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Use cli::cli_abort() everywhere. #502

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merged 15 commits into from
Nov 8, 2023
Merged

Use cli::cli_abort() everywhere. #502

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81c6669
Add snapshot tests
olivroy Oct 30, 2023
b29dd2e
Use correct function name in tests `get_global_graph_attr_info()` ove…
olivroy Oct 30, 2023
3217f2e
Add no_edges to snapshot.
olivroy Oct 30, 2023
76583ce
Remove the last traces of functions removed in DiagrammeR 1.0.6.1
olivroy Oct 30, 2023
6f942b6
Update error messages and snapshots.
olivroy Nov 2, 2023
da99881
Remove usage of `emit_error()` in favour of `cli::cli_abort()`.
olivroy Nov 6, 2023
bfa5ed6
Test refactoring + update snapshots.
olivroy Nov 6, 2023
a52c252
Refactor code
olivroy Nov 6, 2023
62607be
Add news
olivroy Nov 6, 2023
a0178a3
Minimal spellcheck + `devtools::build_readme()` + badges
olivroy Nov 8, 2023
c822cf4
Update URLs
olivroy Nov 8, 2023
e8368d8
Actually use integer (no need for coercion after)
olivroy Nov 8, 2023
8cfbdf2
Update README.Rmd
olivroy Nov 8, 2023
341622c
Update README.md
olivroy Nov 8, 2023
2dbcfc1
Add Olivier as author
olivroy Nov 8, 2023
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2 changes: 2 additions & 0 deletions DiagrammeR.Rproj
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Expand Up @@ -22,3 +22,5 @@ PackageCheckArgs: --as-cran --no-manual
PackageRoxygenize: rd,collate,namespace

UseNativePipeOperator: No

SpellingDictionary: en_US
10 changes: 9 additions & 1 deletion NEWS.md
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@@ -1,5 +1,13 @@
# DiagrammeR (development version)

* DiagrammeR nows uses testthat 3rd edition (@olivroy, #498)

* No longer use deprecated features from igraph and tidyselect (>= 1.2.0) (@olivroy, #497)

* Error messages have been reviewed and now use cli (@olivroy, #499, #502)

* It is now easier to install suggested packages on the fly. DiagrammeR now uses `rlang::check_installed()` internally. (@olivroy, #499)

# DiagrammeR 1.0.10

* Remove dependency on the **influenceR** package, which also means removing the `get_constraint()` and `get_bridging()` graph inspection functions.
Expand Down Expand Up @@ -138,7 +146,7 @@

* Degree data for plots can now be easily obtained using the `get_degree_distribution()` and `get_degree_histogram()` functions

* Global graph attributes are now more easily modifiable using a set of functions for this purpose: `add_global_graph_attrs()`, `clear_global_graph_attrs()`, `delete_global_graph_attrs()`, `get_global_graph_attrs()`, `set_global_graph_attrs()`
* Global graph attributes are now more easily modifiable using a set of functions for this purpose: `add_global_graph_attrs()`, `delete_global_graph_attrs()`, `get_global_graph_attr_info()`.

* Added option to display different text labels on nodes via the `display` node attribute; this is easily set with the `set_node_attr_to_display()` function

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2 changes: 1 addition & 1 deletion R/DiagrammeR.R
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Expand Up @@ -2,7 +2,7 @@
#'
#' @description
#'
#' Make diagrams in R using \href{https://github.com/mdaines/viz.js}{viz.js} or
#' Make diagrams in R using \href{https://github.com/mdaines/viz-js}{viz.js} or
#' \href{https://github.com/mermaid-js/mermaid}{mermaid.js} with infrastructure
#' provided by \href{http://www.htmlwidgets.org/}{htmlwidgets}.
#'
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2 changes: 1 addition & 1 deletion R/add_balanced_tree.R
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Expand Up @@ -290,7 +290,7 @@ add_balanced_tree <- function(
graph_log <-
add_action_to_log(
graph_log = graph_log,
version_id = nrow(graph_log) + 1,
version_id = nrow(graph_log) + 1L,
function_used = fcn_name,
time_modified = time_function_start,
duration = graph_function_duration(time_function_start),
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2 changes: 1 addition & 1 deletion R/add_cycle.R
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Expand Up @@ -264,7 +264,7 @@ add_cycle <- function(
graph_log <-
add_action_to_log(
graph_log = graph_log,
version_id = nrow(graph_log) + 1,
version_id = nrow(graph_log) + 1L,
function_used = fcn_name,
time_modified = time_function_start,
duration = graph_function_duration(time_function_start),
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4 changes: 2 additions & 2 deletions R/add_edge.R
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Expand Up @@ -260,7 +260,7 @@ add_edge <- function(

