revise description + address new cran checks + rm refs to 'simplextree' class

corybrunson · corybrunson · commit 1ab437221a5e · 2022-06-17T10:58:22.000-04:00
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -12,12 +12,19 @@ Authors@R: c(
         given = "Yara",
         family = "Skaf",
         role = c("ctb")))
-Description: This package facilitates coercion (conversion) between data
-    structures used by different packages to represent simplicial complexes.
+Description: Computational topology, which includes topological data analysis
+    (TDA), makes pervasive use of abstract mathematical objects called
+    simplicial complexes; see Edelsbrunner and Harer (2010)
+    <doi:10.1090/mbk/069>.
+    Several R packages and other software libraries used through an R interface
+    construct and use data structures that represent simplicial complexes,
+    including mathematical graphs viewed as 1-dimensional complexes.
+    This package provides coercers (converters) between these data structures.
     Currently supported structures are complete lists of simplices as used by
-    'TDA'; simplex tree instances, both as used by 'simplextree' and by Python
-    GUDHI (by way of 'reticulate'); and the graph/network classes of 'igraph'
-    and 'network' by way of the 'intergraph' package.
+    'TDA'; the simplex trees of Boissonnat and Maria (2014)
+    <doi:10.1007/s00453-014-9887-3> as implemented in 'simplextree' and in
+    Python GUDHI (by way of 'reticulate'); and the graph classes of 'igraph' and
+    'network', by way of the 'intergraph' package.
 Suggests:
     TDA,
     simplextree (>= 0.9.1),
diff --git a/NEWS.md b/NEWS.md
@@ -3,7 +3,7 @@
 This first release includes converters between the following data structures:
 
 * complete lists of simplices, used by the {TDA} package
-* simplex tree instances of class 'Rcpp_SimplexTree' or 'simplextree',
+* simplex tree instances of class 'Rcpp_SimplexTree',
   provided by the {simplextree} package
 * simplex trees as implemented in Python GUDHI through the {reticulate} interface
 * objects of class 'igraph', provided by the {igraph} package
diff --git a/R/as-simplextree.r b/R/as-simplextree.r
@@ -1,4 +1,4 @@
-#' @title Coerce objects to class 'simplextree'
+#' @title Coerce objects to class 'Rcpp_SimplexTree'
 #'
 #' @description Coerce objects to 'Rcpp_SimplexTree' objects, as implemented in
 #'   [the simplextree package][simplextree::simplextree-package].
diff --git a/R/interplex-package.r b/R/interplex-package.r
@@ -17,7 +17,7 @@
 #' * a complete list of simplices,
 #'   as stored as `cmplx` values of filtration objects
 #'   in [the TDA package][TDA::TDA-package]
-#' * an object of class 'Rcpp_SimplexTree' or 'simplextree'
+#' * an object of class 'Rcpp_SimplexTree'
 #'   as implemented
 #'   in [the simplextree package][simplextree::simplextree-package]
 #' * an object of class 'gudhi.simplex_tree.SimplexTree'
diff --git a/R/utils.r b/R/utils.r
@@ -27,7 +27,7 @@ ensure_index <- function(x, index) {
   )
 }
 
-# get list of simplices from a 'simplextree' object
+# get list of simplices from a 'Rcpp_SimplexTree' object
 simplextree_list <- function(x) {
   # extract list of fixed-dimension simplex matrices
   simps <- x$as_list()
diff --git a/README.md b/README.md
@@ -17,7 +17,7 @@ remotes::install_github("corybrunson/interplex")
 {interplex} includes converters between the following data structures:
 
 * complete lists of simplices, used by the [{TDA}](https://cran.r-project.org/package=TDA) package
-* simplex tree instances of class 'Rcpp_SimplexTree' or 'simplextree',
+* simplex tree instances of class 'Rcpp_SimplexTree',
   provided by the [{simplextree}](https://github.com/peekxc/simplextree) package
 * simplex trees in [Python GUDHI](https://gudhi.inria.fr/python/latest/) imported using the [{reticulate}](https://rstudio.github.io/reticulate/) package
 * objects of class 'igraph', provided by the [{igraph}](https://igraph.org/r/) package
diff --git a/cran-comments.md b/cran-comments.md
@@ -16,8 +16,7 @@ There were two NOTEs. One was due to this being a new submission.
 
 The other "[f]ound the following files/directories:" and listed "'lastMiKTeXException'". A web search led me to [{rhub} issue #503](https://github.com/r-hub/rhub/issues/503), which suggests that the issue can be ignored.
 
