Update GitHub templates and workflows

.github/CODE_OF_CONDUCT.md

@@ -82,3 +82,4 @@ For answers to common questions about this code of conduct, see the FAQ at [http
 [Mozilla CoC]: https://github.com/mozilla/diversity
 [FAQ]: https://www.contributor-covenant.org/faq
 [translations]: https://www.contributor-covenant.org/translations
+

.github/CONTRIBUTING.md

@@ -1,6 +1,6 @@
 # Contributing
 
-This outlines how to propose a change to tabula. For more detailed info about contributing to this, and other tesselle packages, please see the [**development contributing guide**](https://www.tesselle.org/contributing.html).
+This outlines how to propose a change to this package. For more detailed info about contributing to this, and other packages, please see the [**development contributing guide**](https://www.tesselle.org/contributing.html).
 
 ## Fixing typos
 
@@ -12,18 +12,18 @@ If you want to make a bigger change, it's a good idea to first file an issue and
 
 ### Pull request process
 
-* Fork the package and clone onto your computer. If you haven't done this before, we recommend using `usethis::create_from_github("tesselle/tabula", fork = TRUE)`.
+* Fork the package and clone onto your computer. If you haven't done this before, we recommend using `usethis::create_from_github("tesselle/PACKAGE", fork = TRUE)`.
 * Install all development dependencies with `devtools::install_dev_deps()`, and then make sure the package passes R CMD check by running `devtools::check()`.  If R CMD check doesn't pass cleanly, it's a good idea to ask for help before continuing.
 * Create a Git branch for your pull request (PR). We recommend using `usethis::pr_init("brief-description-of-change")`.
 * Make your changes, commit to git, and then create a PR by running `usethis::pr_push()`, and following the prompts in your browser. The title of your PR should briefly describe the change. The body of your PR should contain `Fixes #issue-number`.
 * For user-facing changes, add a bullet to the top of `NEWS.md` (i.e. just below the first header). Follow the style described in <https://style.tesselle.org>.
 
 ### Code style
 
-* New code should follow the tesselle [style guide](https://style.tesselle.org).
+* New code should follow the [style guide](https://style.tesselle.org).
 * We use [roxygen2](https://cran.r-project.org/package=roxygen2), with [Markdown syntax](https://cran.r-project.org/web/packages/roxygen2/vignettes/rd-formatting.html), for documentation.
 * We use [testthat](https://cran.r-project.org/package=testthat) for unit tests. Contributions with test cases included are easier to accept.
 
 ## Code of Conduct
 
-Please note that the tabula project is released with a [Contributor Code of Conduct](https://www.tesselle.org/conduct.html). By contributing to this project you agree to abide by its terms.
+Please note that this project is released with a [Contributor Code of Conduct](https://www.tesselle.org/conduct.html). By contributing to this project you agree to abide by its terms.

.github/ISSUE_TEMPLATE/bug_report.md

@@ -1,17 +1,15 @@
 ---
 name: Bug report
-about: Create a report to help us improve
+about: Describe a bug you've seen
 title: ''
 labels: bug
-assignees: nfrerebeau
-
 ---
 
 **Describe the bug**
 A clear and concise description of what the bug is.
 
 **To Reproduce**
-A minimal reproducible example (AKA a reprex). If you've never heard of a [reprex](https://reprex.tidyverse.org/) before, start by reading <https://www.tidyverse.org/help/#reprex>.
+A minimal reproducible example (AKA a reprex).
 
 **Expected behavior**
 A clear and concise description of what you expected to happen.
@@ -21,3 +19,4 @@ If applicable, add screenshots to help explain your problem.
 
 **Additional context**
 Add any other context about the problem here.
+

.github/ISSUE_TEMPLATE/custom.md

@@ -1,10 +1,8 @@
 ---
-name: Custom issue template
-about: Describe this issue template's purpose here.
+name: Custom issue
+about: Ask about a specific problem.
 title: ''
 labels: ''
 assignees: ''
-
 ---
 
-

.github/ISSUE_TEMPLATE/feature_request.md

@@ -1,14 +1,12 @@
 ---
 name: Feature request
-about: Suggest an idea for this project
+about: Make a case for a new feature
 title: ''
 labels: enhancement
-assignees: nfrerebeau
-
 ---
 
 **Is your feature request related to a problem? Please describe.**
-A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+A clear and concise description of what the problem is.
 
