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- generated '_pkgdown.yml' file and populated fields - performed some minor updates to vignettes & README to clean up formatting on pkgdown site - added `tibble` package to Suggests (for use in vignettes) - bumped version number
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| ^data-raw$ | ||
| ^README\.Rmd$ | ||
| ^LICENSE\.md$ | ||
| ^_pkgdown\.yml$ | ||
| ^docs$ | ||
| ^pkgdown$ | ||
| ^\.github$ | ||
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| # Getting help with SomaScan.db | ||
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| Thanks for using SomaScan.db! | ||
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| Before filing an issue, there are a few places to explore | ||
| and pieces to put together to make the process as smooth as possible. | ||
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| ## Make a reprex | ||
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| If we can’t reproduce the bug, we can’t fix it! | ||
| Start by making a minimal **repr**oducible **ex**ample using the [reprex](https://reprex.tidyverse.org/) package. | ||
| If you haven't heard of or used `reprex` before, you're in for a treat! | ||
| Seriously, `reprex` will make all of your R-question-asking endeavors easier | ||
| (which is an excellent ROI for the five to ten minutes it'll take you to learn what it's all about). | ||
| For additional `reprex` pointers, check out the [Get help!](https://www.tidyverse.org/help/). | ||
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| ## Where to ask? | ||
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| Armed with your `reprex`, the next step is to figure out [where to ask](https://www.tidyverse.org/help/#where-to-ask). | ||
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| * If it's a `R` related question: start with [community.rstudio.com](https://community.rstudio.com/) | ||
| and/or [StackOverflow](https://stackoverflow.com). There are more people there to answer questions. | ||
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| * If it's a bug with [SomaScan.db](https://github.com/SomaLogic/SomaScan.db/): you're | ||
| in the right place; please [file an issue](https://github.com/SomaLogic/SomaScan.db/issues/new). | ||
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| * If you're not sure: let the community help you figure it out! | ||
| If your problem _is_ a bug or a feature request, you can easily return | ||
| [here](https://github.com/SomaLogic/SomaScan.db/issues/) and report it. | ||
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| * For _non_-coding related feedback or inquiries please reach out to <techsupport@somalogic.com>. | ||
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| Before opening a new issue, be sure to | ||
| [search issues and pull requests](https://github.com/SomaLogic/SomaScan.db/issues/) | ||
| to make sure the bug hasn't been reported and/or already fixed in the development version. | ||
| By default, the search will be pre-populated with `is:issue is:open`. | ||
| You can [edit the qualifiers](https://help.github.com/articles/searching-issues-and-pull-requests/), | ||
| `is:pr`, `is:closed`, etc., as needed, e.g. you'd simply remove `is:open` to | ||
| search _all_ issues in the repo, open or closed. | ||
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| ## What happens next? | ||
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| We aim to respond to questions or simple bugs within 24 - 48h, particularly | ||
| questions accompanied by a `reprex` can typically be addressed quickly. | ||
| More complex bugs or feature requests can take longer, as they require a | ||
| deeper discussion regarding the software development lifecycle of `SomaScan.db`. | ||
| As mentioned above, you may always reach out to our Global Scientific Engagement | ||
| team at <techsupport@somalogic.com> or for more general inquiries at <support@somalogic.com>. |
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| on: | ||
| push: | ||
| branches: | ||
| - main | ||
| - master | ||
| paths: | ||
| - 'DESCRIPTION' | ||
| - '_pkgdown.yml' | ||
| - 'NEWS.md' | ||
| - 'README.md' | ||
| - 'vignettes/**' | ||
| workflow_dispatch: | ||
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| name: pkgdown | ||
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| jobs: | ||
| pkgdown: | ||
| runs-on: macOS-12 # macOS important Bootstrap/bslib themes | ||
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| env: | ||
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
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| steps: | ||
| - uses: actions/checkout@v3 | ||
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| - uses: r-lib/actions/setup-pandoc@v2 | ||
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| - uses: r-lib/actions/setup-r@v2 | ||
| with: | ||
| use-public-rspm: true | ||
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| - uses: r-lib/actions/setup-r-dependencies@v2 | ||
