Upkeep (#29)

* Add GitHub links to DESCRIPTION

* do upkeep bullets

* Use yaml chunk headers

.Rbuildignore

@@ -8,3 +8,4 @@
 ^pkgdown$
 ^vignettes/articles$
 ^codecov\.yml$
+^CODE_OF_CONDUCT\.md$

.github/workflows/R-CMD-check.yaml

@@ -6,7 +6,9 @@ on:
   pull_request:
     branches: [main, master]
 
-name: R-CMD-check
+name: R-CMD-check.yaml
+
+permissions: read-all
 
 jobs:
   R-CMD-check:
@@ -29,7 +31,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -47,3 +49,4 @@ jobs:
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/pkgdown.yaml

@@ -9,7 +9,9 @@ on:
     types: [published]
   workflow_dispatch:
 
-name: pkgdown
+name: pkgdown.yaml
+
+permissions: read-all
 
 jobs:
   pkgdown:
@@ -22,7 +24,7 @@ jobs:
     permissions:
       contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -41,7 +43,7 @@ jobs:
 
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
         with:
           clean: false
           branch: gh-pages

CODE_OF_CONDUCT.md

@@ -0,0 +1,126 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, caste, color, religion, or sexual
+identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall
+  community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or advances of
+  any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email address,
+  without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+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 tahvdbrand@gmail.com. 
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.1, available at
+<https://www.contributor-covenant.org/version/2/1/code_of_conduct.html>.
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder][https://github.com/mozilla/inclusion].
+
+For answers to common questions about this code of conduct, see the FAQ at
+<https://www.contributor-covenant.org/faq>. Translations are available at <https://www.contributor-covenant.org/translations>.
+
+[homepage]: https://www.contributor-covenant.org

DESCRIPTION

@@ -2,21 +2,14 @@ Package: legendry
 Title: Extended guide options for 'ggplot2'
 Version: 0.0.0.9001
 Authors@R: 
-    person(given = "Teun",
-           family = "van den Brand",
-           role = c("aut", "cre"),
-           email = "tahvdbrand@gmail.com",
+    person("Teun", "van den Brand", , "tahvdbrand@gmail.com", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-9335-7468"))
-Description: A 'ggplot2' extension that focusses on expanding the plotter's 
-    arsenal of guides, such as axes, legends and colour bars.
+Description: A 'ggplot2' extension that focusses on expanding the
+    plotter's arsenal of guides, such as axes, legends and colour bars.
 License: MIT + file LICENSE
-Encoding: UTF-8
-Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
-Config/testthat/edition: 3
-VignetteBuilder: knitr
 URL: https://teunbrand.github.io/legendry/,
     https://github.com/teunbrand/legendry
+BugReports: https://github.com/teunbrand/legendry/issues
 Depends: 
     ggplot2 (>= 3.5.0),
     R (>= 4.1.0)
@@ -31,9 +24,15 @@ Imports:
 Suggests: 
     knitr,
     ragg,
-    svglite,
     rmarkdown,
+    svglite,
     systemfonts,
     testthat (>= 3.0.0),
     vdiffr,
     withr
+VignetteBuilder: 
+    knitr
+Config/testthat/edition: 3
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.2

README.Rmd

@@ -4,7 +4,8 @@ output: github_document
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
-```{r, include = FALSE}
+```{r}
+#| include: false
 knitr::opts_chunk$set(
   collapse = TRUE,
   comment = "#>",
@@ -41,7 +42,8 @@ devtools::install_github("teunbrand/legendry")
 
 Let's first set up a basic plot to experiment with:
 
-```{r basic_plot}
+```{r}
+#| label: basic_plot
 library(legendry)
 
 base <- ggplot(mpg, aes(displ, hwy, colour = cty)) +
@@ -61,7 +63,8 @@ In the example below, we're using two custom variants of vanilla guides, namely
 * The axis guide has an option for bidirectional ticks.
 * The colourbar automatically recognises out-of-bounds values and displays this with a cap.
 
-```{r full_guides}
+```{r}
+#| label: full_guides
 base + 
   scale_colour_viridis_c(
     limits = c(NA, 30),
@@ -77,7 +80,8 @@ The `ggplot2::guide_axis_stack()` is an axis composition function that can be us
 Here, we use a 'primitive' guide (incomplete building block) to display a range on the axis.
 By stacking it with a regular axis the primitive guide is completed.
 
