Bug fixes, remove drop_unused_query_nodes (breaking change)

[oneilsh]

Closes issues #72 #70 #69 #58

[Copilot]

Pull Request Overview

This PR removes the deprecated drop_unused_query_nodes parameter from the expand() family of functions (breaking change), updates all related documentation, tests, and namespace entries, and introduces fixes to preserve the active table context and prevent an infinite loop in the Neo4j engine expansion.

• Remove drop_unused_query_nodes from R function signatures, man pages, vignettes, and tests
• Add active_tbl capture/restore around tidygraph operations to maintain the active context
• Fix Neo4j conditional query grouping to avoid pagination infinite loops

Reviewed Changes

Copilot reviewed 18 out of 18 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
vignettes/monarchr.Rmd	Removed documentation block describing drop_unused_query_nodes
tests/testthat/test-expand.file_engine.R	Deleted tests referencing drop_unused_query_nodes
man/expand_n.Rd	Dropped parameter docs and updated @return tag
man/expand.Rd	Removed drop_unused_query_nodes from Rd entries
R/transitive_reduction.R	Capture and restore active table with active_tbl
R/transitive_closure.R	Short-circuit when no matching edges and restore active_tbl
R/kg_edge_weights.R	Capture and restore active_tbl around mutate calls
R/graph_semsim.R	Capture and restore active_tbl around edge mutation
R/graph_centrality.R	Capture and restore active_tbl around node mutation
R/fetch_nodes.neo4j_engine.R	Wrap conditional in parentheses to fix infinite loop
R/expand_neo4j_engine.R	Removed drop_unused_query_nodes logic
R/expand_n.R	Removed parameter and check_len calls for drop_unused_query_nodes
R/expand_file_engine.R	Removed drop_unused_query_nodes argument and branches
R/expand.tbl_kgx.R	Capture/restore active_tbl when dispatching to engines
R/expand.R	Dropped drop_unused_query_nodes from generic signature
NEWS.md	Notes breaking change and Neo4j bugfix
NAMESPACE	Imported active() from tidygraph
DESCRIPTION	Bumped package version to 2.0

Comments suppressed due to low confidence (2)

man/expand_n.Rd:14

• The @return tag is split across two lines, which can break Rd rendering. Merge into one line, e.g., #' @return A tbl_kgx() graph.

#' @return

R/fetch_nodes.neo4j_engine.R:66

• You’ve fixed the infinite-loop bug by grouping the WHERE clause in parentheses; add a unit test for the Neo4j pagination behavior to prevent future regressions.

query <- paste0("MATCH (n) WHERE (", generate_cypher_conditionals(...), ")")