Fix edge.width not applied to drawn line widths in nplot

.Rbuildignore

@@ -14,3 +14,6 @@ netplot\._.*\.tar\.gz
 ^Rplots\.pdf$
 ^doc$
 ^Meta$
+^AGENTS\.md$
+^\.devcontainer$
+^\.vscode$

.devcontainer/.vscode/settings.json

@@ -0,0 +1,4 @@
+{
+    "r.plot.useHttpgd": true,
+    "r.alwaysUseActiveTerminal": true
+}

.devcontainer/Containerfile

@@ -0,0 +1,19 @@
+FROM ghcr.io/rocker-org/devcontainer/r-ver:4.5
+
+# Architecture-specific variable (built in Docker BuildKit)
+ARG TARGETARCH
+
+# Install quarto-cli and the orange-book extension
+RUN wget https://github.com/quarto-dev/quarto-cli/releases/download/v1.9.35/quarto-1.9.35-linux-${TARGETARCH}.deb && \
+    dpkg -i quarto-1.9.35-linux-${TARGETARCH}.deb && \
+    rm quarto-1.9.35-linux-${TARGETARCH}.deb
+
+# Adding R packages
+RUN install2.r --error knitr rmarkdown markdown igraphdata intergraph \
+  ggraph gridGraphics ggplot2 gridExtra gridBase magrittr tinytest \
+  sna igraph network
+
+RUN apt-get update && apt-get install --no-install-recommends -y \
+  libglpk-dev
+
+CMD ["bash"]

.devcontainer/devcontainer-lock.json

@@ -0,0 +1,9 @@
+{
+  "features": {
+    "ghcr.io/devcontainers/features/github-cli:1": {
+      "version": "1.1.0",
+      "resolved": "ghcr.io/devcontainers/features/github-cli@sha256:d22f50b70ed75339b4eed1ba9ecde3a1791f90e88d37936517e3bace0bbad671",
+      "integrity": "sha256:d22f50b70ed75339b4eed1ba9ecde3a1791f90e88d37936517e3bace0bbad671"
+    }
+  }
+}

.devcontainer/devcontainer.json

@@ -0,0 +1,42 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the
+// README at: https://github.com/devcontainers/templates/tree/main/src/cpp
+{
+	"name": "netplot",
+	"build": {
+		"dockerfile": "Containerfile"
+	},
+	"customizations": {
+		"vscode": {
+			"extensions": [
+				"reditorsupport.r",
+				"rdebugger.r-debugger",
+				"quarto.quarto",
+				"tianyishi.rmarkdown",
+				"github.vscode-github-actions",
+				"ms-vscode.live-server"
+			]
+		}
+	},
+	"mounts": [
+        // Mount the .vscode configuration into the container
+        "source=${localWorkspaceFolder}/.devcontainer/.vscode,target=/workspaces/${localWorkspaceFolderBasename}/.vscode,type=bind,consistency=cached"
+    ],
+	// Features to add to the dev container. More info: https://containers.dev/features.
+	"features": {
+		"ghcr.io/devcontainers/features/github-cli:1": {
+			"version": "1.1.0"
+		}
+	},
+
+	// Use 'forwardPorts' to make a list of ports inside the container available locally.
+	// "forwardPorts": [],
+
+	// Use 'postCreateCommand' to run commands after the container is created.
+	// "postCreateCommand": "gcc -v",
+
+	// Configure tool-specific properties.
+	// "customizations": {},
+
+	// Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
+	"remoteUser": "root"
+}

.github/workflows/ci.yml

@@ -36,7 +36,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v7
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -68,8 +68,14 @@ jobs:
           check-dir: '"check"'
           error-on: '"warning"'
 
+      # Building the tar.gz file for ubuntu-latest and release R version
+      - name: Build package
+        if: ${{ matrix.config.os == 'ubuntu-latest' && matrix.config.r == 'release' }}
+        run: |
+          R CMD build .
+
       # Upload the built package as an artifact
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v7
         if: ${{ matrix.config.os == 'ubuntu-latest' && matrix.config.r == 'release' }}
         with:
           name: ${{ matrix.config.os }}-pkg

