[ci] Move CI to GitHub Actions (fixes #286) (#287)

* [ci] Move CI to GitHub Actions (fixes #286) * fixing OS * shell env vars * missing quotes * comments * pandoc * pdflatex * fix NOTEs about unrecognized files * weird linux stuff I h8 the tidyverse * better mirror * use test.sh * unnecessary installs * better path * Update .github/workflows/ci.yml * misc changes * errors are bad * add pkgdown * poppin * I h8 LaTeX * revert tinytex * stuff * more stuff * explicit exit * fix return codes * fix pandoc stuff * fix masking * remove commented-out stuff * NOT_CRAN * just test on r-release * just test oon r-release * more cleanup * simpler config * Update CONTRIBUTING.md * remove some installs
uptake · Nov 28, 2020 · 96ac2f1 · 96ac2f1
1 parent 1d5a01c
commit 96ac2f1
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -1,7 +1,10 @@
 # Files currently checked into the repo
+^.*\.ci
+^.*\.github
 ^docs$
 ^_pkgdown\.yml$
 ^pkgdown$
+^smoke_tests
 ^cran-comments\.md$
 ^CODE_OF_CONDUCT\.md$
 ^LICENSE\.MD$
@@ -64,4 +67,3 @@ vignettes/*\.pdf
 # Stuff
 .Rbuildignore
 .*\.gitkeep
-
diff --git a/.github/setup.sh b/.github/setup.sh
@@ -0,0 +1,22 @@
+#!/bin/bash
+
+set -e
+
+if [[ "${OS_NAME}" == "ubuntu-latest" ]]; then
+    sudo apt-get update
+    sudo apt-get install \
+        --no-install-recommends \
+        -y \
+        --allow-downgrades \
+            libcurl4-openssl-dev \
+            libfribidi-dev \
+            libharfbuzz-dev \
+            curl \
+        || exit -1
+fi
+
+Rscript -e "
+    options(install.packages.check.source = 'no');
+    install.packages('remotes', repos = 'https://cran.r-project.org')
+    remotes::install_deps(dependencies = TRUE)
+"
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -0,0 +1,47 @@
+name: Tests
+
+on: [push]
+
+jobs:
+  test:
+    name: ${{ matrix.os }} (R ${{ matrix.r-version }})
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 60
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - os: ubuntu-latest
+            r-version: 'release'
+          - os: macos-latest
+            r-version: 'release'
+    steps:
+      - name: checkout repository
+        uses: actions/checkout@v2.3.4
+        with:
+          fetch-depth: 1
+      - name: set up R
+        uses: r-lib/actions/setup-r@v1
+        with:
+          r-version: ${{ matrix.r-version }}
+      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-tinytex@v1
+      - name: set up dependencies
+        shell: bash
+        env:
+          OS_NAME: ${{ matrix.os }}
+        run: $GITHUB_WORKSPACE/.github/setup.sh
+      - name: run tests
+        shell: bash
+        run: $GITHUB_WORKSPACE/test.sh
+      - name: upload coverage
+        if: ${{ matrix.os == 'macos-latest' && matrix.r-version == 'release' }}
+        shell: Rscript {0}
+        run: covr::codecov()
+  # https://github.community/t/is-it-possible-to-require-all-github-actions-tasks-to-pass-without-enumerating-them/117957/4?u=graingert
+  all-successful:
+    runs-on: ubuntu-latest
+    needs: [test]
+    steps:
+    - name: Note that all tests succeeded
+      run: echo "🎉"
diff --git a/.travis.yml b/.travis.yml
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -244,7 +244,7 @@ All comments should be above code, not beside it.
 ***
 ## Running Tests Locally <a name="testing"></a>
 
-We use Travis CI to automatically run unit tests and a serious of other automated checks on every PR commit and merge to `main`. Every `pkgnet` release also goes through a battery of automated tests run on CRAN before becoming officially available through CRAN.
+We use GitHub Actions to automatically run unit tests and a series of other automated checks on every PR commit and merge to `main`. Every `pkgnet` release also goes through a battery of automated tests run on CRAN before becoming officially available through CRAN.
 