| with: | ||
| extra-packages: | | ||
| any::pkgdown | ||
| local::. | ||
| needs: website | ||
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| - name: Install package | ||
| run: | | ||
| R CMD INSTALL --use-vanilla . | ||
| - name: Deploy to GitHub pages 🚀 | ||
| run: | | ||
| git config --local user.name "$GITHUB_ACTOR" | ||
| git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com" | ||
| Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)' |
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| /doc/ | ||
| /Meta/ | ||
| .Rproj.user | ||
| docs | ||
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| url: https://somalogic.github.io/SomaScan.db | ||
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| development: | ||
| mode: auto | ||
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| authors: | ||
| Amanda Hiser: | ||
| href: https://github.com/amanda-hi | ||
| SomaLogic Operating Co., Inc.: | ||
| href: http://www.somalogic.com | ||
| footer: | ||
| roles: [fnd] | ||
| text: "was developed by the Bioinformatics Dept. at" | ||
| sidebar: | ||
| roles: [cre, fnd] | ||
| before: "Special :pray: to:" | ||
| after: ":dna:" | ||
| before: "[SomaScan.db](https://github.com/SomaLogic/SomaScan.db/) is proudly brought to you by:" | ||
| after: ":dna:" | ||
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| footer: | ||
| structure: | ||
| left: [package, developed_by] | ||
| right: built_with | ||
| components: | ||
| logo: "<img src='inst/figures/logo.png' width='20'> " | ||
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| template: | ||
| bootstrap: 5 | ||
| package: tidytemplate | ||
| bslib: | ||
| primary: "#0054AD" | ||
| border-radius: 0.5rem | ||
| btn-border-radius: 0.25rem | ||
| base_font: {google: "Roboto"} | ||
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| home: | ||
| sidebar: | ||
| structure: [links, help, oss, license, citation, authors, dev, toc] | ||
| components: | ||
| oss: | ||
| title: Other Software | ||
| text: > | ||
| [SomaDataIO](https://somalogic.github.io/SomaDataIO/) <br /> | ||
| [SomaPlotr](https://somalogic.github.io/SomaPlotr/) <br /> | ||
| [Canopy](https://github.com/SomaLogic/Canopy/) <br /> | ||
| [DataDelve Statistics](https://somalogic.com/datadelve-statistics/) | ||
| help: | ||
| title: Getting Help | ||
| text: > | ||
| [Ask a question](https://somalogic.github.io/SomaScan.db/SUPPORT.html) <br /> | ||
| [Report a bug](https://github.com/SomaLogic/SomaScan.db/issues) | ||
| links: | ||
| - text: Learn more about SomaScan | ||
| href: http://www.somalogic.com | ||
| - text: Read SomaScan tech notes | ||
| href: http://www.somalogic.com/tech-notes/ | ||
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| navbar: | ||
| structure: | ||
| left: [intro, reference, articles, news] | ||
| right: [search, github] | ||
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| articles: | ||
| - title: Getting Started | ||
| navbar: ~ | ||
| contents: | ||
| - SomaScan-db | ||
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| - title: Example ADAT Workflow Using SomaScan.db | ||
| navbar: ~ | ||
| contents: | ||
| - example_adat_workflow | ||
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| - title: Advanced Exploration of the SomaScan Menu | ||
| navbar: ~ | ||
| contents: | ||
| - advanced_usage_examples | ||
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| reference: | ||
| - title: Query the Database | ||
| desc: > | ||
| Methods for retrieving annotations from the SQLite database. | ||
| contents: | ||
| - keys | ||
| - keytypes | ||
| - columns | ||
| - select | ||
| - mapIds | ||
| - SomaDb-class | ||
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| - title: Data Objects | ||
| desc: > | ||
| Objects provided with `SomaScan.db` | ||
| contents: | ||
| - SomaScan.db | ||
| - somascan_menu | ||
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| - title: Mapping Objects | ||
| desc: > | ||
| Objects containing mappings between database keys (i.e. identifiers). | ||
| contents: | ||
| - SomaScanALIAS2PROBE | ||
| - SomaScanENSEMBL | ||
| - SomaScanENTREZID | ||
| - SomaScanENZYME | ||
| - SomaScanGENENAME | ||
| - SomaScanGO | ||
| - SomaScanMAP | ||
| - SomaScanOMIM | ||
| - SomaScanORGANISM | ||
| - SomaScanPATH | ||
| - SomaScanPMID | ||
| - SomaScanREFSEQ | ||
| - SomaScanSYMBOL | ||
| - SomaTARGETFULLNAME | ||
| - SomaScanUNIPROT | ||
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| - title: Helpers | ||
| desc: > | ||
| Miscellaneous functions for retrieving data or modifying query results. | ||
| contents: | ||
| - addTargetFullName | ||
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| - title: Accessor Functions | ||
| desc: > | ||
| Convenience functions for accessing the database. | ||
| contents: | ||
| - SomaScan_dbconn | ||
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| news: | ||
| - one_page: true |
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