Merge branch 'main' into geom_density-bounds

Author: echasnovski

.Rbuildignore

@@ -3,7 +3,6 @@
 visual_test
 ^.*\.Rproj$
 ^\.Rproj\.user$
-^\.travis\.yml$
 ^/\.gitattributes$
 ^inst/web$
 ^notes$
@@ -22,9 +21,11 @@ visual_test
 ^README\.Rmd$
 ^README-.*\.png$
 ^logo\.png$
-^appveyor\.yml$
 ^\.github$
 ^vignettes/profilings
 ^vignettes/profiling.Rmd$
 ^cran-comments\.md$
 ^LICENSE\.md$
+^vignettes/articles$
+^CRAN-SUBMISSION$
+^docs$

.gitattributes

@@ -1 +1 @@
-/NEWS merge=union
+NEWS.md merge=union

.github/CODE_OF_CONDUCT.md

@@ -0,0 +1,126 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, caste, color, religion, or sexual
+identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall
+  community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or advances of
+  any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email address,
+  without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at [email protected]. 
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.1, available at
+<https://www.contributor-covenant.org/version/2/1/code_of_conduct.html>.
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder][https://github.com/mozilla/inclusion].
+
+For answers to common questions about this code of conduct, see the FAQ at
+<https://www.contributor-covenant.org/faq>. Translations are available at <https://www.contributor-covenant.org/translations>.
+
+[homepage]: https://www.contributor-covenant.org

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

@@ -1,17 +1,17 @@
+# 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
+#
+# NOTE: This workflow is overkill for most R packages and
+# check-standard.yaml is likely a better choice.
+# usethis::use_github_action("check-standard") will install it.
 on:
   push:
-    branches:
-      - master
+    branches: [main, master]
   pull_request:
-    branches:
-      - master
+    branches: [main, master]
 
 name: R-CMD-check
 
-# Increment this version when we want to clear cache
-env:
-  cache-version: v1
-
 jobs:
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
@@ -22,92 +22,53 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: windows-latest, r: '4.0',   vdiffr: true}
-          - {os: macOS-latest,   r: '4.0',   vdiffr: true}
-          - {os: macOS-latest,   r: 'devel', vdiffr: false}
-          - {os: ubuntu-16.04,   r: '4.0',   vdiffr: true,  cran: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"}
-          - {os: ubuntu-16.04,   r: '3.6',   vdiffr: false, cran: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"}
-          - {os: ubuntu-16.04,   r: '3.5',   vdiffr: false, cran: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"}
-          - {os: ubuntu-16.04,   r: '3.4',   vdiffr: false, cran: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"}
-          - {os: ubuntu-16.04,   r: '3.3',   vdiffr: false, cran: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"}
-          - {os: ubuntu-16.04,   r: '3.2',   vdiffr: false, cran: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"}
+          - {os: macOS-latest,   r: 'release'}
+
+          - {os: windows-latest, r: 'release'}
+          # Use 3.6 to trigger usage of RTools35
+          - {os: windows-latest, r: '3.6'}
+
+          # Use latest ubuntu to make it easier to install sf dependencies
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+          - {os: ubuntu-latest,   r: 'oldrel-2'}
+          - {os: ubuntu-latest,   r: 'oldrel-3'}
+          - {os: ubuntu-latest,   r: 'oldrel-4'}
 
     env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      CRAN: ${{ matrix.config.cran }}
-      # don't treat missing suggested packages as error
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
       _R_CHECK_FORCE_SUGGESTS_: false
+      # Some packages might unavailable on the older versions, so let's ignore xref warnings
+      _R_CHECK_RD_XREFS_: false
       # Runs vdiffr test only on the latest version of R
-      VDIFFR_RUN_TESTS: ${{ matrix.config.vdiffr }}
+      VDIFFR_RUN_TESTS: ${{ matrix.config.r == 'release' }}
       VDIFFR_LOG_PATH: "../vdiffr.Rout.fail"
 
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@master
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - 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), "depends.Rds", version = 2)
-        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: ${{ env.cache-version }}-${{ runner.os }}-r-${{ matrix.config.r }}-${{ hashFiles('depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-r-${{ matrix.config.r }}-
-
-      - name: Install system dependencies on Linux
-        if: runner.os == 'Linux'
-        env:
-          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
-        run: |
-          # Use cran:libgit2 PPA to avoid conflicts of libcurl4-gnutls-dev
-          # Remove this after https://github.com/r-lib/actions/pull/97 gets merged
-          sudo add-apt-repository ppa:cran/libgit2
-
-          Rscript -e "remotes::install_github('r-hub/sysreqs')"
-          sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
-          sudo -s eval "$sysreqs"
-
-      - name: Install system dependencies on macOS
-        if: runner.os == 'macOS'
-        run: |
-          # XQuartz is needed by vdiffr
-          brew cask install xquartz
-
-          # To install vdiffr, these three libraries/tools are needed in addition to XQuartz
-          # - freetype (already installed, needed by systemfonts)
-          # - cairo (not installed, needed by gdtools)
-          # - pkg-config (not installed, needed to set proper build settings)
-          brew install pkg-config cairo
-
-          # Since sf dependencies are a bit heavy, install them only when they are needed
-          SF_NEEDS_UPDATED=$(Rscript -e 'if (!"sf" %in% installed.packages()[,"Package"] || "sf" %in% old.packages()[,"Package"]) cat("yes")')
-          if [ "${SF_NEEDS_UPDATED}" == "yes" ]; then
-            brew install udunits gdal
-          fi
-
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-        shell: Rscript {0}
-
-      - name: Check
-        run: rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
-
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@master
+          cache-version: 2
+          extra-packages: >
+            any::rcmdcheck,
+            maps=?ignore-before-r=3.5.0,
+            Hmisc=?ignore-before-r=3.6.0,
+            mapproj=?ignore-before-r=3.5.0,
+            multcomp=?ignore-before-r=3.5.0,
+            quantreg=?ignore-before-r=3.5.0,
+          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/pkgdown.yaml

@@ -1,28 +1,46 @@
+# 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: [main, master]
   release:
     types: [published]
+  workflow_dispatch:
 
 name: pkgdown
 
 jobs:
   pkgdown:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - uses: actions/checkout@v2
-      - uses: r-lib/actions/setup-r@master
-      - uses: r-lib/actions/setup-pandoc@master
-      - name: Install dependencies
-        run: |
-          install.packages("remotes")
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_github("tidyverse/tidytemplate")
-          remotes::install_dev("pkgdown")
-        shell: Rscript {0}
-      - name: Install package
-        run: R CMD INSTALL .
-      - name: Deploy package
-        run: pkgdown::deploy_to_branch(new_process = FALSE)
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs