update roxygen and tests

DESCRIPTION

@@ -10,7 +10,7 @@ Description: dynmethods provides helper functions for containerised trajectory i
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 6.1.1
+RoxygenNote: 7.2.3
 Depends:
   R (>= 3.4.0)
 Imports: 
@@ -23,9 +23,10 @@ Imports:
 Suggests:
   babelwhale,
   dplyr,
-  dynutils,   
+  dynutils,
   knitr,
-  testthat,
+  testthat (>= 3.0.0),
   tibble
 VignetteBuilder: knitr
 Roxygen: list(markdown = TRUE)
+Config/testthat/edition: 3

NAMESPACE

@@ -62,7 +62,11 @@ export(ti_waterfall)
 export(ti_wishbone)
 import(dynwrap)
 importFrom(dynwrap,create_ti_method_container)
+importFrom(purrr,"%>%")
 importFrom(purrr,map)
 importFrom(purrr,map2_dbl)
 importFrom(purrr,map_chr)
+importFrom(purrr,walk)
 importFrom(remotes,parse_github_repo_spec)
+importFrom(utils,compareVersion)
+importFrom(utils,getFromNamespace)

R/dynmethods-package.R

@@ -0,0 +1,11 @@
+#' Wrappers for trajectory inference
+#'
+#' Wrappers for trajectory inference
+#'
+#' @docType package
+#' @name dynmethods
+#'
+#' @import dynwrap
+#' @importFrom purrr %>%
+#' @importFrom utils compareVersion getFromNamespace
+"_PACKAGE"

R/method_install_github_tagged_version.R

@@ -4,7 +4,7 @@
 #' @param versions The desired versions of the package, `NA` if unknown.
 #' @param is_interactive Whether running in an interactive session
 #'
-#' @importFrom purrr map_chr map2_dbl map_chr map
+#' @importFrom purrr map_chr map2_dbl map_chr map walk
 #' @importFrom remotes parse_github_repo_spec
 install_github_tagged_version <- function(remotes, versions = rep(NA, length(remotes)), is_interactive = interactive()) {
   parsed <- purrr::map(remotes, parse_github_repo_spec) %>% purrr::set_names(remotes)

README.Rmd

@@ -17,11 +17,10 @@ methods <- methods %>% filter(!method_source %in% c("control")) # controls are n
 ```
 
 <!-- badges: start -->
-[![R-CMD-check](https://github.com/dynverse/dynmethods/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/dynverse/dynmethods/actions/workflows/R-CMD-check.yaml)  
-[**ℹ️ Tutorials**](https://dynverse.org)  &nbsp;  &nbsp; 
-[**ℹ️ Reference documentation**](https://dynverse.org/reference/dynmethods) 
-
+[![R-CMD-check](https://github.com/dynverse/dynmethods/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/dynverse/dynmethods/actions/workflows/R-CMD-check.yaml)
 [![Codecov test coverage](https://codecov.io/gh/dynverse/dynmethods/branch/master/graph/badge.svg)](https://app.codecov.io/gh/dynverse/dynmethods?branch=master)
+[**ℹ️ Tutorials**](https://dynverse.org) &nbsp; &nbsp;
+[**ℹ️ Reference documentation**](https://dynverse.org/reference/dynmethods)
 <!-- badges: end -->
 
 <br><img src="man/figures/logo.png" align="right" />

data-raw/add_new_container.R

@@ -19,29 +19,28 @@ traj <- dynwrap::infer_trajectory(data, docker_repo, parameters = params, verbos
 dynplot::plot_graph(traj)
 
 
-#' @examples
-#' # you can test whether this method can be evaluated
-#' eval <- dyneval::evaluate_ti_method(data, dynwrap::create_ti_methods_container(paste0("dynverse/ti_", method))(), parameters = params, metrics = c("correlation", "edge_flip", "rf_mse", "featureimp_cor"), verbose = TRUE)
-#' eval$summary
-#' dynplot::plot_graph(eval$models[[1]])
-#' eval$summary$error
-#'
-#' # if it works, you can push the container to docker hub
-#' processx::run("docker", args = c("push", docker_repo), echo = TRUE)
-#'
-#' # rebuild the singularity image
-#' dynbenchmark::setup_singularity_methods()
-#' dynwrap::pull_singularity_ti_method(docker_repo)
-#'
-#' # test the singularity image
-#' traj <- dynwrap::infer_trajectory(data, method, parameters = params, verbose = TRUE)
-#' dynplot::plot_graph(traj)
-#'
-#' # transfer it to prism
-#' qsub::rsync_remote(
-#'   remote_src = FALSE,
-#'   path_src = dynbenchmark::derived_file(c("dynverse/", method, ".simg"), "03-method_characterisation/singularity_images", remote = FALSE),
-#'   remote_dest = TRUE,
-#'   path_dest = dynbenchmark::derived_file(c("dynverse/", method, ".simg"), "03-method_characterisation/singularity_images", remote = TRUE),
-#'   verbose = TRUE
-#' )
+# # you can test whether this method can be evaluated
+# eval <- dyneval::evaluate_ti_method(data, dynwrap::create_ti_methods_container(paste0("dynverse/ti_", method))(), parameters = params, metrics = c("correlation", "edge_flip", "rf_mse", "featureimp_cor"), verbose = TRUE)
+# eval$summary
+# dynplot::plot_graph(eval$models[[1]])
+# eval$summary$error
+#
+# # if it works, you can push the container to docker hub
+# processx::run("docker", args = c("push", docker_repo), echo = TRUE)
+#
+# # rebuild the singularity image
+# dynbenchmark::setup_singularity_methods()
+# dynwrap::pull_singularity_ti_method(docker_repo)
+#
+# # test the singularity image
+# traj <- dynwrap::infer_trajectory(data, method, parameters = params, verbose = TRUE)
+# dynplot::plot_graph(traj)
+#
+# # transfer it to prism
+# qsub::rsync_remote(
+#   remote_src = FALSE,
+#   path_src = dynbenchmark::derived_file(c("dynverse/", method, ".simg"), "03-method_characterisation/singularity_images", remote = FALSE),
+#   remote_dest = TRUE,
+#   path_dest = dynbenchmark::derived_file(c("dynverse/", method, ".simg"), "03-method_characterisation/singularity_images", remote = TRUE),
+#   verbose = TRUE
+# )