cytomining / evalzoo Goto Github PK

I wanted to define a relative data_path in a config to make it user-independent (i.e. avoid overriding results folder and configs on Github), but seems like some paths in evalzoo are defined locally.

E.g., defining data_path: "../1.load/output" and trying to run from another repo gives following:

setwd("matric")
source("run_param.R")
setwd("../../position-effect-correction/2.evalzoo")
run_param("params/params_orf_group.yaml")

gives

Error in abs_path(input) : 
  The file '0.knit-notebooks.Rmd' does not exist.
In addition: Warning message:
In normalizePath(x, winslash = winslash, mustWork = must_work) :
  path[1]="0.knit-notebooks.Rmd": No such file or directory

I was able to make it work with data_path: "../../position-effect-correction/1.load/output" and

run_param("../../position-effect-correction/2.evalzoo/params/params_orf_group.yaml", results_root_dir = "../../position-effect-correction/2.evalzoo/results/")

however, it assumes both repos being located in the same directory, so doesn't fully address issues above.