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Pull request #31: Fixed merge issues caused by linting. Fixed tests
Merge in STAT/prestogp from master to to-git Squashed commit of the following: commit db6cd4f Merge: 55607e2 7da2588 Author: Eric Bair <eric.bair@sciome.com> Date: Sat Jan 13 12:11:56 2024 -0500 Pull request #29: Fixed some bugs caused by the linter Merge in STAT/prestogp from eb-dev to master * commit '7da2588abba4491c1ff490de95e834d00f5df88e': Fixed some bugs caused by the linter commit 7da2588 Author: Eric Bair <eric.bair@sciome.com> Date: Sat Jan 13 01:37:58 2024 -0500 Fixed some bugs caused by the linter commit 55607e2 Merge: c7ed481 81b675d Author: Shail Choksi <shail.choksi@sciome.com> Date: Fri Jan 12 19:37:55 2024 -0500 Pull request #28: Final linting fixes Merge in STAT/prestogp from build-workflow to master * commit '81b675dda9b57f2a362c34876364adf5bcf45560': Fix remaining linting issues Fix all indentation errors Add indentation_linter configuration to lintr config file commit 81b675d Author: sciome-bot <software.tools@sciome.com> Date: Fri Jan 12 19:36:05 2024 -0500 Fix remaining linting issues commit 06673a4 Author: sciome-bot <software.tools@sciome.com> Date: Fri Jan 12 19:23:11 2024 -0500 Fix all indentation errors commit c7ed481 Merge: 723c3eb 7bcfa1a Author: Shail Choksi <shail.choksi@sciome.com> Date: Fri Jan 12 19:02:59 2024 -0500 Pull request #27: Lintr fixes. Added release and sanitizer actions Merge in STAT/prestogp from build-workflow to master * commit '7bcfa1aca78cc6b994cc0227c083357c58d50ca0': (21 commits) Add R_LINTR_LINTER_FILE to lint action to point to global .lintr file More lintr fixes for 1:length, 1:nrow and line length. Disabled object_length_linter WIP: Fix linter warnings for 1:nrow, 1:ncol and 1:length. Increase line length to 160 chars Don't build vignettes during the release action Move release action file to correct directory Add release action Reorder imports in RcppExports file Add missing dependency in Namespace/Description Remove unneeded exports from NAMESPACE Add missing comma in Imports section of DESCRIPTION Add missing comma in imports section of DESCRIPTION Rerun auto-formatter WIP - linting Add ignore rules for .lintr and .github for R build remove linter options from lint action as we have added .lintr project file. Fix all vector_logic_linter warnings Remove line length linter to see the remaining errors/warnings workaround for lintr bug: REditorSupport/languageserver#89 Run auto-lint on vscode enable linting on build-workflow Add missing imports in DESCRIPTION ... commit 29d82cd Author: sciome-bot <software.tools@sciome.com> Date: Fri Jan 12 18:40:17 2024 -0500 Add indentation_linter configuration to lintr config file commit 7bcfa1a Author: sciome-bot <software.tools@sciome.com> Date: Fri Jan 12 18:16:01 2024 -0500 Add R_LINTR_LINTER_FILE to lint action to point to global .lintr file commit b6df473 Author: sciome-bot <software.tools@sciome.com> Date: Fri Jan 12 17:54:50 2024 -0500 More lintr fixes for 1:length, 1:nrow and line length. Disabled object_length_linter commit 6f6f91d Author: sciome-bot <software.tools@sciome.com> Date: Fri Jan 12 17:32:12 2024 -0500 WIP: Fix linter warnings for 1:nrow, 1:ncol and 1:length. Increase line