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Merge pull request #46 from aberHRML/devel
v1.0.0
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| ^\.travis\.yml$ | ||
| ^codecov\.yml$ | ||
| ^\.github$ | ||
| ^_pkgdown\.yml$ | ||
| ^docs$ | ||
| ^pkgdown$ | ||
| ^doc$ | ||
| ^Meta$ | ||
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| @@ -0,0 +1,46 @@ | ||
| # 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: | ||
| branches: [main, master] | ||
| release: | ||
| types: [published] | ||
| workflow_dispatch: | ||
|
|
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| name: pkgdown | ||
|
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| 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 }} | ||
| steps: | ||
| - uses: actions/checkout@v3 | ||
|
|
||
| - uses: r-lib/actions/setup-pandoc@v2 | ||
|
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| - uses: r-lib/actions/setup-r@v2 | ||
| with: | ||
| use-public-rspm: true | ||
|
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| - uses: r-lib/actions/setup-r-dependencies@v2 | ||
| with: | ||
| extra-packages: any::pkgdown, local::. | ||
| needs: website | ||
|
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| - name: Build site | ||
| run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE) | ||
| shell: Rscript {0} | ||
|
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||
| - name: Deploy to GitHub pages 🚀 | ||
| if: github.event_name != 'pull_request' | ||
| uses: JamesIves/github-pages-deploy-action@v4.4.1 | ||
| with: | ||
| clean: false | ||
| branch: gh-pages | ||
| folder: docs |
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| # 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: | ||
| branches: [main, master] | ||
|
|
||
| name: test-coverage | ||
|
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| jobs: | ||
| test-coverage: | ||
| runs-on: ubuntu-latest | ||
| env: | ||
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
|
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||
| steps: | ||
| - uses: actions/checkout@v3 | ||
|
|
||
| - uses: r-lib/actions/setup-r@v2 | ||
| with: | ||
| use-public-rspm: true | ||
|
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||
| - uses: r-lib/actions/setup-r-dependencies@v2 | ||
| with: | ||
| extra-packages: any::covr | ||
| needs: coverage | ||
|
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| - name: Test coverage | ||
| run: | | ||
| covr::codecov( | ||
| quiet = FALSE, | ||
| clean = FALSE, | ||
| install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package") | ||
| ) | ||
| shell: Rscript {0} | ||
|
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| - name: Show testthat output | ||
| if: always() | ||
| run: | | ||
| ## -------------------------------------------------------------------- | ||
| find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true | ||
| shell: bash | ||
|
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||
| - name: Upload test results | ||
| if: failure() | ||
| uses: actions/upload-artifact@v3 | ||
| with: | ||
| name: coverage-test-failures | ||
| path: ${{ runner.temp }}/package |
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| .Rhistory | ||
| .RData | ||
| .Ruserdata | ||
| docs | ||
| inst/doc | ||
| /doc/ | ||
| /Meta/ | ||
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| Package: MFassign | ||
| Title: Molecular Formula Assignment for High Resolution metabolomics | ||
| Version: 0.7.10 | ||
| Package: assignments | ||
| Title: Molecular Formula Assignment For High Resolution ESI-MS Based Metabolomics Data | ||
| Version: 1.0.0 | ||
| Authors@R: person("Jasen", "Finch", email = "jsf9@aber.ac.uk", role = c("aut", "cre")) | ||
| Description: Molecular formula assignment for high resolution metabolomics. | ||
| Description: A molecular formula assignment approach for electrospray ionisation high resolution mass spectrometry based metabolomics data. | ||
| Depends: R (>= 3.5.0), | ||
| ggraph | ||
| Imports: CHNOSZ, | ||
| Imports: cli, | ||
| crayon, | ||
| dplyr, | ||
| furrr, | ||
| future, | ||
| igraph, | ||
| lubridate, | ||
| magrittr, | ||
| stringr, | ||
| tibble, | ||
| metabolyseR, | ||
| methods, | ||
| tidyr, | ||
| crayon, | ||
| mzAnnotation, | ||
| purrr, | ||
| cli, | ||
| lubridate, | ||
| rlang, | ||
| stringr, | ||
| tibble, | ||
| tidygraph, | ||
| igraph, | ||
| ggthemes, | ||
| tidyr | ||
| License: GPL (>= 3) | ||
| Encoding: UTF-8 | ||
| LazyData: true | ||
| Roxygen: list(markdown = TRUE) | ||
| RoxygenNote: 7.2.3 | ||
| Collate: parameters.R assignment.R correlations.R | ||
| addIsoAssign.R transformationAssign.R relationships.R | ||
| graph.R assign.R internals.R components.R | ||
| feature_data.R assignments.R plotAdductDist.R plot_components.R | ||
| plotSpectrum.R reexports.R zzz.R | ||
| Suggests: | ||
| testthat, | ||
| covr, | ||
| ggplot2, | ||
| patchwork, | ||
| mzAnnotation, | ||
| metabolyseR, | ||
| ggraph, | ||
| ggrepel, | ||
| ggtext, | ||
| ggthemes, | ||
| glue, | ||
| graphlayouts, | ||
| future, | ||
| furrr | ||
| Remotes: jasenfinch/mzAnnotation, | ||
| patchwork, | ||
| knitr, | ||
| rmarkdown | ||
| Remotes: aberHRML/mzAnnotation, | ||
| jasenfinch/metabolyseR | ||
| License: GPL (>= 3) | ||
| Encoding: UTF-8 | ||
| LazyData: true | ||
| RoxygenNote: 7.1.1 | ||
| Collate: | ||
| allGenerics.R | ||
| allClasses.R | ||
| prepCorrelations-method.R | ||
| addIsoAssign-method.R | ||
| transformationAssign-method.R | ||
| relationships-method.R | ||
| assignmentParameters.R | ||
| assignMFs.R | ||
| MFgen.R | ||
| MFscore.R | ||
| addIsoScore.R | ||
| addMFs.R | ||
| calcComponents.R | ||
| assignMethods.R | ||
| peakData.R | ||
| LCassignment.R | ||
| MFassign.R | ||
| FIEassignment.R | ||
| doAssignment-method.R | ||
| continueAssignment.R | ||
| show-method.R | ||
| access-methods.R | ||
| summariseAssignment-method.R | ||
| plotNetwork-method.R | ||
| networkComponents.R | ||
| addNames.R | ||
| eliminate.R | ||
| recalcComponents.R | ||
| plotAdductDist-method.R | ||
| plotFeatureSolutions.R | ||
| calcCorrelations-method.R | ||
| filterCorrelations-method.R | ||
| plotSpectrum-method.R | ||
| reexports.R | ||
| Suggests: testthat, | ||
| covr | ||
| URL: https://aberhrml.github.io/assignments/ | ||
| VignetteBuilder: knitr |
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