Support for Databrary 2.0

.Rbuildignore

@@ -9,7 +9,12 @@
 ^_notes$
 ^tmp$
 ^_wip
+^\.lintr$
 ^\.github$
 ^cran-comments\.md$
 ^CRAN-SUBMISSION$
 ^README.Rmd$
+^\.Renviron\.stg$
+^\.Renviron$
+^\.vscode$
+^\.Rprofile$

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

@@ -2,9 +2,9 @@
 # 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, staging]
   pull_request:
-    branches: [main, master]
+    branches: [main, master, staging, development]
 
 name: R-CMD-check
 
@@ -29,7 +29,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - uses: r-lib/actions/setup-pandoc@v2
 

.github/workflows/lint.yaml

@@ -0,0 +1,36 @@
+# 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, staging]
+  pull_request:
+    branches: [main, master, staging, development]
+
+name: lint
+
+permissions: read-all
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v6
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: lintr@3.2.0, any::pkgload, local::.
+          needs: lint
+
+      - name: Lint
+        run: |
+          pkgload::load_all()
+          lintr::lint_package()
+        shell: Rscript {0}
+        env:
+          LINTR_ERROR_ON_LINT: true

.github/workflows/pkgdown.yaml

@@ -1,9 +1,10 @@
 # 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
+# Runs after R-CMD-check succeeds on main/master, or on release, or manually
 on:
-  push:
-    branches: [main, master]
-  pull_request:
+  workflow_run:
+    workflows: [R-CMD-check]
+    types: [completed]
     branches: [main, master]
   release:
     types: [published]
@@ -14,15 +15,20 @@ name: pkgdown
 jobs:
   pkgdown:
     runs-on: ubuntu-latest
+    # Only run when R-CMD-check succeeded (for workflow_run), or for release/manual
+    if: github.event_name != 'workflow_run' || github.event.workflow_run.conclusion == 'success'
     # Only restrict concurrency for non-PR jobs
     concurrency:
-      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+      group: pkgdown-${{ github.event_name != 'workflow_run' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     permissions:
       contents: write
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
+        with:
+          # When triggered by workflow_run, checkout the commit that was checked
+          ref: ${{ github.event_name == 'workflow_run' && github.event.workflow_run.head_sha || github.ref }}
 
       - uses: r-lib/actions/setup-pandoc@v2
 

.github/workflows/test-coverage.yaml

@@ -0,0 +1,71 @@
+# 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:
+  pull_request:
+    branches: [main, master, staging, development]
+
+name: test-coverage
+
+permissions: read-all
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr, any::xml2
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          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)
+          pct <- covr::percent_coverage(cov)
+          cat("Coverage:", pct, "%\n")
+          # TODO: Re-enable coverage threshold once target is met
+          # if (pct < 80) stop("Coverage is below 80% (", pct, "%)")
+          if (pct < 80) {
+            warning("Coverage is below 80% (", pct, "%) - threshold temporarily disabled")
+          } else if (pct < 90) {
+            message("Coverage is below 90% (", pct, "%)")
+          } else {
+            message("Coverage is above 90% (", pct, "%)")
+          }
+        shell: Rscript {0}
+
+      - uses: codecov/codecov-action@v6
+        with:
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
+          files: ./cobertura.xml
+          plugins: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

.gitignore

@@ -1,3 +1,5 @@
+.env
+.env.*
 Meta
 doc
 .Rproj.user
@@ -20,4 +22,5 @@ tmp
 docs
 /doc/
 /Meta/
+.Renviron*
 

.lintr

@@ -0,0 +1,2 @@
+linters: linters_with_defaults(line_length_linter = line_length_linter(120))
+exclusions: list("_wip", "tests/testthat", "vignettes", "R/CONSTANTS.R" = list(object_name_linter = Inf, object_length_linter = Inf), "R/aaa.R" = list(object_name_linter = Inf), "R/auth_utils.R" = list(object_name_linter = Inf), "R/utils.R" = list(object_name_linter = Inf))

DESCRIPTION

@@ -1,12 +1,14 @@
 Type: Package
 Package: databraryr
 Title: Interact with the 'Databrary.org' API
-Version: 0.6.6.9002
+Version: 1.0.0.9000
 Authors@R: c(
     person("Rick", "O. Gilmore", , "rog1@psu.edu", role = c("aut", "cre", "cph")),
     person("Jeffrey", "Spies", , "cran@jeffspies.com", role = "aut"),
+    person("Pawel", "Armatys", "pawel.armatys@montrosesoftware.com", role="aut"),
     person("National Science Foundation OAC-2032713", role = "fnd"),
-    person("National Institutes of Health R01HD094830", role = "fnd")
+    person("National Institutes of Health R01HD094830", role = "fnd"),
+    person("National Science Foundation BCS 2444730, 2444731", role="fnd")
   )
 Maintainer: Rick O. Gilmore <rog1@psu.edu>
 Description: 'Databrary.org' is a restricted access repository for
@@ -23,27 +25,29 @@ Imports:
     httr2 (>= 1.0.0),
     keyring (>= 1.3.2),
     lifecycle (>= 1.0.4),
-    magick (>= 2.8.2),
     magrittr,
     methods (>= 4.3.2),
     options (>= 0.2.0),
     purrr (>= 1.0.2),
     stringr (>= 1.5.1),
     stats,
-    tibble (>= 3.2.1),
-    xfun (>= 0.41)
+    tibble (>= 3.2.1)
 Suggests:
     av (>= 0.9.0),
+    covr (>= 3.6.0),
     ggplot2,
     knitr,
+    lintr (>= 3.0.0),
     openssl,
     readr,
     rmarkdown (>= 2.26),
-    testthat (>= 3.0.0)
+    testthat (>= 3.0.0),
+    withr (>= 2.5.0),
+    xml2 (>= 1.3.0)
 VignetteBuilder: 
     knitr
 Config/testthat/edition: 3
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.3

