Merge pull request #14 from Ulthran/setup-CI

Setup CI
kylebittinger · May 24, 2024 · 1c40d52 · 1c40d52
2 parents a5ad939 + 1350864
commit 1c40d52
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -1,6 +1,9 @@
-^.*\.Rproj$
-^\.Rproj\.user$
-^README\.Rmd$
-^\.travis\.yml$
-^cran-comments\.md$
-^CRAN-RELEASE$
+^renv$
+^renv\.lock$
+^.*\.Rproj$
+^\.Rproj\.user$
+^README\.Rmd$
+^\.travis\.yml$
+^cran-comments\.md$
+^CRAN-RELEASE$
+^\.github$
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -8,10 +8,11 @@ Description: Functions to re-arrange, extract, and work with distances.
 License: GPL-3
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.1.1
+RoxygenNote: 7.2.3
 Suggests:
   testthat,
   tibble,
   tidyr (>= 1.0.0),
   rlang,
-  future.apply
+  future.apply,
+  ggplot2
diff --git a/NAMESPACE b/NAMESPACE
@@ -10,3 +10,7 @@ export(dist_subset)
 export(dist_to_centroids)
 export(pivot_to_matrix)
 export(pivot_to_numeric_matrix)
+importFrom(rlang,as_name)
+importFrom(rlang,ensym)
+importFrom(tibble,column_to_rownames)
+importFrom(tidyr,pivot_wider)
diff --git a/R/dist.R b/R/dist.R
@@ -80,18 +80,7 @@ dist_get <- function (d, idx1, idx2) {
 #' dist_subset(dm4, c("A", "B", "C"))
 #' dist_subset(dm4, c("D", "C", "B", "A"))
 dist_subset <- function (d, idx) {
-  m <- as.matrix(d)
-  l <- length(colnames(m))
-
-  if(is.logical(idx) & length(idx) > l) {
-    message("Logical vector too long for given distance matrix")
-  } else if (is.numeric(idx) & (any(idx < 0) | any(idx >= l + 1))) {
-    message(paste("Numeric vector inputs out of bounds: ", paste(idx[(idx < 0) | (idx >= l)], collapse = ", ")))
-  } else if (any(!(idx %in% colnames(m)))) {
-    message(paste("Character vector inputs don't match matrix column names: ", paste(idx[!(idx %in% colnames(m))], collapse = ", ")))
-  }
-
-  stats::as.dist(m[idx, idx])
+  stats::as.dist(as.matrix(d)[idx, idx])
 }
 
 #' Create a data frame of distances between groups of items.

diff --git a/R/long_format.R b/R/long_format.R
@@ -9,6 +9,10 @@
 #' @param obs_col,feature_col,value_col The same as \code{rows_from},
 #'   \code{cols_from}, and \code{values_from}, respectively.
 #'
+#' @importFrom tidyr pivot_wider
+#' @importFrom tibble column_to_rownames
+#' @importFrom rlang as_name ensym
+#'
 #' @details
 #' The parameters \code{rows_from}, \code{cols_from}, and \code{values_from}
 #' should be provided as bare column names.

diff --git a/README.Rmd b/README.Rmd
@@ -2,7 +2,7 @@
 output: github_document
 ---
 
-<!-- README.md is generated from README.Rmd. Please edit that file -->
+<!-- README.md is generated from README.Rmd. Please edit README.Rmd -->
 
 ```{r, echo = FALSE}
 knitr::opts_chunk$set(
@@ -19,7 +19,10 @@ set.seed(0)
 
 This package provides useful functions for distance matrix objects in R.
 
-[![Travis-CI Build Status](https://travis-ci.org/kylebittinger/usedist.svg?branch=master)](https://travis-ci.org/kylebittinger/usedist)
+<!-- Badges start -->
+[![R-CMD-check](https://github.com/kylebittinger/usedist/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/kylebittinger/usedist/actions/workflows/R-CMD-check.yaml)
+[![Codecov test coverage](https://codecov.io/gh/kylebittinger/usedist/branch/master/graph/badge.svg)](https://app.codecov.io/gh/kylebittinger/usedist?branch=master)
+<!-- Badges end -->
 
 ## Installation
 
@@ -235,4 +238,4 @@ parallel to save time.
 library(future.apply)
 future::plan(future::multisession)
 dist_make(data_matrix, rms_distance)
-```
+```