length to 160 chars commit 2db2e19 Author: sciome-bot <software.tools@sciome.com> Date: Fri Jan 12 16:48:59 2024 -0500 Don't build vignettes during the release action commit c539223 Author: sciome-bot <software.tools@sciome.com> Date: Fri Jan 12 16:39:52 2024 -0500 Move release action file to correct directory commit f83df2b Author: sciome-bot <software.tools@sciome.com> Date: Fri Jan 12 16:36:03 2024 -0500 Add release action commit c84e159 Author: sciome-bot <software.tools@sciome.com> Date: Fri Jan 12 16:04:36 2024 -0500 Reorder imports in RcppExports file commit 0460202 Merge: 245eaa3 43ae272 Author: sciome-bot <software.tools@sciome.com> Date: Fri Jan 12 15:48:30 2024 -0500 Merge branch 'build-workflow' of sciome-bot-git:Spatiotemporal-Exposures-and-Toxicology/PrestoGP into build-workflow commit 245eaa3 Merge: 5355e24 c060815 Author: sciome-bot <software.tools@sciome.com> Date: Fri Jan 12 15:47:42 2024 -0500 Merge branch 'main' of sciome-bot-git:Spatiotemporal-Exposures-and-Toxicology/PrestoGP into build-workflow commit c060815 Merge: 731da76 6d69b69 Author: {SET}group <127860447+Spatiotemporal-Exposures-and-Toxicology@users.noreply.github.com> Date: Thu Jan 11 16:02:52 2024 -0500 Merge pull request #44 from Spatiotemporal-Exposures-and-Toxicology/main-sciome Sciome Update 1/10/2024 commit 6d69b69 Author: sciome-bot <software.tools@sciome.com> Date: Thu Jan 11 14:39:39 2024 -0500 Add missing dependency in Namespace/Description commit bdf52c6 Author: sciome-bot <software.tools@sciome.com> Date: Thu Jan 11 14:30:38 2024 -0500 Remove unneeded exports from NAMESPACE commit 06918b0 Author: sciome-bot <software.tools@sciome.com> Date: Thu Jan 11 14:15:45 2024 -0500 Add missing comma in Imports section of DESCRIPTION ... and 13 more commits
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@@ -5,4 +5,5 @@ | |
| ^\.Rproj\.user$ | ||
| ^doc$ | ||
| ^Meta$ | ||
| ^\.github/ | ||
| ^\.lintr | ||
| ^\.github | ||
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| @@ -0,0 +1,109 @@ | ||
| # This workflow uses actions that are not certified by GitHub. | ||
| # They are provided by a third-party and are governed by | ||
| # separate terms of service, privacy policy, and support | ||
| # documentation. | ||
| # | ||
| # See https://github.com/r-lib/actions/tree/master/examples#readme for | ||
| # additional example workflows available for the R community. | ||
|
|
||
| name: Release New version | ||
|
|
||
| on: | ||
| push: | ||
| tags: | ||
| - '*' | ||
| branches: ["build-workflow"] | ||
| workflow_dispatch: | ||
|
|
||
| jobs: | ||
| create_release: | ||
| name: Create release | ||
| runs-on: ubuntu-latest | ||
| outputs: | ||
| upload_url: ${{ steps.create_release.outputs.upload_url }} | ||
| steps: | ||
| - name: Create release | ||
| id: create_release | ||
| uses: ncipollo/release-action@v1 | ||
| with: | ||
| allowUpdates: true | ||
| build_upload_artefacts: | ||
| runs-on: ${{ matrix.config.os }} | ||
| name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| config: | ||
| - {os: windows-latest, r: 'release'} | ||
| - {os: ubuntu-latest, r: 'release'} | ||
| - {os: macos-latest, r: 'release'} | ||
| # - {os: windows-latest, r: '4.2'} | ||
| # - {os: ubuntu-latest, r: '4.2'} | ||
| # - {os: macos-latest, r: '4.2'} | ||
