Version 1.4.0

.Rbuildignore

@@ -33,4 +33,5 @@
 ^vignettes/used_by*$
 ^revdep$
 ^data-raw$
-^paper$
+^paper$
+^dev$

.github/CONTRIBUTING.md

@@ -0,0 +1,58 @@
+# Contributing to priorsense
+
+This outlines how to propose a change to priorsense and is based on similar
+instructions for tidyverse packages, including the contributing guidelines
+generated by `usethis::use_tidy_contributing()`.
+
+## Fixing typos
+
+You can fix typos, spelling mistakes, or grammatical errors in the documentation
+directly using the GitHub web interface, as long as the changes are made in the
+_source_ file. This generally means you'll need to edit
+[roxygen2 comments](https://roxygen2.r-lib.org/articles/roxygen2.html) in an `.R`,
+not a `.Rd` file. You can find the `.R` file that generates the `.Rd` by reading
+the comment in the first line.
+
+## Bigger changes
+
+If you want to make a bigger change, it's a good idea to first file an issue and
+make sure someone from the team agrees that it’s needed. If you’ve found a bug,
+please file an issue that illustrates the bug with a minimal reproducible
+example (see e.g. the [tidyverse reprex instructions](https://www.tidyverse.org/help/#reprex)).
+The tidyverse guide on [how to create a great issue](https://code-review.tidyverse.org/issues/)
+has more advice.
+
+### Pull request process
+
+If you are new to creating pull requests here are some tips. Using the functions
+from the `usethis` package is not required but can be helpful if this process is
+new to you.
+
+*   Fork the package and clone onto your computer. If you haven't done this before, we recommend using `usethis::create_from_github("stan-dev/priorsense", 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 already used in `NEWS.md`.
+
+### Code style
+
+*  New code should attempt to follow the style used in the package. When in doubt follow the tidyverse [style guide](https://style.tidyverse.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 priorsense project follows the Stan project's
+[Code of Conduct](https://discourse.mc-stan.org/t/announcing-our-new-stan-code-of-conduct/23764).
+By contributing to this project you agree to abide by its terms.
+
+All contributions must follow the [Stan AI Contribution Policy](https://github.com/stan-dev/stan/wiki/AI-Contribution-Policy).

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

@@ -1,12 +1,14 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
     branches: [development]
   pull_request:
     branches: [main, development]
 
-name: R-CMD-check
+name: R-CMD-check.yaml
+
+permissions: read-all
 
 jobs:
   R-CMD-check:
@@ -18,12 +20,9 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          #- {os: macOS-latest, r: 'devel', rtools: ''}
-          #- {os: macOS-latest, r: 'release', rtools: ''}
-          #- {os: windows-latest, r: 'devel', rtools: '45'}
-          #- {os: windows-latest, r: 'release', rtools: '45'}
-          - {os: ubuntu-22.04, r: 'devel', rtools: ''}
-          - {os: ubuntu-22.04, r: 'release', rtools: ''}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
@@ -40,12 +39,13 @@ jobs:
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
 
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v7
 
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
           rtools-version: ${{ matrix.config.rtools }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
       - uses: r-lib/actions/setup-pandoc@v2
         with:
@@ -85,6 +85,6 @@ jobs:
 
       - uses: r-lib/actions/check-r-package@v2
         with:
-          args: 'c("--no-manual", "--as-cran")'
-          error-on: '"warning"'
-          check-dir: '"check"'
+          upload-snapshots: true
+          args: 'c("--no-manual")'
+          build_args: 'c("--no-manual")'

