Merge branch 'develop' of https://github.com/ropensci/babette into de…

…velop

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

@@ -68,23 +68,23 @@ jobs:
         shell: Rscript {0}
 
       - name: Make sure that no files are created in the beautier .cache folder
-        run: testthat::expect_equal(0, length(list.files(rappdirs::user_cache_dir(appname = "beautier"))))
+        run: testthat::expect_length(list.files(rappdirs::user_cache_dir(appname = "beautier")), 0)
         shell: Rscript {0}
 
       - name: Make sure that no files are created in the tracerer .cache folder
-        run: testthat::expect_equal(0, length(list.files(rappdirs::user_cache_dir(appname = "tracerer"))))
+        run: testthat::expect_length(list.files(rappdirs::user_cache_dir(appname = "tracerer")), 0)
         shell: Rscript {0}
 
       - name: Make sure that no files are created in the beastier .cache folder
-        run: testthat::expect_equal(0, length(list.files(rappdirs::user_cache_dir(appname = "beastier"))))
+        run: testthat::expect_length(list.files(rappdirs::user_cache_dir(appname = "beastier")), 0)
         shell: Rscript {0}
 
       - name: Make sure that no files are created in the mauricer .cache folder
-        run: testthat::expect_equal(0, length(list.files(rappdirs::user_cache_dir(appname = "mauricer"))))
+        run: testthat::expect_length(list.files(rappdirs::user_cache_dir(appname = "mauricer")), 0)
         shell: Rscript {0}
 
       - name: Make sure that no files are created in the .cache folder
-        run: testthat::expect_equal(0, length(list.files(rappdirs::user_cache_dir(appname = "babette"))))
+        run: testthat::expect_length(list.files(rappdirs::user_cache_dir(appname = "babette")), 0)
         shell: Rscript {0}
 
       - name: Test coverage

DESCRIPTION

@@ -7,7 +7,6 @@ Authors@R: c(
     person("David", "Winter", role = "rev", comment = "David reviewed the package for rOpenSci, see https://github.com/richelbilderbeek/onboarding/issues/209"),
     person("Jason", "Griffiths", role = "ctb", comment = c(ORCID = "0000-0002-1667-8233")),
     person("Giovanni", "Laudanno", email = "[email protected]", role = "ctb"))
-Maintainer: Richèl J.C. Bilderbeek <[email protected]>
 Description: 'BEAST2' (<https://www.beast2.org>) is a widely used
     Bayesian phylogenetic tool, that uses DNA/RNA/protein data
     and many model priors to create a posterior of jointly estimated 
@@ -19,8 +18,8 @@ Description: 'BEAST2' (<https://www.beast2.org>) is a widely used
 License: GPL-3
 RoxygenNote: 7.2.3
 VignetteBuilder: knitr
-URL: https://docs.ropensci.org/babette/ (website)
-    https://github.com/ropensci/babette/
+URL: https://docs.ropensci.org/babette/ (website),
+    https://github.com/ropensci/babette
 BugReports: https://github.com/ropensci/babette/issues
 Depends:
     beautier (>= 2.6.11),
@@ -30,17 +29,14 @@ Depends:
     tracerer
 Imports:
     phangorn,
-    remotes,
+    rlang (>= 1.1.0),
     stringr,
     xml2
 Suggests:
     ape,
-    curl,
     ggplot2,
-    hunspell,
     knitr,
     lintr,
-    markdown,
     nLTT,
     rappdirs,
     rmarkdown,

NAMESPACE

@@ -16,6 +16,7 @@ export(parse_beast2_output_to_ns)
 export(plot_densitree)
 export(prepare_file_creation)
 export(update_babette)
+import(rlang)
 importFrom(beastier,add_quotes_if_has_spaces)
 importFrom(beastier,are_beast2_input_lines)
 importFrom(beastier,are_beast2_input_lines_deep)

NEWS.md

@@ -14,7 +14,8 @@ Newest versions at top.
 
 ### BUG FIXES
 
-  * None
+  * Removed unused dependencies, and testthat dependency outside tests.
+  * Import rlang for checking conditions.
 
 ### DEPRECATED AND DEFUNCT
 
@@ -359,7 +360,7 @@ create_lambda_param(value = 1.2, estimate = TRUE)
 
 ### MINOR IMPROVEMENTS
 
-  * Follow all [rOpenSci packaging guidelines](https://github.com/ropensci/onboarding/blob/master/packaging_guide.md)
+  * Follow all [rOpenSci packaging guidelines](https://github.com/ropensci/software-review/blob/master/packaging_guide.md)
 
 ### BUG FIXES
 

R/babette-package.R

@@ -602,5 +602,6 @@
 "_PACKAGE"
 
