Merge pull request #433 from mrc-ide/gh-actions

Move CI to github actions

.Rbuildignore

@@ -17,3 +17,6 @@
 ^docker$
 ^buildkite$
 ^images$
+^\.github$
+^figure$
+^cache$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,60 @@
+# 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]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    # Shorter timeout to prevent mac builders hanging for 6 hours!
+    timeout-minutes: 90
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - name: Install libssh
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libssh-dev
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+          extra-repositories: https://mrc-ide.r-universe.dev
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          error-on: '"error"'

.github/workflows/docker.yaml

@@ -0,0 +1,59 @@
+name: Build Docker Image
+
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+jobs:
+  docker:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - id: extract_branch
+        name: Extract branch name
+        shell: bash
+        run: echo "branch=${GITHUB_HEAD_REF:-${GITHUB_REF#refs/heads/}}" >> $GITHUB_OUTPUT
+
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Login to Docker Hub
+        uses: docker/login-action@v3
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - name: Login to GHCR (GitHub Packages)
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Build and push dev containers
+        uses: docker/build-push-action@v5
+        if: github.event_name == 'pull_request'
+        with:
+          file: "./docker/Dockerfile"
+          push: true
+          tags: |
+            mrcide/naomi:${{steps.extract_branch.outputs.branch}}
+            ghcr.io/${{github.repository}}:${{steps.extract_branch.outputs.branch}}
+
+      - name: Build and push prod containers
+        uses: docker/build-push-action@v5
+        if: github.event_name != 'pull_request'
+        with:
+          file: "./docker/Dockerfile"
+          push: true
+          tags: |
+            mrcide/naomi:latest
+            mrcide/naomi:${{steps.extract_branch.outputs.branch}}
+            ghcr.io/${{github.repository}}:latest
+            ghcr.io/${{github.repository}}:${{steps.extract_branch.outputs.branch}}

.github/workflows/pkgdown.yaml

@@ -0,0 +1,53 @@
+# 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:
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    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@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - name: Install libssh
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libssh-dev
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+          extra-repositories: https://mrc-ide.r-universe.dev/bin/linux/jammy/4.3
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        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/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.github/workflows/test-coverage.yaml

@@ -0,0 +1,57 @@
+# 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]
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Install libssh
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libssh-dev
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+          extra-repositories: https://mrc-ide.r-universe.dev
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+          )
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: naomi
 Title: Naomi Model for Subnational HIV Estimates
-Version: 2.9.23
+Version: 2.9.24
 Authors@R:
     person(given = "Jeff",
            family = "Eaton",
@@ -13,35 +13,36 @@ License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Additional_repositories:
-    https://mrc-ide.r-universe.dev
+    https://mrc-ide.r-universe.dev,
+    https://duckdb.r-universe.dev
 Imports:
     DBI,
-    Matrix,
+    Matrix (>= 1.6.5),
     R6,
     TMB,
     assertthat,
     brio,
     data.tree,
     dplyr (>= 1.1.0),
-    duckdb (== 0.9.1),
+    duckdb (>= 0.10.0),
     eppasm (>= 0.7.1),
+    gt,
     first90 (>= 1.6.1),
     forcats,
     fs,
     ggplot2,
-    gt,
-    here,
-    knitr,
     magrittr,
+    methods,
     mvtnorm,
     naomi.options (>= 1.2.0),
     openxlsx,
     plotly,
     prettyunits,
     qs,
     readr (>= 2.0.1),
+    rlang,
     rmarkdown,
     sf,
     spdep (>= 1.1),
@@ -59,27 +60,23 @@ Suggests:
     DiagrammeR,
     covr,
     datamodelr,
+    here,
+    knitr,
     lubridate,
     mockery,
     mockr,
     readxl,
     rvest,
     scales,
     testthat (>= 2.1.0),
+    tibble,
     tidyverse,
     viridis
 VignetteBuilder: knitr
 LinkingTo:
     RcppEigen,
     TMB
 Remotes:
-    bergant/datamodelr,
-    mrc-ide/eppasm,
-    first90=mrc-ide/first90release,
-    reside-ic/traduire,
-    mrc-ide/naomi.options,
-    mrc-ide/mockr,
-    mrc-ide/testthat.buildkite,
-    duckdb/[email protected]
+    bergant/datamodelr
 Config/testthat/edition: 3
 Config/testthat/parallel: true

Makefile

@@ -38,7 +38,7 @@ vignettes/model-workflow.Rmd: vignettes_src/model-workflow.Rmd
 
 vignettes/data-model.Rmd: vignettes_src/data-model.Rmd
 	cp $^ $@
-	mkdir vignettes/figure
+	mkdir -p vignettes/figure
 	./vignettes/script/create_data_model.R
 
 vignettes/hintr-example.Rmd: vignettes_src/hintr-example.R
@@ -51,6 +51,7 @@ vignettes:
 	rm -rf vignettes/figure
 	rm -rf vignettes_src/outputs
 	rm -f vignettes/data-model.Rmd
+	rm -f vignettes/hintr-example.Rmd
 	rm -f vignettes/model-workflow.Rmd
 	rm -f vignettes_src/model-workflow.Rmd
 	make vignettes_install

NAMESPACE

@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(print,naomi_areas)
 export("%>%")
 export(add_output_labels)
 export(age_bar_plotly)

NEWS.md

@@ -1,3 +1,9 @@
+# naomi 2.9.24
+
+* Migrate to github actions
+* Fix R CMD check notes
+* Unpin duckdb version
+
 # naomi 2.9.23
 
 * Update Datim UIDs for Ethiopia 2024 boundary division.

R/areas.R

@@ -160,8 +160,9 @@ create_areas <- function(levels = NULL, hierarchy = NULL, boundaries = NULL,
   v
 }
 
-print.naomi_areas <- function(areas) {
-  print(areas$tree, "area_name")
+#' @export
+print.naomi_areas <- function(x, ...) {
+  print(x$tree, "area_name")
 }
 
 

R/calibrate.R

@@ -496,7 +496,7 @@ calibrate_outputs <- function(output,
                   .expand(naomi_mf$calendar_quarter3, "unaware_plhiv_attend"),
                   .expand(naomi_mf$calendar_quarter1, "aware_plhiv_attend"),
                   .expand(naomi_mf$calendar_quarter2, "aware_plhiv_attend"),
-                  .expand(naomi_mf$calendar_quarter3, "aware_plhiv_attend"),                  
+                  .expand(naomi_mf$calendar_quarter3, "aware_plhiv_attend"),
                   .expand(naomi_mf$calendar_quarter1, "infections"),
                   .expand(naomi_mf$calendar_quarter2, "infections"),
                   .expand(naomi_mf$calendar_quarter3, "infections"),

R/car.R

@@ -42,7 +42,7 @@ create_edge_list <- function(adj_matrix) {
   w <- adj_matrix
 
   ## convert W to a sparse matrix if not already sparse.
-  if(!is(w, "sparseMatrix"))
+  if(!methods::is(w, "sparseMatrix"))
     w <- Matrix(w, sparse = TRUE)
 
   w[upper.tri(w)] <- 0