.github/workflows/website.yml

@@ -1,26 +1,86 @@
-name: netplot website
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
 
-on: [push, pull_request]
+name: pkgdown
 
-env:
-  cntr: usccana/netplot:release
+# Sets permissions of the GITHUB_TOKEN
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+  pull-requests: write
+  actions: read
+
+# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
+# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
 
 jobs:
   build:
-    runs-on: Ubuntu-latest
-
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v6
+
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - name: Container
-        run: docker pull ${cntr}
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
 
-      - name: Building website
-        run: docker run --rm -i -v ${PWD}:/home/mnt -w /home/mnt ${cntr} Rscript -e 'system("R CMD INSTALL .");pkgdown::build_site(install=FALSE)'
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
 
-      - name: Deploy
-        uses: peaceiris/actions-gh-pages@v3
+      # Upload artifact for GitHub Pages deployment (only for pushes to main/master)
+      - name: Upload Pages artifact
+        if: github.event_name != 'pull_request' && (github.ref == 'refs/heads/main' || github.ref == 'refs/heads/master')
+        uses: actions/upload-pages-artifact@v5
         with:
-          github_token: ${{ secrets.GITHUB_TOKEN }}
-          publish_dir: ./docs
+          path: docs
 
+      # Upload artifact for PR preview (only for pull requests)
+      - name: Upload PR artifact
+        if: github.event_name == 'pull_request'
+        uses: actions/upload-artifact@v7
+        with:
+          name: pkgdown-site
+          path: docs
+
+      # Post comment with link to artifact on PRs
+      - name: Post artifact link to PR
+        if: github.event_name == 'pull_request'
+        uses: CDCgov/cfa-actions/post-artifact@v1.2.0
+        with:
+          artifact-name: pkgdown-site
+          gh-token: ${{ secrets.GITHUB_TOKEN }}
+          message: 'Thank you for your contribution @${{ github.actor }} :rocket:! The pkgdown site preview is ready for review :point_right: [Download here]({ artifact-url }) :point_left:!'
+
+  # Deployment job - only runs on pushes to main/master
+  deploy:
+    if: github.event_name != 'pull_request' && (github.ref == 'refs/heads/main' || github.ref == 'refs/heads/master')
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v5

AGENTS.md

@@ -0,0 +1,11 @@
+# What is this project about
+
+This is an R package that uses the `grid` package to create network plots. The package is focused on aesthetics and tries to provide an interface that has a lower footprint in dependencies than other packages, leveraging existing base R packages.
+
+## Development workflow and preferences
+
+- We follow the tinyverse style for code (so minimal dependencies, but still using `roxygen2` for documentation).
+
+- For testing the package, we use `tinytest`.
+
+- For checking the R package, we use `devtools::check()`, and for documenting we call `devtools::document()`.

DESCRIPTION

@@ -17,7 +17,7 @@ Depends:
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.3
 Roxygen: list(markdown = TRUE)
 Imports: 
     graphics,

Makefile

@@ -1,50 +1,16 @@
-VERSION:=$(shell Rscript -e 'x<-readLines("DESCRIPTION");cat(gsub(".+[:]\\s*", "", x[grepl("^Vers", x)]))')
-PKGNAME:=$(shell Rscript -e 'x<-readLines("DESCRIPTION");cat(gsub(".+[:]\\s*", "", x[grepl("^Package", x)]))')
+README.md: README.qmd
+	quarto render README.qmd
 
-install: build
-	cd ../ && \
-		R CMD INSTALL $(PKGNAME)_$(VERSION).tar.gz
-
-$(PKGNAME)_$(VERSION).tar.gz: 
-	cd ../ && R CMD build $(PKGNAME)/
+.PHONY: build check install checkfull checkv clean man docker checkd
 
-build: $(PKGNAME)_$(VERSION).tar.gz
+build: docs
+	R CMD build .
 