# Iteratively set edge attribute values for
# the new edge in the graph
for (i in 1:ncol(edge_aes_tbl)) {
for (i in seq_len(ncol(edge_aes_tbl))) {
graph <-
graph %>%
set_edge_attrs_ws(
Expand Down Expand Up @@ -318,7 +318,7 @@ add_edge <- function(
graph$graph_log <-
add_action_to_log(
graph_log = graph$graph_log,
version_id = nrow(graph$graph_log) + 1,
version_id = nrow(graph$graph_log) + 1L,
function_used = fcn_name,
time_modified = time_function_start,
duration = graph_function_duration(time_function_start),
Expand Down
9 changes: 4 additions & 5 deletions R/add_edge_clone.R
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Expand Up @@ -91,7 +91,7 @@
# to an edge in the graph
if (!(edge %in% graph$edges_df$id)) {

abort(
cli::cli_abort(

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"The value provided in `edge` does not correspond to an edge in the graph.")
}

Expand Down Expand Up @@ -125,12 +125,11 @@
# Create an edge selection for the
# new edge in the graph
graph <-
graph %>%
select_last_edges_created()
select_last_edges_created(graph)

# Iteratively set edge attribute values for
# the new edges in the graph
for (i in 1:ncol(edge_attr_vals)) {
for (i in seq_len(ncol(edge_attr_vals))) {

graph$edges_df[
nrow(graph$edges_df),
Expand All @@ -155,7 +154,7 @@
graph$graph_log <-
add_action_to_log(
graph_log = graph$graph_log,
version_id = nrow(graph$graph_log) + 1,
version_id = nrow(graph$graph_log) + 1L,
function_used = fcn_name,
time_modified = time_function_start,
duration = graph_function_duration(time_function_start),
Expand Down
7 changes: 3 additions & 4 deletions R/add_edge_df.R
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Expand Up @@ -54,7 +54,7 @@
check_graph_valid(graph)

# Validation: Graph contains nodes
check_graph_contains_nodes(graph,extra_msg = " so, edges cannot be added")
check_graph_contains_nodes(graph,extra_msg = "So, edges cannot be added.")

# Get the number of edges ever created for
# this graph
Expand Down Expand Up @@ -92,7 +92,7 @@
graph$graph_log <-
add_action_to_log(
graph_log = graph$graph_log,
version_id = nrow(graph$graph_log) + 1,
version_id = nrow(graph$graph_log) + 1L,
function_used = fcn_name,
time_modified = time_function_start,
duration = graph_function_duration(time_function_start),
Expand All @@ -103,8 +103,7 @@
# Perform graph actions, if any are available
if (nrow(graph$graph_actions) > 0) {
graph <-
graph %>%
trigger_graph_actions()
trigger_graph_actions(graph)

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}

# Write graph backup if the option is set
Expand Down
2 changes: 1 addition & 1 deletion R/add_edges_from_table.R
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Expand Up @@ -298,7 +298,7 @@ add_edges_from_table <- function(
graph$graph_log <-
add_action_to_log(
graph_log = graph$graph_log,
version_id = nrow(graph$graph_log) + 1,
version_id = nrow(graph$graph_log) + 1L,
function_used = fcn_name,
time_modified = time_function_start,
duration = graph_function_duration(time_function_start),
Expand Down
2 changes: 1 addition & 1 deletion R/add_edges_w_string.R
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Expand Up @@ -179,7 +179,7 @@ add_edges_w_string <- function(
graph$graph_log <-
add_action_to_log(
graph_log = graph$graph_log,
version_id = nrow(graph$graph_log) + 1,
version_id = nrow(graph$graph_log) + 1L,
function_used = fcn_name,
time_modified = time_function_start,
duration = graph_function_duration(time_function_start),
Expand Down
11 changes: 5 additions & 6 deletions R/add_forward_edges_ws.R
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Expand Up @@ -66,9 +66,6 @@
# Get the time of function start
time_function_start <- Sys.time()

# Get the name of the function
fcn_name <- get_calling_fcn()

# Validation: Graph object is valid
check_graph_valid(graph)

Expand Down Expand Up @@ -114,11 +111,14 @@
# the graph
edges_added <- edges_graph_2 - edges_graph_1

# Get the name of the function
fcn_name <- get_calling_fcn()

# Update the `graph_log` df with an action
graph$graph_log <-
add_action_to_log(
graph_log = graph$graph_log,
version_id = nrow(graph$graph_log) + 1,
version_id = nrow(graph$graph_log) + 1L,
function_used = fcn_name,
time_modified = time_function_start,
duration = graph_function_duration(time_function_start),
Expand All @@ -129,8 +129,7 @@
# Perform graph actions, if any are available
if (nrow(graph$graph_actions) > 0) {
graph <-
graph %>%
trigger_graph_actions()
trigger_graph_actions(graph)

