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targets

targets #657

Workflow file for this run

# MIT License
# Copyright (c) 2021 Eli Lilly and Company
# Author: William Michael Landau (will.landau at gmail)
# Written with help from public domain (CC0 1.0 Universal) workflow files by Jim Hester:
# * https://github.com/r-lib/actions/blob/master/examples/check-full.yaml
# * https://github.com/r-lib/actions/blob/master/examples/blogdown.yaml
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in all
# copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
on:
push:
branches:
- main
# run at noon every day
schedule:
- cron: '0 12 * * *'
name: targets
jobs:
targets:
runs-on: ubuntu-latest
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
RENV_PATHS_ROOT: ~/.local/share/renv
permissions:
contents: write #gives the action permission to push to targets-runs branch
steps:
- uses: actions/checkout@v4
- uses: r-lib/actions/setup-r@v2
with:
r-version: "renv"
- uses: r-lib/actions/setup-pandoc@v2
- name: Install Quarto
uses: quarto-dev/quarto-actions/setup@v2
- run: |
quarto --version
- name: Install Mac system dependencies
if: runner.os == 'macOS'
run: brew install zeromq
- name: Install Linux system dependencies
if: runner.os == 'Linux'
run: |
sudo apt-get install libcurl4-openssl-dev
sudo apt-get install libssl-dev
sudo apt-get install libzmq3-dev
- name: Cache packages
uses: actions/cache@v4
with:
path: ${{ env.RENV_PATHS_ROOT }}
key: ${{ runner.os }}-renv-${{ hashFiles('**/renv.lock') }}
restore-keys: ${{ runner.os }}-renv-
- name: Restore packages
shell: Rscript {0}
run: |
if (!requireNamespace("renv", quietly = TRUE)) install.packages("renv")
renv::restore()
- name: Check if previous runs exists
id: runs-exist
run: git ls-remote --exit-code --heads origin targets-runs
continue-on-error: true
- name: Checkout previous run
if: steps.runs-exist.outcome == 'success'
uses: actions/checkout@v3
with:
ref: targets-runs
fetch-depth: 1
path: .targets-runs
- name: Restore output files from the previous run
if: steps.runs-exist.outcome == 'success'
run: |
for (dest in scan(".targets-runs/.targets-files", what = character())) {
source <- file.path(".targets-runs", dest)
if (!file.exists(dirname(dest))) dir.create(dirname(dest), recursive = TRUE)
if (file.exists(source)) file.rename(source, dest)
}
shell: Rscript {0}
- name: Run targets pipeline
run: targets::tar_make()
shell: Rscript {0}
env:
CONNECT_SERVER: ${{ secrets.CONNECT_URL }}
CONNECT_API_KEY: ${{ secrets.CONNECT_API_KEY }}
- name: Identify files that the targets pipeline produced
run: git ls-files -mo --exclude=renv > .targets-files
- name: Create the runs branch if it does not already exist
if: steps.runs-exist.outcome != 'success'
run: git checkout --orphan targets-runs
- name: Put the worktree in the runs branch if the latter already exists
if: steps.runs-exist.outcome == 'success'
run: |
rm -r .git
mv .targets-runs/.git .
rm -r .targets-runs
- name: Upload latest run
run: |
git config --local user.name "GitHub Actions"
git config --local user.email "actions@github.com"
rm -r .gitignore .github/workflows
git add --all -- ':!renv'
for file in $(git ls-files -mo --exclude=renv)
do
git add --force $file
done
git commit -am "Run pipeline"
git push origin targets-runs
- name: Prepare failure artifact
if: failure()
run: rm -rf .git .github .targets-files .targets-runs
- name: Post failure artifact
if: failure()
uses: actions/upload-artifact@main
with:
name: ${{ runner.os }}-r${{ matrix.config.r }}-results
path: .