NAMESPACE

@@ -1,54 +1,118 @@
 # Generated by roxygen2: do not edit by hand
 
 export("%>%")
-export(HHMMSSmmm_to_ms)
+export(add_default_record_to_session)
 export(assign_constants)
+export(assign_record_to_file)
+export(bulk_assign_records)
+export(bulk_create_folders)
+export(bulk_create_records)
+export(bulk_create_sessions)
+export(bulk_delete_files)
+export(bulk_delete_folders)
+export(bulk_delete_records)
+export(bulk_delete_sessions)
+export(bulk_rename_files)
+export(bulk_rename_folders)
+export(bulk_rename_sessions)
+export(bulk_unassign_records)
+export(bulk_upload_files)
+export(check_duplicate_files_in_folder)
+export(check_duplicate_files_in_session)
 export(check_ssl_certs)
-export(download_party_avatar)
+export(complete_upload)
+export(create_folder)
+export(create_session)
+export(create_volume_record)
+export(delete_folder)
+export(delete_record_measure)
+export(delete_session)
+export(delete_session_file)
+export(delete_volume_record)
+export(disable_volume_category)
+export(download_folder_asset)
+export(download_folder_asset_from_df)
+export(download_folder_assets_fr_df)
+export(download_folder_zip)
 export(download_session_asset)
+export(download_session_asset_from_df)
 export(download_session_assets_fr_df)
 export(download_session_csv)
 export(download_session_zip)
-export(download_single_session_asset_fr_df)
 export(download_video)
 export(download_volume_zip)
-export(get_asset_segment_range)
+export(enable_volume_category)
+export(get_category_by_id)
 export(get_db_stats)
-export(get_file_duration)
-export(get_party_by_id)
+export(get_folder_by_id)
+export(get_folder_file)
+export(get_funder_by_id)
+export(get_institution_avatar)
+export(get_institution_by_id)
+export(get_institution_statistics)
 export(get_permission_levels)
 export(get_release_levels)
 export(get_session_by_id)
 export(get_session_by_name)
+export(get_session_file)
 export(get_supported_file_types)
+export(get_tag_by_id)
+export(get_upload_status)
+export(get_user_avatar)
+export(get_user_by_id)
+export(get_user_statistics)
 export(get_volume_by_id)
-export(is_institution)
-export(is_person)
+export(get_volume_collaborator_by_id)
+export(get_volume_enabled_categories)
+export(get_volume_record_by_id)
+export(initiate_upload)
 export(list_asset_formats)
 export(list_authorized_investigators)
-export(list_party_affiliates)
-export(list_party_sponsors)
-export(list_party_volumes)
-export(list_session_activity)
+export(list_categories)
+export(list_folder_assets)
+export(list_institution_affiliates)
+export(list_institutions)
 export(list_session_assets)
-export(list_sponsors)
+export(list_user_affiliates)
+export(list_user_history)
+export(list_user_sponsors)
+export(list_user_volumes)
+export(list_users)
 export(list_volume_activity)
 export(list_volume_assets)
-export(list_volume_excerpts)
+export(list_volume_collaborators)
+export(list_volume_folders)
 export(list_volume_funding)
 export(list_volume_info)
 export(list_volume_links)
-export(list_volume_owners)
+export(list_volume_records)
 export(list_volume_session_assets)
 export(list_volume_sessions)
 export(list_volume_tags)
+export(list_volumes)
 export(login_db)
 export(logout_db)
 export(make_default_request)
 export(make_login_client)
+export(patch_folder)
+export(patch_session)
+export(patch_session_file)
+export(remove_default_record_from_session)
+export(resume_bulk)
 export(search_for_funder)
-export(search_for_keywords)
 export(search_for_tags)
+export(search_institutions)
+export(search_users)
+export(search_volumes)
+export(set_record_measure)
+export(set_volume_enabled_categories)
+export(unassign_record_from_file)
+export(update_folder)
+export(update_session)
+export(update_session_file)
+export(update_volume_record)
+export(upload_file)
+export(whoami)
 importFrom(lifecycle,deprecated)
 importFrom(magrittr,"%>%")
 importFrom(methods,is)

NEWS.md

@@ -1,4 +1,8 @@
-# databraryr (development version)
+# databraryr 1.0.0
+
+## Major changes
+
+- Adapted all package functions to Databrary 2.0 API.
 
 # databraryr 0.6.6