From 501db0f80f57b51fea8a27d3f84afcb72b7b34a9 Mon Sep 17 00:00:00 2001 From: wlandau-lilly Date: Fri, 8 Nov 2024 09:58:32 -0500 Subject: [PATCH] make into a quarto project --- .github/workflows/publish.yaml | 35 --- .github/workflows/render.yaml | 38 +++ .gitignore | 2 + DESCRIPTION | 54 ----- LICENSE | 2 +- LICENSE.md | 2 +- NEWS.md | 3 - R/empty.R | 10 - _bookdown.yml | 13 - _output.yml | 17 -- _quarto.yml | 22 ++ classes.Rmd => classes.qmd | 0 codemeta.json | 133 ---------- composition.Rmd => composition.qmd | 5 +- data.Rmd => data.qmd | 0 footer.html | 3 - google_analytics.html | 9 - index.Rmd => index.qmd | 0 inst/CITATION | 19 -- inst/WORDLIST | 324 ------------------------- inst/publish.sh | 10 - man/targets_design_empty.Rd | 18 -- orchestration.Rmd => orchestration.qmd | 0 tests/testthat.R | 4 - tests/testthat/test-empty.R | 3 - 25 files changed, 67 insertions(+), 659 deletions(-) delete mode 100644 .github/workflows/publish.yaml create mode 100644 .github/workflows/render.yaml delete mode 100644 DESCRIPTION delete mode 100644 NEWS.md delete mode 100644 R/empty.R delete mode 100644 _bookdown.yml delete mode 100644 _output.yml create mode 100644 _quarto.yml rename classes.Rmd => classes.qmd (100%) delete mode 100644 codemeta.json rename composition.Rmd => composition.qmd (98%) rename data.Rmd => data.qmd (100%) delete mode 100644 footer.html delete mode 100644 google_analytics.html rename index.Rmd => index.qmd (100%) delete mode 100644 inst/CITATION delete mode 100644 inst/WORDLIST delete mode 100755 inst/publish.sh delete mode 100644 man/targets_design_empty.Rd rename orchestration.Rmd => orchestration.qmd (100%) delete mode 100644 tests/testthat.R delete mode 100644 tests/testthat/test-empty.R diff --git a/.github/workflows/publish.yaml b/.github/workflows/publish.yaml deleted file mode 100644 index 7662d14..0000000 --- a/.github/workflows/publish.yaml +++ /dev/null @@ -1,35 +0,0 @@ -on: - push: - branches: main - -name: publish - -jobs: - publish: - runs-on: macOS-latest - - env: - GITHUB_PAT: ${{ secrets.GITHUBPAT }} - TORCH_INSTALL: 1 - R_REMOTES_NO_ERRORS_FROM_WARNINGS: false - - steps: - - name: Checkout repo - uses: actions/checkout@v4.2.2 - - - name: Setup R - uses: r-lib/actions/setup-r@v2 - - - name: Install system requirements - run: | - brew install pandoc - - - name: Build design specification - run: | - install.packages("bookdown") - bookdown::render_book(input = "index.Rmd", output_format = "bookdown::gitbook") - shell: Rscript {0} - - - name: Publish design specification - run: | - ./inst/publish.sh diff --git a/.github/workflows/render.yaml b/.github/workflows/render.yaml new file mode 100644 index 0000000..29b24b8 --- /dev/null +++ b/.github/workflows/render.yaml @@ -0,0 +1,38 @@ +on: + push: + branches: main + +name: render + +jobs: + render: + runs-on: ubuntu-latest + + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + R_REMOTES_NO_ERRORS_FROM_WARNINGS: false + + steps: + - uses: actions/checkout@v3 + - uses: r-lib/actions/setup-pandoc@v2 + - uses: quarto-dev/quarto-actions/setup@v2 + + - name: Cache results + uses: actions/cache@v2 + with: + path: | + _book + _freeze + key: book-render-${{ hashFiles('**/*qmd') }} + restore-keys: book-render- + + - name: Render + run: quarto render + + - 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: _book diff --git a/.gitignore b/.gitignore index 82f25b6..804f6b7 100644 --- a/.gitignore +++ b/.gitignore @@ -7,3 +7,5 @@ _bookdown_files _targets.R _targets/ targets-manual.Rmd + +/.quarto/ diff --git a/DESCRIPTION b/DESCRIPTION deleted file mode 100644 index 1ae30cb..0000000 --- a/DESCRIPTION +++ /dev/null @@ -1,54 +0,0 @@ -Package: targets.design -Title: Targets R Package Design Specification -Description: This repository contains the design specification of the 'targets' R package. - These