.github/workflows/pkgdown.yaml

@@ -29,50 +29,40 @@ jobs:
       - uses: r-lib/actions/setup-pandoc@v2
 
       - uses: quarto-dev/quarto-actions/setup@v2
-
-      - uses: r-lib/actions/setup-r@v2
+
+      - name: Set up R
+        uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
-
-      - uses: r-lib/actions/setup-r-dependencies@v2
+          extra-repositories: |
+            https://stan-dev.r-universe.dev
+            https://topipa.r-universe.dev
+
+      - name: Install pkgdown dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: |
+          cache-version: 4
+          packages: |
+            deps::.
+            any::sessioninfo
             any::pkgdown
-            local::.
-            XML
-            stan-dev/cmdstanr
-            paul-buerkner/brms
-            topipa/iwmm
-            rcmdcheck
-            rstan
-            checkmate
-            jsonlite
-            nimble
-            posterior
-            processx
-            R6
+          needs: website
+          dependencies: '"all"'
+          extra-packages: |
             BH
-            R2jags
             RcppEigen
             StanHeaders
             RcppParallel
-            withr
-            testthat
-            quarto
-            any::XML
+            stan-dev/cmdstanr
+            topipa/iwmm
+            stan-dev/pkgdown-config
             any::textshaping
-          needs: website
-
-
-      - name: Build site
+
+      - name: Build pkgdown site
         run: |
-          withr::with_envvar(
-            c("NOT_CRAN" = "true"), # this should already be set by setup-r@v2? keeping because vignettes don't build otherwise
-            pkgdown::build_site_github_pages(
-              lazy = FALSE, # change to TRUE if runner times out.
-              run_dont_run = TRUE,
-              new_process = TRUE
-            )
+          pkgdown::build_site_github_pages(
+            install = TRUE,
+            new_process = FALSE
           )
         shell: Rscript {0}
 

.gitignore

@@ -8,6 +8,7 @@ priorsense.Rcheck
 .DS_Store
 docs
 /doc/
+/dev/
 /Meta/
 /pkgdown/
 /..Rcheck/

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: priorsense
 Title: Prior Diagnostics and Sensitivity Analysis
-Version: 1.3.1
-Authors@R: c(person("Noa", "Kallioinen", email = "noa.kallioinen@helsinki.fi", role = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0003-1586-8382")),
+Version: 1.4.0
+Authors@R: c(person("Noa", "Kallioinen", email = "noa.kallioinen@helsinki.fi", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-1586-8382")),
 	     person("Topi", "Paananen", role = c("aut"), comment = c(ORCID = "0000-0002-6542-407X")),
 	     person("Paul-Christian", "Bürkner", role = c("aut"), comment = c(ORCID = "0000-0001-5765-8995")),
 	     person("Aki", "Vehtari", role = c("aut"), comment = c(ORCID = "0000-0003-2164-9469")),
@@ -14,9 +14,9 @@ License: GPL (>= 3)
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE, roclets = c ("namespace", "rd", "srr::srr_stats_roclet"))
-RoxygenNote: 8.0.0
 Imports:
     checkmate (>= 2.3.4),
+    cli,
     ggdist (>= 3.3.3),
     ggh4x (>= 0.3.1),
     ggplot2 (>= 4.0.3),
@@ -29,25 +29,26 @@ Imports:
     tibble (>= 3.3.1),
     utils
 Suggests:
-    bayesplot (>= 1.15.0),
+    bayesplot (>= 1.16.0),
     brms (>= 2.23.0),
     cmdstanr (>= 0.8.1),
     iwmm (>= 0.0.1),
-    nimble (>= 1.4.2),
+    nimble (>= 1.4.3),
     philentropy (>= 0.10.0),
-    quarto (>= 1.4.4),
+    quarto (>= 1.5.1),
     R2jags (>= 0.8),
-    rstan (>= 2.32.6),
-    testthat (>= 3.0.0),
+    rstan (>= 2.32.7),
+    testthat (>= 3.3.2),
     transport (>= 0.15),
-    vdiffr (>= 1.0.8)
+    vdiffr (>= 1.0.9)
 Config/testthat/edition: 3
 Depends:
     R (>= 4.1.0)
 VignetteBuilder: quarto
 Additional_repositories:
     https://topipa.r-universe.dev,
     https://stan-dev.r-universe.dev
-URL: https://n-kall.github.io/priorsense/, https://github.com/n-kall/priorsense
-BugReports: https://github.com/n-kall/priorsense/issues
+URL: https://mc-stan.org/priorsense/, https://mc-stan.org/priorsense
+BugReports: https://github.com/stan-dev/priorsense/issues
 Config/Needs/website: quarto
+Config/roxygen2/version: 8.1.0

NEWS.md

@@ -1,3 +1,9 @@
+priorsense 1.3.1.9000
+---
++ `priorsense` is now an official Stan package, and links to pages and repositories have been updated
++ Plot help text now prints to the console rather than on the plot
++ `powerscale_plot_quantities()` now highlights the line segment closer to 1 when k-hat is high
+
 priorsense 1.3.1
 ---
 + Add new JOSS paper as primary citation for the package.