Merge pull request #291 from stan-dev/patch-for-cran

Minor release v1.10.0

Author: jgabry

.Rbuildignore

@@ -14,4 +14,3 @@ book/*
 docs/*
 Rplots.pdf
 ^\.github$
-^tests/testthat/_snaps$

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

@@ -1,16 +1,15 @@
+# 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:
-      - master
+    branches: [main, master]
   pull_request:
-    branches:
-      - master
+    branches: [main, master, patch-for-cran]
 
 name: R-CMD-check
 
 jobs:
   R-CMD-check:
-    if: "! contains(github.event.head_commit.message, '[ci skip]')"
     runs-on: ${{ matrix.config.os }}
 
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
@@ -19,85 +18,36 @@ jobs:
       fail-fast: false
       matrix:
         config:
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-          - {os: macOS-latest, r: 'release'}
-          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {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
-      RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@master
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
 
-      - uses: r-lib/actions/setup-pandoc@master
-
-      - 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: Cache R packages
-        if: runner.os != 'Windows'
-        uses: actions/cache@v1
+      - uses: r-lib/actions/setup-r-dependencies@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 for linux
-        if: runner.os == 'Linux'
-        env:
-          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
-        run: |
-          Rscript -e "remotes::install_github('r-hub/sysreqs')"
-          sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
-          sudo -s eval "$sysreqs"
-
-      - name: Install system dependencies for mac
-        if: runner.os == 'MacOS'
-        run: |
-           curl -sL  https://mac.r-project.org/libs-4/ |
-           sed -n 's/.*href=\([^>]*x86_64.tar.gz\).*/\1/p' |
-           xargs -I % sh -c 'curl https://mac.r-project.org/libs-4/% --output %; sudo tar fvxz % -C /usr/local --strip 2'
-           ls -la /usr/local/lib
-           ls -la /usr/local/include
-
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-        shell: Rscript {0}
-
-      - name: Session info
-        run: |
-          options(width = 100)
-          pkgs <- installed.packages()[, "Package"]
-          sessioninfo::session_info(pkgs, include_base = TRUE)
-        shell: Rscript {0}
-
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_: false
-          _R_CHECK_FORCE_SUGGESTS_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
-
-      - name: Show testthat output
-        if: always()
-        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
-        shell: bash
-
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@master
+          extra-packages: |
+            any::rcmdcheck
+            any::BH
+            any::RcppEigen
+            any::vdiffr
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          upload-snapshots: true

.github/workflows/codecov.yaml

@@ -0,0 +1,52 @@
+# 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: [main, master]
+  pull_request:
+    branches: [main, master, patch-for-cran]
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: |
+            any::covr
+            any::vdiffr
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+          )
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

.github/workflows/test-coverage.yaml

@@ -1,15 +1,16 @@
 Package: bayesplot
 Type: Package
 Title: Plotting for Bayesian Models
-Version: 1.9.0.9000
-Date: 2022-03-09
+Version: 1.10.0
+Date: 2022-11-15
 Authors@R: c(person("Jonah", "Gabry", role = c("aut", "cre"), email = "jsg2201@columbia.edu"),
              person("Tristan", "Mahr", role = "aut"),
              person("Paul-Christian", "Bürkner", role = "ctb"),
              person("Martin", "Modrák", role = "ctb"),
              person("Malcolm", "Barrett", role = "ctb"),
              person("Frank", "Weber", role = "ctb"),
              person("Eduardo", "Coronado Sroka", role = "ctb"),
+             person("Teemu", "Sailynoja", role = "ctb"),
              person("Aki", "Vehtari", role = "ctb"))
 Maintainer: Jonah Gabry <jsg2201@columbia.edu>
 Description: Plotting functions for posterior analysis, MCMC diagnostics,
@@ -54,7 +55,7 @@ Suggests:
     survival,
     testthat (>= 2.0.0),
     vdiffr (>= 1.0.2)
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.2
 VignetteBuilder: knitr
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)

DESCRIPTION

@@ -188,6 +188,7 @@ import(rlang)
 import(stats)
 importFrom(dplyr,"%>%")
 importFrom(dplyr,across)
+importFrom(dplyr,all_of)
 importFrom(dplyr,arrange)
 importFrom(dplyr,count)
 importFrom(dplyr,full_join)
@@ -205,5 +206,3 @@ importFrom(dplyr,top_n)
 importFrom(dplyr,ungroup)
 importFrom(dplyr,vars)
 importFrom(ggplot2,"%+replace%")
-importFrom(ggridges,geom_density_ridges)
-importFrom(ggridges,geom_density_ridges2)

NAMESPACE

@@ -1,8 +1,19 @@
 <!-- See http://style.tidyverse.org/news.html for advice on writing news -->
 
-# bayesplot 1.9.0.9000
-
-Items for next release go here
+# bayesplot 1.10.0
+
+* New function `mcmc_rank_ecdf()` for rank ecdf plots with confidence bands for
+assessing if two or more chains sample the same distribution (#282,
+@TeemuSailynoja)
+* New functions `ppc_pit_ecdf()`, `ppc_pit_ecdf_grouped()`, PIT ecdf plots with
+confidence bands to assess if `y` and `yrep` contain samples from the same
+distribution. (#282, @TeemuSailynoja)
+* Several `ppc` and `ppd` functions now accept the new `linewidth` argument
+introduced in ggplot2 3.4.0: `ppc_bars()`, `ppc_bars_grouped()`,
+`ppc_intervals()`, `ppc_intervals_grouped()`, `ppd_intervals()`,
+`ppd_intervals_grouped()`.
+* Fix bug in how `mcmc_pairs()` detected hitting `max_treedepth`, thanks to @dmphillippo. (#281)
+* Fix failing tests due to changes in ggplot2 3.4.0 (#289)
 
 # bayesplot 1.9.0
 

NEWS.md

@@ -221,12 +221,12 @@ plot_scheme <- function(scheme = NULL) {
     value = rep(1, length(x))
   )
 
-  ggplot(color_data, aes_(x = ~ name, y = ~ value, fill = ~ group)) +
+  ggplot(color_data, aes(x = .data$name, y = .data$value, fill = .data$group)) +
     geom_bar(
       width = .5,
       stat = "identity",
       color = "white",
-      size = 0.1
+      linewidth = 0.1
     ) +
     scale_fill_manual("", values = unlist(x)) +
     theme_void() +

R/bayesplot-colors.R

@@ -45,8 +45,8 @@ theme_default <-
         panel.grid = element_blank(),
         panel.background = element_blank(),
         panel.border = element_blank(),
-        axis.line = element_line(size = 0.4),
-        axis.ticks = element_line(size = 0.3),
+        axis.line = element_line(linewidth = 0.4),
+        axis.ticks = element_line(linewidth = 0.3),
         strip.background = element_blank(),
         strip.text = element_text(size = rel(0.9)),
         strip.placement = "outside",