 However, these options can lengthen your testing cycle and make the process of contributing tedious. If you wish to run tests locally on whatever machine you are developing `pkgnet` code on, run the following from the repo root:
 

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -31,6 +31,7 @@ Imports:
     visNetwork
 Suggests:
     ggplot2,
+    pkgdown,
     testthat,
     webshot,
     withr

diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
 # pkgnet <img src="man/figures/logo.png" align="right" alt="" width="120" />
 
-[![CRAN\_Status\_Badge](https://www.r-pkg.org/badges/version-last-release/pkgnet)](https://cran.r-project.org/package=pkgnet) [![CRAN\_Download\_Badge](https://cranlogs.r-pkg.org/badges/grand-total/pkgnet)](https://cran.r-project.org/package=pkgnet) [![Build Status](https://img.shields.io/travis/uptake/pkgnet.svg?label=build&logo=travis&branch=main)](https://travis-ci.org/uptake/pkgnet)
+[![CRAN\_Status\_Badge](https://www.r-pkg.org/badges/version-last-release/pkgnet)](https://cran.r-project.org/package=pkgnet) [![CRAN\_Download\_Badge](https://cranlogs.r-pkg.org/badges/grand-total/pkgnet)](https://cran.r-project.org/package=pkgnet) [![GitHub Actions Build Status](https://github.com/uptake/pkgnet/workflows/Tests/badge.svg?branch=main)](https://github.com/uptake/pkgnet/actions?query=workflow%3ATests+branch%3Amain)
 [![Appveyor Build status](https://ci.appveyor.com/api/projects/status/github/uptake/pkgnet?branch=main&svg=true)](https://ci.appveyor.com/project/jameslamb/pkgnet)
 [![codecov](https://codecov.io/gh/uptake/pkgnet/branch/main/graph/badge.svg)](https://codecov.io/gh/uptake/pkgnet) 
 [![Lifecycle badge](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/)

diff --git a/test.sh b/test.sh
@@ -1,15 +1,45 @@
 #!/bin/bash
 
-rm *.tar.gz
-rm ~/thing.txt
-R CMD BUILD .
+set -e pipefail
+
+rm -f *.tar.gz
+R CMD build .
 
 # Work outside of the source directory to avoid false
 # positives (i.e. test the tarball in isolation)
 mkdir -p ~/pkgnet_test_dir
 cp *.tar.gz ~/pkgnet_test_dir
 
+export _R_CHECK_CRAN_INCOMING_=false
 pushd ~/pkgnet_test_dir
-    R CMD CHECK *.tar.gz --as-cran
-    cat ~/thing.txt
-popd
+    R CMD check *.tar.gz --as-cran || exit 1
+
+    LOG_FILE_NAME="pkgnet.Rcheck/00check.log"
+
+    echo ""
+    echo "----- R CMD check logs -----"
+    echo ""
+    cat pkgnet.Rcheck/00check.log
+
+    echo ""
+    echo "----- test outputs -----"
+    echo ""
+    cat pkgnet.Rcheck/tests/testthat.Rout
+
+    if grep -q -R "WARNING" "$LOG_FILE_NAME"; then
+        echo "WARNINGS have been found by R CMD check!"
+        exit 1
+    fi
+
+    ALLOWED_CHECK_NOTES=0
+    NUM_CHECK_NOTES=$(
+        cat ${LOG_FILE_NAME} \
+            | grep -e '^Status: .* NOTE.*' \
+            | sed 's/[^0-9]*//g'
+    )
+    if [[ ${NUM_CHECK_NOTES} -gt ${ALLOWED_CHECK_NOTES} ]]; then
+        echo "Found ${NUM_CHECK_NOTES} NOTEs from R CMD check. Only ${ALLOWED_CHECK_NOTES} are allowed"
+        exit 1
+    fi
+
+popd || exit 0
diff --git a/tests/testthat.R b/tests/testthat.R
@@ -9,13 +9,13 @@ Sys.setenv("R_TESTS" = "")
 
 
 #######  TESTING ON vs. OFF CRAN #############
-# Due to complications on CRAN with handling of temporary packages during testing, TRAVIS
+# Due to complications on CRAN with handling of temporary packages during testing, continuous integration (CI)
 # and local testing will remain the main test processes for pkgnet.
 # See https://github.com/uptake/pkgnet/issues/160 for details on this decision.
 
 cat("testthat.R | NOT_CRAN =", Sys.getenv("NOT_CRAN"), "\n")
 if(identical(Sys.getenv("NOT_CRAN"), "true")){
-    ######## TRAVIS and LOCAL TEST PROCEDURE #############
+    ######## CI and LOCAL TEST PROCEDURE #############
 
