Add `tree` function to print nested structure list-like objects #56

nstrayer · 2021-03-30T15:50:27Z

This PR adds the function tree() (and its helper function tree_label().

The purpose of tree is to replace str() for complex nested structures. The original inspiration was HTML tag lists with children and various other valuable information hanging off of them.

Examples

Printing simple lists

library(tree)

plain_list <- list(
  list(id = "a",
       val = 2),
  list(id = "b",
       val = 1,
       children = list(
         list(id = "b1",
              val = 2.5),
         list(id = "b2",
              val = 8,
              children = list(
                list(id = "b21",
                     val = 4)
              )))))
tree(plain_list)
#> 
#> [list]
#> ├─1:{list}
#> │ ├─id:"a"
#> │ └─val:2
#> └─2:{list}
#>   ├─id:"b"
#>   ├─val:1
#>   └─children:[list]
#>     ├─1:{list}
#>     │ ├─id:"b1"
#>     │ └─val:2.5
#>     └─2:{list}
#>       ├─id:"b2"
#>       ├─val:8
#>       └─children:[list]
#>         └─1:{list}
#>           ├─id:"b21"
#>           └─val:4

Output depth can be limited to avoid information overload

tree(plain_list, max_depth = 2)
#> 
#> [list]
#> ├─1:{list}
#> │ ├─id:"a"
#> │ └─val:2
#> └─2:{list}
#>   ├─id:"b"
#>   ├─val:1
#>   └─children:[list]
#>     ├─1:{list}
#>     └─2:{list}

You can further simplify output by avoiding printing indices for id-less
elements

tree(plain_list, index_arraylike = FALSE)
#> 
#> [list]
#> ├─{list}
#> │ ├─id:"a"
#> │ └─val:2
#> └─{list}
#>   ├─id:"b"
#>   ├─val:1
#>   └─children:[list]
#>     ├─{list}
#>     │ ├─id:"b1"
#>     │ └─val:2.5
#>     └─{list}
#>       ├─id:"b2"
#>       ├─val:8
#>       └─children:[list]
#>         └─{list}
#>           ├─id:"b21"
#>           └─val:4

Prints atomic vectors inline (up to 10 elements)

list_w_vectors <- list(
  name = "vectored list",
  num_vec = 1:10,
  char_vec = letters
)
tree(list_w_vectors)
#> 
#> {list}
#> ├─name:"vectored list"
#> ├─num_vec:1,2,3,4,5,6,7,8,9,10
#> └─char_vec:"a","b","c","d","e","f","g","h","i","j",...(n = 26)

Attempts to work with any list-like object.

For instance: html tag structures

tree(shiny::sliderInput("test", "Input Label", 0, 1, 0.5))
#> 
#> {shiny.tag}
#> ├─name:"div"
#> ├─attribs:{list}
#> │ └─class:"form-group shiny-input-container"
#> └─children:[list]
#>   ├─1:{shiny.tag}
#>   │ ├─name:"label"
#>   │ ├─attribs:{list}
#>   │ │ ├─class:"control-label"
#>   │ │ ├─id:"test-label"
#>   │ │ └─for:"test"
#>   │ └─children:[list]
#>   │   └─1:"Input Label"
#>   └─2:{shiny.tag}
#>     ├─name:"input"
#>     ├─attribs:{list}
#>     │ ├─class:"js-range-slider"
#>     │ ├─id:"test"
#>     │ ├─data-skin:"shiny"
#>     │ ├─data-min:"0"
#>     │ ├─data-max:"1"
#>     │ ├─data-from:"0.5"
#>     │ ├─data-step:"0.01"
#>     │ ├─data-grid:"true"
#>     │ ├─data-grid-num:10
#>     │ ├─data-grid-snap:"false"
#>     │ ├─data-prettify-separator:","
#>     │ ├─data-prettify-enabled:"true"
#>     │ ├─data-keyboard:"true"
#>     │ └─data-data-type:"number"
#>     └─children:[list]

