Streamline package

.Rbuildignore

@@ -11,3 +11,4 @@
 ^\.github$
 (^|/)\.DS\_Store$
 ^\.git($|/)
+^CRAN-SUBMISSION$

.github/workflows/R-CMD-check.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:
+
+name: R-CMD-check.yaml
+
+permissions: read-all
+
+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'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - 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
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: |
+            any::rcmdcheck
+            local::.
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/pkgdown.yaml

@@ -33,7 +33,9 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::pkgdown, local::.
+          extra-packages:  |
+            any::pkgdown
+            local::.
           needs: website
 
       - name: Build site

.github/workflows/test-coverage.yaml

@@ -24,7 +24,10 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::covr, any::xml2
+          extra-packages: |
+            any::covr
+            any::xml2
+            local::.
           needs: coverage
 
       - name: Test coverage
@@ -34,7 +37,6 @@ jobs:
             clean = FALSE,
             install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
           )
-          print(cov)
           covr::to_cobertura(cov)
         shell: Rscript {0}
 

.gitignore

@@ -39,3 +39,5 @@ rsconnect/
 inst/doc
 **/.quarto/
 inst/R.ignore
+cran-comments.md
+CRAN-SUBMISSION

DESCRIPTION

@@ -1,13 +1,13 @@
 Package: dsROCrate
-Title: 'DataSHIELD' RO-Crate Wrapper Functions
+Title: 'DataSHIELD' RO-Crate Governance Functions
 Version: 0.0.1
 Authors@R: c(
     person(given = "Roberto",
            family = "Villegas-Diaz",
            role = c("aut", "cre"),
            email = "r.villegas-diaz@outlook.com",
            comment = c(ORCID = "0000-0001-5036-8661")),
-    person(given = "Rebecca",
+    person(given = "Becca",
            family = "Wilson",
            role = c("aut"),
            comment = c(ORCID = "0000-0003-2294-593X")),
@@ -20,17 +20,19 @@ Authors@R: c(
            role = c("aut"),
            comment = c(ORCID = "0009-0003-2419-1964")),
     person("University of Liverpool", role = c("cph")))
-Description: R package to wrap elements from 'DataSHIELD' analysis into an 
-    RO-Crate.
+Description: Tools for wrapping 'DataSHIELD' analyses into RO-Crate 
+    (Research Object Crate) objects. Provides functions to create structured
+    metadata for federated data analysis projects, enabling governance 
+    tracking of data access, project membership, analysis execution and 
+    output validation across distributed data sources.
 License: MIT + file LICENSE
 Suggests: 
     dsBaseClient,
     DSI,
-    DSMolgenisArmadillo,
     DSOpal,
+    fs,
     knitr,
     MolgenisArmadillo,
-    opalr,
     testthat (>= 3.0.0),
     withr
 Config/testthat/edition: 3
@@ -41,45 +43,19 @@ RoxygenNote: 7.3.3
 Imports: 
     digest,
     dplyr,
+    DSMolgenisArmadillo,
     jsonlite,
-    methods,
+    opalr,
     purrr,
     RcppTOML,
     rmarkdown,
-    rocrateR (>= 0.0.1),
+    rocrateR (>= 0.1.0),
     tibble,
     vtree,
     xptr,
     yaml
 Depends: 
     R (>= 4.1.0)
 VignetteBuilder: knitr
-Collate: 
-    'ArmadilloCredentials-class.R'
-    'audit_cr8tor.R'
-    'audit_safe_people.R'
-    'audit_safe_project.R'
-    'audit_study.R'
-    'dsROCrate-package.R'
-    'dsROCrate.R'
-    'rocrate_report.R'
-    'safe_data.R'
-    'safe_output.R'
-    'safe_people.R'
-    'safe_project.R'
-    'safe_setting.R'
-    'utils-armadillo.R'
-    'utils-connection.R'
-    'utils-cr8tor.R'
-    'utils-date.R'
-    'utils-digest.R'
-    'utils-opal.R'
-    'utils-rocrate.R'
-    'utils-rocrateR.R'
-    'utils-safe_data.R'
-    'utils-safe_output.R'
-    'utils-safe_people.R'
-    'utils-safe_project.R'
-    'utils-safe_setting.R'
-    'utils-show.R'
-    'utils-tibble.R'
+URL: https://github.com/FederatedMethods/dsROCrate
+BugReports: https://github.com/FederatedMethods/dsROCrate/issues

LICENSE

@@ -0,0 +1,2 @@
+YEAR: 2026
+COPYRIGHT HOLDER: University of Liverpool

LICENSE.md

@@ -1,6 +1,6 @@
 # MIT License
 
-Copyright (c) 2025 dsROCrate authors
+Copyright (c) 2026 University of Liverpool
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

NAMESPACE

@@ -1,12 +1,13 @@
 # Generated by roxygen2: do not edit by hand
 
-S3method(audit_safe_people,default)
-S3method(audit_safe_people,opal)
-S3method(audit_safe_project,default)
-S3method(audit_safe_project,opal)
-S3method(audit_study,default)
-S3method(audit_study,list)
-S3method(audit_study,opal)
+S3method(audit,ArmadilloCredentials)
+S3method(audit,character)
+S3method(audit,cr8tor)
+S3method(audit,list)
+S3method(audit,opal)
+S3method(audit,rocrate)
+S3method(audit_engine,cr8tor)
+S3method(audit_engine,opal)
 S3method(extract_safe_data,opal)
 S3method(extract_safe_data,rocrate)
 S3method(extract_safe_output,opal)
@@ -29,10 +30,13 @@ S3method(flatten_safe_setting,default)
 S3method(flatten_safe_setting,rocrate)
 S3method(init,opal)
 S3method(init,rocrate)
-S3method(rocrate_report,character)
-S3method(rocrate_report,default)
-S3method(rocrate_report,list)
-S3method(rocrate_report,rocrate)
+S3method(parse_user_profiles,ArmadilloCredentials)
+S3method(print,cr8tor_bundle)
+S3method(project_exists,ArmadilloCredentials)
+S3method(report,character)
+S3method(report,default)
+S3method(report,list)
+S3method(report,rocrate)
 S3method(safe_data,character)
 S3method(safe_data,default)
 S3method(safe_data,opal)
@@ -45,6 +49,7 @@ S3method(safe_people,character)
 S3method(safe_people,default)
 S3method(safe_people,opal)
 S3method(safe_people,rocrate)
+S3method(safe_project,ArmadilloCredentials)
 S3method(safe_project,character)
 S3method(safe_project,default)
 S3method(safe_project,opal)
@@ -55,19 +60,13 @@ S3method(safe_setting,default)
 S3method(safe_setting,opal)
 S3method(safe_setting,rocrate)
 export(armadillo_login)
-export(audit_cr8tor)
-export(audit_safe_people)
-export(audit_safe_project)
-export(audit_study)
+export(audit)
 export(init)
-export(load_cr8tor_bundle)
-export(rocrate_report)
+export(report)
 export(safe_data)
 export(safe_output)
 export(safe_people)
 export(safe_project)
 export(safe_setting)
-exportMethods(safe_project)
-import(methods)
 importFrom(rocrateR,get_entity)
 importFrom(utils,write.csv)

NEWS.md

@@ -0,0 +1,6 @@
+# dsROCrate 0.0.1
+
+* Initial CRAN submission.
+* This version contains standard functions for auditing (`audit()`), reporting
+(`report()`) and extracting five safe principle components (`safe_*()`).
+* This version currently only supports OBiBa's Opal as the backend.