Preparing for CRAN release

.devcontainer/Containerfile

@@ -1,4 +1,4 @@
-FROM rocker/tidyverse:4.5.1
+FROM ghcr.io/rocker-org/devcontainer/tidyverse:4.5
 
 # RUN \
 #   echo 'options(repos=c(CRAN="https://packagemanager.posit.co/cran/__linux__/bookworm/latest"))' >> ~/.Rprofile && \

.devcontainer/devcontainer.json

@@ -11,7 +11,8 @@
 				"reditorsupport.r",
 				"rdebugger.r-debugger",
 				"quarto.quarto",
-				"tianyishi.rmarkdown"
+				"tianyishi.rmarkdown",
+				"github.vscode-github-actions"
 			]
 		}
 	},

.github/workflows/copilot-setup-steps.yml

@@ -0,0 +1,42 @@
+name: "Copilot Setup Steps"
+
+# Automatically run the setup steps when they are changed to allow for easy validation, and
+# allow manual testing through the repository's "Actions" tab
+on:
+  workflow_dispatch:
+  push:
+    paths:
+      - .github/workflows/copilot-setup-steps.yml
+  pull_request:
+    paths:
+      - .github/workflows/copilot-setup-steps.yml
+
+jobs:
+  # The job MUST be called `copilot-setup-steps` or it will not be picked up by Copilot.
+  copilot-setup-steps:
+    runs-on: ubuntu-latest
+
+    # Set the permissions to the lowest permissions possible needed for your steps.
+    # Copilot will be given its own token for its operations.
+    permissions:
+      # If you want to clone the repository as part of your setup steps, for example to install dependencies, you'll need the `contents: read` permission. If you don't clone the repository in your setup steps, Copilot will do this for you automatically after the steps complete.
+      contents: read
+
+    # You can define any steps you want, and they will run before the agent starts.
+    # If you do not check out your code, Copilot will do this for you.
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v6
+
+      - name: Set up R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: 'release'
+
+      - name: Install dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: |
+            any::rcmdcheck
+            any::tinytest
+          needs: check

.github/workflows/coverage.yaml

@@ -0,0 +1,35 @@
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: Coverage
+
+jobs:
+  coverage:
+    runs-on: ubuntu-latest
+    name: Coverage
+
+    steps:
+      - uses: actions/checkout@v5
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2.9.0
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: |
+            any::covr
+          needs: check
+
+      - name: Running coverage
+        run: |
+          # Run coverage
+          covr::codecov(
+            token = Sys.getenv("CODECOV_TOKEN")
+            )
+        shell: Rscript {0}
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/pkgdown.yaml

@@ -11,16 +11,27 @@ on:
 
 name: pkgdown
 
+# 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:
-  pkgdown:
+  build:
     runs-on: ubuntu-latest
-    # Only restrict concurrency for non-PR jobs
-    concurrency:
-      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -39,10 +50,39 @@ jobs:
         run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}
 
-      - name: Deploy to GitHub pages 🚀
-        if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@v4.4.1
+      # 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@v3
         with:
-          clean: false
-          branch: gh-pages
-          folder: 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@v4
+        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@v4

.github/workflows/r.yml

@@ -13,6 +13,28 @@ on:
 name: R-CMD-check
 
 jobs:
+  R-binary:
+    runs-on: ubuntu-latest
+
+    name: R binary version
+    steps:
+      - uses: actions/checkout@v5
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+
+      - name: Build package
+        run: R CMD build .
+
+      - name: Upload artifact
+        uses: actions/upload-artifact@v6
+        with:
+          name: defm-ubuntu-tar-gz
+          path: defm_*.tar.gz
+
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
 
@@ -39,7 +61,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
 
       - uses: r-lib/actions/setup-pandoc@v2
 

DESCRIPTION

@@ -9,7 +9,11 @@ Authors@R: c(
         "Department of Veterans Affairs - Rehabilitation, Research, and Development Service",
         role = "fnd",
         comment = "Award/W81XWH-18-PH/TBIRP-LIMBIC under Award No. I01 RX003443"
-        ))
+        ),
+    person(
+        "U.S. Army Medical Research Acquisition Activity", role = "fnd",
+        comment = "ORION project, Award #W81XWH1910615")
+    )
 Description: Multi-binary response models are a class of models that allow for the estimation of multiple binary outcomes simultaneously. This package provides functions to estimate and simulate these models using the Discrete Exponential-Family Models [DEFM] framework. In it, we implement the models described in Vega Yon, Valente, and Pugh (2023) <doi:10.48550/arXiv.2211.00627>. DEFMs include Exponential-Family Random Graph Models [ERGMs], which characterize graphs using sufficient statistics, which is also the core of DEFMs. Using sufficient statistics, we can describe the data through meaningful motifs, for example, transitions between different states, joint distribution of the outcomes, etc. 
 URL: https://github.com/UofUEpiBio/defm,
         https://uofuepibio.github.io/defm/
@@ -28,5 +32,3 @@ Depends:
     stats4
 Suggests: 
     texreg, tinytest, barry
-Remotes:
-    USCBiostats/barryr

Makefile

@@ -9,7 +9,6 @@ help:
 	@echo "  make debug        Install package with debug flags"
 	@echo "  make clean        Clean up generated files"
 	@echo "  make README.md    Generate README.md from README.Rmd"
-	@echo "  make inst/NEWS    Generate inst/NEWS from NEWS.md"
 	@echo "  make docker-run   Run a docker container with R and barry installed"
 	@echo "  make docker-check All checks inside a docker container"
 
@@ -33,15 +32,8 @@ clean:
 	Rscript --vanilla -e 'devtools::clean_dll()'; \
 		rm -rf *.Rcmdcheck 
 
-README.md: README.Rmd
-	Rscript --vanilla -e 'rmarkdown::render("README.Rmd")'
-
 .PHONY: build update clean
 
-inst/NEWS: NEWS.md
-	Rscript -e "rmarkdown::pandoc_convert('NEWS.md', 'plain', output='inst/NEWS')" && \
-		head -n 80 inst/NEWS
-
 
 docker-run:
 	docker run --rm -ti -v $(PWD):/mnt -w/mnt gvegayon/defm:latest bash
@@ -59,3 +51,6 @@ docker-check-all:
 	RD CMD build . && \
 		DEFM_CONFIG="-DBARRY_DEBUG" _R_CHECK_FORCE_SUGGESTS_=false \
 		RD CMD check defm_*.tar.gz
+
+README.md: README.qmd
+	quarto render README.qmd

NEWS.md

@@ -1,3 +1,10 @@
+# defm 0.2.1.0
+
+* Returning to CRAN.
+
+* The `defm` now uses the same versioning as the [`barry`](https://github.com/USCbiostats/barry) library (first three numbers). The last number is the patch.
+
+
 # defm 0.1-1
 
 * Added a `NEWS.md` file to track changes to the package.