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}

# Write graph backup if the option is set
Expand Down
4 changes: 2 additions & 2 deletions R/add_full_graph.R
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Expand Up @@ -410,7 +410,7 @@ add_full_graph <- function(
graph_log <-
add_action_to_log(
graph_log = graph_log,
version_id = nrow(graph_log) + 1,
version_id = nrow(graph_log) + 1L,
function_used = fcn_name,
time_modified = time_function_start,
duration = graph_function_duration(time_function_start),
Expand Down Expand Up @@ -452,7 +452,7 @@ add_full_graph <- function(
graph_log <-
add_action_to_log(
graph_log = graph_log,
version_id = nrow(graph_log) + 1,
version_id = nrow(graph_log) + 1L,
function_used = fcn_name,
time_modified = time_function_start,
duration = graph_function_duration(time_function_start),
Expand Down
2 changes: 1 addition & 1 deletion R/add_global_graph_attrs.R
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Expand Up @@ -116,7 +116,7 @@ add_global_graph_attrs <- function(
graph$graph_log <-
add_action_to_log(
graph_log = graph$graph_log,
version_id = nrow(graph$graph_log) + 1,
version_id = nrow(graph$graph_log) + 1L,
function_used = fcn_name,
time_modified = time_function_start,
duration = graph_function_duration(time_function_start),
Expand Down
2 changes: 1 addition & 1 deletion R/add_gnm_graph.R
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Expand Up @@ -254,7 +254,7 @@ add_gnm_graph <- function(
graph_log <-
add_action_to_log(
graph_log = graph_log,
version_id = nrow(graph_log) + 1,
version_id = nrow(graph_log) + 1L,
function_used = fcn_name,
time_modified = time_function_start,
duration = graph_function_duration(time_function_start),
Expand Down
2 changes: 1 addition & 1 deletion R/add_gnp_graph.R
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Expand Up @@ -250,7 +250,7 @@ add_gnp_graph <- function(
graph_log <-
add_action_to_log(
graph_log = graph_log,
version_id = nrow(graph_log) + 1,
version_id = nrow(graph_log) + 1L,
function_used = fcn_name,
time_modified = time_function_start,
duration = graph_function_duration(time_function_start),
Expand Down
8 changes: 4 additions & 4 deletions R/add_graph_action.R
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Expand Up @@ -66,7 +66,7 @@ add_graph_action <- function(
# Create a character expression for the
# function to evaluate at every graph
# transformation step
if (length(fcn_args) == 0) {
if (length(fcn_args) == 0L) {
char_expr <-
paste0(
fcn,
Expand Down Expand Up @@ -111,8 +111,8 @@ add_graph_action <- function(
# Create a data frame row with the new graph action
new_graph_action <-
data.frame(
action_index = ifelse(nrow(graph$graph_actions) == 0, 1,
max(graph$graph_actions$action_index) + 1),
action_index = ifelse(nrow(graph$graph_actions) == 0L, 1L,
max(graph$graph_actions$action_index) + 1L),
action_name = action_name %||% NA_character_,
expression = char_expr,
stringsAsFactors = FALSE)
Expand All @@ -128,7 +128,7 @@ add_graph_action <- function(
graph$graph_log <-
add_action_to_log(
graph_log = graph$graph_log,
version_id = nrow(graph$graph_log) + 1,
version_id = nrow(graph$graph_log) + 1L,
function_used = fcn_name,
time_modified = time_function_start,
duration = graph_function_duration(time_function_start),
Expand Down
2 changes: 1 addition & 1 deletion R/add_grid_2d.R
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Expand Up @@ -272,7 +272,7 @@ add_grid_2d <- function(
graph_log <-
add_action_to_log(
graph_log = graph_log,
version_id = nrow(graph_log) + 1,
version_id = nrow(graph_log) + 1L,
function_used = fcn_name,
time_modified = time_function_start,
duration = graph_function_duration(time_function_start),
Expand Down
10 changes: 3 additions & 7 deletions R/add_grid_3d.R
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Expand Up @@ -129,12 +129,8 @@ add_grid_3d <- function(
# Create an edge data frame for the grid graph
grid_edges <-
create_edge_df(
from = grid %>%
get_edge_df() %>%
dplyr::pull(from),
to = grid %>%
get_edge_df() %>%
dplyr::pull(to),
from = get_edge_df(grid)$from,
to = get_edge_df(grid)$to,
rel = rel)

