v1.2.1

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: autograph
 Title: Automatic Plotting and Theming of Many Graphs
-Version: 1.2.0
+Version: 1.2.1
 Description: Visual exploration and presentation of networks should not be difficult.
    This package includes functions for plotting networks and network-related metrics with sensible and pretty defaults.
    It includes 'ggplot2'-based plot methods for many popular network package classes.

NEWS.md

@@ -1,3 +1,17 @@
+# autograph 1.2.1
+
+## Layouts
+
+- Fixed "valence" layout returning a poor layout for some random starts
+  - The nodes now start on a circle, so one run resembles the next
+  - The repulsion force between two close nodes is now bounded
+  - Each step is now capped and cools over the iterations
+
+## Tests
+
+- Fixed the tutorial test failing on a deprecation warning that the tutorial code does not raise itself
+- Fixed the "valence" layout test depending on the random seed
+
 # autograph 1.2.0
 
 ## Package

R/layout_valence.R

@@ -41,7 +41,13 @@ layout_valence <- function(.data, times = 500, center = NULL, circular = FALSE,
       rep(1, manynet::net_ties(graph))
   weights[is.na(weights)] <- 1
 
-  coords <- matrix(stats::runif(n * 2, min = -1, max = 1), ncol = 2)
+  # The nodes start on a circle rather than at random points, so that the
+  # layout is stable from one run to the next. A random start can place two
+  # nodes on top of each other, which the repulsion force then throws apart.
+  # A small jitter breaks the symmetry of the circle.
+  angle <- 2 * pi * seq_len(n) / n
+  coords <- cbind(cos(angle), sin(angle)) +
+    matrix(stats::runif(n * 2, min = -0.01, max = 0.01), ncol = 2)
 
   for (i in 1:times) {
     delta <- matrix(0, nrow = n, ncol = 2)
@@ -52,7 +58,10 @@ layout_valence <- function(.data, times = 500, center = NULL, circular = FALSE,
         vec <- coords[k, ] - coords[j, ]
         dist <- sqrt(sum(vec^2)) + 1e-4
         dir <- vec / dist
-        force <- repulsion_coef / dist^2
+        # The distance is floored, since two nodes that start close together
+        # would otherwise repel each other with a force large enough to throw
+        # the whole layout apart, which it never recovers from.
+        force <- repulsion_coef / max(dist, 0.1)^2
 
         delta[j, ] <- delta[j, ] - force * dir
         delta[k, ] <- delta[k, ] + force * dir
@@ -75,8 +84,13 @@ layout_valence <- function(.data, times = 500, center = NULL, circular = FALSE,
       delta[t_id, ] <- delta[t_id, ] - force * dir
     }
 
-    # Position update with damping
-    coords <- coords + 0.1 * delta
+    # Position update with damping, a capped step, and cooling.
+    # The cap keeps one large force from moving a node further than the layout
+    # is wide, and the cooling lets the layout settle over the iterations.
+    step <- sqrt(rowSums(delta^2))
+    limit <- ifelse(step > 1, 1 / step, 1)
+    temp <- 1 - (i - 1) / times
+    coords <- coords + 0.1 * temp * delta * limit
   }
   coords <- as.data.frame(coords)
   names(coords) <- c("x", "y")

cran-comments.md

@@ -1,3 +1,22 @@
+## Resubmission
+
+This is a resubmission of 1.2.0, which failed the incoming checks with a test error
+on Windows and on Debian. Both are fixed here.
+
+* `layout_valence()` started its nodes at random points, and a start that placed two
+  nodes close together gave a force large enough to spoil the layout. The nodes now
+  start on a circle, the force is bounded, and the test sets a seed.
+* On Windows, the tutorial test failed on a deprecation warning that the tutorial code
+  does not raise itself: `netrics::tie_by_closeness()` (0.4.1) calls
+  `manynet::to_ties()`, which manynet deprecates in 2.3.0. netrics 1.0.0, to be
+  submitted, calls the current function. The test now fails only if the tutorial calls
+  a deprecated function itself, so it passes with either netrics version.
+
+The full test suite passes with each of these three pairs: manynet 2.2.3 with
+netrics 0.4.0, manynet 2.3.1 with netrics 0.4.1 (the pair that failed on Windows),
+and manynet 2.3.0 with netrics 1.0.0. manynet 2.3.1 and netrics 1.0.0 are to be
+submitted; this version does not require either of them.
+
 ## Test environments
 
 * local R installation, aarch64-apple-darwin20, R 4.5.1

tests/testthat/helper-tutorials.R

@@ -89,6 +89,25 @@ check_tute_functions <- function(path, skip = "ergm\\(|grapht\\("){
       if (!grepl("deprecate|defunct|moved", msg, ignore.case = TRUE)) {
         w <- NULL
       }
+
+      # Only fail if the tutorial calls the deprecated function itself. A
+      # dependency that calls a deprecated function of its own dependency
+      # raises the same warning, and no edit to this tutorial can silence it.
+      if (!is.null(w)) {
+        code <- paste(deparse(exprs[[i]]), collapse = " ")
+        # The name a deprecation warning reports, in either the base R form
+        # ("'to_ties' is deprecated") or the {lifecycle} form
+        # ("`to_ties()` was deprecated in manynet 2.3.0").
+        hits <- regmatches(msg, gregexpr(
+          "[`'\"][^`'\"]+[`'\"][^[:alpha:]]*(is|was|has been)[[:space:]]+(deprecated|defunct|moved)",
+          msg))[[1]]
+        named <- gsub("^[`'\"]([^`'\"]+)[`'\"].*$", "\\1", hits)
+        named <- gsub("\\(\\)$", "", named)
+        if (length(named) > 0 &&
+            !any(vapply(named, grepl, logical(1), x = code, fixed = TRUE))) {
+          w <- NULL
+        }
+      }
     }
 
     # Now test what happened

tests/testthat/test-layout_valence.R

@@ -1,4 +1,5 @@
 test_that("valence layout works", {
+  set.seed(123)
   edges <- data.frame(from = c("A", "B"),
                       to   = c("B", "C"),
                       weight = c(3, 3),