Merge branch 'dev'

Author: maelle

.github/workflows/dev.yml

@@ -9,6 +9,8 @@ name: Render-Book-from-dev
 
 jobs:
   bookdown:
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     name: Render-Book
     runs-on: macOS-latest
     steps:

.github/workflows/pr.yml

@@ -8,6 +8,10 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     name: Render Book
     runs-on: macOS-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      NETLIFY_AUTH_TOKEN: ${{ secrets.NETLIFY_AUTH_TOKEN }}
+      NETLIFY_SITE_ID: ${{ secrets.NETLIFY_SITE_ID }}
     if: github.repository == 'ropensci/dev_guide'
     steps:
       - name: Is this a fork
@@ -46,24 +50,18 @@ jobs:
       - name: Move files around
         run: Rscript -e 'file.copy(from = "pdfbook/ropensci-dev-guide.pdf", to = "_book/ropensci-dev-guide.pdf")' -e 'purrr::walk(list.files("images", full.names = TRUE), file.copy, to = "_book/images")'
 
-      - uses: actions/setup-node@v1
-
-      - name: Install Netlify CLI
-        run: npm install netlify-cli -g
-
-      - name: Deploy to Netlify (test)
-        run: DEPLOY_URL=$(netlify deploy --site ${{ secrets.NETLIFY_SITE_ID }} --auth ${{ secrets.NETLIFY_AUTH_TOKEN }} --dir=docs --json | jq '.deploy_url' --raw-output);echo "DEPLOY_URL=${DEPLOY_URL}" >> $GITHUB_ENV
-
-      - name: Update commit status
-        run: |
-          curl --request POST \
-          --url https://api.github.com/repos/${{ github.repository }}/statuses/${{ github.event.pull_request.head.sha }} \
-          --header 'authorization: Bearer ${{ secrets.GITHUB_TOKEN }}' \
-          --header 'Accept: application/vnd.github.antiope-preview+json' \
-          --header 'content-type: application/json' \
-          --data '{
-            "state": "success",
-            "target_url": "${{ env.DEPLOY_URL }}",
-            "context": "Netlify"
-            }'
-
+      - name: Deploy to Netlify
+        id: netlify-deploy
+        uses: nwtgck/[email protected]
+        with:
+          publish-dir: './_book'
+          production-branch: master
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          deploy-message:
+            'Deploy from GHA: ${{ github.event.pull_request.title || github.event.head_commit.message }} (${{ github.sha }})'
+          # these all default to 'true'
+          enable-pull-request-comment: false
+          enable-commit-comment: false
+          # enable-commit-status: true
+          #o verwrites-pull-request-comment: true
+        timeout-minutes: 1

