diff --git a/.github/ISSUE_TEMPLATE/feature_request_template.md b/.github/ISSUE_TEMPLATE/feature_request_template.md new file mode 100644 index 00000000..21d2a926 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/feature_request_template.md @@ -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 using the appropriate tag(s) +including the one for this package. + +**Note**. Update the issue title to summarize the feature request. + +## 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. + +## Additional context + +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 diff --git a/.github/ISSUE_TEMPLATE/issue_template.md b/.github/ISSUE_TEMPLATE/issue_template.md index 6e857c69..becde438 100644 --- a/.github/ISSUE_TEMPLATE/issue_template.md +++ b/.github/ISSUE_TEMPLATE/issue_template.md @@ -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 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. + +
-## 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 ``` +
-## 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. -The output of `sessioninfo::session_info()` includes relevant GitHub installation information and other details that are missed by `sessionInfo()`. diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml index 530497b3..001279ec 100644 --- a/.github/workflows/check-bioc.yml +++ b/.github/workflows/check-bioc.yml @@ -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' @@ -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: @@ -79,12 +79,12 @@ 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 }} @@ -92,7 +92,7 @@ jobs: ## 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 - name: Query dependencies run: | @@ -102,19 +102,19 @@ jobs: - 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 "$GITHUB_ACTOR@users.noreply.github.com" - 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: ${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-results path: check + ## Note that DOCKER_PASSWORD is really a token for your dockerhub + ## account, not your actual dockerhub account password. + ## This comes from + ## https://seandavi.github.io/BuildABiocWorkshop/articles/HOWTO_BUILD_WORKSHOP.html#6-add-secrets-to-github-repo + ## Check https://github.com/docker/build-push-action/tree/releases/v1 + ## for more details. - uses: docker/build-push-action@v1 if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && runner.os == 'Linux' " with: diff --git a/README.Rmd b/README.Rmd index dc8c6e2a..e314bd89 100644 --- a/README.Rmd +++ b/README.Rmd @@ -17,13 +17,19 @@ knitr::opts_chunk$set( [![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://www.tidyverse.org/lifecycle/#stable) -[![BioC status](http://bioconductor.org/shields/build/release/data-experiment/spatialLIBD.svg)](http://bioconductor.org/checkResults/release/data-experiment-LATEST/spatialLIBD/) -[![BioC dev status](http://bioconductor.org/shields/build/devel/data-experiment/spatialLIBD.svg)](http://bioconductor.org/checkResults/devel/data-experiment-LATEST/spatialLIBD/) +[![Bioc release status](http://www.bioconductor.org/shields/build/release/data-experiment/spatialLIBD.svg)](https://bioconductor.org/checkResults/release/data-experiment-LATEST/spatialLIBD) +[![Bioc devel status](http://www.bioconductor.org/shields/build/devel/data-experiment/spatialLIBD.svg)](https://bioconductor.org/checkResults/devel/data-experiment-LATEST/spatialLIBD) +[![Bioc downloads rank](https://bioconductor.org/shields/downloads/release/spatialLIBD.svg)](http://bioconductor.org/packages/stats/bioc/spatialLIBD/) +[![Bioc support](https://bioconductor.org/shields/posts/spatialLIBD.svg)](https://support.bioconductor.org/tag/spatialLIBD) +[![Bioc history](https://bioconductor.org/shields/years-in-bioc/spatialLIBD.svg)](https://bioconductor.org/packages/release/data-experiment/html/spatialLIBD.html#since) +[![Bioc last commit](https://bioconductor.org/shields/lastcommit/devel/data-experiment/spatialLIBD.svg)](http://bioconductor.org/checkResults/devel/data-experiment-LATEST/spatialLIBD/) +[![Bioc dependencies](https://bioconductor.org/shields/dependencies/release/spatialLIBD.svg)](https://bioconductor.org/packages/release/data-experiment/html/spatialLIBD.html#since) [![Codecov