 ## usethis namespace: start
+#' @import rlang
 ## usethis namespace: end
 NULL

R/bbt_continue.R

@@ -114,7 +114,7 @@ bbt_continue <- function(
     beast2_options$input_filename,
     "beast2_options$input_filename"
   )
-  testthat::expect_true(
+  check_true(
     beastier::is_beast2_input_file(beast2_options$input_filename)
   )
   beautier::check_file_exists(
@@ -132,7 +132,12 @@ bbt_continue <- function(
       beautier::get_alignment_id(fasta_filename), ".log"
     )
   }
-  testthat::expect_true(!is.na(inference_model$mcmc$tracelog$filename))
+
+  if (is.na(inference_model$mcmc$tracelog$filename)) {
+    stop(
+      "Expected inference_model$mcmc$tracelog$filename not to be missing."
+    )
+  }
   if (!file.exists(normalizePath(inference_model$mcmc$tracelog$filename))) {
     stop(
       "'mcmc$tracelog$filename' not found. \n",
@@ -152,7 +157,7 @@ bbt_continue <- function(
     pattern = "\\$\\(tree\\)",
     replacement = beautier::get_alignment_id(fasta_filename)
   )
-  testthat::expect_true(file.exists(inference_model$mcmc$treelog$filename) &&
+  check_true(file.exists(inference_model$mcmc$treelog$filename) &&
     length(
       paste0(
         "'mcmc$treelog$filename' not found. \n",
@@ -162,7 +167,7 @@ bbt_continue <- function(
       )
     )
   )
-  testthat::expect_true(file.exists(beast2_options$output_state_filename) &&
+  check_true(file.exists(beast2_options$output_state_filename) &&
     length(
       paste0(
         "beast2_output_state_filename not found. \n",
@@ -189,9 +194,15 @@ bbt_continue <- function(
   n_trees_in_file <- tracerer::count_trees_in_file(
     inference_model$mcmc$treelog$filename
   )
-  testthat::expect_true(inherits(out[[1]], "multiPhylo"))
+
+  if (!inherits(out[[1]], "multiPhylo")) {
+    stop("Expected out to be a multiPhylo object.")
+  }
   n_trees_in_output <- length(out[[1]])
-  testthat::expect_equal(n_trees_in_file, n_trees_in_output)
+
+  if (n_trees_in_file != n_trees_in_output) {
+    stop("Expected n_trees_in_files to be equal to n_trees_in_output")
+  }
 
   # Process the package specific output,
   # for example, add an 'ns' atributed for Nested Sampling

R/bbt_run_from_model.R

@@ -127,8 +127,10 @@ bbt_run_from_model <- function(
       beautier::get_alignment_id(fasta_filename), ".log"
     )
   }
-  testthat::expect_true(!is.na(inference_model$mcmc$tracelog$filename))
-  testthat::expect_true(
+  if (is.na(inference_model$mcmc$tracelog$filename)) {
+    stop("inference_model$mcmc$tracelog$filename should not be missing.")
+  }
+  check_true(
     file.exists(normalizePath(inference_model$mcmc$tracelog$filename)) &&
     length(
       paste0(
@@ -156,7 +158,8 @@ bbt_run_from_model <- function(
       )
     )
   )
-  testthat::expect_true(file.exists(beast2_options$output_state_filename) &&
+  # Should this be if (!file.exists) stop(paste0(...))?
+  check_true(file.exists(beast2_options$output_state_filename) &&
     length(
       paste0(
         "beast2_output_state_filename not found. \n",
@@ -183,9 +186,13 @@ bbt_run_from_model <- function(
   n_trees_in_file <- tracerer::count_trees_in_file(
     inference_model$mcmc$treelog$filename
   )
-  testthat::expect_true(inherits(out[[1]], "multiPhylo"))
+  if (!inherits(out[[1]], "multiPhylo")) {
+    stop("out[[1]] should be multiPhylo.")
+  }
   n_trees_in_output <- length(out[[1]])
-  testthat::expect_equal(n_trees_in_file, n_trees_in_output)
+  if (n_trees_in_file != n_trees_in_output) {
+    stop("n_trees_in_file should be equal to n_trees_in_output.")
+  }
 
   # Process the package specific output,
   # for example, add an 'ns' atributed for Nested Sampling

R/bbt_self_test.R

@@ -15,7 +15,10 @@
 bbt_self_test <- function(
   beast2_options = beastier::create_beast2_options()
 ) {
-  testthat::expect_true(beastier::is_beast2_installed())
+
+  if (!beastier::is_beast2_installed()) {
+    stop("Beast2 must be installed for bbt_self_test.")
+  }
   inference_model <- beautier::create_test_inference_model()
   babette::bbt_run_from_model(
     fasta_filename = beautier::get_fasta_filename(),

R/check_true_false.R

@@ -0,0 +1,43 @@
+# Created by modifying check_bool from import-standalone-type-check.
+check_true <- function(x,
+                       ...,
+                       allow_na = FALSE,
+                       allow_null = FALSE,
+                       arg = caller_arg(x),
+                       call = caller_env()) {
+
+  if (!missing(x) && !isFALSE(x) &&.standalone_types_check_dot_call(ffi_standalone_is_bool_1.0.7, x, allow_na, allow_null)) {
+    return(invisible(NULL))
+  }
+
+  stop_input_type(
+    x,
+    c("`TRUE`"),
+    ...,
+    allow_na = allow_na,
+    allow_null = allow_null,
+    arg = arg,
+    call = call
+  )
+}
+# Adapted from standalone-types-check.R
+check_false <- function(x,
+                        ...,
+                        allow_na = FALSE,
+                        allow_null = FALSE,
+                        arg = caller_arg(x),
+                        call = caller_env()) {
+  if (!missing(x) && !isTRUE(x) && .standalone_types_check_dot_call(ffi_standalone_is_bool_1.0.7, x, allow_na, allow_null)) {
+    return(invisible(NULL))
+  }
+
+  stop_input_type(
+    x,
+    c("`FALSE`"),
+    ...,
+    allow_na = allow_na,
+    allow_null = allow_null,
+    arg = arg,
+    call = call
+  )
+}