.zenodo.json

@@ -2,67 +2,82 @@
     "description": "Extended version of the rOpenSci packaging guide. This book is a guide for authors, maintainers, reviewers and editors of rOpenSci. The first section of the book contains our guidelines for creating and testing R packages. The second section is dedicated to rOpenSci's software peer review process: what it is, our policies, and specific guides for authors, editors and reviewers throughout the process. The third and last section features our best practice for nurturing your package once it has been onboarded: how to collaborate with other developers, how to document releases, how to promote your package and how to leverage GitHub as a development platform. The third section also features a chapter for anyone wishing to start contributing to rOpenSci packages.",
     "license": {"id":"CC-BY-4.0"},
     "title": "rOpenSci Packages: Development, Maintenance, and Peer Review",
-    "version": "0.6.0",
+    "version": "0.7.0",
     "upload_type": "software",
-    "publication_date": "2021-02-22",
+    "publication_date": "2021-11-16",
     "publication_type": "book",
     "creators": [
         {
             "name": "rOpenSci"
         },
         {
-            "name": "Brooke Anderson",
+            "name": "Anderson, Brooke",
             "affiliation": "Colorado State University"
         },
         {
-            "name": "Scott Chamberlain",
+            "name": "Chamberlain, Scott",
             "affiliation": "rOpenSci",
             "orcid": "0000-0003-1444-9135"
         },
         {
-            "name": "Laura DeCicco",
+            "name": "DeCicco, Laura",
             "affiliation": "USGS",
             "orcid": "0000-0002-3915-9487"
         },
         {
-            "name": "Julia Gustavsen",
-            "affiliation": "SOPHiA GENETICS",
+            "name": "Gustavsen, Julia",
+            "affiliation": "Agroscope",
             "orcid": "0000-0002-4764-4802"
         },
         {
-            "name": "Anna Krystalli",
+            "name": "Krystalli, Anna",
             "affiliation": "University of Sheffield RSE",
             "orcid": "0000-0002-2378-4915"
         },
         {
-            "name": "Mauro Lepore",
+            "name": "Lepore, Mauro",
             "affiliation": "2 Degrees Investing Initiative",
             "orcid": "0000-0002-1986-7988"
         },
         {
-            "name": "Lincoln Mullen",
+            "name": "Mullen, Lincoln",
             "affiliation": "George Mason University",
             "orcid": "0000-0001-5103-6917"
         },
         {
-            "name": "Karthik Ram",
+            "name": "Ram, Karthik",
             "affiliation": "rOpenSci",
             "orcid": "0000-0002-0233-1757"
         },
         {
-            "name": "Noam Ross",
+            "name": "Ross, Noam",
             "affiliation": "EcoHealth Alliance",
             "orcid": "0000-0002-2136-0000"
         },
         {
-            "name": "Ma\u00eblle Salmon",
+            "name": "Salmon, Ma\u00eblle",
             "affiliation": "rOpenSci",
             "orcid": "0000-0002-2815-0399"
         },
         {
-            "name": "Melina Vidoni",
+            "name": "Vidoni, Melina",
             "affiliation": "RMIT University (School of Science)",
             "orcid": "0000-0002-4099-1430"
+        },
+        {
+            "name": "Riederer, Emily",
+            "affiliation": "Capital One",
+            "orcid": ""
+        },
+        {
+            "name": "Sparks, Adam",
+            "affiliation": "Department of Primary Industries and Regional Development",
+            "orcid": "0000-0002-0061-8359"
+        },
+        {
+            "name": "Hollister, Jeff",
+            "affiliation": "US Environmental Protection Agency",
+            "orcid": "0000-0002-9254-9740"
         }
     ],
     "access_right": "open"

DESCRIPTION

@@ -4,18 +4,20 @@ Title: rOpenSci Packages: Development, Maintenance, and Peer Review
 Description: rOpenSci Packages: Development, Maintenance, and Peer Review
 Version: 0.0.1
 Imports:
-  airtabler,
-  htmltools,
-  bookdown,
-  purrr,
-  humaniformat,
-  bslib,
-  downlit,
-  xml2,
-  zen4R
-Remotes: 
-  bergant/airtabler,
-  rstudio/htmltools,
-  rstudio/bookdown,
-  rstudio/bslib,
-  r-lib/downlit
+    airtabler,
+    htmltools,
+    bookdown,
+    purrr,
+    humaniformat,
+    bslib,
+    downlit,
+    xml2,
+    rvest,
+    usethis,
+    rlang (>= 0.4.11.9000)
+Remotes:  
+    bergant/airtabler,
+    rstudio/htmltools,
+    rstudio/bookdown,
+    r-lib/downlit,
+    r-lib/rlang

_bookdown.yml

@@ -7,6 +7,7 @@ rmd_files: ["index.Rmd", "pkg_building.Rmd",
            "softwarereview_intro.Rmd", "softwarereview_policies.Rmd",
            "softwarereview_author.Rmd",
            "softwarereview_reviewer.Rmd", "softwarereview_editor.Rmd",
+           "softwarereview_editor_management.Rmd",
            "maintenance_collaboration.Rmd",
            "maintenance_changing_maintainers.Rmd","maintenance_releases.Rmd",
            "maintenance_marketing.Rmd", "maintenance_github_grooming.Rmd",

