Spring cleaning 🧼 (#52)

* Update DESCRIPTION, CoC * Update README, vignette * Update GH actions
rstudio · Mar 7, 2023 · 1498c88 · 1498c88
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diff --git a/.github/CODE_OF_CONDUCT.md b/.github/CODE_OF_CONDUCT.md
@@ -59,7 +59,7 @@ representative at an online or offline event.
 ## Enforcement
 
 Instances of abusive, harassing, or otherwise unacceptable behavior may be
-reported to the community leaders responsible for enforcement at codeofconduct@rstudio.com. 
+reported to the community leaders responsible for enforcement at codeofconduct@posit.co. 
 All complaints will be reviewed and investigated promptly and fairly.
 
 All community leaders are obligated to respect the privacy and security of the

diff --git a/.github/workflows/R-CMD-check-hard.yaml b/.github/workflows/R-CMD-check-hard.yaml
@@ -31,7 +31,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-pandoc@v2
 

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -22,21 +22,21 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest,   r: 'release'}
+          - {os: macos-latest,   r: 'release'}
 
           - {os: windows-latest, r: 'release'}
 
-          - {os: ubuntu-18.04,   r: 'devel', http-user-agent: 'release'}
-          - {os: ubuntu-18.04,   r: 'release'}
-          - {os: ubuntu-18.04,   r: 'oldrel-1'}
-          - {os: ubuntu-18.04,   r: 'oldrel-2'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+          - {os: ubuntu-latest,   r: 'oldrel-2'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-pandoc@v2
 

diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -20,7 +20,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-pandoc@v2
 

diff --git a/.github/workflows/pr-commands.yaml b/.github/workflows/pr-commands.yaml
@@ -14,7 +14,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/pr-fetch@v2
         with:
@@ -51,7 +51,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/pr-fetch@v2
         with:

diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -15,7 +15,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-r@v2
         with:

diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,18 +2,19 @@ Package: bundle
 Title: Serialize Model Objects with a Consistent Interface
 Version: 0.1.0.9000
 Authors@R: c(
-    person("Julia", "Silge", , "julia.silge@rstudio.com", role = c("aut", "cre"),
+    person("Julia", "Silge", , "julia.silge@posit.co", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-3671-836X")),
     person("Simon", "Couch", , "[email protected]", role = "aut"),
     person("Qiushi", "Yan", , "[email protected]", role = "aut"),
-    person("Max", "Kuhn", , "max@rstudio.com", role = "aut"),
-    person("RStudio", role = c("cph", "fnd"))
+    person("Max", "Kuhn", , "max@posit.co", role = "aut"),
+    person(given = "Posit Software, PBC", role = c("cph", "fnd"))
   )
 Description: Typically, models in 'R' exist in memory and can be saved via
-    regular 'R' serialization. However, some models store information in 
-    locations that cannot be saved using 'R' serialization alone. The goal of 
-    'bundle' is to provide a common interface to capture this information, 
-    situate it within a portable object, and restore it for use in new settings.
+    regular 'R' serialization. However, some models store information in
+    locations that cannot be saved using 'R' serialization alone. The goal
+    of 'bundle' is to provide a common interface to capture this
+    information, situate it within a portable object, and restore it for
+    use in new settings.
 License: MIT + file LICENSE
 URL: https://github.com/rstudio/bundle, https://rstudio.github.io/bundle/
 BugReports: https://github.com/rstudio/bundle/issues
@@ -42,8 +43,8 @@ Suggests:
     renv,
     rmarkdown,
     stacks,
-    testthat (>= 3.0.0),
     tensorflow,
+    testthat (>= 3.0.0),
     torch,
     torchvision,
     uwot,

diff --git a/README.Rmd b/README.Rmd
@@ -41,8 +41,8 @@ install.packages("bundle")
 And the development version from [GitHub](https://github.com/) with:
 
 ``` r
-# install.packages("devtools")
-devtools::install_github("rstudio/bundle")
+# install.packages("pak")
+pak::pak("rstudio/bundle")
 ```
 