test coverage](https://codecov.io/gh/LieberInstitute/spatialLIBD/branch/master/graph/badge.svg)](https://codecov.io/gh/LieberInstitute/spatialLIBD?branch=master) [![R build status](https://github.com/LieberInstitute/spatialLIBD/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/LieberInstitute/spatialLIBD/actions) -[![Support site activity, last 6 months: tagged questions/avg. answers per question/avg. comments per question/accepted answers, or 0 if no tagged posts.](http://www.bioconductor.org/shields/posts/spatialLIBD.svg)](https://support.bioconductor.org/t/spatialLIBD/) [![GitHub issues](https://img.shields.io/github/issues/LieberInstitute/spatialLIBD)](https://github.com/LieberInstitute/spatialLIBD/issues) [![DOI](https://zenodo.org/badge/225913568.svg)](https://zenodo.org/badge/latestdoi/225913568) + + Welcome to the `spatialLIBD` project! It is composed of: diff --git a/README.md b/README.md index 32bfd80c..c1ece4d4 100644 --- a/README.md +++ b/README.md @@ -7,21 +7,28 @@ [![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://www.tidyverse.org/lifecycle/#stable) -[![BioC -status](http://bioconductor.org/shields/build/release/data-experiment/spatialLIBD.svg)](http://bioconductor.org/checkResults/release/data-experiment-LATEST/spatialLIBD/) -[![BioC dev -status](http://bioconductor.org/shields/build/devel/data-experiment/spatialLIBD.svg)](http://bioconductor.org/checkResults/devel/data-experiment-LATEST/spatialLIBD/) +[![Bioc release +status](http://www.bioconductor.org/shields/build/release/data-experiment/spatialLIBD.svg)](https://bioconductor.org/checkResults/release/data-experiment-LATEST/spatialLIBD) +[![Bioc devel +status](http://www.bioconductor.org/shields/build/devel/data-experiment/spatialLIBD.svg)](https://bioconductor.org/checkResults/devel/data-experiment-LATEST/spatialLIBD) +[![Bioc downloads +rank](https://bioconductor.org/shields/downloads/release/spatialLIBD.svg)](http://bioconductor.org/packages/stats/bioc/spatialLIBD/) +[![Bioc +support](https://bioconductor.org/shields/posts/spatialLIBD.svg)](https://support.bioconductor.org/tag/spatialLIBD) +[![Bioc +history](https://bioconductor.org/shields/years-in-bioc/spatialLIBD.svg)](https://bioconductor.org/packages/release/data-experiment/html/spatialLIBD.html#since) +[![Bioc last +commit](https://bioconductor.org/shields/lastcommit/devel/data-experiment/spatialLIBD.svg)](http://bioconductor.org/checkResults/devel/data-experiment-LATEST/spatialLIBD/) +[![Bioc +dependencies](https://bioconductor.org/shields/dependencies/release/spatialLIBD.svg)](https://bioconductor.org/packages/release/data-experiment/html/spatialLIBD.html#since) [![Codecov test coverage](https://codecov.io/gh/LieberInstitute/spatialLIBD/branch/master/graph/badge.svg)](https://codecov.io/gh/LieberInstitute/spatialLIBD?branch=master) [![R build status](https://github.com/LieberInstitute/spatialLIBD/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/LieberInstitute/spatialLIBD/actions) -[![Support site activity, last 6 months: tagged questions/avg. answers -per question/avg. comments per question/accepted answers, or 0 if no -tagged -posts.](http://www.bioconductor.org/shields/posts/spatialLIBD.svg)](https://support.bioconductor.org/t/spatialLIBD/) [![GitHub issues](https://img.shields.io/github/issues/LieberInstitute/spatialLIBD)](https://github.com/LieberInstitute/spatialLIBD/issues) [![DOI](https://zenodo.org/badge/225913568.svg)](https://zenodo.org/badge/latestdoi/225913568) + Welcome to the `spatialLIBD` project! It is composed of: diff --git a/inst/app/www/README.md b/inst/app/www/README.md index 115d3a04..e64f3653 100644 --- a/inst/app/www/README.md +++ b/inst/app/www/README.md @@ -7,21 +7,28 @@ [![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://www.tidyverse.org/lifecycle/#stable) -[![BioC -status](http://bioconductor.org/shields/build/release/data-experiment/spatialLIBD.svg)](http://bioconductor.org/checkResults/release/data-experiment-LATEST/spatialLIBD/) -[![BioC dev -status](http://bioconductor.org/shields/build/devel/data-experiment/spatialLIBD.svg)](http://bioconductor.org/checkResults/devel/data-experiment-LATEST/spatialLIBD/) +[![Bioc