Skip to content

Commit

Permalink
Merge pull request #23 from thomasyu888/add-cicd
Browse files Browse the repository at this point in the history 
Add CI/CD to push package to our cran servers
  • Loading branch information
@thomasyu888
thomasyu888 authored Jun 13, 2023
2 parents e85d840 + 32dcb95 commit 8134cb7
Show file tree
Hide file tree
Showing 2 changed files with 272 additions and 5 deletions.
260 changes: 260 additions & 0 deletions .github/workflows/build.yml
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,260 @@
# build and test synapserutils. Additionally deploys to S3 RAN server on GitHub release.

name: build

on:
push:
# we build/test all pushed branches, but not tags.
# we only push tags with releases, and we handle releases explicitly
branches:
- '**'
tags-ignore:
- '**'

pull_request:

release:
types:
- 'published'

jobs:
build:

runs-on: ${{ matrix.os }}
outputs:
package_version: ${{ steps.shared-env.outputs.package_version }}
r_minor_version: ${{ steps.shared-env.outputs.r_minor_version }}

strategy:
matrix:
os: [ubuntu-22.04, macos-12, windows-2022]
r: [4.1.3, 4.2.3, 4.3.0]

steps:
- name: checkout
uses: actions/checkout@v3

- name: setup-r
uses: r-lib/actions/setup-r@v2
with:
r-version: ${{ matrix.r }}
architecture: 'x64'

- name: shared-env
id: shared-env
shell: bash
run: |
PACKAGE_NAME=synapserutils
echo "PACKAGE_NAME=$PACKAGE_NAME" >> $GITHUB_ENV
PACKAGE_VERSION=$(grep "Version: " DESCRIPTION | awk '{print $2'})
# if this was triggered by a release and the release tag
# looks like semver then we use that for the package version.
RELEASE_TAG=${{ github.event.release.tag_name }}
if [[ $RELEASE_TAG =~ ^v?([[:digit:]\.]+)(-rc)? ]]; then
RELEASE_VERSION="${BASH_REMATCH[1]}.$GITHUB_RUN_NUMBER"
# a release version overrides the package version
# for purposes of creating artifacts
PACKAGE_VERSION=$RELEASE_VERSION
DATE=`date +%Y-%m-%d`
# replace DESCRIPTION with $VERSION & $DATE
# sed -i not portable on OSX so we wash through some temp files instead
sed "s|^Version: .*$|Version: $PACKAGE_VERSION|g" DESCRIPTION > DESCRIPTION.temp
sed "s|^Date: .*$|Date: $DATE|g" DESCRIPTION.temp > DESCRIPTION2.temp
rm DESCRIPTION
mv DESCRIPTION2.temp DESCRIPTION
rm DESCRIPTION.temp
fi
echo "BRANCH_VERSION=$BRANCH_VERSION" >> $GITHUB_ENV
echo "PACKAGE_VERSION=$PACKAGE_VERSION" >> $GITHUB_ENV
R_VERSION=${{matrix.r}}
R_MAJOR_VERSION=$(echo $R_VERSION | cut -f1 -d".")
R_MINOR_VERSION=$R_MAJOR_VERSION.$(echo $R_VERSION | cut -f2 -d".")
echo "R_VERSION=$R_VERSION" >> $GITHUB_ENV
echo "R_MAJOR_VERSION=$R_MAJOR_VERSION" >> $GITHUB_ENV
echo "R_MINOR_VERSION=$R_MINOR_VERSION" >> $GITHUB_ENV
# replace backslashes with forward slashes for windows.
# windows bash will handle forward slashes fine and this
# makes it easier to unify the path handling.
R_LIBS_USER_SANITIZED=$(echo $R_LIBS_USER | sed 's/\\/\//g')
echo "R_LIBS_USER=$R_LIBS_USER_SANITIZED" >> $GITHUB_ENV
echo "::set-output name=package_version::$PACKAGE_VERSION"
echo "::set-output name=r_minor_version::$R_MINOR_VERSION"
- name: setup-r-mac-12
if: ${{matrix.os == 'macos-12'}}
run: |
R_LIBS_USER=${GITHUB_WORKSPACE}/R_LIBS
rm -rf R_LIBS_USER
mkdir -p $R_LIBS_USER
echo "R_LIBS_USER=$R_LIBS_USER" >> $GITHUB_ENV
echo "R=R" >> $GITHUB_ENV
# - name: install-test-config
# shell: bash
# run: |
# if [ -z "${{ secrets.encrypted_d17283647768_key }}" ] || [ -z "${{ secrets.encrypted_d17283647768_key }}" ]; then
# echo "No test configuration decryption keys available, skipping integration tests"
# exit 1
# fi
# # decrypt the encrypted test synapse configuration
# openssl aes-256-cbc -K ${{ secrets.encrypted_d17283647768_key }} -iv ${{ secrets.encrypted_d17283647768_iv }} -in test.synapseConfig.enc -out test.synapseConfig -d
# mv test.synapseConfig ~/.synapseConfig
- name: install-pandoc
uses: r-lib/actions/setup-pandoc@v2