 ## Overview
@@ -51,7 +51,7 @@ We often imagine a trained model as a somewhat "standalone" R object---given som
 
 We need some way to preserve access to those references. The bundle package provides a consistent interface for _bundling_ model objects with their references so that they can be safely saved and re-loaded in production:
 
-```{r diagram-04, echo = FALSE, fig.alt = "A replica of the previous diagram, where the arrow previously connecting the model object in R session one and the standalone model object in R session two is connected by a verb called bundle. The bundle function outputs an object called a bundle.", out.width = '100%'}
+```{r diagram-04, echo = FALSE, fig.alt = "A diagram showing a rectangle, labeled model object, and another rectangle, labeled predictions. The two are connected by an arrow from model object to predictions, with the label 'predict'. There are two boxes labeled reference, connected to the arrow labeled predict with dotted arrows, to show that, most of the time, we don't need to think about including them in our workflow. There are two boxes, labeled R Session number one, and R session number two. In focus is the arrow from the model object, in R Session number one, to a model object in R session number two. This arrow connecting the model object in R session one and the model object in R session two is connected by a verb called bundle. The bundle function outputs an object called a bundle.", out.width = '100%'}
 knitr::include_graphics("man/figures/diagram_04.png")
 ```
 

diff --git a/README.md b/README.md
@@ -32,8 +32,8 @@ install.packages("bundle")
 And the development version from [GitHub](https://github.com/) with:
 
 ``` r
-# install.packages("devtools")
-devtools::install_github("rstudio/bundle")
+# install.packages("pak")
+pak::pak("rstudio/bundle")
 ```
 
 ## Overview
@@ -57,7 +57,7 @@ package provides a consistent interface for *bundling* model objects
 with their references so that they can be safely saved and re-loaded in
 production:
 
-<img src="man/figures/diagram_04.png" alt="A replica of the previous diagram, where the arrow previously connecting the model object in R session one and the standalone model object in R session two is connected by a verb called bundle. The bundle function outputs an object called a bundle." width="100%" />
+<img src="man/figures/diagram_04.png" alt="A diagram showing a rectangle, labeled model object, and another rectangle, labeled predictions. The two are connected by an arrow from model object to predictions, with the label 'predict'. There are two boxes labeled reference, connected to the arrow labeled predict with dotted arrows, to show that, most of the time, we don't need to think about including them in our workflow. There are two boxes, labeled R Session number one, and R session number two. In focus is the arrow from the model object, in R Session number one, to a model object in R session number two. This arrow connecting the model object in R session one and the model object in R session two is connected by a verb called bundle. The bundle function outputs an object called a bundle." width="100%" />
 
 For more on this diagram, see the [main bundle
 vignette](https://rstudio.github.io/bundle/articles/bundle.html).
@@ -96,14 +96,14 @@ mod
 #> parsnip model object
 #> 
 #> ##### xgb.Booster
-#> raw: 8 Kb 
+#> raw: 8.1 Kb 
 #> call:
 #>   xgboost::xgb.train(params = list(eta = 0.3, max_depth = 6, gamma = 0, 
 #>     colsample_bytree = 1, colsample_bynode = 0.3, min_child_weight = 1, 
-#>     subsample = 1, objective = "reg:squarederror"), data = x$data, 
-#>     nrounds = 5, watchlist = x$watchlist, verbose = 0, nthread = 1)
+#>     subsample = 1), data = x$data, nrounds = 5, watchlist = x$watchlist, 
+#>     verbose = 0, nthread = 1, objective = "reg:squarederror")
 #> params (as set within xgb.train):
-#>   eta = "0.3", max_depth = "6", gamma = "0", colsample_bytree = "1", colsample_bynode = "0.3", min_child_weight = "1", subsample = "1", objective = "reg:squarederror", nthread = "1", validate_parameters = "TRUE"
+#>   eta = "0.3", max_depth = "6", gamma = "0", colsample_bytree = "1", colsample_bynode = "0.3", min_child_weight = "1", subsample = "1", nthread = "1", objective = "reg:squarederror", validate_parameters = "TRUE"
 #> xgb.attributes:
 #>   niter
 #> callbacks:
@@ -113,11 +113,11 @@ mod
 #> nfeatures : 10 
 #> evaluation_log:
 #>  iter training_rmse
-#>     1     14.640496
-#>     2     10.911261
-#>     3      8.226121
-#>     4      6.231544
-#>     5      4.761105
+#>     1     14.631798
+#>     2     10.865171
+#>     3      8.130434
+#>     4      6.150935
+#>     5      4.681918
 ```
 