-```{r primitives}
+```{r}
+#| label: primitives
 # A partial guide to display a bracket
 efficient_bracket <- primitive_bracket(
   # Keys determine what is displayed
@@ -98,7 +102,8 @@ In the example below we compose a 'sandwich': a central guide flanked by two oth
 Because our bracket is a primitive, it does not matter what aesthetic it displays and we can re-use it for the sandwich.
 I've yet to write the vignette on composition.
 
-```{r composition}
+```{r}
+#| label: composition
 base + 
   scale_colour_viridis_c(
     guide = compose_sandwich(
@@ -109,3 +114,7 @@ base +
   )
 ```
 
+## Code of Conduct
+
+Please note that the legendry project is released with a [Contributor Code of Conduct](https://teunbrand.github.io/legendry/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.
+

README.md

@@ -114,3 +114,10 @@ base +
 ```
 
 <img src="man/figures/README-composition-1.svg" width="80%" style="display: block; margin: auto;" />
+
+## Code of Conduct
+
+Please note that the legendry project is released with a [Contributor
+Code of
+Conduct](https://teunbrand.github.io/legendry/CODE_OF_CONDUCT.html). By
+contributing to this project, you agree to abide by its terms.

vignettes/articles/guide_composition.Rmd

@@ -2,15 +2,17 @@
 title: "A guide to guide composition"
 ---
 
-```{r, include = FALSE}
+```{r}
+#| include: false
 knitr::opts_chunk$set(
   collapse = TRUE,
   comment = "#>",
   dev = "ragg_png"
 )
 ```
 
-```{r setup}
+```{r}
+#| label: setup
 library(legendry)
 ```
 
@@ -135,14 +137,16 @@ last_plot() +
 By giving them the `primitive_`-prefix, we have made it impossible to use them by name inside function that don't expect them.
 This acts as a little bit of discouragement from using primitives as complete guides.
 
-```{r, error=TRUE}
+```{r}
+#| error: true
 standard + 
   guides(x.sec = "ticks")
 ```
 
 However, you *can* use primitives by name inside guide composition functions, *or* use their full constructor function.
 
-```{r, fig.keep = "last"}
+```{r}
+#| fig-keep: last
 standard +
   guides(x.sec = compose_stack("ticks"))
 
@@ -187,7 +191,8 @@ last_plot() + theme(legend.text.position = "left")
 It should also be noted that if the guide has a label-supression mechanism, the 'opposite' guide will be drawn with surpressed labels. 
 The mechanism is in place in guides like `guide_axis()`/`guide_axis_base()` for display in for example `facet_grid(axis.labels = "margins")`.
 
-```{r, fig.keep = "last"}
+```{r}
+#| fig-keep: last
 standard +
   aes(colour = cty) +
   scale_colour_viridis_c(

vignettes/articles/keys.Rmd

@@ -2,15 +2,17 @@
 title: "Key information"
 ---
 
-```{r, include = FALSE}
+```{r}
+#| include: false
 knitr::opts_chunk$set(
   collapse = TRUE,
   comment = "#>",
   dev = "ragg_png"
 )
 ```
 
-```{r setup}
+```{r}
+#| label: setup
 library(legendry)
 ```
 

vignettes/articles/tour.Rmd

@@ -2,14 +2,16 @@
 title: "A guided tour"
 ---
 
-```{r, include = FALSE}
+```{r}
+#| include: false
 knitr::opts_chunk$set(
   collapse = TRUE,
   comment = "#>"
 )
 ```
 
-```{r setup}
+```{r}
+#| label: setup
 library(legendry)
 library(scales)
 ```
@@ -265,7 +267,9 @@ In the plot below, the `cty` variable has a few observation below the lower limi
 Typically, these are displayed in the `na.value = "grey"` colour.
 The bars display that these data are out-of-bounds by the gray 'caps' at the two ends of the bar.
 
-```{r, dev = 'png', dev.args=list(type = 'cairo')}
+```{r}
+#| dev-args: !expr list(type = "cairo")
+#| fig-format: png
 standard +
   scale_colour_viridis_c(
     limits = c(10, 30),