- name: install-python-dependencies
shell: bash
if: ${{runner.os == 'Windows'}}
run: |
pip install pandas
pip install synapseclient
- uses: r-lib/actions/setup-r-dependencies@v2
with:
cache: true
cache-version: 1
architecture: 'x64'

- name: linux-build-package
if: ${{runner.os == 'linux'}}
run: |
R CMD build ./
R CMD INSTALL ./ --library=$R_LIBS_USER --no-test-load
echo "ARTIFACT_EXTENSION=tar.gz" >> $GITHUB_ENV
- name: mac-build-package
if: ${{runner.os == 'macOS'}}
run: |
R CMD build ./
R CMD INSTALL --build ${PACKAGE_NAME}_${PACKAGE_VERSION}.tar.gz --library=$R_LIBS_USER --no-test-load
echo "ARTIFACT_EXTENSION=tgz" >> $GITHUB_ENV
- name: windows-build-package
if: ${{runner.os == 'Windows'}}
shell: bash
run: |
R CMD build ./
R CMD INSTALL --build ${PACKAGE_NAME}_${PACKAGE_VERSION}.tar.gz --library=$R_LIBS_USER --no-test-load --no-multiarch
echo "ARTIFACT_EXTENSION=zip" >> $GITHUB_ENV
# - name: run-tests
# shell: bash
# run: |
# echo ".libPaths(c('$R_LIBS_USER', .libPaths()));" > runTests.R
# echo "setwd(sprintf('%s/tests', getwd()));" >> runTests.R
# echo "source('testthat.R')" >> runTests.R
# echo "library(synapserutils);" >> runTests.R
# echo "detach(\"package:synapserutils\", unload=TRUE);" >> runTests.R
# echo "library(synapserutils)" >> runTests.R
# R --vanilla < runTests.R
# rm runTests.R
- name: artifact-name
shell: bash
run: |
# we format our artifact names so we align to the same pattern
# used by the deploy gist written to work with jenkins.
ARTIFACT_NAME="${PACKAGE_NAME}_${PACKAGE_VERSION}.${ARTIFACT_EXTENSION}"
OS_LABEL=$(echo ${{runner.os}} | tr '[:upper:]' '[:lower:]')
if [[ "$OS_LABEL" == "macos" ]]; then
OS_LABEL="mac"
fi
UPLOAD_NAME="label=${OS_LABEL}-RVERS-${{ steps.shared-env.outputs.r_minor_version }}"
echo "ARTIFACT_NAME=$ARTIFACT_NAME" >> $GITHUB_ENV
echo "UPLOAD_NAME=$UPLOAD_NAME" >> $GITHUB_ENV
- name: upload-artifact
uses: actions/upload-artifact@v2
with:
name: ${{env.UPLOAD_NAME}}
path: ${{env.ARTIFACT_NAME}}

deploy:
runs-on: ubuntu-22.04
needs: build
if: github.event_name == 'release'
outputs:
s3_ran: ${{ steps.deploy-to-target.outputs.s3_ran }}

steps:
- name: check-deployment-target
id: check-deployment-target
if: ${{github.event.action == 'published'}}
shell: bash
run: |
DEPLOY_TARGET=""
RELEASE_VERSION=""
RELEASE_TAG=${{ github.event.release.tag_name }}
if [[ $RELEASE_TAG =~ ^v?([[:digit:]\.]+)(-rc)? ]]; then
RELEASE_VERSION="${BASH_REMATCH[1]}"
echo $RELEASE_VERSION
if [[ -n "$RELEASE_VERSION" ]]; then
if [[ "${{ github.event.release.prerelease }}" == "true" ]]; then
DEPLOY_TARGET="staging"
else
DEPLOY_TARGET="prod"
fi
fi
fi
- name: download-artifacts
uses: actions/download-artifact@v2
if: ${{steps.check-deployment-target.outputs.deploy_target != ''}}
with:
path: deploy_artifacts