 **Describe the solution you'd like**
 A clear and concise description of what you want to happen.
@@ -18,3 +16,4 @@ A clear and concise description of any alternative solutions or features you've
 
 **Additional context**
 Add any other context or screenshots about the feature request here.
+

.github/pull_request_template.md

@@ -18,3 +18,4 @@ methods/functions, include an example if possible to do in brief form -->
 
 <!--- Did you remember to include tests? Unless you're just changing
 grammar, please include new tests for your change -->
+

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

@@ -1,9 +1,11 @@
 on:
   push:
     branches:
+      - main
       - master
   pull_request:
     branches:
+      - main
       - master
 
 name: R-CMD-check
@@ -32,9 +34,9 @@ jobs:
           - {os: ubuntu-20.04,   r: '3.3',     vdiffr: false, xref: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
 
     env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       # don't treat missing suggested packages as error
       _R_CHECK_FORCE_SUGGESTS_: false
       # Some packages might unavailable on the older versions, so let's ignore xref warnings
@@ -60,7 +62,7 @@ jobs:
           writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
         shell: Rscript {0}
 
-      - name: Cache R packages
+      - name: Restore R package cache
         if: runner.os != 'Windows'
         uses: actions/cache@v2
         with:
@@ -116,3 +118,4 @@ jobs:
         with:
           name: ${{ runner.os }}-r${{ matrix.config.r }}-results
           path: check
+

.github/workflows/drat.yaml

@@ -0,0 +1,92 @@
+# https://github.com/r-hyperspec/hySpc.chondro/blob/develop/.github/workflows/drat--insert-package.yaml
+
+on:
+  release:
+    types:
+      - published
+
+name: drat
+
+jobs:
+  drat:
+    runs-on: ubuntu-20.04
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      REPO: ${{ github.event.repository.name }}
+      RELEASE: ${{ github.event.release.tag_name }}
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v1
+
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Restore R package cache
+        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 system dependencies
+        run: |
+          while read -r cmd
+          do
+            eval sudo $cmd
+          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
+
+      - name: Install dependencies
+        run: |
+          remotes::install_deps(dependencies = TRUE)
+          install.packages(c("pkgbuild", "drat"))
+        shell: Rscript {0}
+
+      - name: Build source package
+        run: |
+          dir.create("build", showWarnings = FALSE)
+          pkgbuild::build(dest_path = "build", binary = FALSE, vignettes = TRUE, manual = FALSE)
+        shell: Rscript {0}
+
+      - name: Configure git
+        # https://stackoverflow.com/a/60548651/633251
+        env:
+          TOKEN: ${{ secrets.ACCESS_TOKEN }}
+        run: |
+          git config --global url."https://${TOKEN}:x-oauth-basic@github.com/".insteadOf "https://github.com/"
+          git config --global user.email "${REPO}@tesselle.org"
+          git config --global user.name "${REPO}"
+          
+      - name: Clone tesselle/packages
+        if: success()
+        run: |
+          rm -rf tmp
+          git clone https://github.com/tesselle/packages.git tmp
+          
+      - name: Insert package
+        if: success()
+        run: |
+          targz <- list.files(path = "build", pattern = "\\.tar\\.gz", full.names = TRUE)
+          drat::insertPackage(file = targz, repodir = "tmp", action = "archive", location = "docs")
+        shell: Rscript {0}
+
+      - name: Deploy
+        if: success()
+        run: |
+          cd tmp
+          git add *
+          # .tar.gz files are globally blocked (git ignored) by git,
+          # must add manually and force it
+          git add -f *.tar.gz
+          git commit -m "Add ${REPO} ${RELEASE}"
+          git push origin master
+          

.github/workflows/pkgdown.yaml

@@ -25,7 +25,7 @@ jobs:
           writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
         shell: Rscript {0}
 
