Merge pull request #12 from openstatsware/chapter5-edits

Audrey's inputs for chapter 5

Author: audreyyeoCH

slides/01_intro.qmd

@@ -273,7 +273,7 @@ knitr::include_graphics("resources/pkg_graph.png")
   [`r fontawesome::fa("linkedin")`](https://www.linkedin.com/in/philippe-boileau-773270205/)
   [`r fontawesome::fa("globe")`](https://pboileau.ca/)
 - In the current version, changes were done by (later authors):
-  Audrey T. Yeo
+  Audrey Yeo Te-ying
   [`r fontawesome::fa("linkedin")`](https://www.linkedin.com/in/audreyyeo8000/)
   [`r fontawesome::fa("github")`](https://github.com/audreyyeocH)
   Alessandro Gasparini

slides/05_publication.qmd

@@ -20,9 +20,12 @@ author: Audrey T. Yeo
 
 - `pkgdown` makes it quick and easy to build a website for your package
 - After installing `pkgdown`, run `usethis::use_pkgdown()` to get started
+- Alternatively, run `usethis::use_pkgdown_github_pages()`
+  - Adds (and writes) `pkgdown.yml`, `docs` folder, and "pkgdown" to `.Rbuildignore` and `docs` to `gitignore`. Also initialises empty branch `gh-pages` in chosen repo and activates GitHub Pages for repo [^1].
 - Main configuration happens in `_pkgdown.yml` file
 - Many customizations can be applied, but bulk of work during development is
   updating the `reference` section with names of `.Rd` files
+[^1]: `usethis::use_pkgdown_github_pages()` performs these actions additionally to `usethis::use_pkgdown()`.
 
 ## Example `_pkgdown.yml` File
 
@@ -198,19 +201,20 @@ rhub::rhub_platforms()
 
 ## GitHub Actions
 
-- It is also possible to use GitHub Actions to run `R CMD check`
+- It is also possible to use [GitHub Actions](https://docs.github.com/en/actions) to run `R CMD check`
 - Free for public repositories, paid service for private repositories
 - Checks will be run every time someone pushes a commit to a repository hosted on GitHub
 - Easy setup from your R console: `usethis::use_github_action_check_standard()`
+  - ( runs a standard `R CMD check ` on three major operating systems. )
 - Script and documentation are developed and maintained by the `r-lib` organization [here](https://github.com/r-lib/actions/tree/v2/check-r-package)
 
 # GitHub
 
 ## Tags
 
 - Tags are a feature of Git, i.e., not specific to GitHub
-- Git can tag specific points in the code history as being important
-- Typically, for each release, create a tag `vx.y.z`
+- Git can tag (or "bookmark") specific points in the code history as being important
+- Typically, for each release, create a tag `vx.y.z` (MAJOR.Minor.patch format)
 - The value here is that users can later check out the package
   in the state of this release version
   - Download in R: `remotes::install_github("org/package", ref = "vx.y.z")`
@@ -222,12 +226,17 @@ rhub::rhub_platforms()
 
 ## Releases
 
-- Based on Git tags, and a feature of GitHub
+- [Releases](https://docs.github.com/en/repositories/releasing-projects-on-github/about-releases) are based on Git tags, and a feature of GitHub
 - Are "deployable software packages to make them available for a wider audience
   to download and use"
 - Contain release notes and links to the binary package files for download
   - However, for R packages these `tar.gz` package files are rarely used
     directly
+    
+```{Bash}
+#| eval: false
+git diff v0.3.14 v0.3.15 # checking for difference in mmrm release
+```
 
 ## Releases: Example
 
@@ -239,7 +248,8 @@ rhub::rhub_platforms()
 
 - The [Bioconductor](https://www.bioconductor.org/) project develops, supports,
   and disseminates open source software for the analysis of biological assays
-- Like CRAN, Bioconductor has additional package requirements
+- Like CRAN, Bioconductor has additional package requirements. 
+  One can only submit either to CRAN or Bioconductor. 
 - Packages are peer reviewed by community members
 - New packages and updates to existing packages are released semi-annually
 - Software is expected to be interoperable with other Bioconductor packages
@@ -254,17 +264,74 @@ rhub::rhub_platforms()
 - [CRAN Repository Policy](https://cran.r-project.org/web/packages/policies.html)
 - [Bioconductor packages](https://contributions.bioconductor.org/index.html)
 
