Merge pull request #22 from jasenfinch/devel

v1.0.8
jasenfinch · Feb 1, 2022 · a1014b6 · a1014b6
2 parents 98813f7 + 8fa743f
commit a1014b6
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Showing 93 changed files with 128 additions and 12,058 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -6,3 +6,5 @@
 ^codecov\.yml$
 ^doc$
 ^Meta$
+^_pkgdown\.yml$
+^pkgdown$
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -1,15 +1,10 @@
-# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
-# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches:
-      - main
-      - master
-      - devel
+    branches: [main, master,devel]
   pull_request:
-    branches:
-      - main
-      - master
+    branches: [main, master]
 
 name: R-CMD-check
 
@@ -23,74 +18,41 @@ 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: r-lib/actions/setup-pandoc@v1
+
       - uses: r-lib/actions/setup-r@v1
         with:
           r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
 
-      - 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: Cache R packages
-        if: runner.os != 'Windows'
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v1
         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-
-
+          extra-packages: rcmdcheck
+
       - name: Install system dependencies
         if: runner.os == 'Linux'
         run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
           sudo apt install mono-xbuild
-
-      - name: Install dependencies
+          
+      - name: Setup R dependencies
         run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran(c("rcmdcheck","goodpractice"))
           rawrr::installRawFileReaderDLLs()
           rawrr::buildRawrrExe()
           msconverteR::get_pwiz_container()
         shell: Rscript {0}
 
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
-
-      - name: Good practice
-        run: goodpractice::goodpractice()
-        shell: Rscript {0}
-
-      - name: Test coverage
-        run: covr::codecov()
-        shell: Rscript {0}
-
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
-        with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+      - uses: r-lib/actions/check-r-package@v1
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -0,0 +1,47 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - uses: r-lib/actions/setup-r@v1
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v1
+        with:
+          extra-packages: pkgdown
+          needs: website
+
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt install mono-xbuild
+          
+      - name: Setup R dependencies
+        run: |
+          rawrr::installRawFileReaderDLLs()
+          rawrr::buildRawrrExe()
+          msconverteR::get_pwiz_container()
+        shell: Rscript {0}
+
+      - name: Deploy package
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
+          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -0,0 +1,42 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/master/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]
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v1
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v1
+        with:
+          extra-packages: covr
+
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt install mono-xbuild
+          
+      - name: Setup R dependencies
+        run: |
+          rawrr::installRawFileReaderDLLs()
+          rawrr::buildRawrrExe()
+          msconverteR::get_pwiz_container()
+        shell: Rscript {0}
+
+      - name: Test coverage
+        run: covr::codecov()
+        shell: Rscript {0}
diff --git a/.gitignore b/.gitignore
@@ -5,3 +5,4 @@ grover.txt
 .mzML
 doc
 Meta
+docs
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: grover
 Title: Web API Framework for Mass Spectrometry Data Transfer
-Version: 1.0.7
+Version: 1.0.8
 Authors@R: 
     person(given = "Jasen",
            family = "Finch",
@@ -39,6 +39,7 @@ Suggests:
     prettydoc,
     testthat,
     covr
-Remotes: wilsontom/msconverteR
+Remotes: wilsontom/msconverteR,
+        bioc::rawrr
 VignetteBuilder: knitr
-RoxygenNote: 7.1.1
+RoxygenNote: 7.1.2
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+# grover 1.0.8
+
+* Added Bioconductor package [`rawrr](https://bioconductor.org/packages/release/bioc/html/rawrr.html) as a `bioc` remote to ensure the package can be installed correctly using [`pak`](https://pak.r-lib.org/) and [`renv`](https://rstudio.github.io/renv/articles/renv.html).
+
 # grover 1.0.7
 
 * Added `biocViews` field to the DESCRIPTION to ensure the [`rawrr](https://bioconductor.org/packages/release/bioc/html/rawrr.html) Bioconductor dependency is installed automatically.

diff --git a/README.md b/README.md
@@ -2,9 +2,11 @@
 # grover
 
 <!-- badges: start -->
-[![Lifecycle: maturing](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/#maturing)
-[![R build status](https://github.com/jasenfinch/grover/workflows/R-CMD-check/badge.svg)](https://github.com/jasenfinch/grover/actions)
+[![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
+[![R-CMD-check](https://github.com/jasenfinch/grover/workflows/R-CMD-check/badge.svg)](https://github.com/jasenfinch/grover/actions)
 [![Codecov test coverage](https://codecov.io/gh/jasenfinch/grover/branch/master/graph/badge.svg)](https://codecov.io/gh/jasenfinch/grover?branch=master)
+[![license](https://img.shields.io/badge/license-GNU%20GPL%20v3.0-blue.svg)](https://github.com/jasenfinch/grover/blob/master/DESCRIPTION)
+[![GitHub release](https://img.shields.io/github/release/jasenfinch/grover.svg)](https://GitHub.com/jasenfinch/grover/releases/)
 <!-- badges: end -->
 
 ### Overview

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -0,0 +1,4 @@
+url: https://jasenfinch.github.io/grover/
+template:
+  bootstrap: 5
+