Preparing for CRAN release

.Rbuildignore

@@ -18,7 +18,7 @@
 .*\.doc
 .*\.pdf
 # Misc
-README[.]Rmd
+README[.](R|q)md
 ^README\_files$
 [.]travis[.]yml
 ^appveyor\.yml$
@@ -39,4 +39,5 @@ makefile
 ^netdiffuseR\.tar\.gz$
 ^\.github
 netdiffuseR\.Rcheck
-
+^\.devcontainer$
+^\.vscode$

.devcontainer/.vscode/settings.json

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

.devcontainer/Dockerfile

@@ -0,0 +1,16 @@
+FROM rocker/tidyverse:4.4.0
+
+# RUN \
+#   echo 'options(repos=c(CRAN="https://packagemanager.posit.co/cran/__linux__/bookworm/latest"))' >> ~/.Rprofile && \
+#   Rscript --vanilla -e 'getOption("repos")'
+
+# Adding R packages
+RUN install2.r Rcpp sna network networkDynamic Matrix MASS MatchIt SparseM igraph \
+  viridisLite covr testthat knitr rmarkdown ape RSiena survival RcppArmadillo
+
+RUN install2.r languageserver httpgd
+
+RUN apt-get update && apt-get install --no-install-recommends -y valgrind gdb \
+  libglpk-dev
+
+CMD ["bash"]

.devcontainer/devcontainer.json

@@ -0,0 +1,36 @@
+// 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": "epiworldR",
+	"build": {
+		"dockerfile": "Dockerfile"
+	},
+	"customizations": {
+		"vscode": {
+			"extensions": [
+				"reditorsupport.r",
+				"rdebugger.r-debugger",
+				"quarto.quarto",
+				"tianyishi.rmarkdown"
+			]
+		}
+	},
+	"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": {},
+
+	// 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/r.yml

@@ -26,6 +26,7 @@ jobs:
           - {os: macOS-latest, r: 'release'}
           - {os: ubuntu-latest, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
           - {os: ubuntu-latest, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-latest, r: 'devel', valgrind: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
@@ -70,16 +71,44 @@ jobs:
         shell: Rscript {0}
 
       - name: Check
+        if: ${{ matrix.config.valgrind != true }}
         env:
           _R_CHECK_CRAN_INCOMING_REMOTE_: false
         run: |
           options(crayon.enabled = TRUE)
           rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "error", check_dir = "check")
         shell: Rscript {0}
 
+      - name: Setup valgrind
+        if: ${{ matrix.config.valgrind == true }}
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y valgrind --no-install-recommends
+        shell: bash
+
+      - name: Check with Valgrind
+        if: ${{ matrix.config.valgrind == true }}
+        env:
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
+        run: |
+          options(crayon.enabled = TRUE)
+          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran", "--use-valgrind"), error_on = "error", check_dir = "check")
+        shell: Rscript {0}
+
       - name: Upload check results
         if: failure()
         uses: actions/upload-artifact@main
         with:
           name: ${{ runner.os }}-r${{ matrix.config.r }}-results
           path: check
+
+      - name: Build the package
+        if: ${{ matrix.config.os == 'ubuntu-latest' && (matrix.config.r == 'release' || matrix.config.r == 'devel') && (matrix.config.valgrind != true) }}
+        run: R CMD build .
+
+      - uses: actions/upload-artifact@v4
+        if: ${{ matrix.config.os == 'ubuntu-latest' && (matrix.config.r == 'release' || matrix.config.r == 'devel') && (matrix.config.valgrind != true) }}
+        with:
+          name: netdiffuseR-built-package-${{ matrix.config.os }}-${{ matrix.config.r }}
+          path: netdiffuseR_*.tar.gz
+          retention-days: 7