-The check also flagged the unrecognized word "simplicial", pluralized "simplices".
-This is a standard term in discrete topology.
+In addition to several surnames, the check also flagged the unrecognized words "GUDHI", which is a Python package; "TDA", the standard initialism for "topological data analysis"; and "simplicial", pluralized "simplices", which is a standard term in discrete topology.
 
 ### Win-Builder
 
@@ -34,7 +33,3 @@ The method `as_py_gudhi.Rcpp_SimplexTree()` operates differently depending on th
 ## Reverse dependencies
 
 This is a new submission with no reverse dependencies.
-
-## References
-
-There are no references (other than dependencies) to cite for the methods in this package. The data structures coerced between are documented, including with references, in their respective packages.
diff --git a/man/as_simplextree.Rd b/man/as_simplextree.Rd
diff --git a/man/interplex.Rd b/man/interplex.Rd
diff --git a/tests/testthat/test-cmplx-list.r b/tests/testthat/test-cmplx-list.r
@@ -25,7 +25,7 @@ test_that("list-to-'network' conversion preserves vertices", {
   expect_true(all(sort_el(cp_rf_el) == sort_el(network::as.edgelist(nw_rf))))
 })
 
-test_that("list-to-'simplextree' conversion preserves 0,1-simplices", {
+test_that("list-to-'Rcpp_SimplexTree' conversion preserves 0,1-simplices", {
   skip_if_not_installed("simplextree")
   st_rf <- as_simplextree(cp_rf)
   expect_equal(cp_rf_vc, st_rf$n_simplices[[1L]])
diff --git a/tests/testthat/test-igraph-class.r b/tests/testthat/test-igraph-class.r
@@ -13,7 +13,7 @@ test_that("'igraph'-to-'network' conversion preserves vertices", {
   expect_true(all(ig_kt_el == network::as.edgelist(nw_kt)))
 })
 
-test_that("'igraph'-to-'simplextree' conversion preserves 0,1-simplices", {
+test_that("'igraph'-to-'Rcpp_SimplexTree' conversion preserves 0,1-simplices", {
   skip_if_not_installed("simplextree")
   st_kt <- as_simplextree(ig_kt)
   expect_equal(igraph::gorder(ig_kt), st_kt$n_simplices[[1L]])
@@ -48,7 +48,7 @@ test_that("'igraph'-to-'network' conversion preserves attributes", {
   expect_true("id" %in% network::list.vertex.attributes(nw_kt))
 })
 
-test_that("'igraph'-to-'simplextree' conversion uses indices", {
+test_that("'igraph'-to-'Rcpp_SimplexTree' conversion uses indices", {
   skip_if_not_installed("simplextree")
   st_kt <- as_simplextree(ig_kt, index = "id")
   ig_id <- igraph::vertex_attr(ig_kt, "id")
diff --git a/tests/testthat/test-network-class.r b/tests/testthat/test-network-class.r
@@ -13,7 +13,7 @@ test_that("'network'-to-'igraph' conversion preserves vertices", {
   expect_true(all(nw_flo_el == igraph::as_edgelist(ig_flo)))
 })
 
-test_that("'network'-to-'simplextree' conversion preserves 0,1-simplices", {
+test_that("'network'-to-'Rcpp_SimplexTree' conversion preserves 0,1-simplices", {
   skip_if_not_installed("simplextree")
   st_flo <- as_simplextree(nw_flo)
   expect_equal(network::network.size(nw_flo), st_flo$n_simplices[[1L]])
@@ -48,7 +48,7 @@ test_that("'network'-to-'igraph' conversion preserves attributes", {
   expect_true("id" %in% igraph::vertex_attr_names(ig_flo))
 })
 
-test_that("'network'-to-'simplextree' conversion uses indices", {
+test_that("'network'-to-'Rcpp_SimplexTree' conversion uses indices", {
   skip_if_not_installed("simplextree")
   st_flo <- as_simplextree(nw_flo, index = "id")
   nw_id <- network::get.vertex.attribute(nw_flo, "id")
diff --git a/tests/testthat/test-py-gudhi.r b/tests/testthat/test-py-gudhi.r
@@ -23,7 +23,7 @@ test_that("GUDHI-to-'network' conversion preserves vertices", {
   expect_true(all(gd_el == sort_el(network::as.edgelist(nw_ex))))
 })
 
