Merge pull request #10 from bschilder/main

Add rworkflows CI + Get closer to passing rcmdchecks

.Rbuildignore

@@ -3,3 +3,12 @@
 ^LICENSE\.md$
 ^meta$
 ^docs$
+
+^\.lintr$
+^\.github$
+^\.vscode$
+
+## For GitHub Actions Windows runner
+node_modules$
+package-lock\.json$
+package\.json$

.github/workflows/rworkflows.yml

@@ -0,0 +1,57 @@
+name: rworkflows
+'on':
+  push:
+    branches:
+    - master
+    - main
+    - devel
+    - RELEASE_**
+  pull_request:
+    branches:
+    - master
+    - main
+    - devel
+    - RELEASE_**
+jobs:
+  rworkflows:
+    permissions: write-all
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+    container: ${{ matrix.config.cont }}
+    strategy:
+      fail-fast: ${{ false }}
+      matrix:
+        config:
+        - os: ubuntu-latest
+          bioc: devel
+          r: auto
+          cont: ghcr.io/bioconductor/bioconductor_docker:devel
+          rspm: ~
+        - os: macOS-latest
+          bioc: release
+          r: auto
+          cont: ~
+          rspm: ~
+        - os: windows-latest
+          bioc: release
+          r: auto
+          cont: ~
+          rspm: ~
+    steps:
+    - uses: neurogenomics/rworkflows@master
+      with:
+        run_bioccheck: ${{ false }}
+        run_rcmdcheck: ${{ true }}
+        as_cran: ${{ true }}
+        run_vignettes: ${{ true }}
+        has_testthat: ${{ true }}
+        run_covr: ${{ true }}
+        run_pkgdown: ${{ true }}
+        has_runit: ${{ false }}
+        has_latex: ${{ false }}
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run_docker: ${{ true }}
+        DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }}
+        runner_os: ${{ runner.os }}
+        cache_version: cache-v1
+        docker_registry: ghcr.io

DESCRIPTION

@@ -1,24 +1,35 @@
 Package: monarchr
 Type: Package
-Title: What the Package Does (Title Case)
-Version: 0.2.0
-Author: Who wrote it
-Maintainer: The package maintainer <[email protected]>
-Description: More about what it does (maybe more than one line)
-    Use four spaces when indenting paragraphs within the Description.
+Title: Monarch Knowledge Graph Queries
+Description: R package for easy access, manipulation, and analysis of
+		Monarch KG data Resources.
+Version: 0.2.1
+Authors@R:
+    c(
+  person(given = "Shawn",
+           family = "O'Neil",
+           role = c("aut","cre"),
+           email = "[email protected]",
+           comment = c(ORCID = "0000-0001-6220-7080")),
+    person(given = "Brian",
+           family = "Schilder",
+           role = c("aut","ctb"),
+           email = "[email protected]",
+           comment = c(ORCID = "0000-0001-5949-2191"))
+     ) 
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
-Suggests: 
-    testthat (>= 3.0.0)
 Config/testthat/edition: 3
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
+VignetteBuilder: knitr
 Imports: 
     assertthat,
     colorDF,
     dotenv,
     dplyr,
+    tidyr,
     ggiraph,
     ggraph,
     httr,
@@ -33,3 +44,6 @@ Imports:
     tidygraph,
     vcr,
     yaml
+Suggests: 
+    testthat (>= 3.0.0),
+    knitr

NAMESPACE

@@ -3,6 +3,7 @@
 S3method(explode,tbl_kgx)
 S3method(select_nodes,monarch_kg)
 export(cypher_query)
+export(cypher_query_df)
 export(edges)
 export(fetch_edges)
 export(monarch_search)