-      - name: Cache R packages
+      - name: Restore R package cache
         uses: actions/cache@v2
         with:
           path: ${{ env.R_LIBS_USER }}
@@ -47,3 +47,4 @@ jobs:
           git config --local user.email "actions@github.com"
           git config --local user.name "GitHub Actions"
           Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'
+

.github/workflows/test-coverage.yaml

@@ -29,7 +29,7 @@ jobs:
           writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
         shell: Rscript {0}
 
-      - name: Cache R packages
+      - name: Restore R package cache
         uses: actions/cache@v2
         with:
           path: ${{ env.R_LIBS_USER }}
@@ -46,3 +46,4 @@ jobs:
       - name: Test coverage
         run: covr::codecov()
         shell: Rscript {0}
+

README.Rmd

@@ -35,9 +35,9 @@ knitr::opts_chunk$set(
 
 An easy way to examine archaeological count data. **tabula** provides a convenient and reproducible toolkit for relative and absolute dating and analysis of (chronological) patterns. It includes functions for matrix seriation (reciprocal ranking, CA-based seriation), chronological modeling and dating of archaeological assemblages and/or objects. Beyond these, the package provides several tests and measures of diversity: heterogeneity and evenness (Brillouin, Shannon, Simpson, etc.), richness and rarefaction (Chao1, Chao2, ACE, ICE, etc.), turnover and similarity (Brainerd-Robinson, etc.). The package make it easy to visualize count data and statistical thresholds: rank vs. abundance plots, heatmaps, Ford (1962) and Bertin (1977) diagrams.
 
-To cite **tabula** in publications please use:
-
-> Frerebeau, N. (2019). tabula: An R Package for Analysis, Seriation, and Visualization of Archaeological Count Data. *Journal of Open Source Software*, 4(44), 1821. DOI [10.21105/joss.01821](https://doi.org/10.21105/joss.01821).
+```{r citation, echo=FALSE}
+utils::citation("tabula")
+```
 
 ## Installation
 

README.md

@@ -40,12 +40,25 @@ and rarefaction (Chao1, Chao2, ACE, ICE, etc.), turnover and similarity
 data and statistical thresholds: rank vs. abundance plots, heatmaps,
 Ford (1962) and Bertin (1977) diagrams.
 
-To cite **tabula** in publications please use:
-
-> Frerebeau, N. (2019). tabula: An R Package for Analysis, Seriation,
-> and Visualization of Archaeological Count Data. *Journal of Open
-> Source Software*, 4(44), 1821. DOI
-> [10.21105/joss.01821](https://doi.org/10.21105/joss.01821).
+    #> 
+    #> To cite tabula in publications use:
+    #> 
+    #>   Frerebeau, Nicolas (2019). tabula: An R Package for Analysis,
+    #>   Seriation, and Visualization of Archaeological Count Data. Journal of
+    #>   Open Source Software, 4(44), 1821. DOI 10.21105/joss.01821.
+    #> 
+    #> A BibTeX entry for LaTeX users is
+    #> 
+    #>   @Article{,
+    #>     title = {{tabula}: An R Package for Analysis, Seriation, and Visualization of Archaeological Count Data},
+    #>     author = {Nicolas Frerebeau},
+    #>     year = {2019},
+    #>     journal = {Journal of Open Source Software},
+    #>     volume = {4},
+    #>     number = {44},
+    #>     page = {1821},
+    #>     doi = {10.21105/joss.01821},
+    #>   }
 
 ## Installation
 

_pkgdown.yml

@@ -31,9 +31,6 @@ reference:
 - title: Getters and Setters
   contents:
   - has_concept("mutator")
-- title: Data
-  contents:
-  - has_concept("datasets")
 
 navbar:
   type: default
@@ -55,5 +52,5 @@ navbar:
   - text: Changelog
     href: news/index.html
   right:
-  - icon: fa-github fa-lg
-    href: https://github.com/nfrerebeau/tabula
+  - icon: fab fa-github fa-lg
+    href: https://github.com/tesselle/tabula