "%>%", "mutate", "rename", "filter", "case_when")
+importFrom("stats", "time")
+importFrom("rlang", ".data")
 import(methods, Rcpp)
 
-S3method(print,rraces)
 export(Simulation)
-export(set_initial_cell)
-export(create_simulation)
 export(plot_state)
-export(add_species)
+export(plot_tissue)
+export(plot_firings)

R/ggplot_config.R

@@ -1,19 +1,20 @@
-my_theme = function(){
+my_theme <- function() {
   ggplot2::theme_linedraw(base_size = 10) +
     ggplot2::theme(
-      legend.position = 'bottom'
+      legend.position = "bottom"
     )
 }
 
-get_species_colors = function(x){
-  nm = sort(x)
-
-  nmc = RColorBrewer::brewer.pal(x %>% length(), "Set1")
-
-  if(length(nm) < length(nmc)) 
-    nmc = nmc[1:length(nm)]
-
-  names(nmc) = nm
-
+get_species_colors <- function(x) {
+  nm <- sort(x)
+
+  nmc <- RColorBrewer::brewer.pal(x %>% length(), "Set1")
+
+  if (length(nm) < length(nmc)) {
+    nmc <- nmc[1:length(nm)]
+  }
+
+  names(nmc) <- nm
+
   return(nmc)
 }

R/globals.R

@@ -0,0 +1 @@
+utils::globalVariables()