-inst/NEWS: NEWS.md
-	Rscript -e "rmarkdown::pandoc_convert('NEWS.md', 'plain', output='inst/NEWS')"&& \
-	head -n 80 inst/NEWS
+check: docs
+	Rscript -e "devtools::check()"
 
-README.md: README.Rmd
-	Rscript -e 'rmarkdown::render("README.Rmd")'
+install: docs
+	Rscript -e "devtools::install()"
 
-.PHONY: checfull checkv clean
-
-check: $(PKGNAME)_$(VERSION).tar.gz
-	R CMD check --no-vignettes --no-manual $(PKGNAME)_$(VERSION).tar.gz
-
-checkfull: R/*.R inst/NEWS README.md
-	R CMD build . \&& 
-		R CMD check --as-cran $(PKGNAME)_$(VERSION).tar.gz
-
-checkv: $(PKGNAME)_$(VERSION).tar.gz
-	R CMD check --as-cran --use-valgrind $(PKGNAME)_$(VERSION).tar.gz
-
-clean:
-	cd ../ && \
-		rm -rf $(PKGNAME).Rcheck $(PKGNAME)_$(VERSION).tar.gz
-
-.PHONY: man docker
-man: R/* 
-	Rscript --vanilla -e 'roxygen2::roxygenize()'
-
-docker:
-	docker run -v$(pwd):/pkg/ -w/pkg --rm -i uscbiostats/fmcmc:latest make check
-
-checkd:
-	apt update && \
-		tlmgr install amsmath && \
-		install2.r igraph gridGraphics gridBase gridExtra magrittr tinytest sna \
-		ggraph rmarkdown knitr intergraph igraphdata pkgdown markdown && \
-		apt install libglpk-dev --no-install-recommends -y && \
-		R CMD build . && \
-		R CMD check --no-manual $(PKGNAME)_$(VERSION).tar.gz
+docs:
+	Rscript -e "devtools::document()"

NEWS.md

@@ -1,5 +1,21 @@
 # netplot 0.3-0
 
+* `nplot.network()` now uses the `"weight"` edge attribute for `edge.width`
+  by default (like `nplot.igraph()` already did), so edge widths reflect edge
+  weights instead of being drawn uniformly. `edge.width` values are also
+  explicitly re-applied to each edge grob after color post-processing to keep
+  the drawn line widths robust. Closes #17.
+
+* `edge.width.range`, `vertex.size.range`, and `vertex.label.range` now accept
+  `NULL` to suppress scaling and use the supplied values as-is.
+
+* Fixed `vertex.rot`, which was truncated to an integer and so ignored
+  fractional (radian) rotations; the named `"square"` shape orientation was
+  corrected as well.
+
+* `edge.line.lty` is now validated to be length 1 or one value per plotted
+  edge, and is subset correctly when `sample.edges` drops edges.
+
 * Invalid arguments passed to `nplot()` now raise an error.
 
 * Figures with legends are not drawn twice.

R/geometry.R

@@ -2,13 +2,17 @@
 #' @param size Numeric vector. Size of the node (radious).
 #' @param rel Numeric vector of length 3. Relative size for the minimum and maximum
 #' of the plot, and curvature of the scale. The third number is used as `size^rel[3]`.
+#' If `NULL`, scaling is suppressed.
 #'
 #' @details
 #' This function is to be called after [plot.new], as it takes the parameter `usr`
 #' from the
 #' @noRd
 rescale_size <- function(size, rel=c(.01, .05, 1)) {
 
+  if (is.null(rel))
+    return(size)
+
   # Checking the rel size
   if (length(rel) == 2)
     rel <- c(rel, 1)
@@ -204,4 +208,3 @@ map_attribute_to_shape <- function(x) {
   names(sides_lookup)[as.numeric(factor(x))]
 
 }
-