| env: | ||
| R_KEEP_PKG_SOURCE: yes | ||
| steps: | ||
| # see this for details: https://msmith.de/2020/03/12/r-cmd-check-github-actions.html | ||
| - name: Configure git | ||
| run: git config --global core.autocrlf false | ||
| - uses: actions/checkout@v3 | ||
| - uses: r-lib/actions/setup-pandoc@v2 | ||
| - uses: r-lib/actions/setup-tinytex@v2 | ||
| - uses: r-lib/actions/setup-r@v2 | ||
| - uses: r-lib/actions/setup-r-dependencies@v2 | ||
| with: | ||
| cache-version: 2 | ||
| extra-packages: | | ||
| any::ggplot2 | ||
| any::rcmdcheck | ||
| any::roxygen2 | ||
| needs: | | ||
| check | ||
| roxygen2 | ||
| - name: Read VERSION file | ||
| if: runner.os != 'macOs' | ||
| id: getversion | ||
| shell: bash | ||
| run: | | ||
| echo "VERSION=$(cat DESCRIPTION | grep -Po '(?<=Version\:\s).*')" >> $GITHUB_OUTPUT | ||
| - name: Read VERSION file (macOS) | ||
| if: runner.os == 'macOs' | ||
| id: getversion_mac | ||
| run: | | ||
| echo "VERSION=$(sed -n 's/Version:[[:space:]]*//p' DESCRIPTION | tr -d '[:space:]')" >> $GITHUB_OUTPUT | ||
| - name: Build package (Windows) | ||
| if: runner.os == 'Windows' | ||
| shell: cmd | ||
| run: R CMD build --no-build-vignettes . | ||
| - name: Build package | ||
| if: runner.os == 'Linux' || runner.os == 'macOs' | ||
| run: R CMD build --no-build-vignettes . | ||
| - name: Test Install (Windows) | ||
| if: runner.os == 'Windows' | ||
| shell: cmd | ||
| run: R CMD INSTALL --build PrestoGP_${{ steps.getversion.outputs.VERSION }}.tar.gz | ||
| - name: Test Install (Linux) | ||
| if: runner.os == 'Linux' | ||
| run: R CMD INSTALL --build PrestoGP_${{ steps.getversion.outputs.VERSION }}.tar.gz | ||
| - name: Test Install (macOs) | ||
| if: runner.os == 'macOs' | ||
| run: R CMD INSTALL --build PrestoGP_${{ steps.getversion_mac.outputs.VERSION }}.tar.gz | ||
| - uses: svenstaro/upload-release-action@v2 | ||
| if: runner.os == 'macOs' | ||
| with: | ||
| tag: ${{ github.ref }} | ||
| file: PrestoGP_${{ steps.getversion_mac.outputs.VERSION }}.tgz | ||
| asset_name: "PrestoGP_${{ steps.getversion_mac.outputs.VERSION }}-x86_64-macOs-R.${{ matrix.config.r }}.tgz" | ||
| - uses: svenstaro/upload-release-action@v2 | ||
| if: runner.os == 'Linux' | ||
| with: | ||
| tag: ${{ github.ref }} | ||
| file: "PrestoGP_${{ steps.getversion.outputs.VERSION }}_R_x86_64-pc-linux-gnu.tar.gz" | ||
| asset_name: PrestoGP_${{ steps.getversion.outputs.VERSION }}-x86_64-linux-R.${{ matrix.config.r }}.zip | ||
| - uses: svenstaro/upload-release-action@v2 | ||
| if: runner.os == 'Windows' | ||
| with: | ||
| tag: ${{ github.ref }} | ||
| file: PrestoGP_${{ steps.getversion.outputs.VERSION }}.zip | ||
| asset_name: PrestoGP_${{ steps.getversion.outputs.VERSION }}-windows-R.${{ matrix.config.r }}.zip | ||
|
|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,13 @@ | ||
| linters: linters_with_defaults( | ||
| line_length_linter(160L), | ||
| commented_code_linter = NULL, | ||
| object_name_linter = NULL, | ||
| cyclocomp_linter = NULL, | ||
| object_length_linter = NULL, | ||
| indentation_linter( | ||
| indent = 2L, | ||
| hanging_indent_style = "never", | ||
| assignment_as_infix = FALSE | ||
| ) | ||
| ) | ||
| encoding: "UTF-8" |
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