From 4f317736f47f1fd489a4022f43434ab3926b8963 Mon Sep 17 00:00:00 2001 From: Felix MIL <34234913+Felixmil@users.noreply.github.com> Date: Wed, 24 Jul 2024 10:49:05 +0200 Subject: [PATCH] Add codecov token (#1465) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * forward repo secret to reusable workflow * Delete refactored actions * 🤖 Update Core Files. --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> --- .github/workflows/R-CMD-check.yaml | 75 --------------------------- .github/workflows/main-workflow.yaml | 1 + .github/workflows/pkgdown.yaml | 44 ---------------- .github/workflows/test-coverage.yaml | 58 --------------------- inst/lib/ConsoleApp.deps.json | 52 +++++++++---------- inst/lib/ConsoleApp.dll | Bin 4096 -> 4096 bytes inst/lib/PKSim.Assets.Images.dll | Bin 916480 -> 916480 bytes inst/lib/PKSim.Assets.dll | Bin 174592 -> 174592 bytes inst/lib/PKSim.CLI.Core.dll | Bin 76288 -> 76288 bytes inst/lib/PKSim.Core.dll | Bin 1473536 -> 1473536 bytes inst/lib/PKSim.Infrastructure.dll | Bin 729600 -> 729600 bytes inst/lib/PKSim.Presentation.dll | Bin 1114112 -> 1114112 bytes inst/lib/PKSim.R.dll | Bin 22016 -> 22016 bytes 13 files changed, 27 insertions(+), 203 deletions(-) delete mode 100644 .github/workflows/R-CMD-check.yaml delete mode 100644 .github/workflows/pkgdown.yaml delete mode 100644 .github/workflows/test-coverage.yaml diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml deleted file mode 100644 index 739333a0a..000000000 --- a/.github/workflows/R-CMD-check.yaml +++ /dev/null @@ -1,75 +0,0 @@ -# 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/* diff --git a/.github/workflows/main-workflow.yaml b/.github/workflows/main-workflow.yaml index 0b0c66d0e..84dc0aa63 100644 --- a/.github/workflows/main-workflow.yaml +++ b/.github/workflows/main-workflow.yaml @@ -30,6 +30,7 @@ jobs: if: ${{ !cancelled() }} needs: [update-core-files] uses: Open-Systems-Pharmacology/Workflows/.github/workflows/test-coverage.yaml@main + secrets: inherit pkgdown: diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml deleted file mode 100644 index 0b527de5b..000000000 --- a/.github/workflows/pkgdown.yaml +++ /dev/null @@ -1,44 +0,0 @@ -# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples -# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help -on: - workflow_call: - -name: pkgdown - -permissions: read-all - -jobs: - pkgdown: - runs-on: ubuntu-latest - # Only restrict concurrency for non-PR jobs - concurrency: - group: pkgdown-${{ 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 diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml deleted file mode 100644 index 5085ebe56..000000000 --- a/.github/workflows/test-coverage.yaml +++ /dev/null @@ -1,58 +0,0 @@ -# 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 diff --git a/inst/lib/ConsoleApp.deps.json b/inst/lib/ConsoleApp.deps.json index 63393dda0..291934e48 100644 --- a/inst/lib/ConsoleApp.deps.json +++ b/inst/lib/ConsoleApp.deps.json @@ -12,7 +12,7 @@ "OSPSuite.R": "12.0.300", "OSPSuite.SimModel.Ubuntu22": "4.0.0.59", "OSPSuite.SimModelSolver_CVODES.Ubuntu22": "4.1.0.9", - "PKSim.R": "12.0.293" + "PKSim.R": "12.0.294" }, "runtime": { "ConsoleApp.dll": {} @@ -1331,7 +1331,7 @@ "System.Xml.ReaderWriter": "4.3.0" } }, - "PKSim.Assets/12.0.293": { + "PKSim.Assets/12.0.294": { "dependencies": { "OSPSuite.Assets": "12.0.300", "OSPSuite.Assets.Images": "12.0.300", @@ -1341,7 +1341,7 @@ "PKSim.Assets.dll": {} } }, - "PKSim.Assets.Images/12.0.293": { + "PKSim.Assets.Images/12.0.294": { "dependencies": { "OSPSuite.Assets": "12.0.300", "OSPSuite.Assets.Images": "12.0.300", @@ -1351,18 +1351,18 @@ "PKSim.Assets.Images.dll": {} } }, - "PKSim.CLI.Core/12.0.293": { + "PKSim.CLI.Core/12.0.294": { "dependencies": { "OSPSuite.Assets": "12.0.300", "OSPSuite.Core": "12.0.300", "OSPSuite.Utility": "4.1.0.6", - "PKSim.Core": "12.0.293" + "PKSim.Core": "12.0.294" }, "runtime": { "PKSim.CLI.Core.dll": {} } }, - "PKSim.Core/12.0.293": { + "PKSim.Core/12.0.294": { "dependencies": { "Newtonsoft.Json": "12.0.3", "OSPSuite.Assets": "12.0.300", @@ -1370,14 +1370,14 @@ "OSPSuite.Core": "12.0.300", "OSPSuite.Infrastructure.Import": "12.0.300", "OSPSuite.Utility": "4.1.0.6", - "PKSim.Assets": "12.0.293", + "PKSim.Assets": "12.0.294", "System.ComponentModel.Annotations": "4.7.0" }, "runtime": { "PKSim.Core.dll": {} } }, - "PKSim.Infrastructure/12.0.293": { + "PKSim.Infrastructure/12.0.294": { "dependencies": { "FluentNHibernate": "2.1.2", "LumenWorksCsvReader": "4.0.0", @@ -1396,30 +1396,30 @@ "OSPSuite.Infrastructure.Serialization": "12.0.300", "OSPSuite.Presentation.Serialization": "12.0.300", "OSPSuite.Utility": "4.1.0.6", - "PKSim.Assets": "12.0.293", - "PKSim.Core": "12.0.293", - "PKSim.Presentation": "12.0.293" + "PKSim.Assets": "12.0.294", + "PKSim.Core": "12.0.294", + "PKSim.Presentation": "12.0.294" }, "runtime": { "PKSim.Infrastructure.dll": {} } }, - "PKSim.Presentation/12.0.293": { + "PKSim.Presentation/12.0.294": { "dependencies": { "OSPSuite.Assets": "12.0.300", "OSPSuite.Core": "12.0.300", "OSPSuite.Presentation": "12.0.300", "OSPSuite.TeXReporting": "3.0.0.5", "OSPSuite.Utility": "4.1.0.6", - "PKSim.Assets": "12.0.293", - "PKSim.Assets.Images": "12.0.293", - "PKSim.Core": "12.0.293" + "PKSim.Assets": "12.0.294", + "PKSim.Assets.Images": "12.0.294", + "PKSim.Core": "12.0.294" }, "runtime": { "PKSim.Presentation.dll": {} } }, - "PKSim.R/12.0.293": { + "PKSim.R/12.0.294": { "dependencies": { "OSPSuite.Assets": "12.0.300", "OSPSuite.Core": "12.0.300", @@ -1427,9 +1427,9 @@ "OSPSuite.SimModel": "4.0.0.59", "OSPSuite.SimModelSolver_CVODES": "4.1.0.9", "OSPSuite.Utility": "4.1.0.6", - "PKSim.CLI.Core": "12.0.293", - "PKSim.Core": "12.0.293", - "PKSim.Infrastructure": "12.0.293", + "PKSim.CLI.Core": "12.0.294", + "PKSim.Core": "12.0.294", + "PKSim.Infrastructure": "12.0.294", "System.Data.SQLite.Core": "1.0.112" }, "runtime": { @@ -2319,37 +2319,37 @@ "path": "system.xml.xmldocument/4.3.0", "hashPath": "system.xml.xmldocument.4.3.0.nupkg.sha512" }, - "PKSim.Assets/12.0.293": { + "PKSim.Assets/12.0.294": { "type": "project", "serviceable": false, "sha512": "" }, - "PKSim.Assets.Images/12.0.293": { + "PKSim.Assets.Images/12.0.294": { "type": "project", "serviceable": false, "sha512": "" }, - "PKSim.CLI.Core/12.0.293": { + "PKSim.CLI.Core/12.0.294": { "type": "project", "serviceable": false, "sha512": "" }, - "PKSim.Core/12.0.293": { + "PKSim.Core/12.0.294": { "type": "project", "serviceable": false, "sha512": "" }, - "PKSim.Infrastructure/12.0.293": { + "PKSim.Infrastructure/12.0.294": { "type": "project", "serviceable": false, "sha512": "" }, - "PKSim.Presentation/12.0.293": { + "PKSim.Presentation/12.0.294": { "type": "project", "serviceable": false, "sha512": "" }, - 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