specifications describe the internal architecture, the data storage model, - and the orchestration and branching model. The goal is to help developers contribute - to core elements of the package. Developers are encouraged to to read - the rendered output at . -Version: 1.8.0.9009 -License: MIT + file LICENSE -URL: https://books.ropensci.org/targets-design, - https://github.com/ropensci-books/targets-design -BugReports: https://github.com/ropensci-books/targets-design/issues -Authors@R: c( - person( - given = c("William", "Michael"), - family = "Landau", - role = c("aut", "cre"), - email = "will.landau@gmail.com", - comment = c(ORCID = "0000-0003-1878-3253") - ), - person( - given = "Samantha", - family = "Oliver", - role = "rev", - comment = c(ORCID = "0000-0001-5668-1165") - ), - person( - given = "Tristan", - family = "Mahr", - role = "rev", - comment = c(ORCID = "0000-0002-8890-5116") - ), - person( - family = "Eli Lilly and Company", - role = "cph" - )) -Depends: - R (>= 3.5.0) -Imports: - bookdown (>= 0.21), - tarchetypes (>= 0.0.1), - targets (>= 0.0.1), -Suggests: - knitr (>= 1.30), - rmarkdown (>= 2.4), - testthat (>= 2.3.2) -Remotes: - ropensci/tarchetypes, - ropensci/targets -Encoding: UTF-8 -Language: en-US -Roxygen: list(markdown = TRUE) -RoxygenNote: 7.1.1 -VignetteBuilder: knitr diff --git a/LICENSE b/LICENSE index b231b9f..9244f14 100644 --- a/LICENSE +++ b/LICENSE @@ -1,2 +1,2 @@ -YEAR: 2020 +YEAR: 2024 COPYRIGHT HOLDER: Eli Lilly and Company diff --git a/LICENSE.md b/LICENSE.md index 614c900..c9bb514 100644 --- a/LICENSE.md +++ b/LICENSE.md @@ -1,6 +1,6 @@ # MIT License -Copyright (c) 2020 Eli Lilly and Company +Copyright (c) 2024 Eli Lilly and Company Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/NEWS.md b/NEWS.md deleted file mode 100644 index 29de58a..0000000 --- a/NEWS.md +++ /dev/null @@ -1,3 +0,0 @@ -# targets.design 0.0.1 - -* First version diff --git a/R/empty.R b/R/empty.R deleted file mode 100644 index b3f2685..0000000 --- a/R/empty.R +++ /dev/null @@ -1,10 +0,0 @@ -#' @title Empty function -#' @export -#' @description This is a bookdown manual. It only -#' borrows R package infrastructure for devops purposes. -#' @return Nothing. -#' @examples -#' targets_design_empty() -targets_design_empty <- function() { - invisible() -} diff --git a/_bookdown.yml b/_bookdown.yml deleted file mode 100644 index 52e9cb8..0000000 --- a/_bookdown.yml +++ /dev/null @@ -1,13 +0,0 @@ -book_filename: "targets-design" -repo: "https://ropensci.github.io/targets-design" -language: - ui: - chapter_name: "Chapter " -delete_merged_file: true -rmd_files: [ - "index.Rmd", - "data.Rmd", - "classes.Rmd", - "composition.Rmd", - "orchestration.Rmd" -] diff --git a/_output.yml b/_output.yml deleted file mode 100644 index d24b416..0000000 --- a/_output.yml +++ /dev/null @@ -1,17 +0,0 @@ -bookdown::gitbook: - config: - sharing: - github: yes - facebook: false - toc: - collapse: subsection - before: | -
  • The targets R Package Design Documents
    • - after: | -
  • Published with bookdown
    • - edit: - link: https://github.com/ropensci/targets-design/edit/main/%s - text: "Edit this chapter" - history: - link: https://github.com/ropensci/targets-design/commits/main/%s - text: "Chapter edit history" diff --git a/_quarto.yml b/_quarto.yml new file mode 100644 index 0000000..ca87640 --- /dev/null +++ b/_quarto.yml @@ -0,0 +1,22 @@ +project: + type: book + +book: + title: "The {targets} R package design specification" + author: "Will Landau" + site-url: https://books.ropensci.org/targets-design/ + repo-url: https://github.com/ropensci-books/targets-design/ + repo-branch: main + repo-actions: [edit] + sharing: [twitter, facebook, linkedin] + page-footer: "How to get help:
    Copyright 2024, Eli Lilly and Company" + chapters: + - index.qmd + - data.qmd + - classes.qmd + - composition.qmd + - orchestration.qmd + +format: + html: + theme: cosmo diff --git a/classes.Rmd b/classes.qmd similarity index 100% rename from classes.Rmd rename to classes.qmd diff --git a/codemeta.json b/codemeta.json deleted file mode 100644 index b53c86c..0000000 --- a/codemeta.json +++ /dev/null @@ -1,133 +0,0 @@ -{ - "@context": [ - "https://doi.org/10.5063/schema/codemeta-2.0", - "http://schema.org" - ], - "@type": "SoftwareSourceCode", - "identifier": "targets.design", - "description": "This repository contains the design documents of the 'targets' R package.\n These specifications describe the internal architecture, the data storage model,\n and the orchestration and branching model. The goal is to help developers contribute\n to core elements of the package. Developers are encouraged to to read\n the rendered output at .", - "name": "targets.design: Targets R Package Design Documents", - "codeRepository": "https://github.com/ropensci-books/targets-design", - "relatedLink": "https://books.ropensci.org/targets-design", - "issueTracker": "https://github.com/ropensci-books/targets-design/issues", - "license": "https://spdx.org/licenses/MIT", - "version": "0.0.1", - "programmingLanguage": { - "@type": "ComputerLanguage", - "name": "R", - "url": "https://r-project.org" - }, - "runtimePlatform": "R version 4.0.3 (2020-10-10)", - "author": [ - { - "@type": "Person", - "givenName": ["William", "Michael"], - "familyName": "Landau", - "email": "will.landau@gmail.com", - "@id": "https://orcid.org/0000-0003-1878-3253" - } - ], - "contributor": {}, - "copyrightHolder": [ - { - "@type": "Organization", - "name": "Eli Lilly and Company" - } - ], - "funder": {}, - "maintainer": [ - { - "@type": "Person", - "givenName": ["William", "Michael"], - "familyName": "Landau", - "email": "will.landau@gmail.com", - "@id": "https://orcid.org/0000-0003-1878-3253" - } - ], - "softwareSuggestions": [ - { - "@type": "SoftwareApplication", - "identifier": "knitr", - "name": "knitr", - "version": ">= 1.30", - "provider": { - "@id": "https://cran.r-project.org", - "@type": "Organization", - "name": "Comprehensive R Archive Network (CRAN)", - "url": "https://cran.r-project.org" - }, - "sameAs": "https://CRAN.R-project.org/package=knitr" - }, - { - "@type": "SoftwareApplication", - "identifier": "rmarkdown", - "name": "rmarkdown", - "version": ">= 2.4", - "provider": { - "@id": "https://cran.r-project.org", - "@type": "Organization", - "name": "Comprehensive R Archive Network (CRAN)", - "url": "https://cran.r-project.org" - }, - "sameAs": "https://CRAN.R-project.org/package=rmarkdown" - }, - { - "@type": "SoftwareApplication", - "identifier": "testthat", - "name": "testthat", - "version": ">= 2.3.2", - "provider": { - "@id": "https://cran.r-project.org", - "@type": "Organization", - "name": "Comprehensive R Archive Network (CRAN)", - "url": "https://cran.r-project.org" - }, - "sameAs": "https://CRAN.R-project.org/package=testthat" - } - ], - "softwareRequirements": [ - { - "@type": "SoftwareApplication", - "identifier": "R", - "name": "R", - "version": ">= 3.5.0" - }, - { - "@type": "SoftwareApplication", - "identifier": "bookdown", - "name": "bookdown", - "version": ">= 0.21", - "provider": { - "@id": "https://cran.r-project.org", - "@type": "Organization", - "name": "Comprehensive R Archive Network (CRAN)", - "url": "https://cran.r-project.org" - }, - "sameAs": "https://CRAN.R-project.org/package=bookdown" - }, - { - "@type": "SoftwareApplication", - "identifier": "tarchetypes", - "name": "tarchetypes", - "version": ">= 0.0.1", - "sameAs": "https://github.com/ropensci/tarchetypes" - }, - { - "@type": "SoftwareApplication", - "identifier": "targets", - "name": "targets", - "version": ">= 