Attributes can be shown (but arent by default)

list_w_attrs <- structure(
  list(
    structure(
      list(id = "a",
           val = 2),
      level = 2,
      name = "first child"
    ),
    structure(
      list(id = "b",
           val = 1,
           children = list(
             list(id = "b1",
                  val = 2.5),
             list(id = "b2",
                  val = 8,
                  children = list(
                    list(id = "b21",
                         val = 4)
                  )))),
      level = 2,
      name = "second child",
      class = "custom-class"
    )),
  level = "1",
  name = "root"
)
tree(list_w_attrs, show_attributes = TRUE)
#> 
#> [list]
#> ├─1:{list}
#> │ ├─id:"a"
#> │ ├─val:2
#> │ ├┄<attr>names:"id","val"
#> │ ├┄<attr>level:2
#> │ └┄<attr>name:"first child"
#> ├─2:{custom-class}
#> ┊ ├─id:"b"
#> ┊ ├─val:1
#> ┊ ├─children:[list]
#> ┊ ┊ ├─1:{list}
#> ┊ ┊ │ ├─id:"b1"
#> ┊ ┊ │ ├─val:2.5
#> ┊ ┊ │ └┄<attr>names:"id","val"
#> ┊ ┊ └─2:{list}
#> ┊ ┊   ├─id:"b2"
#> ┊ ┊   ├─val:8
#> ┊ ┊   ├─children:[list]
#> ┊ ┊   ┊ └─1:{list}
#> ┊ ┊   ┊   ├─id:"b21"
#> ┊ ┊   ┊   ├─val:4
#> ┊ ┊   ┊   └┄<attr>names:"id","val"
#> ┊ ┊   └┄<attr>names:"id","val","children"
#> ┊ ├┄<attr>names:"id","val","children"
#> ┊ ├┄<attr>level:2
#> ┊ ├┄<attr>name:"second child"
#> ┊ └┄<attr>class:"custom-class"
#> ├┄<attr>level:"1"
#> └┄<attr>name:"root"

You can customize the tree appearance by swapping out unicode characters

Find characters at
unicode-table.com.

tree(plain_list,
     char_vertical = "\u2551",
     char_horizontal = "\u2550",
     char_branch = "\u2560",
     char_final_branch = "\u255A")
#> 
#> [list]
#> ╠═1:{list}
#> ║ ╠═id:"a"
#> ║ ╚═val:2
#> ╚═2:{list}
#>   ╠═id:"b"
#>   ╠═val:1
#>   ╚═children:[list]
#>     ╠═1:{list}
#>     ║ ╠═id:"b1"
#>     ║ ╚═val:2.5
#>     ╚═2:{list}
#>       ╠═id:"b2"
#>       ╠═val:8
#>       ╚═children:[list]
#>         ╚═1:{list}
#>           ╠═id:"b21"
#>           ╚═val:4

You can also pass custom style functions for class and value printing
that transform text. E.g. using crayon to style.

library(crayon)
tree(plain_list, 
     class_printer = white$bgBlue,
     val_printer = underline$red)

Screenshot of output in consoles with styling support.

Limitations/Drawbacks

Built entirely outside of `lobstr` at first:

Since I assumed no dependencies there very well may be some rlang niceties that could make the code much more maintainable.
No shared code with the already existing shared tree printing code that is used in functions like ast()

Testing

Most tests while building function were snapshot tests which are not compatible with the current testhat version for lobstr.
Many of the non-snapshot tests rely on the lack of some results which is a bit confusing to reason about and make sure that the tests themselves don't break. Not sure how to fix this.

…jects

…lipped through

…a warning not an error

…eaned up to avoid breaking tree vertical continuity

…ls arent awkwardly on the same line

hadley

A few initial comment; will be easier to respond with more details once you've changed the tests.

R/tree.R

tests/testthat/test-tree.R

hadley · 2021-04-05T16:41:13Z

tests/testthat/test-tree.R

+#   )
+# })
+
+test_that("Max depth can be enforced", {


I think pretty much all of these should be converted to snapshot tests, with the object included in the snapshot code. That'll make it much easier for me to review the precise display decisions.

