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add R Markdown - knitr cache example & show default booleans
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Vincent Clemson
parent
14bc367517
commit
e5e58a06aa
2 changed files with 83 additions and 39 deletions
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@ -31,8 +31,8 @@ If you are using this inside a container, a POSIX-compliant `tar` needs to be in
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* `key` - An explicit key for restoring and saving the cache
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* `restore-keys` - An ordered list of keys to use for restoring stale cache if no cache hit occurred for key. Note
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`cache-hit` returns false in this case.
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* `reeval` - A boolean. Whether to reevaluate the `key` argument in the action's post run script when saving cache. Set to `true` if you would like your cache key set after your job's steps are complete.
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* `only-restore` - A boolean. Whether to only perform cache restoration and not the save post run script.
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* `reeval` - A boolean. Default set to `false`. Whether to reevaluate the `key` argument in the action's post run script when saving cache. Set to `true` if you would like your cache key set after your job's steps are complete.
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* `only-restore` - A boolean. Default set to `false`. Whether to only perform cache restoration and not the save post run script.
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### Outputs
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118
examples.md
118
examples.md
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@ -1,42 +1,44 @@
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# Examples
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- [C# - NuGet](#c---nuget)
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- [D - DUB](#d---dub)
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- [POSIX](#posix)
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- [Windows](#windows)
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- [Deno](#deno)
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- [Linux](#linux)
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- [macOS](#macos)
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- [Windows](#windows-1)
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- [Elixir - Mix](#elixir---mix)
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- [Erlang - Rebar3](#erlang--rebar3)
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- [Go - Modules](#go---modules)
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- [Linux](#linux-1)
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- [macOS](#macos-1)
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- [Windows](#windows-2)
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- [Haskell - Cabal](#haskell---cabal)
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- [Haskell - Stack](#haskell---stack)
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- [Java - Gradle](#java---gradle)
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- [Java - Maven](#java---maven)
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- [Node - npm](#node---npm)
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- [Node - Lerna](#node---lerna)
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- [Node - Yarn](#node---yarn)
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- [Node - Yarn 2](#node---yarn-2)
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- [OCaml/Reason - esy](#ocamlreason---esy)
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- [PHP - Composer](#php---composer)
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- [Python - pip](#python---pip)
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- [Simple example](#simple-example)
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- [Multiple OS's in a workflow](#multiple-oss-in-a-workflow)
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- [Multiple OS's in a workflow with a matrix](#multiple-oss-in-a-workflow-with-a-matrix)
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- [Using pip to get cache location](#using-pip-to-get-cache-location)
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- [Python - pipenv](#python---pipenv)
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- [R - renv](#r---renv)
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- [Ruby - Bundler](#ruby---bundler)
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- [Rust - Cargo](#rust---cargo)
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- [Scala - SBT](#scala---sbt)
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- [Swift, Objective-C - Carthage](#swift-objective-c---carthage)
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- [Swift, Objective-C - CocoaPods](#swift-objective-c---cocoapods)
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- [Swift - Swift Package Manager](#swift---swift-package-manager)
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- [Examples](#examples)
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- [C# - NuGet](#c---nuget)
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- [D - DUB](#d---dub)
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- [POSIX](#posix)
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- [Windows](#windows)
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- [Deno](#deno)
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- [Linux](#linux)
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- [macOS](#macos)
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- [Windows](#windows-1)
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- [Elixir - Mix](#elixir---mix)
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- [Erlang - Rebar3](#erlang---rebar3)
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- [Go - Modules](#go---modules)
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- [Linux](#linux-1)
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- [macOS](#macos-1)
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- [Windows](#windows-2)
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- [Haskell - Cabal](#haskell---cabal)
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- [Haskell - Stack](#haskell---stack)
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- [Java - Gradle](#java---gradle)
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- [Java - Maven](#java---maven)
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- [Node - npm](#node---npm)
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- [Node - Lerna](#node---lerna)
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- [Node - Yarn](#node---yarn)
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- [Node - Yarn 2](#node---yarn-2)