+## Quick quiz (One correct answer only)
+
+::: columns
+::: {.column width="40%"}
+1. I am cloning / forking a repo that has an MIT Licence. Which license shall I use if I want to make modification and distribute my new package ? 
+a. MIT Licence
+b. one of any copyleft Licences
+c. no licence assumes transfer of my rights from the original repo
+:::
+
+::: {.column width="10%"}
+:::
+
+::: {.column width="40%"}
+2. I want to build a website for my package. Which file can I *mainly* configure my website in ? 
+\
+\
+\
+a. `_pkgdown.yml` file
+b. .gitignore
+c. any .Rd file
+:::
+:::
+
+## Quick quiz (Solutions) 
+
+::: columns
+::: {.column width="40%"}
+1. I am cloning / forking a repo that has an MIT Licence. Which license shall I use if I want to make modification and distribute my new package ? 
+a. MIT Licence
+b. **any licence**
+c. no licence because that assumes transfer of my rights from the original repo's MIT Licence
+:::
+
+::: {.column width="10%"}
+:::
+
+::: {.column width="40%"}
+2. I want to build a website for my package. Which file can I *mainly* configure my website in ? 
+\
+\
+\
+a. **`_pkgdown.yml` file**
+b. .gitignore
+c. any .Rd file
+:::
+:::
+
 # Exercise
 
-Use the same repository created from template [https://github.com/kkmann/simulatr](https://github.com/kkmann/simulatr)
+Use your project from *chapter 2* :
+
+- Run CRAN-like checks in RStudio: 
+  - Go to Tools -> Project Options -> Build Tools -> "Check package - R CMD check additional options" : -> type "--as-cran"
+
+- Alternatively, use `--as-cran` in argument in console :
+
+```{r}
+#| eval: false
+rcmdcheck::rcmdcheck("myrootdir", args = "--as-cran")
+```
 
-- Run CRAN-like checks in RStudio: use `--as-cran` in check options
 - Look at the CI/CD checks reported on your GitHub repository
   - Where are the `R CMD check` results?
 - Enable GitHub page through `use_pkgdown_github_pages`
+  - (nested in this [`use_pkgdown_github_pages`](https://pkgdown.r-lib.org/articles/pkgdown.html) includes : `use_pkgdown()`, `use_github_pages()`, `use_github_action("pkgdown")`)
 - Deploy the website with `pkgdown`
-  - Need to change remote to `git`
-- Deploy the website through `use_github_action("pkgdown")`
+- Set up a GitHub action to deploy website `use_github_action("pkgdown")`
   - (Optional) Check the automatic GitHub page deploy action
 
 # License information {.smaller}
@@ -275,6 +342,8 @@ Use the same repository created from template [https://github.com/kkmann/simulat
 - In the current version, changes were done by (later authors):
   Liming Li [`r fontawesome::fa("github")`](https://github.com/clarkliming),
   Philippe Boileau [`r fontawesome::fa("globe")`](https://pboileau.ca/),
-  Alessandro Gasparini [`r fontawesome::fa("linkedin")`](https://www.linkedin.com/in/ellessenne) [`r fontawesome::fa("github")`](https://www.github.com/ellessenne) [`r fontawesome::fa("globe")`](https://www.ellessenne.xyz/)
+  Alessandro Gasparini [`r fontawesome::fa("linkedin")`](https://www.linkedin.com/in/ellessenne) [`r fontawesome::fa("github")`](https://www.github.com/ellessenne) [`r fontawesome::fa("globe")`](https://www.ellessenne.xyz/), Audrey Yeo Te-ying
+  [`r fontawesome::fa("linkedin")`](https://www.linkedin.com/in/audreyyeo8000/)
+  [`r fontawesome::fa("github")`](https://github.com/audreyyeocH)
 
 {{< include _license_footer.qmd >}}