Done! For ones where I reuse the same object a few times for testing different options I just made the snapshot an expression that declared the object as a variable and passed it twice.
E.g.

expect_snapshot({ deep_list <- list( list( id = "b", val = 1, children = list( list(id = "b1",val = 2.5), list( id = "b2", val = 8, children = list( list(id = "b21", val = 4) ) ) ) ), list(id = "a", val = 2) ) tree(deep_list, max_depth = 1) tree(deep_list, max_depth = 2) tree(deep_list, max_depth = 3) tree(deep_list, max_length = 0) tree(deep_list, max_length = 2) tree(deep_list, max_depth = 1, max_length = 4) })

Works fine but didn't know if that was frowned upon.

R/tree.R

hadley · 2021-04-05T16:51:10Z

R/tree.R

+    # Environments also tend to have the same trouble as functions. For instance
+    # the srcobject attached to a function's attributes is an environment but
+    # doesn't report as one to s3.
+    tree_label.environment(x)


But tree_label.environment just calls format.default? I think it would be better to at least optionally recurse into environments.

Agreed. I had put it off because it felt hard due to not knowing when to stop recusing. I think I have a good heuristic for stopping now:

... if (is_environment(x)) { # If we're looking at an environment, we add its parent as child parent <- env_parent(x) already_seen_parent <- any(as.logical(lapply(counter_env$envs_seen, identical, parent))) # Stop recursion into environments when we get to either the calling # environment, the global environment, or an empty environment if ( !( already_seen_parent | identical(parent, rlang::caller_env()) | identical(parent, rlang::empty_env()) | identical(parent, rlang::global_env()) ) ) { counter_env$envs_seen <- c(counter_env$envs_seen, parent) children <- c(children, parent = env_parent(x)) } } ...

E.g.:

library(rlang) ea <- env(d = 4, e = 5) lobstr::tree(env(ea, a = 1, b = 2, c = 3)) #> <environment: 0x7f91ba1a4ab8> #> ├─a: 1 #> ├─b: 2 #> ├─c: 3 #> └─parent: <environment: 0x7f91aa4d42e0> #> ├─d: 4 #> └─e: 5

I don't think it makes sense to show the parent -- for example, if you show the tree for shiny:::.globals (which is an environment), it'll show a bunch of environments that aren't relevant. I also think that if you do show parents, stopping at the global env or caller env can be misleading to users.

To add a bit more: I think it's very uncommon when using environments to care what's in the parent env. That only really is relevant in closures. In the vast majority of cases, when an environment is used as a data structure, the parent env is not relevant, since $ and [[ indexing won't look in the parent.

Yeah, I don't think you need to recurse into the parent either.

Once you ignore the parent, you're less likely to encounter other special environments, but I'd suggest following the same heuristics as obj_size(): https://github.com/r-lib/lobstr/blob/master/src/size.cpp#L157-L159

Recursing into parent was removed in ce4128a, also matches the forbidden environments from obj_size().

hadley · 2021-04-05T16:51:56Z

R/tree.R

+#'
+#' @export
+tree_label <- function(x, val_printer, class_printer, remove_newlines){
+  UseMethod("tree_label")


Hmmmm, it's not clear to me that you actually want to use S3 dispatch at all here.

The motivation for using S3 dispatch was to enable external developers to hook up custom printing functions for their classes. For instance maybe Shiny.tag wants to print as <h1/> etc..

Without that motivation, it does feel like creating unnecessary namespace exports.

It also feels like if the goal is truly to most accurately represent the structure then we wouldn't want custom printing for classes. However, if we wanted to have the function serve as a base for different tree-printing applications then maybe we should either keep the S3 dispatch or come up with another customization interface.

…tion in future

tests/testthat/_snaps/tree.md

hadley · 2021-04-06T16:32:40Z

tests/testthat/_snaps/tree.md

+      {list}
+      ├─name:"vectored list"
+      ├─num_vec:1,2,3,4,5,6,7,8,9,10
+      └─char_vec:"a","b","c","d","e","f","g","h","i","j",...(n = 26)


What if this was char_vec[26]? i.e. always put the length on the left hand side.

