Satisfy devtools::check() and add CI

.Rbuildignore

@@ -1,2 +1,9 @@
+^\.github$
+^.*\.html$
+^.*\.Rmd$
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^.*\.yml$
+^CODE_OF_CONDUCT\.md$
+^CONTRIBUTING\.md$
+^LICENSE\.md$

.github/workflows/check.yaml

@@ -0,0 +1,76 @@
+on: [push, pull_request]
+
+name: check
+
+jobs:
+  check:
+    runs-on: macOS-latest
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUBPAT }}
+      AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
+      AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+      AWS_DEFAULT_REGION: ${{ secrets.AWS_DEFAULT_REGION }}
+      TORCH_INSTALL: 1
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: false
+
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v2
+
+      - name: Setup R
+        uses: r-lib/actions/setup-r@master
+
+      - name: Install system requirements
+        run: |
+          brew install pandoc
+          brew install pandoc-citeproc
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        uses: actions/cache@v2
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+
+      - name: Install dependencies
+        run: |
+          install.packages(c("remotes"))
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("covr")
+        shell: Rscript {0}
+
+      - name: Cache bookdown results
+        uses: actions/cache@v1
+        with:
+          path: _bookdown_files
+          key: bookdown-${{ hashFiles('**/*Rmd') }}
+          restore-keys: bookdown-
+
+      - name: Check
+        env:
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
+          _R_CHECK_FORCE_SUGGESTS_: false
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Bookdown
+        env:
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
+          _R_CHECK_FORCE_SUGGESTS_: false
+        run: bookdown::render_book(input = "index.Rmd", output_format = "bookdown::gitbook")
+        shell: Rscript {0}
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@master
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check

.github/workflows/publish.yaml

@@ -0,0 +1,61 @@
+on:
+  push:
+    branches: main
+
+name: publish
+
+jobs:
+  publish:
+    runs-on: macOS-latest
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUBPAT }}
+      AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
+      AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+      AWS_DEFAULT_REGION: ${{ secrets.AWS_DEFAULT_REGION }}
+      TORCH_INSTALL: 1
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: false
+
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v2
+
+      - name: Setup R
+        uses: r-lib/actions/setup-r@master
+
+      - name: Install system requirements
+        run: |
+          brew install pandoc
+          brew install pandoc-citeproc
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        uses: actions/cache@v2
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+
+      - name: Install dependencies
+        run: |
+          install.packages(c("remotes"))
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("covr")
+        shell: Rscript {0}
+
+      - name: Cache bookdown results
+        uses: actions/cache@v1
+        with:
+          path: _bookdown_files
+          key: bookdown-${{ hashFiles('**/*Rmd') }}
+          restore-keys: bookdown-
+
+      - name: Publish manual
+        run: |
+          ./inst/publish.sh

.gitignore

@@ -6,3 +6,4 @@ _book
 _bookdown_files
 _targets.R
 _targets/
+targets-manual.Rmd

DESCRIPTION

@@ -0,0 +1,46 @@
+Package: targets.manual
+Title: Targets R Package User Manual
+Description: This repository is the 'bookdown' project of the targets R
+  package user manual. It contains in-depth discussion and walkthroughs
+  of the main features of 'targets' and advice about best practices.
+Version: 0.0.0.9000
+License: MIT + file LICENSE
+URL: https://wlandau.github.io/targets-manual,
+  https://github.com/wlandau/targets-manual
+BugReports: https://github.com/wlandau/targets-manual/issues
+Authors@R: c(
+  person(
+    given = c("William", "Michael"),
+    family = "Landau",
+    role = c("aut", "cre"),
+    email = "[email protected]",
+    comment = c(ORCID = "0000-0003-1878-3253")
+  ),
+  person(
+    family = "Eli Lilly and Company",
+    role = "cph"
+  ))
+Depends:
+  R (>= 3.5.0)
+Imports:
+  biglm (>= 0.9.2),
+  bookdown (>= 0.19),
+  fs (>= 1.4.1),
+  purrr (>= 0.3.4),
+  tarchetypes,
+  targets,
+  tidyverse (>= 1.3.0),
+  visNetwork (>= 2.0.9),
+  withr (>= 2.2.0)
+Suggests:
+  knitr (>= 1.30),
+  rmarkdown (>= 2.4),
+  testthat (>= 2.3.2)
+Remotes:
+  wlandau/tarchetypes,
+  wlandau/targets
+Encoding: UTF-8
+Language: en-US
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.1.1.9000
+VignetteBuilder: knitr

LICENSE

@@ -0,0 +1,2 @@
+YEAR: 2020
+COPYRIGHT HOLDER: Eli Lilly and Company

NAMESPACE

@@ -0,0 +1,3 @@
+# Generated by roxygen2: do not edit by hand
+
+export(targets_manual_empty)

R/empty.R

@@ -0,0 +1,10 @@
+#' @title Empty function
+#' @export
+#' @description This is a bookdown manual. It only
+#'   borrows R package infrastructure for devops purposes.
+#' @return Nothing.
+#' @examples
+#' targets_manual_empty()
+targets_manual_empty <- function() {
+  invisible()
+}

files.Rmd

@@ -119,11 +119,11 @@ save_plot_and_return_path <- function() {
 
 R Markdown reports are a little more challenging because they often depend on upstream targets. To integrate an R Markdown report with a `targets` pipeline, you must use `tar_read()` and `tar_load()` in active code chunks to explicitly name the targets that the report depends on. (Do not use `tar_read_raw()` or `tar_load_raw()` for this.) The report from the [minimal example](https://github.com/wlandau/targets-minimal) looks like this.
 
-![](./images/knitr-source.png)
+![](./man/figures/knitr-source.png)
 
 Above, the report depends on targets `fit` and `hist`. The use of `tar_read()` and `tar_load()` allows us to run the report outside the pipeline. (Again, do not use `tar_read_raw()` or `tar_load_raw()` for this.) As long as `_targets/` folder has data on the required targets from a previous `tar_make()`, you can open the RStudio IDE, edit the report, and click the Knit button like you would for any other R Markdown report.
 
-![](./images/knitr-ide.png)
+![](./man/figures/knitr-ide.png)
 
 To connect the target with the pipeline, we define a special kind of target using `tar_render()` from the [`tarchetypes`](https://github.com/wlandau/tarchetypes) package instead of the usual `tar_target()`, which
 
@@ -186,7 +186,7 @@ tar_pipeline(
 tar_visnetwork()
 ```
 
-![](./images/knitr-graph.png)
+![](./man/figures/knitr-graph.png)
 
 ### Parameterized R Markdown
 

index.Rmd

@@ -15,10 +15,10 @@ output:
 url: "https://wlandau.github.io/targets-manual"
 description: "In-depth discussion of the major functionality of targets."
 github-repo: "wlandau/targets-manual"
-cover-image: /images/logo.png
-apple-touch-icon: "images/apple-touch-icon.png"
+cover-image: /man/figures/logo.png
+apple-touch-icon: "man/figures/apple-touch-icon.png"
 apple-touch-icon-size: 120
-favicon: "images/favicon.ico"
+favicon: "man/figures/favicon.ico"
 always_allow_html: yes
 ---