# Before deoloying to RAN (which is an S3 bucket), authenticate to AWS using GitHub OIDC
- name: Assume AWS Role
uses: aws-actions/configure-aws-credentials@v1
with:
aws-region: us-east-1
role-to-assume: arn:aws:iam::325565585839:role/sagebase-github-oidc-sage-bionetworks-synapser
role-session-name: GitHubActions-${{ github.repository_owner }}-${{ github.event.repository.name }}-${{ github.run_id }}
role-duration-seconds: 1200

- name: deploy-to-target
id: deploy-to-target
if: ${{steps.check-deployment-target.outputs.deploy_target != ''}}
shell: bash
run: |
# we use a gist to upload and the gist internally uses R so we need R on this runner.
# TODO maybe create a docker image to run this with R preloaded (and/or an action).
sudo apt-get -y update && sudo apt-get -y install r-base
export ARTIFACTS_DIR=deploy_artifacts
if [[ "$DEPLOY_TARGET" == "staging" ]]; then
export S3_RAN=staging-ran.synapse.org
elif [[ "$DEPLOY_TARGET" == "prod" ]]; then
export S3_RAN=ran.synapse.org
fi
curl -s https://raw.githubusercontent.com/Sage-Bionetworks/CI-Build-Tools/master/r-pkg/deploy.sh | bash
echo "::set-output name=s3_ran::$S3_RAN"
# on each of our matrix platforms, download the newly uploaded package from RAN
check-deploy:
needs:
[build, deploy]

strategy:
matrix:
os: [ubuntu-22.04, windows-2022, macos-12]
r: [4.1.3, 4.2.2]

runs-on: ${{ matrix.os }}

steps:
- name: checkout
uses: actions/checkout@v3

- name: setup-r
uses: r-lib/actions/setup-r@v2
with:
r-version: ${{ matrix.r }}

- name: check-install
shell: bash
run: |
RAN="http://${{ needs.deploy.outputs.s3_ran }}"
VERSION_TO_CHECK="${{ needs.build.outputs.package_version }}"
PACKAGE="synapserutils"
echo "if (available.packages(repos='$RAN')['$PACKAGE','Version'] != '$VERSION_TO_CHECK') { quit(save = 'no', status = 1) }" > test.R
echo "try(remove.packages('$PACKAGE'), silent=T)" >> test.R
echo "install.packages('reticulate', repos=c('https://cloud.r-project.org/'))" >> test.R
echo "reticulate::virtualenv_create('r-reticulate')" >> test.R
echo "reticulate::use_virtualenv('r-reticulate')" >> test.R
echo "install.packages('$PACKAGE', repos=c('$RAN', 'https://cloud.r-project.org/'))" >> test.R
echo "library('$PACKAGE')" >> test.R
R --vanilla < test.R
17 changes: 12 additions & 5 deletions DESCRIPTION
View file
Original file line number Diff line number Diff line change
@@ -1,18 +1,25 @@
Package: synapserutils
Type: Package
Title: Collection of utilities building on top of synapser
Version: 0.1.6
Version: 1.0.0
Date: 2019-05-31
Authors@R: c(
person("Kimyen", "Ladia", role = c("aut", "cre"), email = "kimyen.ladia@sagebase.org"),
person("Thomas", "Yu", role = c("aut", "cre"), email = "thomas.yu@sagebase.org"),
person("Sage Bionetworks", role = c("cph"))
)
Maintainer: Kimyen Ladia <kimyen.ladia@sagebase.org>
Maintainer: Thomas Yu <thomas.yu@sagebase.org>
Description: Provides convenience R functions for interacting with Synapse.
License: Apache License 2.0
Encoding: UTF-8
Imports: reticulate (>= 0.2)
# Depends: synapser (>= 0.2)
Imports:
reticulate(>= 1.25),
synapser
Depends:
R(>= 4.0),
synapser(>= 1.0.0)
Remotes:
[email protected],
Sage-Bionetworks/synapser@update-client-version
Suggests: testthat, knitr, rmarkdown
URL: https://www.synapse.org
BugReports: https://github.com/Sage-Bionetworks/synapserutils/issues
Expand Down

0 comments on commit 8134cb7

Please sign in to comment.