What happens if each individual string is very long?

I ended up changing the vector printing to wrap in square brackets and then (if truncated) put the length at the end. Putting the length at the start felt like it interfered with ease-of-reading and meant that we needed to put it for every vector, which if they are short feels excessive.

<list> ├─name: "vectored list" ├─num_vec: (n:10) 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 └─char_vec: (n:26) "a", "b", "c", "d", "e", "f", "g", "h", "i", "j", ...

vs

<list> ├─name: "vectored list" ├─num_vec: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10] └─char_vec: ["a", "b", "c", "d", "e", "f", "g", "h", "i", "j", ...] n:26

I'm not deadset in this viewpoint though.

How about using something like pillar::obj_sum():

├─name<chr [1]>: "vectored list" ├─num_vec<int [10]>: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 └─char_vec<chr [26]>: "a", "b", "c", "d", "e", "f", "g", "h", "i", "j", ...

I'd prefer not to use [] just because that'd be introducing a new convention which we haven't used elsewhere.

Oh I definitely like that better.

Done with one exception. I feel like adding the same <type [length]> prefix for all the scalar atomics is a bit busier than necessary so I default to printing those as before; with an option to enable more verbose behavior.

Default keeps scalar atomics nice and clean (type's are still inferable with printing behavior)

lobstr::tree( list(name = "vectored list", num_vec = 1:10) ) #> <list> #> ├─name: "vectored list" #> └─num_vec<int [10]>: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10

But the more verbose (and accurate to underyling structure) printing is available with an argument

lobstr::tree( list(name = "vectored list", num_vec = 1:10), hide_scalar_types = FALSE ) #> <list> #> ├─name<chr [1]>: "vectored list" #> └─num_vec<int [10]>: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10

Do you think this is a fair compromise between terseness and conveying info about the element?

tests/testthat/_snaps/tree.md

hadley · 2021-04-06T16:36:09Z

tests/testthat/_snaps/tree.md

+      {list}
+      ├─normal string:"first element"
+      ├─really long string:"abcdefghijklmnopqrstuvwxyzabcdef..."
+      └─vec of long strings:"a long


Should this show \n insteadd?

I ended up using a unicode symbol to show where newlines existed instead of just wiping them out.

{list} ├─normal string: "first element" ├─really long string: "abcdefghijklmnopqrstuvwxyzabcdef..." └─vec of long strings: ["a long↵and m...", "a fine length", "another long..."]

I figured it's less horizontal space taken up and a bit easier to parse on a glance. That being said I can see why we may want to simply use \n instead.

Hmmmm, interesting. Again, I don't have any concerns except that we haven't used it before elsewhere.

(This is another example where you want to balance the length on individual elements with the number of elements displayed)

hadley · 2021-04-06T20:20:50Z

Fixes #2. Should we call it rst()?

wch · 2021-04-06T20:25:10Z

Does rst stand for anything or is it just an anagram of str?

…element not just those in array-like structures

… arrow

… els> at the end for truncated vectors

…t to snapshot test

…an ellipsis to show more exists

…r types

wch · 2021-04-08T20:28:14Z

R/tree.R

+  already_seen <- rlang::is_environment(x) &&
+    any(vapply(counter_env$envs_seen, identical, x, FUN.VALUE = NA))
+
+  if (!already_seen && rlang::is_environment(x)) {
+    # If this environment is new, add it to the seen
+    counter_env$envs_seen[[length(counter_env$envs_seen) + 1]] <- x
+  }


I think it would be clearer to have:

already_seen <- FALSE if (is_environment(x)) { already_seen <- any(vapply(counter_env$envs_seen, identical, x, FUN.VALUE = NA)) if (!already_seen) { counter_env$envs_seen[[length(counter_env$envs_seen) + 1]] <- x } }

And for clarity FUN.VALUE = logical(1)

I've recently been using NA/NA_character_/NA_integer_ etc., because the literal value has less overhead than a function call. The drawback is that for logicals, it's NA instead of NA_logical_, so it's not as obvious what the type is.