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- [OCaml/Reason - esy](#ocamlreason---esy)
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- [PHP - Composer](#php---composer)
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- [Python - pip](#python---pip)
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- [Simple example](#simple-example)
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- [Multiple OS's in a workflow](#multiple-oss-in-a-workflow)
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- [Multiple OS's in a workflow with a matrix](#multiple-oss-in-a-workflow-with-a-matrix)
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- [Using pip to get cache location](#using-pip-to-get-cache-location)
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- [Python - pipenv](#python---pipenv)
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- [R - renv](#r---renv)
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- [R Markdown - knitr cache](#r-markdown---knitr-cache)
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- [Ruby - Bundler](#ruby---bundler)
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- [Rust - Cargo](#rust---cargo)
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- [Scala - SBT](#scala---sbt)
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- [Swift, Objective-C - Carthage](#swift-objective-c---carthage)
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- [Swift, Objective-C - CocoaPods](#swift-objective-c---cocoapods)
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- [Swift - Swift Package Manager](#swift---swift-package-manager)
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## C# - NuGet
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@ -515,6 +517,48 @@ For renv, the cache directory will vary by OS. The `RENV_PATHS_ROOT` environment
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restore-keys: ${{ steps.get-version.outputs.os-version }}-${{ steps.get-version.outputs.r-version }}-${{inputs.cache-version }}-
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```
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## R Markdown - knitr cache
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For [R Markdown](https://bookdown.org/yihui/rmarkdown-cookbook/cache.html) and [Quarto](https://quarto.org/docs/computations/caching.html#knitr-cache), [knitr](https://yihui.org/knitr/options/#cache) creates a directory of cached code chunk variables & output for chunks where the chunk option `cache=TRUE` is set. The cache directory is typically located in the directory of the input file being rendered. It is named by concating the input `.Rmd` or `.qmd` file name with `_cache` appended.
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See the composite action implementation [prncevince/r-actions/setup-knitr-cache](https://github.com/prncevince/r-actions/tree/main/setup-knitr-cache) and corresponding [example](https://github.com/prncevince/r-actions/blob/main/.github/workflows/knitr-cache.yaml) [workflows](https://github.com/prncevince/test-workflow-knitr-cache/blob/main/.github/workflows/knitr-cache.yaml).
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Here, we set `reeval` to `true`. This instructs the action to reevalute the cache `key` input variable before saving the cache during the action's post script run when determing if we have met a cache hit. When using knitr caching, we do this because the knitr cache is typically ignored from the Git repo, and invalidation is determined by much more than a diff on the input file. Thus, it makes more sense to evaluate our cache key after knitr code chunk evaluation has completed. For more info on knitr cache invalidation, see [On Cache Invalidation](https://yihui.org/en/2018/06/cache-invalidation/).
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```yaml
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jobs:
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setup-knitr-cache:
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- uses: actions/checkout@v3
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- uses: r-lib/actions/setup-pandoc@v2
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- name: Install system dependencies on Linux
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if: runner.os == 'Linux'
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run: |
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sudo apt-get update -y
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sudo apt-get install -y libcurl4-openssl-dev libharfbuzz-dev libfribidi-dev
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- uses: r-lib/actions/setup-r@v2
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with:
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r-version: latest
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- name: Get R and OS version
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id: restore-partials
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shell: Rscript {0}
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run: |
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cat("##[set-output name=os-version;]", sessionInfo()$running, "\n", sep = "")
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cat("##[set-output name=r-version;]", R.Version()$version.string, sep = "")
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- name: Install R Markdown
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shell: Rscript {0}
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run: install.packages("rmarkdown")
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- name: Restore knitr cache
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uses: actions/cache@v3
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with:
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reeval: true
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path: rmd-file-name_cache
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key: ${{ github.action }}-${{ github.workflow }}-${{ steps.restore-partials.outputs.os-version }}-${{ steps.restore-partials.outputs.r-version }}-${{ hashFiles(format('{0}/**', rmd-file-name_cache)) }}
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restore-keys: ${{ github.action }}-${{ github.workflow }}-${{ steps.restore-partials.outputs.os-version }}-${{ steps.restore-partials.outputs.r-version }}-
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- name: Render R Markdown & Build knitr cache
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shell: Rscript {0}
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run: rmarkdown::render(input = "rmd-file-name.Rmd")
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```
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## Ruby - Bundler
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Caching gems with Bundler correctly is not trivial and just using `actions/cache`
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