fix: R encoding of pathlib.Path objects (#1201)

* feat: support converting Path objects for R

* test: test for converting Path objects to R

* Update script.py

* test: Snakemake test for R encoding pathlib.Path objects (missing files)

* fix: touch file to make expected-results dir appear in git

Co-authored-by: Johannes Köster <johannes.koester@uni-due.de>

tests/test_converting_path_for_r_script/Snakefile

@@ -0,0 +1,18 @@
+
+from pathlib import Path
+
+
+rule all:
+  input:
+    out_file="out-file.txt"
+
+
+rule step1:
+  input:
+    text_file=Path("text-file.txt")
+  params:
+    param_dir=Path("dir")
+  output:
+    out_file=Path("out-file.txt")
+  script:
+    "r-script.R"

tests/test_converting_path_for_r_script/r-script.R

@@ -0,0 +1,9 @@
+
+infile <- snakemake@input[["text_file"]]
+
+# Check the read value is as expected in R.
+param_dir <- snakemake@params[["param_dir"]]
+stopifnot(param_dir == "dir")
+
+outfile <- snakemake@output[["out_file"]]
+file.create(outfile)

tests/tests.py

@@ -1340,5 +1340,9 @@ def test_github_issue1158():
     )
 
 
+def test_converting_path_for_r_script():
+    run(dpath("test_converting_path_for_r_script"), cores=1)
+
+
 def test_ancient_dag():
     run(dpath("test_ancient_dag"))