 Note that simply saving and loading the model results in changes to the
@@ -129,7 +129,7 @@ saveRDS(mod, temp_file)
 mod2 <- readRDS(temp_file)
 
 compare(mod, mod2, ignore_formula_env = TRUE)
-#> `old$fit$handle` is <pointer: 0x147aa3740>
+#> `old$fit$handle` is <pointer: 0x102ff7800>
 #> `new$fit$handle` is <pointer: 0x0>
 #> 
 #> `old$fit$handle` is attr(,"class")
@@ -176,13 +176,13 @@ r(
 #> # A tibble: 7 × 1
 #>   .pred
 #>   <dbl>
-#> 1  22.1
-#> 2  20.6
-#> 3  16.5
-#> 4  14.1
-#> 5  16.5
-#> 6  11.8
-#> 7  18.8
+#> 1  22.4
+#> 2  22.4
+#> 3  19.0
+#> 4  19.4
+#> 5  16.6
+#> 6  11.2
+#> 7  22.4
 ```
 
 For a more in-depth demonstration of the package, see the [main
@@ -195,14 +195,14 @@ This project is released with a [Contributor Code of
 Conduct](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html).
 By contributing to this project, you agree to abide by its terms.
 
--   For questions and discussions about our packages, modeling, and
-    machine learning, please [post on RStudio
-    Community](https://community.rstudio.com/new-topic?category_id=15&tags=question).
+- For questions and discussions about our packages, modeling, and
+  machine learning, please [post on RStudio
+  Community](https://community.rstudio.com/new-topic?category_id=15&tags=question).
 
--   If you think you have encountered a bug, please [submit an
-    issue](https://github.com/rstudio/bundle/issues).
+- If you think you have encountered a bug, please [submit an
+  issue](https://github.com/rstudio/bundle/issues).
 
--   Either way, learn how to create and share a
-    [reprex](https://reprex.tidyverse.org/articles/articles/learn-reprex.html)
-    (a minimal, reproducible example), to clearly communicate about your
-    code.
+- Either way, learn how to create and share a
+  [reprex](https://reprex.tidyverse.org/articles/articles/learn-reprex.html)
+  (a minimal, reproducible example), to clearly communicate about your
+  code.
diff --git a/vignettes/bundle.Rmd b/vignettes/bundle.Rmd
@@ -200,7 +200,7 @@ We've done the work of figuring that out, and it turns out the interface is a li
 
 What if we could just use the same function for any R object, and it would _just work_?
 
-```{r diagram-03, echo = FALSE, fig.alt = "A diagram showing the same set of rectangles, representing a prediction problem, as before. This version of the diagram adds two boxes, labeled R Session numbe r one, and R session number two. In R session number two, we have a new rectangle labeled standalone model object. In focus is the arrow from the model object, in R Session number one, to the standalone model object in R session number two.", out.width = '100%'}
+```{r diagram-03, echo = FALSE, fig.alt = "A diagram showing the same set of rectangles, representing a prediction problem, as before. This version of the diagram adds two boxes, labeled R Session number one, and R session number two. In R session number two, we have a new rectangle labeled standalone model object. In focus is the arrow from the model object, in R Session number one, to the standalone model object in R session number two.", out.width = '100%'}
 knitr::include_graphics("figures/diagram_03.png")
 ```