0.0.1", - "sameAs": "https://github.com/ropensci/targets" - } - ], - "releaseNotes": "https://github.com/ropensci-books/targets-design/blob/master/NEWS.md", - "fileSize": "1120.876KB", - "developmentStatus": "https://www.repostatus.org/#active", - "review": { - "@type": "Review", - "url": "https://github.com/ropensci/software-review/issues/401", - "provider": "https://ropensci.org" - }, - "readme": "https://github.com/ropensci-books/targets-design/blob/main/README.md", - "keywords": ["targets", "r", "rstats", "workflow", "reproducibility", "high-performance-computing", "pipeline", "make"] -} diff --git a/composition.Rmd b/composition.qmd similarity index 98% rename from composition.Rmd rename to composition.qmd index 0570517..039e26a 100644 --- a/composition.Rmd +++ b/composition.qmd @@ -26,10 +26,11 @@ Command | ✓ | ✓ | ✓ | ✓ | ✓ | Settings | ✓ | ✓ | ✓ | ✓ | ✓ | Value | ✓ | ✓ | ✓ | ✓ | ✓ | Metrics | ✓ | ✓ | ✓ | | | -Store | ✓ | ✓ | ✓ | | | +Store | ✓ | ✓ | ✓ | | ✓ | +File | ✓ | ✓ | ✓ | | | Subpipeline | ✓ | ✓ | ✓ | | | Junction | | ✓ | | | ✓ | -Cue | ✓ | ✓ | ✓ | | | +Cue | ✓ | ✓ | ✓ | | ✓ | Patternview | | | | | ✓ | The class inheritance hierarchy of targets is below, and the [orchestration chapter](#orchestration) explains why the package is designed this way. diff --git a/data.Rmd b/data.qmd similarity index 100% rename from data.Rmd rename to data.qmd diff --git a/footer.html b/footer.html deleted file mode 100644 index cbd68e9..0000000 --- a/footer.html +++ /dev/null @@ -1,3 +0,0 @@ -
    - Copyright Eli Lilly and Company -
    diff --git a/google_analytics.html b/google_analytics.html deleted file mode 100644 index 96d509b..0000000 --- a/google_analytics.html +++ /dev/null @@ -1,9 +0,0 @@ - - - diff --git a/index.Rmd b/index.qmd similarity index 100% rename from index.Rmd rename to index.qmd diff --git a/inst/CITATION b/inst/CITATION deleted file mode 100644 index 248f20e..0000000 --- a/inst/CITATION +++ /dev/null @@ -1,19 +0,0 @@ -citHeader("The targets design specification is part of targets. To cite targets, see below:") - -citEntry( - entry = "Article", - title = "The targets R package: a dynamic Make-like function-oriented pipeline toolkit for reproducibility and high-performance computing", - author = "William Michael Landau", - journal = "Journal of Open Source Software", - year = 2021, - volume = 6, - number = 57, - pages = 2959, - url = "https://doi.org/10.21105/joss.02959", - textVersion = paste( - "Landau, W. M., (2021). The targets R package: a dynamic Make-like", - "function-oriented pipeline toolkit for reproducibility and", - "high-performance computing. Journal of Open Source Software,", - "6(57), 2959, https://doi.org/10.21105/joss.02959" - ) -) diff --git a/inst/WORDLIST b/inst/WORDLIST deleted file mode 100644 index 76010e8..0000000 --- a/inst/WORDLIST +++ /dev/null @@ -1,324 +0,0 @@ -’ -’s -Acknowledgements -acyclic -addin -advisor -ailProbPaper -al -algo -ALTREP -Ane -args -Args -autoclean -Axthelm -backoff -Badi -Baltagi -batchtools -bdbfcddb -Bengtsson -Bioinformatics -Boneri -bookdown -Bostock -brancher -Broman -Broman's -bugfix -Bugfix -bugfixes -Bugfixes -cancelled -changelog -Changelog -checksum -checksums -Checksum -Checksums -childlist -chmod -Clarkberg -clustermq -codecov -codeless -coef -coercible -compendia -config -connectedness -counterintuitive -cpu -cranlogs -CRAN -CRAN's -creatable -customizable -cyclomatic -da -DataFest -deduplicate -del -demografia -deps -dequeue -dequeued -deregister -dereferenced -deterministically -devops -devtools -discoverability -docstring -Dobbyn -doi -dplyr -DSL -drakeplanner -DropBox -dt -Ebihara -Ecdat -Econometrics -econometrics -efcaguab -else's -eng -envir -errored -et -ETag -eval -expr -extensibility -f15face7d72c15c2d1098da959492bdbfcddb425 -Factual's -Falster -faq -FitzJohn -flowlines -fst -ftp -Gametophytes -Genotype -ggplot -github -GitLab -globals -gridlines -gsp -gzip -Halotype -HDF -HDF5 -hotfix -HPC -hpc -http -https -igraph -Igraph -IndianaCHE -Inivisibly -instantiation -Intercross -init -io -Jarad -Jeroen -joelnitta -JOSS -joss -Karthik -kbroman -Kendon -Keras -keras -Kirill -Kirill's -knitr -Knitr -lapply -learnings -lifecycle -loadd -Loadd -Lowndes -Maëlle -Makefile -Makefiles -makinoi -Marwick -mbostock -mc -mclapply -md -memoise -Memoise -Memoize -memoize -memoization -Memoization -memoized -Metaflow -metaprogram -metaprogrammed -metaprogramming -modularity -mtcars -Müller -multisession -Munnell -namespaced -Nantz -NHDPlus -Niemi -Nitta -nolint -nsw -Ooms -OOP -OneDrive -ORCID -OSF -outdatedness -overengineering -packrat -Packrat -pandoc -parallelizable -parallelization -parallelize -parallelizing -parLapply -passwd -patternview -Payseur -pditmmaso -PhantomJS -Pharma -Phylogenetic -phyloQTLpaper -Pinnoi -pleurosoriopsis -Pleurorosiopsis -Polypodiaceae -POSIXct -pre -preCCProbPaper -preclean -precomputed -prelocal -preprocess -preprocessed -preprocesses -prettycode -prework -programmatically -Programmatically -PSOCK -quasiquotation -quickstart -Quickstart -Rbuildignore -RDS -README -Recombinant -reimagine -reimagining -reimplement -replicability -reproducibility -Reproducibility -reproducibly -rerender -RL -rmarkdown -Rmd -RMSPE -roadmap -ropensci -rOpenSci -RStudio -Rtools -Rüeger -runthrough -Sankey -Saunak -scalability -scalable -Schratzur -shinyapps -Sina -sitrep -skippable -SLURM -SSP -Stallman -Stawitz -storr -Storr -subclass -subcomponents -subflow -subfolder -subgraphs -Subgraphs -Subpipeline -subplan -sugiyama -Sungjin -tempfile -templating -tensorflow -tibble -tibbles -tidyeval -tidyselect -Tidyverse -tidyverse -tiernanmartin -tmpl -toc -toolkits -traceback -txtq -UD -un -unhandled -Univa -unparsable -unserialize -unserialized -untimed -untransformed -validators -vectorization -vectorized -versioning -VignetteEncoding -VignetteEngine -VignetteIndexEntry -vis -visNetwork -voto -walkthrough -walkthroughs -webshot -whitelist -widehat -wip -withTimeout -wlandau -workflowr -workplan -workspace -workspaces -YAML -yaml -yml -Yub -zenodo -zeromq -ZeroMQ diff --git a/inst/publish.sh b/inst/publish.sh deleted file mode 100755 index 6ba9262..0000000 --- a/inst/publish.sh +++ /dev/null @@ -1,10 +0,0 @@ -git config --global user.email "will.landau@gmail.com" -git config --global user.name "wlandau" -[ -z "${GITHUB_PAT}" ] && exit 0 -git clone -b gh-pages https://${GITHUB_PAT}@github.com/ropensci-books/targets-design.git gh-pages -cd gh-pages -ls -a | grep -Ev "^\.$|^..$|^\.git$" | xargs rm -rf -cp -r ../_book/* ./ -git add * -git commit -am "Update the design docs" || true -git push origin gh-pages diff --git a/man/targets_design_empty.Rd b/man/targets_design_empty.Rd deleted file mode 100644 index 26095a7..0000000 --- a/man/targets_design_empty.Rd +++ /dev/null @@ -1,18 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/empty.R -\name{targets_design_empty} -\alias{targets_design_empty} -\title{Empty function} -\usage{ -targets_design_empty() -} -\value{ -Nothing. -} -\description{ -This is a bookdown manual. It only -borrows R package infrastructure for devops purposes. -} -\examples{ -targets_design_empty() -} diff --git a/orchestration.Rmd b/orchestration.qmd similarity index 100% rename from orchestration.Rmd rename to orchestration.qmd diff --git a/tests/testthat.R b/tests/testthat.R deleted file mode 100644 index c21be15..0000000 --- a/tests/testthat.R +++ /dev/null @@ -1,4 +0,0 @@ -library(testthat) -library(targets.design) - -test_check("targets.design") diff --git a/tests/testthat/test-empty.R b/tests/testthat/test-empty.R deleted file mode 100644 index 228fc97..0000000 --- a/tests/testthat/test-empty.R +++ /dev/null @@ -1,3 +0,0 @@ -test_that("empty", { - expect_null(targets_design_empty()) -})