Modify terminal state from markov chain (#45)

* add badges and debug covr

* Update R-CMD-check.yml

* fix allowed actors?

* ok forgot to only run check on ubuntu

* try and see if i can combine the installation

* Update markovProbability.R

add the default value of terminal_state

* solving the problem of name with value NULL

* soloving problem2

The number of terminal_state varies, when it equals to 1, the probabilities@x[probabilities@x < 0] <- 0 will throw an error

* Update markovProbability.R

* the function returns index of the waypoint not the index of cell

* Update vignette_02.rmd

* Update markovProbability.R

* debugs

store the terminal_state in metadata so that the function downstream could retrieve it when needed.

* test.R

add test of markovProbability

* Update test-projectPseudotimeToCell.R

* Update projectPseudotimeToCell.R

---------

Co-authored-by: Zewen Kelvin Tuong <[email protected]>

R/projectPseudotimeToCell.R

@@ -64,7 +64,7 @@
 projectPseudotimeToCell <- function(milo, pb_milo, term_states = NULL, pseudotime_key = "pseudotime", suffix = "") {
     if(is.null(term_states))
     {
-      if(is.null(metadata(pb_milo)$branch.tips)) # ncov start
+      if(is.null(metadata(pb_milo)$branch.tips)) # nocov start
       {
         abort("Parameter Error: Please provide term_state, which should align with parameter terminal_state in function markovProbability")
       } # nocov end