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Merge pull request #27 from aberHRML/devel
v2.0.0
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| Original file line number | Diff line number | Diff line change |
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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 | ||
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| - 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/[email protected] | ||
| with: | ||
| clean: false | ||
| branch: gh-pages | ||
| folder: docs |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,50 @@ | ||
| # 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] | ||
|
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| 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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|---|---|---|
| @@ -1,59 +1,29 @@ | ||
| Package: mzAnnotation | ||
| Title: Signal Annotation Tools for High Resolution Metabolomics | ||
| Version: 1.7.5 | ||
| Title: Tools for Putative Annotation of Electrospray Ionisation High Resolution Mass Spectrometry Data | ||
| Version: 2.0.0 | ||
| Authors@R: | ||
| person(given = "Jasen", | ||
| family = "Finch", | ||
| role = c("aut", "cre"), | ||
| email = "[email protected]") | ||
| Description: Tools for the putative annotation of high resolution metabolomics m/z. | ||
| data. | ||
| biocViews: MassSpectrometry, Metabolomics | ||
| URL: https://jasenfinch.github.io/mzAnnotation/ | ||
| BugReports: https://github.com/jasenfinch/mzAnnotation/issues | ||
| Description: Tools to aid the putative annotation of electrospray ionisation high resolution mass spectrometry data. These include molecular formula generation, relationship calculation and isotopic distribution calculation. | ||
| URL: http://aberhrml.github.io/mzAnnotation/ | ||
| BugReports: https://github.com/aberHRML/mzAnnotation/issues | ||
| Depends: R (>= 3.5) | ||
| Imports: | ||
| Rcpp, | ||
| CHNOSZ, | ||
| tibble, | ||
| dplyr, | ||
| magrittr, | ||
| purrr, | ||
| rlang, | ||
| Rcpp, | ||
| stringr, | ||
| tidyr, | ||
| methods, | ||
| callr | ||
| tidyr | ||
| License: GPL (>= 3) | ||
| Encoding: UTF-8 | ||
| RoxygenNote: 7.1.1 | ||
| LazyData: true | ||
| Suggests: testthat, | ||
| covr, | ||
| zlibbioc | ||
| Roxygen: list(markdown = TRUE) | ||
| RoxygenNote: 7.2.3 | ||
| LinkingTo: Rcpp | ||
| Collate: allGenerics.R | ||
| allClasses.R | ||
| adductTransfromMF.R | ||
| aminoAcids.R | ||
| calcAccurateMass.R | ||
| calcAdducts.R | ||
| calcM.R | ||
| calcMZ.R | ||
| checks.R | ||
| convert.R | ||
| data.R | ||
| descriptors.R | ||
| elementFrequencies-method.R | ||
| filter-methods.R | ||
| generateMF.R | ||
| get-methods.R | ||
| ionisationProducts.R | ||
| isotopeDistribution.R | ||
| metaboliteDB.R | ||
| mzAnnotation.R | ||
| PIPsearch.R | ||
| ppmError.R | ||
| RcppExports.R | ||
| relationshipCalculator.R | ||
| show-method.R | ||
| transformMF.R | ||
| Suggests: testthat, | ||
| covr |
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