Merge branch 'r-sharp-r6' into pksim-installation-vignette

.Rbuildignore

@@ -34,5 +34,6 @@ tests\^spelling
 ^BinaryFiles$
 ^README\.Rmd$
 ^vignettes/images/simulation_lifecycle_flowcharts\.drawio$
+^update_core_files.R
 ^\.github$
 ^codecov\.yml$

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

@@ -0,0 +1,75 @@
+# 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:
+  workflow_call:
+
+name: R-CMD-check
+
+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
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
+          error-on: 'c("error")'
+
+      - name: Build package
+        if: ${{ success() }}
+        run: |
+          output_dir <- file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "built_package")
+          dir.create(output_dir)
+          devtools::build(binary = TRUE, path = output_dir)
+        shell: Rscript {0}
+
+      - name: Get package version from DESCRIPTION file and set as environment variable
+        run: |
+          echo "PKG_VERSION=$(grep -oP '(?<=Version: )\d+\.\d+\.\d+\.*\d*' DESCRIPTION)" >> $GITHUB_ENV
+        shell: bash
+
+      - name: get R version and set as environment variable
+        run: |
+          echo "R_VERSION=$(Rscript -e 'cat(R.version$major, R.version$minor, sep = ".")')" >> $GITHUB_ENV
+        shell: bash
+
+      - name: Upload built package
+        if: ${{ success() }}
+        uses: actions/upload-artifact@v4
+        with:
+          name: ospsuite-v${{ env.PKG_VERSION }}-${{runner.os}}-r_${{ env.R_VERSION }}
+          path: ${{ runner.temp }}/built_package/*

.github/workflows/main-workflow.yaml

@@ -12,35 +12,23 @@ jobs:
     uses: ./.github/workflows/bump-dev-version.yaml
     secrets: inherit
 
-  R-CMD-Check:
-    if: ${{ always() }}
+  update-core-files:
+    if: ${{ !cancelled() && github.event_name == 'pull_request' }}
     needs: [bump-dev-version]
-    uses: Open-Systems-Pharmacology/Workflows/.github/workflows/R-CMD-check-build.yml@main
-    with:
-      install-pksim: true
-      install-rClr: true
-      extra-packages: |
-        ospsuite.utils=github::Open-Systems-Pharmacology/OSPSuite.RUtils
-        tlf=github::Open-Systems-Pharmacology/TLF-Library
+    uses: ./.github/workflows/update-core-files.yaml
+
+  R-CMD-Check:
+    if: ${{ !cancelled() }}
+    needs: [update-core-files]
+    uses: ./.github/workflows/R-CMD-check.yaml
 
   test-coverage:
-    if: ${{ always() }}
-    needs: [R-CMD-Check]
-    uses: Open-Systems-Pharmacology/Workflows/.github/workflows/test-pkg-and-coverage.yml@main
-    with:
-      install-pksim: true
-      install-rClr: true
-      extra-packages: |
-        ospsuite.utils=github::Open-Systems-Pharmacology/OSPSuite.RUtils
-        tlf=github::Open-Systems-Pharmacology/TLF-Library
+    if: ${{ !cancelled() }}
+    needs: [update-core-files]
+    uses: ./.github/workflows/test-coverage.yaml
+
 
   pkgdown:
-    if: ${{ always() }}
-    needs: [R-CMD-Check]
-    uses: Open-Systems-Pharmacology/Workflows/.github/workflows/pkgdown.yml@main
-    with:
-      install-pksim: true
-      install-rClr: true
-      extra-packages: |
-        ospsuite.utils=github::Open-Systems-Pharmacology/OSPSuite.RUtils
-        tlf=github::Open-Systems-Pharmacology/TLF-Library
+    if: ${{ !cancelled() }}
+    needs: [update-core-files]
+    uses: ./.github/workflows/pkgdown.yaml

.github/workflows/pkgdown.yaml

@@ -0,0 +1,44 @@
+# 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:
+  workflow_call:
+
+name: pkgdown
+
+permissions: read-all
+
+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 }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - 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/github-pages-deploy-action@v4.5.0
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.github/workflows/test-coverage.yaml

@@ -0,0 +1,58 @@
+# 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:
+  workflow_call:
+
+name: test-coverage
+
+permissions: read-all
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - 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")
+          )
+          covr::to_cobertura(cov)
+        shell: Rscript {0}
+
+      - uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          file: ./cobertura.xml
+          plugin: 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

