Use GitHub actions instead of Travis (#396)

* Add R-CMD-check and linting workflows

* Update CI login helper functions

Rather than checking whether they run on travis, check whether they're run on
CI. Both travis and github actions have a "CI" env var set to "true".

* Use API key from secret

* Remove .travis.yml

* Try different way to get python packages installed

* Update .Rprofile to check for CI

Also removes repos; we don't use synapser anymore so I don't think this is needed

* Turn off reticulate autoconfigure

* Put CRAN mirror back

* Put synapseclient name in quotes

.Rprofile

@@ -1,12 +1,11 @@
 .First <- function() {
   options(
     repos = c(
-      CRAN = "https://cran.rstudio.com/",
-      Sage = "http://ran.synapse.org"
+      CRAN = "https://cran.rstudio.com/"
     )
   )
 }
 
-if (!identical(Sys.getenv("TRAVIS"), "true")) { # don't run on travis
+if (!identical(Sys.getenv("CI"), "true")) { # don't run on travis
   source("renv/activate.R")
 }

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

@@ -0,0 +1,105 @@
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macOS-latest,   r: 'devel'}
+          - {os: macOS-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-16.04,   r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+          - {os: ubuntu-16.04,   r: '3.6',     rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+          - {os: ubuntu-16.04,   r: '3.5',     rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+          - {os: ubuntu-16.04,   r: '3.4',     rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+      SYNAPSE_USER: ${{ secrets.SYNAPSE_USER }}
+      SYNAPSE_APIKEY: ${{ secrets.SYNAPSE_APIKEY }}
+      RETICULATE_AUTOCONFIGURE: 'FALSE'
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@master
+        with:
+          r-version: ${{ matrix.config.r }}
+
+      - 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
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-r-${{ matrix.config.r }}-${{ hashFiles('depends.Rds') }}
+          restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-
+
+      - name: Install system dependencies (Linux)
+        if: runner.os == 'Linux'
+        run: |
+          export DEBIAN_FRONTEND=noninteractive
+          sudo apt-get -y update
+          sudo apt-get install -y make python-minimal pandoc pandoc-citeproc git-core libv8-dev libxml2-dev libcurl4-openssl-dev libssl-dev libssh2-1-dev zlib1g-dev
+
+      - name: Install system dependencies (macOS)
+        if: runner.os == 'macOS' && matrix.config.r == 'devel'
+        run: |
+          brew install V8
+
+      - name: Install dependencies
+        run: |
+          library(remotes)
+          deps <- readRDS("depends.Rds")
+          deps[["installed"]] <- vapply(deps[["package"]], remotes:::local_sha, character(1))
+          update(deps)
+          remotes::install_cran("rcmdcheck")
+        shell: Rscript {0}
+
+      - name: Install Miniconda
+        run: |
+          Rscript -e "remotes::install_github('rstudio/reticulate')"
+          Rscript -e "reticulate::install_miniconda()"
+
+      - name: Add Miniconda to .Rprofile on macOS
+        if: runner.os == 'macOS'
+        run: echo "options(reticulate.conda_binary = reticulate:::miniconda_conda())" >> .Rprofile
+
+      - name: Install Python deps
+        run: |
+          Rscript -e "reticulate::conda_create('r-reticulate', packages = c('python==3.7.0'))"
+          Rscript -e "remotes::install_local()"
+          Rscript -e "reticulate::py_install('pandas', pip = TRUE)"
+          Rscript -e "reticulate::py_install('synapseclient', pip = TRUE)"
+
+      - 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
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check

.github/workflows/lint.yaml

@@ -0,0 +1,44 @@
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+
+name: lint
+
+jobs:
+  lint:
+    runs-on: macOS-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@master
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        uses: actions/cache@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-
+
+      - name: Install dependencies
+        run: |
+          install.packages(c("remotes"))
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("lintr")
+        shell: Rscript {0}
+
+      - name: Lint
+        run: lintr::lint_package()
+        shell: Rscript {0}

R/utils.R

@@ -1,6 +1,6 @@
 ## Check if we are running on travis
-on_travis <- function() {
-  if (identical(Sys.getenv("TRAVIS"), "true")) {
+on_ci <- function() {
+  if (identical(Sys.getenv("CI"), "true")) {
     return(TRUE)
     # nocov start
   } else {
@@ -10,11 +10,11 @@ on_travis <- function() {
 }
 
 ## Look up env vars and log in to Synapse
-syn_travis_login <- function(syn) {
-  ## Credentials are encrypted on travis
-  user <- Sys.getenv("SYNAPSE_USER")
-  pass <- Sys.getenv("SYNAPSE_PASSWORD")
-  syn$login(email = user, password = pass)
+syn_ci_login <- function(syn) {
+  ## Credentials are encrypted
+  user   <- Sys.getenv("SYNAPSE_USER")
+  apikey <- Sys.getenv("SYNAPSE_APIKEY")
+  syn$login(email = user, apiKey = apikey)
 }
 
 attempt_instantiate <- function() {
@@ -29,8 +29,8 @@ attempt_instantiate <- function() {
 ## org, or with regular synLogin() if not on travis. If on travis but not within
 ## Sage, do nothing.
 attempt_login <- function(syn, ...) {
-  if (on_travis() & !is.null(syn)) {
-    try(syn_travis_login(syn), silent = TRUE)
+  if (on_ci() & !is.null(syn)) {
+    try(syn_ci_login(syn), silent = TRUE)
   } else if (reticulate::py_module_available("synapseclient") & !is.null(syn)) {
     syn$login(...)
   } else {

tests/testthat/test-utils.R

@@ -3,14 +3,14 @@ context("utils.R")
 syn <- attempt_instantiate()
 attempt_login(syn)
 
-test_that("on_travis() returns TRUE on Travis", {
-  expect_equal(on_travis(), isTRUE(as.logical(Sys.getenv("TRAVIS"))))
+test_that("on_ci() returns TRUE on Travis", {
+  expect_equal(on_ci(), isTRUE(as.logical(Sys.getenv("CI"))))
 })
 
 test_that("login works on travis in main repo", {
   ## Lots of other things will fail too if it doesn't, but doesn't hurt to have
   ## a dedicated test
-  skip_if_not(on_travis())
+  skip_if_not(on_ci())
 
   ## In this one we do need to ensure it only runs for builds on upstream repo,
   ## not forks
@@ -20,7 +20,7 @@ test_that("login works on travis in main repo", {
   )
   skip_if_not(owner == "Sage-Bionetworks", "Testing on upstream repo")
 
-  login <- try(syn_travis_login(syn), silent = TRUE)
+  login <- try(syn_ci_login(syn), silent = TRUE)
   expect_false(inherits(login, "try-error"))
 })