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Update to the latest version of biocthis()
Basically with: ```R biocthis::use_bioc_github_action() biocthis::use_bioc_pkgdown_css() biocthis::use_bioc_issue_template() biocthis::use_bioc_feature_request_template() biocthis::use_bioc_badges() ## had to customize a few things devtools::build_readme() ## Manually coping changes from README.md to inst/app/www/README.md ```
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,37 @@ | ||
| --- | ||
| name: Feature Request | ||
| about: Suggest an idea for this package | ||
| title: "[Feature Request] A short description of the feature" | ||
| labels: '' | ||
| assignees: '' | ||
| --- | ||
|
|
||
| Please ask questions about how to use `spatialLIBD` on the Bioconductor | ||
| Support Site at <https://support.bioconductor.org> using the appropriate tag(s) | ||
| including the one for this package. | ||
|
|
||
| **Note**. Update the issue title to summarize the feature request. | ||
|
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| ## Is the feature request related to a problem? | ||
|
|
||
| Please provide a clear and concise description of what the problem | ||
| is. Ex. I'm always frustrated when [...] | ||
|
|
||
| ## Describe the solution | ||
|
|
||
| A clear and concise description of what you want to happen. | ||
|
|
||
| ## Describe any alternatives considered | ||
|
|
||
| A clear and concise description of any alternative solutions or | ||
| features you've considered. | ||
|
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| ## Additional context | ||
|
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| Add any other context about the feature request here. You may include web links | ||
| (e.g., from GitHub) to: | ||
|
|
||
| * raw code | ||
| * a commit | ||
| * code inside a commit | ||
| * code from an R package |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,56 +1,73 @@ | ||
| --- | ||
| name: Bug report or feature request | ||
| about: Describe a bug you've seen or make a case for a new feature | ||
| title: "[BUG] Your bug or feature request" | ||
| name: Bug Report | ||
| about: Describe the bug in detail | ||
| title: "[BUG] A short description of the bug" | ||
| labels: '' | ||
| assignees: '' | ||
| --- | ||
|
|
||
| Please briefly describe your problem and what output you expect. If you have a question, please don't use this form. Instead, ask on <https://support.bioconductor.org/> using the appropriate tag(s) including one for this package. | ||
| Please ask questions about how to use `spatialLIBD` on the | ||
| [Bioconductor Support Site](https://support.bioconductor.org) using the | ||
| appropriate tag(s) including the one for this package. | ||
|
|
||
| ## Context | ||
| **Note**. Update the issue title to concisely describe the bug. | ||
|
|
||
| Provide some context for your bug report or feature request. This could be the: | ||
| ## Describe the bug | ||
|
|
||
| * link to raw code, example: https://github.com/lcolladotor/osca_LIIGH_UNAM_2020/blob/master/00-template.Rmd#L24-L28 | ||
| * link to a commit, example: https://github.com/lcolladotor/osca_LIIGH_UNAM_2020/commit/6aa30b22eda614d932c12997ba611ba582c435d7 | ||
| * link to a line of code inside a commit, example: https://github.com/lcolladotor/osca_LIIGH_UNAM_2020/commit/6aa30b22eda614d932c12997ba611ba582c435d7#diff-e265269fe4f17929940e81341b92b116R17 | ||
| * link to code from an R package, example: https://github.com/LieberInstitute/spatialLIBD/blob/master/R/run_app.R#L51-L55 | ||
| Please provide a clear and concise description of what the bug is. | ||
|
|
||
| ## Code | ||
| ### Provide a minimally reproducible example (reprex) | ||
|
|
||
| Include the code you ran and comments | ||
| Provide a clear and concise description of the bug. It can be easily (but not | ||
| necessarily) illustrated with a minimally reproducible example using the | ||
| [`reprex` package](https://reprex.tidyverse.org/articles/learn-reprex.html). | ||
|
|
||
| ```R | ||
| ## prompt an error | ||
| stop('hola') | ||
| For tips on creating a reprex, see this | ||
| [StackOverflow link](https://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example). | ||
|
|
||
| ## check the error trace | ||