NEWS.md

@@ -0,0 +1,15 @@
+# monarchr 0.2.1
+
+* Add rworkflows GHA for automated checking, site building, and Docker container creation.
+* Update *.Rbuildignore*.
+* Add NEWS file.
+* Add Title, Description, and Authors to *DESCRIPTION*.
+	- Hope you don't mind me adding our names here @oneilsh, I anticipate making lots of contributions!
+* Add `tidyr` Import to *DESCRIPTION*.
+* Add vignettes header info.
+* Fix `edges` docs by adding title.
+* Add `VignetteBuilder: knitr` to *DESCRIPTION*.
+* Fix `cypher_query` example by adding `ids`
+* Fix `cypher_query_df` example by adding `ids`
+* Export `cypher_query_df`
+* Get `monarchR` closer to passing rcmdcheck (methods for edges/nodes not yet being recognized)

R/cypher_query.R

@@ -63,7 +63,7 @@ stitch_vectors <- function(x) {
 #' query <- "MATCH (s) -[p]- (o) return s, p, o LIMIT 2"
 #' parameters <- NULL
 #' g <- cypher_query(query, parameters)
-#'
+#' ids <- c("MONDO:0007525", "MONDO:0020066", "MONDO:0034021")
 #' query = "MATCH (n) WHERE n.id IN $ids RETURN n"
 #' parameters = list(ids = ids)
 #' g <- cypher_query(query, parameters)
@@ -162,9 +162,11 @@ cypher_query <- function(query, parameters = NULL, ...) {
 #' @param parameters A list of parameters for the Cypher query. Default is an empty list.
 #' @param ... Additional arguments passed to the function.
 #' @return A data frame containing the result of the Cypher query.
+#' @export
 #' @examples
 #' query <- "MATCH (n) RETURN n LIMIT 10"
-#' parameters <- list()
+#' ids <- c("MONDO:0007525", "MONDO:0020066", "MONDO:0034021")
+#' parameters <- list(ids = ids)
 #' result <- cypher_query_df(query, parameters)
 #' @importFrom neo2R cypher
 cypher_query_df <- function(query, parameters = list(), ...) {

R/utils.R

@@ -1,3 +1,5 @@
+#' Get tbl_kgx graph nodes table.
+#'
 #' @importFrom tidygraph as_tibble
 #' @examples
 #' g <- monarch_search("fanconi anemia", limit = 1)
@@ -6,6 +8,8 @@ nodes.tbl_kgx <- function(x, ...) {
   tidygraph::as_tibble(x, active = "nodes")
 }
 
+#' Get tbl_kgx graph edges table.
+#'
 #' @importFrom tidygraph as_tibble
 #' @examples
 #' g <- monarch_search("fanconi anemia", limit = 1)
@@ -29,6 +33,9 @@ nodes <- function(x, ...) {
   UseMethod("nodes")
 }
 
+#' Get graph edges table.
+#'
+#' @return A tibble with the edges of the graph
 #' @importFrom tidygraph as_tibble
 #' @export
 #' @examples

vignettes/Basics.Rmd

@@ -1,8 +1,13 @@
 ---
 title: "MonarchR Basics"
 author: "Shawn T O'Neil"
-date: "2024-02-17"
-output: html_document
+date: "<h4>Vignette updated: <i>`r format( Sys.Date(), '%b-%d-%Y')`</i></h4>"
+output:
+  rmarkdown::html_document
+vignette: >
+  %\VignetteIndexEntry{Basics}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
 ---
 
 ```{r setup, include=FALSE}
@@ -243,5 +248,5 @@ eds_search %>%                                                 # starting with a
 	explode() %>%                                                # split into a list of 5 single-node graphs
 	lapply(fetch_edges) %>%                                      # fetch neighborhood edges for each graph 
 	lapply(nodes) %>%                                            # extract nodes df from each graph
-	lapply(function(nodes_df) {filter(nodes_df, is.na(source))}) # remove original seached nodes from each df
+	lapply(function(nodes_df) {filter(nodes_df, is.na(source))}) # remove original searched nodes from each df
 ```