vimc · richfitz · Jul 4, 2023 · Jul 4, 2023 · Jul 4, 2023 · Jul 4, 2023
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -1,16 +1,14 @@
-# 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
+    branches: [main, master]
 
-name: Check
+name: R-CMD-check.yaml
+
+permissions: read-all
 
 jobs:
   R-CMD-check:
@@ -22,113 +20,33 @@ jobs:
       fail-fast: false
       matrix:
         config:
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-          - {os: macOS-latest, r: 'release'}
-          - {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: ubuntu-20.04, r: 'oldrel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          - {os: ubuntu-20.04, r: '3.6', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {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 }}
-      VAULTR_TEST_SERVER_INSTALL: true
-      VAULTR_TEST_SERVER_PORT: 18200
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
-
-      - uses: r-lib/actions/setup-r@v1
-        with:
-          r-version: ${{ matrix.config.r }}
-
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: actions/checkout@v4
 
-      - 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-pandoc@v2
 
-      - name: Cache R packages
-        if: runner.os != 'Windows'
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r@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: Set env
-        run: echo "VAULTR_TEST_SERVER_BIN_PATH=$GITHUB_WORKSPACE/.vault" >> $GITHUB_ENV
-
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          git config --global user.email "[email protected]"
-          git config --global user.name "GitHub Actions"
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
-
-      - name: "[macOS] system dependencies"
-        if: runner.os == 'macOS'
-        run: |
-          brew install libgit2
-
-      - name: Install openssl (Windows)
-        if: runner.os == 'Windows'
-        run: |
-          install.packages("openssl", type = "binary")
-        shell: Rscript {0}
-
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-        shell: Rscript {0}
-
-      - name: Install RSQlite
-        run: |
-          remotes::install_cran("RSQLite")
-        shell: Rscript {0}
-
-      - name: Install vault
-        if: runner.os != 'Windows'
-        run: |
-          vaultr::vault_test_server_install()
-        shell: Rscript {0}
-
-      - name: Copy reference data
-        run: |
-          ./scripts/copy_reference
-
-      - 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}
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
 
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          extra-packages: any::rcmdcheck
+          needs: check
 
-  check-orderly-server:
-
-    runs-on: ubuntu-20.04
-
-    needs: R-CMD-check
-
-    steps:
-      - uses: convictional/[email protected]
+      - uses: r-lib/actions/check-r-package@v2
         with:
-          owner: vimc
-          repo: orderly.server
-          ref: master
-          github_token: ${{ secrets.REPO_DISPATCH_TOKEN }}
-          client_payload: "{\"orderly_version\": \"${{ github.event_name == 'push' && 'master' || github.head_ref }}\"}"
-          workflow_file_name: R-CMD-check.yaml
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -1,68 +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
+    branches: [main, master]
   pull_request:
-    branches:
-      - main
-      - master
+    branches: [main, master]
 
-name: test-coverage
+name: test-coverage.yaml
+
+permissions: read-all
 
 jobs:
   test-coverage:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      VAULTR_TEST_SERVER_INSTALL: true
-      VAULTR_TEST_SERVER_PORT: 18200
 
     steps:
-      - uses: actions/checkout@v2
-
-      - uses: r-lib/actions/setup-r@v1
-
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: actions/checkout@v4
 
-      - 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
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r@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: Set env
-        run: echo "VAULTR_TEST_SERVER_BIN_PATH=$GITHUB_WORKSPACE/.vault" >> $GITHUB_ENV
+          use-public-rspm: true
 
-      - name: Install dependencies
-        run: |
-          install.packages(c("remotes"))
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("covr")
-          vaultr::vault_test_server_install()
-        shell: Rscript {0}
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr, any::xml2
+          needs: coverage
 
-      - name: Install RSQlite
+      - name: Test coverage
         run: |
-          remotes::install_cran("RSQLite")
+          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: Copy reference data
+      - uses: codecov/codecov-action@v5
+        with:
+          # 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: ${{ secrets.CODECOV_TOKEN }}
+
+      - name: Show testthat output
+        if: always()
         run: |
-          ./scripts/copy_reference
+          ## --------------------------------------------------------------------
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
 