| traceback() | ||
| ``` | ||
| ## Expected behavior | ||
|
|
||
| ## Small reproducible example | ||
| A clear and concise description of what you expected to happen. | ||
|
|
||
| If you copy the lines of code that lead to your error, you can then run [`reprex::reprex()`](https://reprex.tidyverse.org/reference/reprex.html) which will create a small website with code you can then easily copy-paste here in a way that will be easy to work with later on. | ||
| ## R Session Information | ||
|
|
||
| ```R | ||
| ## prompt an error | ||
| stop('hola') | ||
| #> Error in eval(expr, envir, enclos): hola | ||
| Please report the output of either `sessionInfo()` or | ||
| `sessioninfo::session_info()` here. | ||
|
|
||
| <details> | ||
|
|
||
| ## check the error trace | ||
| traceback() | ||
| #> No traceback available | ||
| ```R | ||
| options(width = 120) | ||
| ## insert session info here | ||
| # sessioninfo::session_info() ## provides GitHub, pandoc, and other details | ||
| # sessionInfo() ## base R function in case you don't want to install sessioninfo | ||
| ``` | ||
|
|
||
| </details> | ||
|
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||
| ## R session information | ||
| Indicate whether `BiocManager::valid()` returns `TRUE`. | ||
|
|
||
| Remember to include your full R session information. | ||
| - [ ] `BiocManager::valid()` is `TRUE` | ||
|
|
||
| ```R | ||
| options(width = 120) | ||
| sessioninfo::session_info() | ||
| ``` | ||
| **Note**. To avoid potential issues with version mixing and reproducibility, do | ||
| not install packages from `GitHub`. | ||
|
|
||
| ## Additional Context | ||
|
|
||
| Provide some additional context for the bug report. You may include web links | ||
| (e.g., from GitHub) to: | ||
|
|
||
| * raw code | ||
| * a commit | ||
| * code inside a commit | ||
| * code from an R package | ||
|
|
||
| ## Is the package installed via bioconda? | ||
|
|
||
| We find that [bioconda](https://bioconda.github.io/) installations can often be | ||
| problematic due to the nature of the setup environment and potential for version | ||
| mixing. | ||
|
|
||
| The preferred method for installing Bioconductor software through `BiocManager` | ||
| and we do not support issues related to `bioconda` installations at this time. | ||
|
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||
| The output of `sessioninfo::session_info()` includes relevant GitHub installation information and other details that are missed by `sessionInfo()`. |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -36,7 +36,7 @@ name: R-CMD-check-bioc | |
| env: | ||
| has_testthat: 'true' | ||
| run_covr: 'true' | ||
| run_pkgdown: 'false' | ||
| run_pkgdown: 'true' | ||
| has_RUnit: 'false' | ||
| cache-version: 'cache-v1' | ||
| run_docker: 'false' | ||
|
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@@ -52,9 +52,9 @@ jobs: | |
| fail-fast: false | ||
| matrix: | ||
| config: | ||
| - { os: ubuntu-latest, r: '4.2', bioc: '3.15', cont: "bioconductor/bioconductor_docker:RELEASE_3_15", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" } | ||
| #- { os: macOS-latest, r: '4.2', bioc: '3.15'} | ||
| #- { os: windows-latest, r: '4.2', bioc: '3.15'} | ||
| - { os: ubuntu-latest, r: '4.2', bioc: '3.16', cont: "bioconductor/bioconductor_docker:RELEASE_3_16", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" } | ||
| - { os: macOS-latest, r: '4.2', bioc: '3.16'} | ||
| - { os: windows-latest, r: '4.2', bioc: '3.16'} | ||
| ## Check https://github.com/r-lib/actions/tree/master/examples | ||
| ## for examples using the http-user-agent | ||
| env: | ||
|
|
@@ -79,20 +79,20 @@ jobs: | |
| ## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml | ||
| ## If they update their steps, we will also need to update ours. | ||
| - name: Checkout Repository | ||
| uses: actions/checkout@v2 | ||
| uses: actions/checkout@v3 | ||
|
|
||
| ## R is already included in the Bioconductor docker images | ||
| - name: Setup R from r-lib | ||
| if: runner.os != 'Linux' | ||
| uses: r-lib/actions/setup-r@master | ||
| uses: r-lib/actions/setup-r@v2 | ||
| with: | ||
| r-version: ${{ matrix.config.r }} | ||
| http-user-agent: ${{ matrix.config.http-user-agent }} | ||
|
|
||