…on into themselves

…at cant.

hadley · 2021-04-13T12:08:25Z

@nstrayer if you fix the build failures, I think this is in a good place to merge, and we can continue iterating in future PRs.

…ist-like objects passing through as.list unscathed

wch · 2021-05-12T22:16:06Z

R/tree.R

+  if (rlang::is_environment(x)) {
+    # Environments are funky as they dont have names before conversion to list
+    # but do after, so let them handle their conversion
+    return (as.list(x))


This might need to be as.list.environment(), because if the environment has a class (like with R6 objects), as.list() will not dispatch to as.list.environment().

Also need to consider whether or not to set all.names = TRUE

I had no idea the default was FALSE for that. Updated to TRUE. Since the purpose of tree is to show the true underlying structure of objects it seems only natural we would expose dot prefixed children.

wch · 2021-05-12T22:30:28Z

R/tree.R

@@ -268,6 +268,22 @@ is_printable_env <- function(x) {
    )
 }

+tree_as_list <- function(x){


What kind of objects can this take as input? I'm asking because the removal of all attributes (other than names) may have unexpected results. For example:

x <- matrix(1:6, 2, 3) attributes(x) #> $dim #> [1] 2 3 x <- data.frame(x=1:3, y=4:6) attributes(x) #> $names #> [1] "x" "y" #> #> $class #> [1] "data.frame" #> #> $row.names #> [1] 1 2 3

Stripping attributes seems like the right approach to me. The tree is fundamentally about the underlying data not the lies that S3 might be telling you about it.

It's only used to make sure we can properly iterate over the children. We already pull off attributes before doing this if they are requested with show_attributes = TRUE.

Can you add a comment about what kind of objects this function can take as input? That'll help future readers to understand what should be happening in this function.

So I realized that I only called this function once. (I had wrapped attributes(x) in it, but since attributes() always returns a list I didn't need to there.) So I moved the function inline and streamlined it a bit.

... # Coerce current object to a plain list. This is necessary as some s3 # classes override `[[` and return funky stuff like themselves (see s3 class # "package_version") children <- if (is_printable_env(x)) { # Environments are funky as they don't have names before conversion to list # but do after, so let them handle their conversion. # We use all.names = TRUE in an effort to fully explain the object as.list.environment(x, all.names = TRUE) } else { # By wiping all attributes except for the names we force the object to be # a plain list. This is inspired by the (now depreciated) rlang::as_list(). attributes(x) <- list(names = names(x)) as.list(x) } ...

…n" children

… more usefull comments

… would not show proper branch structure

Different versions of R have different arguments for strArgs so just define a function so we know the args wont change

…acter support breaking snapshots

nstrayer · 2021-05-13T22:48:35Z

All checks are passing -- finally! So baring name changes this should be good to go.

nstrayer added 8 commits March 30, 2021 11:35

Add tree function to print nested structure of arbitrary list-like ob…

dab5dfb

…jects

Removed (out of date) docs from tree_internal function

b80a8df

Made ellipsis documentation explicit and checked for arguments that s…

16f6974

…lipped through

Fixed mistake of not updating el -> x in roxygen

269ed77

Made the unknown arguments test a bit more robust and turned it into …

45c937d

…a warning not an error

Character strings that contain new-lines or are super long are now cl…

9ea6e7a

…eaned up to avoid breaking tree vertical continuity

Made max length shorter for strings in character vectors

dcb5312

Put newline at end of cat so there's no space before and the next cal…

e4b1fea

…ls arent awkwardly on the same line

hadley reviewed Apr 5, 2021

View reviewed changes

nstrayer added 11 commits April 6, 2021 10:23

Merge remote-tracking branch 'original_repo/master'

