Update and fix importsFrom list

ropensci · Sep 26, 2023 · d2a9d19 · d2a9d19
1 parent 2437cbf
commit d2a9d19
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Showing 3 changed files with 38 additions and 1 deletion.
diff --git a/NAMESPACE b/NAMESPACE
@@ -190,6 +190,7 @@ importFrom(beautier,check_treelog_values)
 importFrom(beautier,compare_lines)
 importFrom(beautier,count_trailing_spaces)
 importFrom(beautier,create_alpha_param)
+importFrom(beautier,create_b_pop_sizes_param)
 importFrom(beautier,create_bd_tree_prior)
 importFrom(beautier,create_beast2_beast_xml)
 importFrom(beautier,create_beast2_input)
@@ -238,6 +239,7 @@ importFrom(beautier,create_distr_one_div_x)
 importFrom(beautier,create_distr_poisson)
 importFrom(beautier,create_distr_uniform)
 importFrom(beautier,create_exp_distr)
+importFrom(beautier,create_freq_param)
 importFrom(beautier,create_gamma_distr)
 importFrom(beautier,create_gamma_site_model)
 importFrom(beautier,create_gtr_site_model)
@@ -250,6 +252,7 @@ importFrom(beautier,create_jc69_site_model)
 importFrom(beautier,create_jc69_subst_model_xml)
 importFrom(beautier,create_kappa_1_param)
 importFrom(beautier,create_kappa_2_param)
+importFrom(beautier,create_kappa_param)
 importFrom(beautier,create_lambda_param)
 importFrom(beautier,create_laplace_distr)
 importFrom(beautier,create_log_normal_distr)
@@ -266,8 +269,11 @@ importFrom(beautier,create_ns_mcmc)
 importFrom(beautier,create_one_div_x_distr)
 importFrom(beautier,create_param)
 importFrom(beautier,create_param_alpha)
+importFrom(beautier,create_param_b_pop_sizes)
 importFrom(beautier,create_param_beta)
 importFrom(beautier,create_param_clock_rate)
+importFrom(beautier,create_param_freq)
+importFrom(beautier,create_param_kappa)
 importFrom(beautier,create_param_kappa_1)
 importFrom(beautier,create_param_kappa_2)
 importFrom(beautier,create_param_lambda)
@@ -291,6 +297,7 @@ importFrom(beautier,create_rate_categories_state_node_xml)
 importFrom(beautier,create_rate_cg_param)
 importFrom(beautier,create_rate_ct_param)
 importFrom(beautier,create_rate_gt_param)
+importFrom(beautier,create_rln_clock_branch_rate_model_xml)
 importFrom(beautier,create_rln_clock_model)
 importFrom(beautier,create_s_param)
 importFrom(beautier,create_scale_param)
@@ -307,6 +314,7 @@ importFrom(beautier,create_site_model_tn93)
 importFrom(beautier,create_site_model_xml)
 importFrom(beautier,create_site_models)
 importFrom(beautier,create_site_models_from_names)
+importFrom(beautier,create_strict_clock_branch_rate_model_xml)
 importFrom(beautier,create_strict_clock_model)
 importFrom(beautier,create_strict_clock_rate_scaler_operator_xml)
 importFrom(beautier,create_subst_model_xml)
@@ -360,6 +368,9 @@ importFrom(beautier,get_clock_model_name)
 importFrom(beautier,get_clock_model_names)
 importFrom(beautier,get_clock_models_ids)
 importFrom(beautier,get_crown_age)
+importFrom(beautier,get_default_beast_namespace)
+importFrom(beautier,get_default_beast_namespace_v2_4)
+importFrom(beautier,get_default_beast_namespace_v2_6)
 importFrom(beautier,get_distr_n_params)
 importFrom(beautier,get_distr_names)
 importFrom(beautier,get_fasta_filename)
@@ -401,6 +412,7 @@ importFrom(beautier,has_xml_opening_tag)
 importFrom(beautier,has_xml_short_closing_tag)
 importFrom(beautier,indent)
 importFrom(beautier,is_alpha_param)