appendix.Rmd

@@ -2,6 +2,38 @@
 
 # NEWS {#booknews}
 
+## dev
+
+* 2021-11-04, add mentions of stat software review to software review intro and to the first book page (#342).
+
+* 2021-11-04, mention pkgcheck in the author guide (@mpadge, #343).
+
+* 2021-11-04, add editors' responsabilities including  Editor etiquette for commenting on packages on which you aren't handling/reviewing (@jhollist, #354). 
+
+* 2021-11-04, give precise examples of tools for installation instructions (remotes, pak, R-universe).
+
+* 2021-11-04, add more bot guidance (less work for editors).
+
+* 2021-10-07, add guidance for editorial management (recruiting, inviting, onboarding, offboarding editors).
+
+* 2021-09-14, add a requirement that there is at least one _HTML_ vignette.
+
+* 2021-09-03, add some recommendations around git. (@annakrystalli, #341)
+
+* 2021-07-14, clarify the categories data extraction and munging by adding examples. (@noamross, #337)
+
+* 2021-05-20, add guidance around setting up your package to foster a community, inspired by the recent rOpenSci community call. (with help from `@Bisaloo`, #289, #308)
+
+* 2021-04-27, no longer ask reviewers to ask covr as it'll be done by automatic tools, but ask them to pay attention to tests skipped.
+
+* 2021-04-02, add citation guidance.
+
+* 2021-04-02, stop asking reviewers to run goodpractice as this is part of editorial checks.
+
+* 2021-03-23, launched a new form for reviewer volunteering.
+
+* 2021-02-24, add guidance around the use of `@ropensci-review-bot`.
+
 ## 0.6.0
 
 * 2021-02-04, add guidance to enforce package versioning and tracking of changes through review (`@annakrystalli`, #305)
@@ -204,25 +236,40 @@
 
 * Added a `NEWS.md` file to track changes to the book.
 
+```{r, echo=FALSE, message=FALSE, warning=FALSE}
+fs::dir_create("templaaates")
+save_one <- function(file) {
+  download.file(
+    sprintf("https://raw.githubusercontent.com/ropensci/software-review/master/.buffy/templates/%s", file),
+    file.path("templaaates", file)
+  )
+}
+
+lapply(
+  c("approved.md", "editor.md", "review-es.md", "review.md", "reviewer-approval.md"),
+  save_one
+)
+```
+
 # Review template {#reviewtemplate}
 
 ```markdown
-```{r, eval = !knitr::is_latex_output(), child="templates/review.md"}
+```{r, eval = !knitr::is_latex_output(), child="templaaates/review.md"}
 ```
 ```
 
-```{r, eval = knitr::is_latex_output(), child="templates/review.md"}
+```{r, eval = knitr::is_latex_output(), child="templaaates/review.md"}
 
 ```
 
 # Review template in Spanish {#reviewtemplatees}
 
 ```markdown
-```{r, eval = !knitr::is_latex_output(), child="templates/review-es.md"}
+```{r, eval = !knitr::is_latex_output(), child="templaaates/review-es.md"}
 ```
 ```
 
-```{r, eval = knitr::is_latex_output(), child="templates/review-es.md"}
+```{r, eval = knitr::is_latex_output(), child="templaaates/review-es.md"}
 
 ```
 
@@ -232,11 +279,11 @@
 
 
 ```markdown
-```{r, eval = !knitr::is_latex_output(), child="templates/editor.md"}
+```{r, eval = !knitr::is_latex_output(), child="templaaates/editor.md"}
 ```
 ```
 
-```{r, eval = knitr::is_latex_output(), child="templates/editor.md"}
+```{r, eval = knitr::is_latex_output(), child="templaaates/editor.md"}
 
 ```
 
@@ -257,23 +304,23 @@ Editors may make use of the e-mail template below in recruiting reviewers.
 