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: netdiffuseR
 Title: Analysis of Diffusion and Contagion Processes on Networks
-Version: 1.22.7
+Version: 1.23.0
 Authors@R: c(
   person("George", "Vega Yon", email="[email protected]", role=c("aut", "cre"),
     comment=c(ORCID = "0000-0002-3171-0844", what="Rewrite functions with Rcpp, plus new features")
@@ -51,7 +51,7 @@ Suggests:
     survival
 VignetteBuilder: knitr
 LinkingTo: Rcpp, RcppArmadillo
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Encoding: UTF-8
 URL: https://github.com/USCCANA/netdiffuseR,
  https://USCCANA.github.io/netdiffuseR/
@@ -64,6 +64,7 @@ Collate:
     'adjmat.r'
     'bass.r'
     'bootnet.r'
+    'citer_environment.R'
     'data.r'
     'diffnet-c.R'
     'diffnet-class.r'

Makefile

@@ -1,29 +1,32 @@
-VERSION:=$(shell Rscript -e 'x<-readLines("DESCRIPTION");cat(gsub(".+[:]\\s*", "", x[grepl("^Vers", x)]))')
-
-install: netdiffuseR_$(VERSION).tar.gz
-	R CMD INSTALL netdiffuseR_$(VERSION).tar.gz
-
-netdiffuseR_$(VERSION).tar.gz: */*.R inst/NEWS README.md
+help:
+	@echo "Makefile for netdiffuseR package"
+	@echo "Usage:"
+	@echo "  make install     - Install the package"
+	@echo "  make build       - Build the package source tarball"
+	@echo "  make check       - Check the package with R CMD check"
+	@echo "  make checkv      - Check the package with R CMD check using Valgrind"
+	@echo "  make clean       - Clean up the build artifacts"
+	@echo "  make docs        - Generate documentation"
+
+install: 
+	R CMD INSTALL .
+
+build:
 	R CMD build . 
 
-inst/NEWS: NEWS.md
-	Rscript -e "rmarkdown::pandoc_convert('NEWS.md', 'plain', output='inst/NEWS')"&& \
-	head -n 80 inst/NEWS
-
 README.md: README.Rmd
 	Rscript -e 'rmarkdown::render("README.Rmd")'
 
-.PHONY: check checkv clean
-
 check: netdiffuseR_$(VERSION).tar.gz
 	R CMD check --as-cran netdiffuseR_$(VERSION).tar.gz
 
 checkv: netdiffuseR_$(VERSION).tar.gz
 	R CMD check --as-cran --use-valgrind netdiffuseR_$(VERSION).tar.gz
 
 clean:
-	rm -rf netdiffuseR.Rcheck
+	rm -rf netdiffuseR.Rcheck src/*.so src/*.o
 
-man/moran.Rd: R/* src/*.cpp src/*.h
-	Rscript --vanilla -e 'roxygen2::roxygenize()'
+docs:
+	Rscript --vanilla -e 'devtools::document()'
 
+.PHONY: check checkv clean install docs

NEWS.md

@@ -1,3 +1,10 @@
+# Changes in netdiffuseR version 1.23.0 (2025-06-10)
+
+* New methods for simulating multi-diffusion models.
+
+* It is now possible to simulate diffusions with general disadoption functions.
+
+
 # Changes in netdiffuseR version 1.22.7 (2024-09-18)
 
 * Minor changes to testing (skip warnings).

R/citer_environment.R

@@ -0,0 +1,20 @@
+# file_version: f6ffa5cc103728c81c977e9101df287d
+# citer_version: 0.0.9000
+# DO NOT EDIT THIS BY HAND!
+# This document was automatically generated by the `citer` package.
+# tools::md5sum()
+
+# Citer Environment Setup
+citation_on_load <- function() {
+
+  pkg_name <- "netdiffuseR"
+
+  packageStartupMessage(
+    "Thank you for using ", pkg_name, "! ",
+    "Please consider citing it in your work.\n",
+    "You can find the citation information by running\n  citation(\"",
+    pkg_name,
+    "\")"
+  )
+
+}