| ## pandoc is already included in the Bioconductor docker images | ||
| - name: Setup pandoc from r-lib | ||
| if: runner.os != 'Linux' | ||
| uses: r-lib/actions/setup-pandoc@master | ||
| uses: r-lib/actions/setup-pandoc@v2 | ||
|
|
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| - name: Query dependencies | ||
| run: | | ||
|
|
@@ -102,19 +102,19 @@ jobs: | |
|
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| - name: Restore R package cache | ||
| if: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'" | ||
| uses: actions/cache@v2 | ||
| uses: actions/cache@v3 | ||
| with: | ||
| path: ${{ env.R_LIBS_USER }} | ||
| key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_15-r-4.2-${{ hashFiles('.github/depends.Rds') }} | ||
| restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_15-r-4.2- | ||
| key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-${{ hashFiles('.github/depends.Rds') }} | ||
| restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2- | ||
|
|
||
| - name: Cache R packages on Linux | ||
| if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' " | ||
| uses: actions/cache@v2 | ||
| uses: actions/cache@v3 | ||
| with: | ||
| path: /home/runner/work/_temp/Library | ||
| key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_15-r-4.2-${{ hashFiles('.github/depends.Rds') }} | ||
| restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_15-r-4.2- | ||
| key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-${{ hashFiles('.github/depends.Rds') }} | ||
| restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2- | ||
|
|
||
| - name: Install Linux system dependencies | ||
| if: runner.os == 'Linux' | ||
|
|
@@ -176,7 +176,7 @@ jobs: | |
| gha_repos <- if( | ||
| .Platform$OS.type == "unix" && Sys.info()["sysname"] != "Darwin" | ||
| ) c( | ||
| "AnVIL" = "https://bioconductordocker.blob.core.windows.net/packages/3.15/bioc", | ||
| "AnVIL" = "https://bioconductordocker.blob.core.windows.net/packages/3.16/bioc", | ||
| BiocManager::repositories() | ||
| ) else BiocManager::repositories() | ||
|
|
@@ -276,25 +276,41 @@ jobs: | |
| if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux' | ||
| run: R CMD INSTALL . | ||
|
|
||
| - name: Build and deploy pkgdown site | ||
| - name: Build pkgdown site | ||
| if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux' | ||
| run: | | ||
| git config --local user.name "$GITHUB_ACTOR" | ||
| git config --local user.email "[email protected]" | ||
| Rscript -e "pkgdown::deploy_to_branch(new_process = FALSE)" | ||
| shell: bash {0} | ||
| run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE) | ||
| shell: Rscript {0} | ||
| ## Note that you need to run pkgdown::deploy_to_branch(new_process = FALSE) | ||
| ## at least one locally before this will work. This creates the gh-pages | ||
| ## branch (erasing anything you haven't version controlled!) and | ||
| ## makes the git history recognizable by pkgdown. | ||
|
|
||
| - name: Install deploy dependencies | ||
| if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux' | ||
| run: | | ||
| apt-get update && apt-get -y install rsync | ||
| - name: Deploy pkgdown site to GitHub pages 🚀 | ||
| if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux' | ||
| uses: JamesIves/github-pages-deploy-action@releases/v4 | ||
| with: | ||
| clean: false | ||
| branch: gh-pages | ||
| folder: docs | ||
|
|
||
| - name: Upload check results | ||
| if: failure() | ||
| uses: actions/upload-artifact@master | ||
| with: | ||
| name: ${{ runner.os }}-biocversion-RELEASE_3_15-r-4.2-results | ||
| name: ${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-results | ||
| path: check | ||
|
|
||
| ## Note that DOCKER_PASSWORD is really a token for your dockerhub | ||
| ## account, not your actual dockerhub account password. | ||
| ## This comes from | ||
| ## https://seandavi.github.io/BuildABiocWorkshop/articles/HOWTO_BUILD_WORKSHOP.html#6-add-secrets-to-github-repo | ||
| ## Check https://github.com/docker/build-push-action/tree/releases/v1 | ||
| ## for more details. | ||
| - uses: docker/build-push-action@v1 | ||
| if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && runner.os == 'Linux' " | ||
| with: | ||
|
|
||
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