Merge branch 'master' into mrc-5074

.Rbuildignore

@@ -15,3 +15,4 @@
 ^tests/testthat/testdata/sensitive$
 ^buildkite$
 ^naomi$
+^\.github$

.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: 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
+
+      - 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
+
+      - name: Start Redis
+        uses: shogo82148/actions-setup-redis@v1
+        with:
+          redis-version: "5.x"
+
+      - name: Build test data
+        run: Rscript ./scripts/build_test_data
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          error-on: '"error"'

.github/workflows/R-integration-test.yaml

@@ -0,0 +1,63 @@
+# 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: Integration test
+
+jobs:
+  integration:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {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
+
+      - 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::devtools
+
+      - name: Start Redis
+        uses: shogo82148/actions-setup-redis@v1
+        with:
+          redis-version: "5.x"
+
+      - name: Build test data
+        run: |
+          ./scripts/build_test_data
+
+      - name: Install hintr
+        run: |
+          Rscript -e 'devtools::install()'
+
+      - name: Run integration tests
+        run: |
+          ./scripts/test_integration

.github/workflows/docker.yaml

@@ -0,0 +1,66 @@
+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 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: Clone Naomi
+        uses: actions/checkout@master
+        with:
+          repository: mrc-ide/naomi
+          ## ${{ github.token }} is scoped to the current repository, so we
+          ## need to provide our own PAT
+          token: ${{ secrets.NAOMI_GH_PAT }}
+          path: naomi
+
+      - name: Build and push dev containers
+        uses: docker/build-push-action@v5
+        if: github.event_name == 'pull_request'
+        with:
+          context: .
+          file: "./docker/Dockerfile"
+          push: true
+          tags: |
+            mrcide/hintr:${{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/hintr:latest
+            mrcide/hintr:${{steps.extract_branch.outputs.branch}}
+            ghcr.io/${{github.repository}}:latest
+            ghcr.io/${{github.repository}}:${{steps.extract_branch.outputs.branch}}

.github/workflows/pkgdown.yaml

@@ -0,0 +1,47 @@
+# 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
+
+      - 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 +1,60 @@
+# 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: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - 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: Start Redis
+        uses: shogo82148/actions-setup-redis@v1
+        with:
+          redis-version: "5.x"
+
+      - name: Build test data
+        run: |
+          ./scripts/build_test_data
+
+      - 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

@@ -12,7 +12,7 @@ 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 
 Imports:
     data.table,
@@ -22,9 +22,10 @@ Imports:
     glue,
     ids,
     jsonlite (>= 1.2.2),
-    naomi (>= 2.9.23),
+    naomi (>= 2.9.24),
     naomi.options (>= 1.1.0),
     porcelain (>= 0.1.8),
+    qs,
     R6,
     readxl,
     rrq (>= 0.7.0),
@@ -36,19 +37,19 @@ Imports:
     zip
 Suggests:
     callr,
+    cli,
     covr,
     httr,
     jsonvalidate,
-    mockr,
     mockery,
+    pkgload,
     ps,
     redux,
     ssh,
     testthat (>= 2.1.0),
+    tidyselect,
     withr
 Remotes:
-    mrc-ide/geojsonio,
-    mrc-ide/rrq,
-    mrc-ide/mockr
+    mrc-ide/naomi,
 Config/testthat/edition: 3
 Config/testthat/parallel: true

R/adr_metadata.R

@@ -1,22 +1,15 @@
 adr_metadata <- function(queue) {
   function(id) {
     tryCatch({
-      res <- queue$result(id)
-      if (is_error(res) || is.null(res$path)) {
-        msg <- res$message
-        if (is.null(msg)) {
-          msg <- t_("FAILED_ADR_METADATA")
-        }
-        hintr_error(msg, "OUTPUT_GENERATION_FAILED")
-      }
+      res <- get_download_result(queue, id, "FAILED_ADR_METADATA")
       list(type = scalar(res$metadata$type),
            description = scalar(res$metadata$description))
     },
     error = function(e) {
       if (is_porcelain_error(e)) {
         stop(e)
       } else {
-        hintr_error(e$message, "FAILED_TO_RETRIEVE_RESULT")
+        hintr_error(api_error_msg(e), "FAILED_TO_RETRIEVE_RESULT")
       }
     })
   }