-test_that("GUDHI-to-'simplextree' conversion preserves all simplices", {
+test_that("GUDHI-to-'Rcpp_SimplexTree' conversion preserves all simplices", {
   skip_if_not_installed("simplextree")
   st_ex <- as_simplextree(gd_ex)
   expect_equal(gd_ex$num_vertices(), st_ex$n_simplices[[1L]])
diff --git a/tests/testthat/test-simplextree-class.r b/tests/testthat/test-simplextree-class.r
@@ -1,33 +1,33 @@
-context("'simplextree' objects")
+context("'Rcpp_SimplexTree' objects")
 
 skip_if_not_installed("simplextree")
 
 st_ex <- simplextree::simplex_tree()
 st_ex$insert(list(1:2, 2:5, 5:6, c(4,7), c(5,7), 6:7, 7:9))
 st_sl <- simplextree_list(st_ex)
 
-test_that("'simplextree'-to-'igraph' conversion preserves vertices", {
+test_that("'Rcpp_SimplexTree'-to-'igraph' conversion preserves vertices", {
   skip_if_not_installed("igraph")
   ig_ex <- as_igraph(st_ex)
   expect_equal(st_ex$n_simplices[[1L]], igraph::gorder(ig_ex))
   expect_true(all(st_ex$edges == sort_el(igraph::as_edgelist(ig_ex))))
 })
 
-test_that("'simplextree'-to-'network' conversion preserves vertices", {
+test_that("'Rcpp_SimplexTree'-to-'network' conversion preserves vertices", {
   skip_if_not_installed("network")
   nw_ex <- as_network(st_ex)
   expect_equal(st_ex$n_simplices[[1L]], network::network.size(nw_ex))
   expect_true(all(st_ex$edges == sort_el(network::as.edgelist(nw_ex))))
 })
 
-test_that("'simplextree'-to-list conversion preserves 0,1-simplices", {
+test_that("'Rcpp_SimplexTree'-to-list conversion preserves 0,1-simplices", {
   cp_ex <- as_cmplx(st_ex)
   expect_equal(st_ex$n_simplices[[1L]], length(unique(unlist(cp_ex))))
   expect_true(all(st_ex$edges ==
                     t(sapply(cp_ex[sapply(cp_ex, length) == 2L], identity))))
 })
 
-test_that("'simplextree'-to-GUDHI conversion preserves all simplices", {
+test_that("'Rcpp_SimplexTree'-to-GUDHI conversion preserves all simplices", {
   skip_if_not_installed("reticulate")
   gd_ex <- as_py_gudhi(st_ex)
   expect_equal(length(st_ex$vertices), gd_ex$num_vertices())
@@ -39,14 +39,14 @@ test_that("'simplextree'-to-GUDHI conversion preserves all simplices", {
 st_ex$clear()
 st_ex$insert(list(3:5, c(5, 8, 13), c(3, 13), 13:14, 14:15))
 
-test_that("'simplextree'-to-'igraph' conversion encodes indices", {
+test_that("'Rcpp_SimplexTree'-to-'igraph' conversion encodes indices", {
   skip_if_not_installed("igraph")
   ig_ex <- as_igraph(st_ex, index = "id")
   expect_true("id" %in% igraph::vertex_attr_names(ig_ex))
   expect_equal(st_ex$vertices, igraph::vertex_attr(ig_ex, "id"))
 })
 
-test_that("'simplextree'-to-'network' conversion encodes indices", {
+test_that("'Rcpp_SimplexTree'-to-'network' conversion encodes indices", {
   skip_if_not_installed("network")
   nw_ex <- as_network(st_ex, index = "id")
   expect_true("id" %in% network::list.vertex.attributes(nw_ex))

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-#' @title Coerce objects to class 'simplextree'`
	`1`	`+#' @title Coerce objects to class 'Rcpp_SimplexTree'`
`2`	`2`	`#'`
`3`	`3`	`#' @description Coerce objects to 'Rcpp_SimplexTree' objects, as implemented in`
`4`	`4`	`#' [the simplextree package][simplextree::simplextree-package].`
Original file line number	Diff line number	Diff line change
`@@ -27,7 +27,7 @@ ensure_index <- function(x, index) {`
`27`	`27`	`)`
`28`	`28`	`}`
`29`	`29`
`30`		`-# get list of simplices from a 'simplextree' object`
	`30`	`+# get list of simplices from a 'Rcpp_SimplexTree' object`
`31`	`31`	`simplextree_list <- function(x) {`
`32`	`32`	`# extract list of fixed-dimension simplex matrices`
`33`	`33`	`simps <- x$as_list()`