release +status](http://www.bioconductor.org/shields/build/release/data-experiment/spatialLIBD.svg)](https://bioconductor.org/checkResults/release/data-experiment-LATEST/spatialLIBD) +[![Bioc devel +status](http://www.bioconductor.org/shields/build/devel/data-experiment/spatialLIBD.svg)](https://bioconductor.org/checkResults/devel/data-experiment-LATEST/spatialLIBD) +[![Bioc downloads +rank](https://bioconductor.org/shields/downloads/release/spatialLIBD.svg)](http://bioconductor.org/packages/stats/bioc/spatialLIBD/) +[![Bioc +support](https://bioconductor.org/shields/posts/spatialLIBD.svg)](https://support.bioconductor.org/tag/spatialLIBD) +[![Bioc +history](https://bioconductor.org/shields/years-in-bioc/spatialLIBD.svg)](https://bioconductor.org/packages/release/data-experiment/html/spatialLIBD.html#since) +[![Bioc last +commit](https://bioconductor.org/shields/lastcommit/devel/data-experiment/spatialLIBD.svg)](http://bioconductor.org/checkResults/devel/data-experiment-LATEST/spatialLIBD/) +[![Bioc +dependencies](https://bioconductor.org/shields/dependencies/release/spatialLIBD.svg)](https://bioconductor.org/packages/release/data-experiment/html/spatialLIBD.html#since) [![Codecov test coverage](https://codecov.io/gh/LieberInstitute/spatialLIBD/branch/master/graph/badge.svg)](https://codecov.io/gh/LieberInstitute/spatialLIBD?branch=master) [![R build status](https://github.com/LieberInstitute/spatialLIBD/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/LieberInstitute/spatialLIBD/actions) -[![Support site activity, last 6 months: tagged questions/avg. answers -per question/avg. comments per question/accepted answers, or 0 if no -tagged -posts.](http://www.bioconductor.org/shields/posts/spatialLIBD.svg)](https://support.bioconductor.org/t/spatialLIBD/) [![GitHub issues](https://img.shields.io/github/issues/LieberInstitute/spatialLIBD)](https://github.com/LieberInstitute/spatialLIBD/issues) [![DOI](https://zenodo.org/badge/225913568.svg)](https://zenodo.org/badge/latestdoi/225913568) + Welcome to the `spatialLIBD` project! It is composed of: diff --git a/man/figures/README-access_data-1.png b/man/figures/README-access_data-1.png index bbdcf8db..acbb5e4e 100644 Binary files a/man/figures/README-access_data-1.png and b/man/figures/README-access_data-1.png differ diff --git a/pkgdown/extra.css b/pkgdown/extra.css new file mode 100644 index 00000000..19caa82e --- /dev/null +++ b/pkgdown/extra.css @@ -0,0 +1,99 @@ +/* +Developed and maintained by Kevin Rue-Albrecht (@kevinrue) +Borrowed by Leo from https://github.com/iSEE/iSEEhub/blob/main/pkgdown/extra.css +See https://github.com/lcolladotor/biocthis/issues/34 for more details. +*/ + +/* +#0092ac blue +#00758a darker blue (active menu) +#c4d931 green (on blue) +#87b13f green (on white) +*/ + +.headroom { + background-color: #0092ac; +} + +.navbar-default .navbar-link { + color: #ffffff; +} + +.navbar-default .navbar-link:hover { + color: #c4d931; +} + +.navbar-default .navbar-nav>.active>a, +.navbar-default .navbar-nav>.active>a:hover, +.navbar-default .navbar-nav>.active>a:focus { + color: #c4d931; + background-color: #00758a; +} + +.navbar-default .navbar-nav>.open>a, +.navbar-default .navbar-nav>.open>a:hover, +.navbar-default .navbar-nav>.open>a:focus { + color: #c4d931; + background-color: #00758a; +} + +.dropdown-menu>.active>a, +.dropdown-menu>.active>a:hover, +.dropdown-menu>.active>a:focus { + color: #c4d931; + background-color: #00758a; +} + +.navbar-default .navbar-nav>li>a:hover, +.navbar-default .navbar-nav>li>a:focus { + color: #c4d931; +} + +.dropdown-menu>li>a:hover { + color: #87b13f; + background-color: #ffffff; +} + +.navbar-default .navbar-nav>li>a { + color: #ffffff; +} + +h1 { + color: #87b13f; +} + +h2 { + color: #1a81c2; +} + +h3 { + color: #1a81c2; + font-weight: bold; +} + +.btn-copy-ex { + color: #ffffff; + background-color: #0092ac; + border-color: #0092ac; +} + +.btn-copy-ex:hover { + color: #ffffff; + background-color: #00758a; + border-color: #00758a; +} + +.btn-copy-ex:active:focus { + color: #c4d931; + background-color: #00758a; + border-color: #0092ac; +} + +p>.fa, +p>.fas { + color: #0092ac; +} + +img { + width: auto; +}