+importFrom(beautier,is_b_pop_sizes_param)
 importFrom(beautier,is_bd_tree_prior)
 importFrom(beautier,is_beauti_options)
 importFrom(beautier,is_beta_distr)
@@ -416,6 +428,7 @@ importFrom(beautier,is_distr)
 importFrom(beautier,is_distr_name)
 importFrom(beautier,is_exp_distr)
 importFrom(beautier,is_freq_equilibrium_name)
+importFrom(beautier,is_freq_param)
 importFrom(beautier,is_gamma_distr)
 importFrom(beautier,is_gamma_site_model)
 importFrom(beautier,is_gtr_site_model)
@@ -455,6 +468,7 @@ importFrom(beautier,is_inv_gamma_distr)
 importFrom(beautier,is_jc69_site_model)
 importFrom(beautier,is_kappa_1_param)
 importFrom(beautier,is_kappa_2_param)
+importFrom(beautier,is_kappa_param)
 importFrom(beautier,is_lambda_param)
 importFrom(beautier,is_laplace_distr)
 importFrom(beautier,is_log_normal_distr)
@@ -476,8 +490,11 @@ importFrom(beautier,is_on_travis)
 importFrom(beautier,is_one_bool)
 importFrom(beautier,is_one_div_x_distr)
 importFrom(beautier,is_one_double)
+importFrom(beautier,is_one_empty_string)
 importFrom(beautier,is_one_int)
 importFrom(beautier,is_one_na)
+importFrom(beautier,is_one_string)
+importFrom(beautier,is_one_string_that_is_a_number)
 importFrom(beautier,is_param)
 importFrom(beautier,is_param_name)
 importFrom(beautier,is_phylo)

diff --git a/R/babette-package.R b/R/babette-package.R
@@ -50,6 +50,7 @@
 #'   }
 #' }
 #' @note the imports are created by script 'scripts/create_imports.R'
+#'
 #' @importFrom beautier are_clock_models
 #' @importFrom beautier are_equal_mcmcs
 #' @importFrom beautier are_equal_screenlogs
@@ -130,6 +131,7 @@
 #' @importFrom beautier compare_lines
 #' @importFrom beautier count_trailing_spaces
 #' @importFrom beautier create_alpha_param
+#' @importFrom beautier create_b_pop_sizes_param
 #' @importFrom beautier create_bd_tree_prior
 #' @importFrom beautier create_beast2_beast_xml
 #' @importFrom beautier create_beast2_input
@@ -178,6 +180,7 @@
 #' @importFrom beautier create_distr_poisson
 #' @importFrom beautier create_distr_uniform
 #' @importFrom beautier create_exp_distr
+#' @importFrom beautier create_freq_param
 #' @importFrom beautier create_gamma_distr
 #' @importFrom beautier create_gamma_site_model
 #' @importFrom beautier create_gtr_site_model
@@ -190,6 +193,7 @@
 #' @importFrom beautier create_jc69_subst_model_xml
 #' @importFrom beautier create_kappa_1_param
 #' @importFrom beautier create_kappa_2_param
+#' @importFrom beautier create_kappa_param
 #' @importFrom beautier create_lambda_param
 #' @importFrom beautier create_laplace_distr
 #' @importFrom beautier create_log_normal_distr
@@ -206,8 +210,11 @@
 #' @importFrom beautier create_one_div_x_distr
 #' @importFrom beautier create_param
 #' @importFrom beautier create_param_alpha
+#' @importFrom beautier create_param_b_pop_sizes
 #' @importFrom beautier create_param_beta
 #' @importFrom beautier create_param_clock_rate
+#' @importFrom beautier create_param_freq
+#' @importFrom beautier create_param_kappa
 #' @importFrom beautier create_param_kappa_1
 #' @importFrom beautier create_param_kappa_2
 #' @importFrom beautier create_param_lambda
@@ -231,6 +238,7 @@
 #' @importFrom beautier create_rate_cg_param
 #' @importFrom beautier create_rate_ct_param
 #' @importFrom beautier create_rate_gt_param
+#' @importFrom beautier create_rln_clock_branch_rate_model_xml
 #' @importFrom beautier create_rln_clock_model
 #' @importFrom beautier create_s_param
 #' @importFrom beautier create_scale_param
@@ -247,6 +255,7 @@
 #' @importFrom beautier create_site_model_xml
 #' @importFrom beautier create_site_models
 #' @importFrom beautier create_site_models_from_names
+#' @importFrom beautier create_strict_clock_branch_rate_model_xml
 #' @importFrom beautier create_strict_clock_model
 #' @importFrom beautier create_strict_clock_rate_scaler_operator_xml
 #' @importFrom beautier create_subst_model_xml
@@ -300,6 +309,9 @@
 #' @importFrom beautier get_clock_model_names
 #' @importFrom beautier get_clock_models_ids
 #' @importFrom beautier get_crown_age
+#' @importFrom beautier get_default_beast_namespace
+#' @importFrom beautier get_default_beast_namespace_v2_4
+#' @importFrom beautier get_default_beast_namespace_v2_6
 #' @importFrom beautier get_distr_n_params
 #' @importFrom beautier get_distr_names
 #' @importFrom beautier get_fasta_filename
@@ -341,6 +353,7 @@
 #' @importFrom beautier has_xml_short_closing_tag
 #' @importFrom beautier indent
 #' @importFrom beautier is_alpha_param
+#' @importFrom beautier is_b_pop_sizes_param
 #' @importFrom beautier is_bd_tree_prior
 #' @importFrom beautier is_beauti_options
 #' @importFrom beautier is_beta_distr
@@ -356,6 +369,7 @@
 #' @importFrom beautier is_distr_name
 #' @importFrom beautier is_exp_distr
 #' @importFrom beautier is_freq_equilibrium_name
+#' @importFrom beautier is_freq_param
 #' @importFrom beautier is_gamma_distr
 #' @importFrom beautier is_gamma_site_model
 #' @importFrom beautier is_gtr_site_model
@@ -395,6 +409,7 @@
 #' @importFrom beautier is_jc69_site_model
 #' @importFrom beautier is_kappa_1_param
 #' @importFrom beautier is_kappa_2_param
+#' @importFrom beautier is_kappa_param
 #' @importFrom beautier is_lambda_param
 #' @importFrom beautier is_laplace_distr
 #' @importFrom beautier is_log_normal_distr
@@ -416,8 +431,11 @@
 #' @importFrom beautier is_one_bool
 #' @importFrom beautier is_one_div_x_distr
 #' @importFrom beautier is_one_double
+#' @importFrom beautier is_one_empty_string
 #' @importFrom beautier is_one_int
 #' @importFrom beautier is_one_na
+#' @importFrom beautier is_one_string
+#' @importFrom beautier is_one_string_that_is_a_number
 #' @importFrom beautier is_param
 #' @importFrom beautier is_param_name
 #' @importFrom beautier is_phylo
@@ -578,6 +596,7 @@
 #' @importFrom mauricer is_beast2_ns_pkg_installed
 #' @importFrom mauricer is_beast2_pkg_installed
 #' @importFrom mauricer uninstall_beast2_pkg
+#'
 #' @author Richèl J.C. Bilderbeek
 #' @keywords internal
 "_PACKAGE"

diff --git a/scripts/create_imports.R b/scripts/create_imports.R
@@ -1,3 +1,4 @@
+#!/bin/env Rscript
 ###############################################################################
 # beautier
 ###############################################################################
@@ -37,7 +38,7 @@ beastier_function_names <- stringr::str_subset(
 )
 beastier_function_names <- stringr::str_subset(
   beastier_function_names,
-  "remove_beautier_folder|create_beautier_tempfolder",
+  "remove_beautier_folder|create_beautier_tempfolder|is_on_appveyor|is_on_ci|is_on_travis",
   negate = TRUE
 )
 beastier_text <- paste("#' @importFrom beastier", beastier_function_names)