a1a2837

Switched to Recall for recursive calls in case we change name of func…

40ecd2d

…tion in future

Converted most tests to snapshot tests

b4e3d20

Fixed indenting to use tidyverse standard

dfb4550

Renamed index_arraylike to index_unnamed

4576280

Return object printed so tree can be used in pipes

00847e8

Added option for max-length of printing

8e8e9a7

Added max_length tests

0e88d47

replaced the base is.* functions with rlang's underscored versions

2b79563

Added spaces after every if statement before the parens

b70accb

Swapped out my hacky unnamed argument checking to the ellipsis package

e54d098

hadley reviewed Apr 6, 2021

View reviewed changes

Substantially less hacky way of enforcing max_length

9e6ac57

nstrayer added 6 commits April 6, 2021 16:52

index_unamed now does what it's name implies and indexes any unnamed …

6279aaf

…element not just those in array-like structures

Updated default value of index_unnamed to be FALSE

63bc4e1

Instead of simply erasing newlines they are replaced with a down-left…

45290b3

… arrow

Atomic vectors get wrapped in square brackets with an optional n:<num…

49e2fcc

… els> at the end for truncated vectors

Updated tests with new spacing rules and converted missing values tes…

791acef

…t to snapshot test

Early termination due to max-length being reached is now marked with …

cd4c863

…an ellipsis to show more exists

nstrayer added 5 commits April 8, 2021 13:59

New atomic vector printing

77bb48d

More optimized array append

5913e27

attributes now print as attr(,"id") to avoid conflict with <> used fo…

02772da

…r types

Simplified function argument snapshot test

32c687a

Accidentally was adding every object seen to seen_envs list

afaa4f7

wch reviewed Apr 8, 2021

View reviewed changes

nstrayer added 8 commits April 8, 2021 16:30

Fixes but where single-length non-atomics will cause infinite recursi…

2469f17

…on into themselves

Fixed up recursion logic to say what should go through rather than wh…

926e6f9

…at cant.

Clarified logic around if an environment has already been seen

7c5d46e

Added support for printing of expressions

d034040

Added formula printing as well

e212545

Moved the separated tree_label methods next to each-other in file

05fdae2

Reformmated using styler to make sure I match tidyverse styleguide

e2a0dbf

Rebuilt docs

5ebab19

Switched to more robust list conversion function due to some tricky l…

5d7bcb1

…ist-like objects passing through as.list unscathed

wch reviewed May 12, 2021

View reviewed changes

nstrayer added 9 commits May 13, 2021 12:31

Set all.names = TRUE in as.list.environment() so we don't omit "hidde…

ac2f5d2

…n" children

Moved tree_as_list() inline, simplified its implementation, and added…

5586cef

… more usefull comments

Fixed bug where attributes with children followed by other attributes…

e9a921d

… would not show proper branch structure

Ran styleR

4342a1b

Remove test that used shiny::input_slider

40deb1a

Namespaced some env calls in tests

7d791bf

Fixed all issues from running R CMD Check locally

ab3652b

Switch to explicit function definition for argument printing test

971b44b

Different versions of R have different arguments for strArgs so just define a function so we know the args wont change

Skip all but one tree test on windows due to lack of "fancy" box char…

df3b36e

…acter support breaking snapshots

hadley approved these changes May 17, 2021

View reviewed changes

nstrayer merged commit 91ff8b5 into r-lib:master May 17, 2021

Add tree function to print nested structure list-like objects #56

Add tree function to print nested structure list-like objects #56

Conversation

nstrayer commented Mar 30, 2021 • edited Loading

Examples

Printing simple lists

Output depth can be limited to avoid information overload

Prints atomic vectors inline (up to 10 elements)

Attempts to work with any list-like object.

Attributes can be shown (but arent by default)

You can customize the tree appearance by swapping out unicode characters

Limitations/Drawbacks

Built entirely outside of lobstr at first:

Testing

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hadley Apr 7, 2021 • edited Loading

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hadley commented Apr 6, 2021

wch commented Apr 6, 2021

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hadley commented Apr 13, 2021

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hadley May 13, 2021 • edited Loading

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nstrayer commented May 13, 2021

Add `tree` function to print nested structure list-like objects #56

Add `tree` function to print nested structure list-like objects #56

nstrayer commented Mar 30, 2021 •

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Built entirely outside of `lobstr` at first:

nstrayer Apr 7, 2021 •

edited

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hadley Apr 7, 2021 •

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hadley May 13, 2021 •

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