-      - 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
@@ -1,6 +1,6 @@
-Package: orderly
+Package: orderly1
 Title: Lightweight Reproducible Reporting
-Version: 1.6.1
+Version: 1.7.0
 Description: Order, create and store reports from R.  By defining a
     lightweight interface around the inputs and outputs of an
     analysis, a lot of the repetitive work for reproducible research

diff --git a/R/batch.R b/R/batch.R
@@ -3,7 +3,7 @@
 ##' Run one report multiple times with different sets of parameters.
 ##'
 ##' @param name Name of the report to run (see
-##'   [orderly::orderly_list()]).  A leading `src/` will be
+##'   [orderly1::orderly_list()]).  A leading `src/` will be
 ##'   removed if provided, allowing easier use of autocomplete.
 ##'   Alternatively, the default of `NULL` is useful if you have
 ##'   already set the working directory to be the source directory.
@@ -17,18 +17,18 @@
 ##'   during preparation e.g. because of missing parameters this will
 ##'   error and stop all subsequent parameter sets.
 ##'
-##' @param ... Additional args passed to [orderly::orderly_run()]
+##' @param ... Additional args passed to [orderly1::orderly_run()]
 ##'
-##' @seealso [orderly::orderly_run()] for details of report running
+##' @seealso [orderly1::orderly_run()] for details of report running
 ##'
 ##' @export
 ##' @return List of ids of newly created reports
 ##'
 ##' @examples
 ##'
-##' path <- orderly::orderly_example("demo")
+##' path <- orderly1::orderly_example("demo")
 ##' params <- data.frame(nmin = c(0.2, 0.25))
-##' ids <- orderly::orderly_batch("other", params, root = path)
+##' ids <- orderly1::orderly_batch("other", params, root = path)
 orderly_batch <- function(name = NULL, parameters = NULL,
                           continue_on_error = TRUE, ...) {
   if (NROW(parameters) < 1) {

diff --git a/R/bundle.R b/R/bundle.R
@@ -24,7 +24,7 @@
 ##'   `orderly_bundle_pack` or `orderly_bundle_run`)
 ##'
 ##' @param name Name of the report to pack (see
-##'   [orderly::orderly_list()].  A leading `src/` will be removed if
+##'   [orderly1::orderly_list()].  A leading `src/` will be removed if
 ##'   provided, allowing easier use of autocomplete.
 ##'
 ##' @inheritParams orderly_run
@@ -39,35 +39,35 @@
 ##'
 ##' @export
 ##' @examples
-##' path <- orderly::orderly_example("minimal")
+##' path <- orderly1::orderly_example("minimal")
 ##'
 ##' # A working directory to export bundles to:
 ##' workdir <- tempfile()
 ##'
 ##' # Pack up the "example" report to go:
-##' res <- orderly::orderly_bundle_pack(workdir, "example", root = path)
+##' res <- orderly1::orderly_bundle_pack(workdir, "example", root = path)
 ##'
 ##' # The return value is a list with the id and the path to the zip
 ##' # file created:
 ##' res
 ##'
 ##' # A list of reports bundled in this directory and their status
-##' orderly::orderly_bundle_list(workdir)
+##' orderly1::orderly_bundle_list(workdir)
 ##'
 ##' # Run the bundle (this would ordinarily be done on another computer)
-##' zip <- orderly::orderly_bundle_run(res$path, workdir)
+##' zip <- orderly1::orderly_bundle_run(res$path, workdir)
 ##' zip
 ##'
 ##' # The status has now been updated to reflect the status
-##' orderly::orderly_bundle_list(workdir)
+##' orderly1::orderly_bundle_list(workdir)
 ##'
 ##' # We can import this into the orderly tree
-##' orderly::orderly_bundle_import(zip$path, root = path)
+##' orderly1::orderly_bundle_import(zip$path, root = path)
 ##'
 ##' # This has now been included in your orderly archive and the
 ##' # workdir can be safely deleted
 ##' unlink(workdir, recursive = TRUE)
-##' orderly::orderly_list_archive(path)
+##' orderly1::orderly_list_archive(path)
 orderly_bundle_pack <- function(path, name, parameters = NULL,
                               envir = NULL, root = NULL, locate = TRUE,
                               message = NULL, instance = NULL,