 
 ```markdown
-```{r, eval = !knitr::is_latex_output(), child="templates/approved.md"}
+```{r, eval = !knitr::is_latex_output(), child="templaaates/approved.md"}
 ```
 ```
 
-```{r, eval = knitr::is_latex_output(), child="templates/approved.md"}
+```{r, eval = knitr::is_latex_output(), child="templaaates/approved.md"}
 
 ```
 
 # Reviewer approval comment template {#approval2template}
 
 
 ```markdown
-```{r, eval = !knitr::is_latex_output(), child="templates/reviewer-approval.md"}
+```{r, eval = !knitr::is_latex_output(), child="templaaates/reviewer-approval.md"}
 ```
 ```
 
-```{r, eval = knitr::is_latex_output(), child="templates/reviewer-approval.md"}
+```{r, eval = knitr::is_latex_output(), child="templaaates/reviewer-approval.md"}
 
 ```
 
@@ -298,6 +345,10 @@ Editors may make use of the e-mail template below in recruiting reviewers.
 
 ```
 
+```{r, echo=FALSE, message=FALSE, warning=FALSE}
+fs::dir_delete("templaaates")
+```
+
 # How to set a redirect {#redirect}
 
 ## Non GitHub pages site (e.g. Netlify)

images/airtable.png

@@ -1,6 +1,6 @@
 --- 
 title: "rOpenSci Packages: Development, Maintenance, and Peer Review"
-author: "rOpenSci software review editorial team (current and alumni): Brooke Anderson, Scott Chamberlain, Laura DeCicco, Julia Gustavsen, Anna Krystalli, Mauro Lepore, Lincoln Mullen, Karthik Ram, Emily Riederer, Noam Ross, Maëlle Salmon, Melina Vidoni"
+author: "rOpenSci software review editorial team (current and alumni): Brooke Anderson, Scott Chamberlain, Laura DeCicco, Julia Gustavsen, Jeff Hollister, Anna Krystalli, Mauro Lepore, Lincoln Mullen, Karthik Ram, Emily Riederer, Noam Ross, Maëlle Salmon, Adam Sparks, Melina Vidoni"
 date: "`r Sys.Date()`"
 site: bookdown::bookdown_site
 documentclass: book
@@ -30,12 +30,13 @@ knitr::include_graphics("images/cover.png")
 
 ```{r zenodo, echo=FALSE, results = 'asis', warning=FALSE}
 cat("\n```bibtex\n")
-zenodo <- zen4R::ZenodoManager$new(
-  token = Sys.getenv("ZENODO_TOKEN")
-)
-guide <- zenodo$getDepositionByConceptDOI("10.5281/zenodo.2553043")
-guide$exportAsBibTeX("dev_citation")
-cat(readLines("dev_citation_BibTeX.bib"), sep = "\n")
+u <- "https://zenodo.org/record/2553043" # universal URL redirects to latest
+s <- rvest::session(u)
+u <- paste0(s$url, "/export/hx") # redirected
+out <- rvest::read_html(u)
+bibentry <- rvest::html_text(rvest::html_element(out, "pre"))
+writeLines(strsplit(bibentry, "\n")[[1]], "dev_citation_BibTeX.bib")
+cat(bibentry)
 cat("\n```\n")
 ```
 
@@ -47,7 +48,7 @@ Welcome! This book is a guide for authors, maintainers, reviewers and editors of
 
 The [first section of the book](#building) contains our guidelines for creating and testing R packages. 
 
-The [second section](#softwarereviewintro) is dedicated to rOpenSci's software peer review process: what it is, our policies, and specific guides for authors, editors and reviewers throughout the process.
+The [second section](#softwarereviewintro) is dedicated to rOpenSci's software peer review process: what it is, our policies, and specific guides for authors, editors and reviewers throughout the process. For _statistical software review_, refer to the [project webpage and resources](https://ropensci.org/stat-software-review/).
 
 The [third and last section](#collaboration) features our best practice for nurturing your package once it has been onboarded: how to collaborate with other developers, how to document releases, how to promote your package and how to leverage GitHub as a development platform. The third section also features a [chapter for anyone wishing to start contributing to rOpenSci packages](#contributingguide).