# Create the grid graph
Expand Down Expand Up @@ -273,7 +269,7 @@ add_grid_3d <- function(
graph_log <-
add_action_to_log(
graph_log = graph_log,
version_id = nrow(graph_log) + 1,
version_id = nrow(graph_log) + 1L,
function_used = fcn_name,
time_modified = time_function_start,
duration = graph_function_duration(time_function_start),
Expand Down
2 changes: 1 addition & 1 deletion R/add_growing_graph.R
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Expand Up @@ -250,7 +250,7 @@ add_growing_graph <- function(
graph_log <-
add_action_to_log(
graph_log = graph_log,
version_id = nrow(graph_log) + 1,
version_id = nrow(graph_log) + 1L,
function_used = fcn_name,
time_modified = time_function_start,
duration = graph_function_duration(time_function_start),
Expand Down
2 changes: 1 addition & 1 deletion R/add_islands_graph.R
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Expand Up @@ -243,7 +243,7 @@ add_islands_graph <- function(
graph_log <-
add_action_to_log(
graph_log = graph_log,
version_id = nrow(graph_log) + 1,
version_id = nrow(graph_log) + 1L,
function_used = fcn_name,
time_modified = time_function_start,
duration = graph_function_duration(time_function_start),
Expand Down
2 changes: 1 addition & 1 deletion R/add_n_node_clones.R
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Expand Up @@ -171,7 +171,7 @@ add_n_node_clones <- function(
graph$graph_log <-
add_action_to_log(
graph_log = graph$graph_log,
version_id = nrow(graph$graph_log) + 1,
version_id = nrow(graph$graph_log) + 1L,
function_used = fcn_name,
time_modified = time_function_start,
duration = graph_function_duration(time_function_start),
Expand Down
2 changes: 1 addition & 1 deletion R/add_n_nodes.R
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Expand Up @@ -125,7 +125,7 @@ add_n_nodes <- function(
graph$graph_log <-
add_action_to_log(
graph_log = graph$graph_log,
version_id = nrow(graph$graph_log) + 1,
version_id = nrow(graph$graph_log) + 1L,
function_used = fcn_name,
time_modified = time_function_start,
duration = graph_function_duration(time_function_start),
Expand Down
5 changes: 1 addition & 4 deletions R/add_n_nodes_ws.R
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Expand Up @@ -94,9 +94,6 @@ add_n_nodes_ws <- function(
# Get the time of function start
time_function_start <- Sys.time()

# Get the name of the function
fcn_name <- get_calling_fcn()

# Validation: Graph object is valid
check_graph_valid(graph)

Expand Down Expand Up @@ -393,7 +390,7 @@ add_n_nodes_ws <- function(
graph$graph_log <-
add_action_to_log(
graph_log = graph$graph_log,
version_id = nrow(graph$graph_log) + 1,
version_id = nrow(graph$graph_log) + 1L,
function_used = fcn_name,
time_modified = time_function_start,
duration = graph_function_duration(time_function_start),
Expand Down
8 changes: 4 additions & 4 deletions R/add_node.R
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Expand Up @@ -163,7 +163,7 @@ add_node <- function(
graph$graph_log <-
add_action_to_log(
graph_log = graph$graph_log,
version_id = nrow(graph$graph_log) + 1,
version_id = nrow(graph$graph_log) + 1L,
function_used = fcn_name,
time_modified = time_function_start,
duration = graph_function_duration(time_function_start),
Expand Down Expand Up @@ -303,7 +303,7 @@ add_node <- function(
graph$graph_log <-
add_action_to_log(
graph_log = graph$graph_log,
version_id = nrow(graph$graph_log) + 1,
version_id = nrow(graph$graph_log) + 1L,
function_used = fcn_name,
time_modified = time_function_start,
duration = graph_function_duration(time_function_start),
Expand Down Expand Up @@ -441,7 +441,7 @@ add_node <- function(
graph$graph_log <-
add_action_to_log(
graph_log = graph$graph_log,
version_id = nrow(graph$graph_log) + 1,
version_id = nrow(graph$graph_log) + 1L,
function_used = fcn_name,
time_modified = time_function_start,
duration = graph_function_duration(time_function_start),
Expand Down Expand Up @@ -595,7 +595,7 @@ add_node <- function(
graph$graph_log <-
add_action_to_log(
graph_log = graph$graph_log,
version_id = nrow(graph$graph_log) + 1,
version_id = nrow(graph$graph_log) + 1L,
function_used = fcn_name,
time_modified = time_function_start,
duration = graph_function_duration(time_function_start),
Expand Down
2 changes: 1 addition & 1 deletion R/add_node_clones_ws.R
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Expand Up @@ -246,7 +246,7 @@ add_node_clones_ws <- function(
graph$graph_log <-
add_action_to_log(
graph_log = graph$graph_log,
version_id = nrow(graph$graph_log) + 1,
version_id = nrow(graph$graph_log) + 1L,
function_used = fcn_name,
time_modified = time_function_start,
duration = graph_function_duration(time_function_start),
Expand Down
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