.github/workflows/update-core-files.yaml

@@ -0,0 +1,34 @@
+on:
+  workflow_call:
+
+name: R-CMD-check
+
+permissions: write-all
+
+
+jobs:
+  update-core-files:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          repository: ${{ github.event.pull_request.head.repo.full_name }}
+          ref: ${{ github.event.pull_request.head.ref }}
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: download-and-unzip-core-files
+        run: source("update_core_files.R")
+        shell: Rscript {0}
+
+      - uses: EndBug/add-and-commit@v9
+        if: ${{ success() }}
+        with:
+          message: '🤖 Update Core Files.'
+          default_author: github_actions
+          add: 'inst/lib'

.gitignore

@@ -42,7 +42,12 @@ vignettes/*.pdf
 
 # Shiny token, see https://shiny.rstudio.com/articles/shinyapps.html
 rsconnect/
-doc
+
 Meta
+
+# Website output folder
 docs
-inst/doc
+doc
+
+# test artifacts
+tests/testthat/*.pdf

DESCRIPTION

@@ -3,7 +3,7 @@ Package: ospsuite
 Title: R package to manipulate OSPSuite Models
 Version: 12.0.0.9002
 Authors@R: 
-    c(person("Open-Systems-Pharmacology Community", role = "cph"),
+    c(person("Open-Systems-Pharmacology Community", role = c("cph", "fnd")),
       person("Michael", "Sevestre", role = c("aut", "cre"), email = "michael@design2code.ca"),
       person("Pavel", "Balazki", role = "aut"),
       person("Juri", "Solodenko", role = "aut", comment = c(ORCID = "0000-0001-6922-588X")),
@@ -19,8 +19,8 @@ URL: https://github.com/open-systems-pharmacology/ospsuite-r,
 BugReports: 
     https://github.com/open-systems-pharmacology/ospsuite-r/issues
 Depends: 
-    R (>= 3.6),
-    rClr (>= 0.9.1),
+    R (>= 4.1),
+    rSharp
 Imports: 
     dplyr (>= 1.0.0),
     ospsuite.utils (>= 1.5.0),
@@ -47,7 +47,7 @@ Suggests:
 Language: en-US
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Roxygen: list(markdown = TRUE)
 VignetteBuilder: knitr
 Config/testthat/edition: 3
@@ -141,5 +141,6 @@ Collate:
     'zzz.R'
     'zzz_deprecated.R'
 Remotes: 
-    Open-Systems-Pharmacology/OSPSuite.RUtils,
-    Open-Systems-Pharmacology/TLF-Library
+    Open-Systems-Pharmacology/rSharp,
+    ospsuite.utils=Open-Systems-Pharmacology/OSPSuite.RUtils,
+    tlf=Open-Systems-Pharmacology/TLF-Library

NAMESPACE

@@ -152,7 +152,7 @@ export(validateDimension)
 export(validateUnit)
 import(data.table)
 import(ospsuite.utils)
-import(rClr)
+import(rSharp)
 import(tidyr)
 import(tlf)
 import(xml2)

NEWS.md

@@ -4,6 +4,7 @@
 
   - `{openxlsx}`
   - `{lifecyle}`
+  - `{rSharp`}
 
 
 ## New features
@@ -21,13 +22,19 @@
   - Added a function `exportSteadyStateToXLS()` to export steady state values
     calculated for one simulation using the `getSteadyState()` to an Excel file
     that can be imported in MoBi.
+
+  - The package does not require a local installation of PK-Sim any more. All required 
+  dependencies are shipped with the package.
+
+  - The package fully supports Linux.
 
 ## Breaking Changes
 
   - The single argument of the `getBaseUnit()` function is now named
     `quantityOrDimension` (was `dimension` previously). It can now use objects
     of class `Quantity` as inputs, to be consistent with the `toBaseUnit()`
     function.
+  - The package gains a new dependency `{rSharp}`
 
 ## Major Changes
 
@@ -44,6 +51,7 @@
   - `plotPopulationTimeProfile()` has a new `aggregation` argument that allow
     the user to choose between quantiles, arithmetic and geometric aggregations
     of y.
+  - The package loses dependency `{rClr}`
 
 
 ## Minor improvements and bug fixes