vimc · richfitz · Jul 14, 2025 · Jul 11, 2025 · Jul 11, 2025 · Jul 11, 2025
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -1,16 +1,13 @@
-# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
-# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+# 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
+    branches: [main, master]
   pull_request:
-    branches:
-      - main
-      - master
 
-name: R-CMD-check
+name: R-CMD-check.yaml
+
+permissions: read-all
 
 jobs:
   R-CMD-check:
@@ -22,73 +19,45 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {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'}
 
     env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      ORDERLYWEB_TEST_TOKEN: ${{ secrets.ORDERLYWEB_TEST_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - 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
 
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+      - name: Set up Python
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.7
+          python-version: 3.11
 
       - name: Set up orderly-web
+        if: runner.os == 'Linux'
         run: |
           pip3 install constellation
-          pip3 install orderly-web
+          pip3 install git+https://github.com/vimc/orderly-web-deploy.git
           orderly-web start --pull inst/config
 
-      - uses: r-lib/actions/setup-pandoc@v1
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        if: runner.os != 'Windows'
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
-
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-        shell: Rscript {0}
-
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
+      - uses: r-lib/actions/check-r-package@v2
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -1,52 +1,49 @@
+# 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
+    branches: [main, master]
+  pull_request:
+  release:
+    types: [published]
+  workflow_dispatch:
 
-name: pkgdown
+name: pkgdown.yaml
+
+permissions: read-all
 
 jobs:
   pkgdown:
-    runs-on: macOS-latest
+    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 }}
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v2
-
-      - uses: r-lib/actions/setup-r@v1
+      - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
 
-      - name: Cache R packages
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install libs
-        run: |
-          brew install libgit2
-
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          install.packages("pkgdown", type = "binary")
-        shell: Rscript {0}
+          extra-packages: any::pkgdown, local::.
+          needs: website
 
-      - name: Install package
-        run: R CMD INSTALL .
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
 
-      - name: Deploy package
-        run: |
-          git config --local user.email "actions@github.com"
-          git config --local user.name "GitHub Actions"
-          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -1,68 +1,73 @@
+# 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
+    branches: [main, master]
   pull_request:
-    branches:
-      - main
-      - master
 
-name: test-coverage
+name: test-coverage.yaml
+
+permissions: read-all
 
 jobs:
   test-coverage:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      ORDERLYWEB_TEST_TOKEN: ${{ secrets.ORDERLYWEB_TEST_TOKEN }}
+
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
 
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+      - name: Set up Python
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.7
+          python-version: 3.11
 
       - name: Set up orderly-web
         run: |
           pip3 install constellation
-          pip3 install orderly-web
+          pip3 install git+https://github.com/vimc/orderly-web-deploy.git
           orderly-web start --pull inst/config
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr, any::xml2
+          needs: coverage
 
-      - name: Query dependencies
+      - name: Test coverage
         run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          print(cov)
+          covr::to_cobertura(cov)
         shell: Rscript {0}
 
-      - name: Cache R packages
-        uses: actions/cache@v2
+      - uses: codecov/codecov-action@v5
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+          # Fail if error if not on PR, or if on PR and token is given
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
+          files: ./cobertura.xml
+          plugins: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
 
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
+      - name: Show testthat output
+        if: always()
         run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
+          ## --------------------------------------------------------------------
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
 
-      - name: Install dependencies
-        run: |
-          install.packages(c("remotes"))
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("covr")
-        shell: Rscript {0}
-
-      - name: Test coverage
-        run: covr::codecov()
-        shell: Rscript {0}
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,22 +1,22 @@
 Package: orderlyweb
 Title: Orderly Support for 'OrderlyWeb'
-Version: 0.1.15
+Version: 0.1.16
 Authors@R:
     c(person(given = "Rich",
              family = "FitzJohn",
              role = c("aut", "cre"),
              email = "rich.fitzjohn@gmail.com"),
       person("Imperial College of Science, Technology and Medicine",
              role = "cph"))
-Description: Client for 'OrderlyWeb' for use from the 'orderly'
+Description: Client for 'OrderlyWeb' for use from the 'orderly1'
     package.  Allows downloading of reports, running remote reports
     and other interaction with the remote report repository.
 Imports:
     R6,
     gert,
     httr,
     jsonlite,
-    orderly (>= 1.2.19),
+    orderly1 (>= 1.2.19),
     progress,
     zip
 Suggests:
@@ -29,4 +29,4 @@ BugReports: https://github.com/vimc/orderlyweb/issues
 Encoding: UTF-8
 LazyData: true
 Remotes:
-    vimc/orderly
+    vimc/orderly1
diff --git a/README.md b/README.md
@@ -2,13 +2,13 @@
 
 <!-- badges: start -->
 [![Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip)
-[![R build status](https://github.com/vimc/orderlyweb/workflows/R-CMD-check/badge.svg)](https://github.com/vimc/orderlyweb/actions)
-[![codecov.io](https://codecov.io/github/vimc/orderlyweb/coverage.svg?branch=master)](https://codecov.io/github/vimc/orderlyweb?branch=master)
+[![R-CMD-check](https://github.com/vimc/orderlyweb/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/vimc/orderlyweb/actions/workflows/R-CMD-check.yaml)
+[![Codecov test coverage](https://codecov.io/gh/vimc/orderlyweb/graph/badge.svg)](https://app.codecov.io/gh/vimc/orderlyweb)
 <!-- badges: end -->
 
 > R client support for OrderlyWeb
 
-The R package [`orderly`](https://github.com/vimc/orderly) has a [web interface called OrderlyWeb](https://github.com/vimc/orderly-web); this package provides support for `orderly` to interact with `OrderlyWeb` in order to download reports from a remote server and run them remotely
+The R package [`orderly1`](https://github.com/vimc/orderly1) has a [web interface called OrderlyWeb](https://github.com/vimc/orderly-web); this package provides support for `orderly1` to interact with `OrderlyWeb` in order to download reports from a remote server and run them remotely
 
 ### Testing
 

diff --git a/scripts/demo.R b/scripts/demo.R
@@ -1,4 +1,4 @@
 path <- tempfile()
 dir.create(path)
 
-path <- orderly:::create_orderly_demo(quiet = TRUE)
+path <- orderly1:::create_orderly_demo(quiet = TRUE)
diff --git a/tests/testthat/test-integration.R b/tests/testthat/test-integration.R
@@ -388,7 +388,7 @@ test_that("can pack a bundle", {
   expect_equal(dirname(res), tempdir())
   expect_match(basename(res), "^[0-9]{8}-[0-9]{6}-[[:xdigit:]]{8}\\.zip$")
 
-  ans <- orderly::orderly_bundle_run(res, echo = FALSE)
+  ans <- orderly1::orderly_bundle_run(res, echo = FALSE)
   expect_equal(ans$id, sub("\\.zip$", "", basename(res)))
   expect_false(ans$id %in% cl$report_versions("minimal"))