     # Check if setup and helper funs have been run.
     # If in R CMD CHECK, they may not have been run yet.
@@ -26,7 +26,7 @@ if(identical(Sys.getenv("NOT_CRAN"), "true")){
         library(pkgnet)
         ## ******************************************************************************************
         ## THIS IS THIS SAME CONTENT as setup_setTestEnv.R but neccessary to paste here due to
-        ## travis checks.
+        ## CI checks.
         ## ******************************************************************************************
 
         # [DEBUG] write("PKGNET_REBUILD triggered", file = "~/thing.txt", append = TRUE)
@@ -70,7 +70,7 @@ if(identical(Sys.getenv("NOT_CRAN"), "true")){
 
         ## ******************************************************************************************
         ## THIS IS THIS SAME CONTENT as teardown_setTestEnv.R but neccessary to paste here due to
-        ## travis checks.
+        ## CI checks.
         ## ******************************************************************************************
 
         # [DEBUG] write("PKGNET_REBUILD tear-down triggered", file = "~/thing.txt", append = TRUE)

diff --git a/tests/testthat/setup-setTestEnv.R b/tests/testthat/setup-setTestEnv.R
@@ -4,7 +4,7 @@
 
 cat("setup-setTestEnv.R | NOT_CRAN =", Sys.getenv("NOT_CRAN"), "\n")
 if(identical(Sys.getenv("NOT_CRAN"), "true")){
-    ######## TRAVIS and LOCAL TEST PROCEDURE #############
+    ######## CI and LOCAL TEST PROCEDURE #############
 
     # record original libpaths in order to reset later.
     # This should be unnecessary since tests are conducted within a seperate enviornment.

diff --git a/tests/testthat/test-AbstractPackageReporter.R b/tests/testthat/test-AbstractPackageReporter.R
@@ -67,7 +67,9 @@ test_that(".is.PackageReporter correctly identifies package reporters", {
     expect_true(pkgnet:::.is.PackageReporter(DependencyReporter$new()))
     expect_true(pkgnet:::.is.PackageReporter(FunctionReporter$new()))
     expect_true(pkgnet:::.is.PackageReporter(InheritanceReporter$new()))
-    expect_true(pkgnet:::.is.PackageReporter(SummaryReporter$new()))
+
+    # using :: to avoid masking by testthat::SummaryReporter
+    expect_true(pkgnet:::.is.PackageReporter(pkgnet::SummaryReporter$new()))
 
     DependencyTabloid <- R6::R6Class(
         classname = "DependencyTabloid"

diff --git a/tests/testthat/test-CreatePackageVignette.R b/tests/testthat/test-CreatePackageVignette.R
@@ -100,10 +100,11 @@ test_that("Test that CreatePackageVignette runs end-to-end with non-default repo
     )
     outputPath <- tempfile(pattern = "vignette", fileext = ".html")
 
+    # using :: to avoid masking by testthat::SummaryReporter
     expect_true({
         CreatePackageVignette(pkg = pkgPath
                               , pkg_reporters = list(
-                                  SummaryReporter$new()
+                                  pkgnet::SummaryReporter$new()
                                   , DependencyReporter$new()
                               )
                               , vignette_path = vignettePath

diff --git a/tests/testthat/test-PackageReport.R b/tests/testthat/test-PackageReport.R
@@ -87,7 +87,7 @@ test_that('PackageReport works with pkg_path', {
     )
     reporterObj$DependencyReporter <- DependencyReporter$new()
     expect_true(reporterObj$pkg_path == MILNE_PKG_PATH)
-    # The below test fails on macOS Travis for some mysterious reason.
+    # The below test fails on macOS CI for some mysterious reason.
     #expect_true(reporterObj$DependencyReporter$.__enclos_env__$private$pkg_path == MILNE_PKG_PATH)
 
 })

diff --git a/tests/testthat/test-cran-true.R b/tests/testthat/test-cran-true.R
@@ -1,5 +1,5 @@
 context("always true for cran")
-# Due to complications on CRAN with handling of temporary packages during testing, TRAVIS
+# Due to complications on CRAN with handling of temporary packages during testing, CI
 # and local testing will remain the main test processes for pkgnet.
 # See https://github.com/uptake/pkgnet/issues/160 for details on this decision.