Skip to content

Commit d8be6ee

Browse files
cicdguycicdguy
authored
Initialize the package template (#9)
* Init template * Remove rogue dep * Add shiny, plumber examples * Doc fixes * Doc fixes * Add plumber test
1 parent 5e333ed commit d8be6ee

32 files changed

+1145
-0
lines changed

‎.Rbuildignore

+10
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,10 @@
1+
^.*\.Rproj$
2+
^\.Rproj\.user$
3+
^_pkgdown\.yml$
4+
^vignettes/hello\.Rmd$
5+
^docs$
6+
^\.github$
7+
README.*
8+
^\.lintr$
9+
^staged_dependencies\.yaml$
10+
coverage.*

‎.github/workflows/build-check-install.yaml

+205
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,205 @@
1+
name: R CMD Check
2+
3+
on:
4+
push:
5+
tags:
6+
- "v*"
7+
branches:
8+
- main
9+
- pre-release
10+
pull_request:
11+
12+
jobs:
13+
build-install-check:
14+
runs-on: ubuntu-latest
15+
container:
16+
image: ${{ matrix.config.image }}:${{ matrix.config.tag }}
17+
name: ${{ matrix.config.image }}, version ${{ matrix.config.tag }}
18+
strategy:
19+
fail-fast: false
20+
matrix:
21+
config:
22+
- {image: ghcr.io/insightsengineering/rstudio_4.1.0_bioc_3.13, tag: 'latest'}
23+
24+
steps:
25+
- name: Check if Docker image meets requirements
26+
run: |
27+
lsb=$(lsb_release -d)
28+
[[ ! $lsb =~ "Ubuntu" ]] && exit 1
29+
30+
required_pkgs="r-base curl git"
31+
for PKG in $required_pkgs
32+
do {
33+
DPKG_PAGER=cat dpkg -l $PKG
34+
}
35+
done
36+
shell: bash
37+
38+
- name: Gather info from PR
39+
uses: actions/github-script@v5
40+
id: get-pr
41+
if: github.event_name == 'pull_request'
42+
with:
43+
script: |
44+
const request = {
45+
owner: context.repo.owner,
46+
repo: context.repo.repo,
47+
pull_number: context.issue.number
48+
}
49+
core.info(`Getting PR #${request.pull_number} from ${request.owner}/${request.repo}`)
50+
try {
51+
const result = await github.rest.pulls.get(request)
52+
return result.data
53+
} catch (err) {
54+
core.setFailed(`Request failed with error ${err}`)
55+
}
56+
57+
- name: Checkout repo during PR
58+
uses: actions/checkout@v2
59+
if: github.event_name == 'pull_request'
60+
with:
61+
repository: ${{ fromJSON(steps.get-pr.outputs.result).head.repo.full_name }}
62+
ref: ${{ fromJSON(steps.get-pr.outputs.result).head.ref }}
63+
path: ${{ github.event.repository.name }}
64+
65+
- name: Checkout repo from push
66+
uses: actions/checkout@v2
67+
if: github.event_name == 'push'
68+
with:
69+
path: ${{ github.event.repository.name }}
70+
71+
- name: Print branch name
72+
run: |
73+
cd ${{ github.event.repository.name }}
74+
git branch --show-current
75+
shell: bash
76+
77+
- name: Run Staged dependencies
78+
uses: insightsengineering/staged-dependencies-action@v1
79+
env:
80+
GITHUB_PAT: ${{ secrets.REPO_GITHUB_TOKEN }}
81+
SD_REPO_PATH: ${{ github.event.repository.name }}
82+
83+
- name: Installed packages
84+
run: |
85+
Rscript -e 'sessionInfo();as.data.frame(installed.packages()[,c("LibPath","Version")])'
86+
shell: bash
87+
88+
- name: Build R package
89+
run: |
90+
R CMD build ${{ github.event.repository.name }}
91+
echo "PKGBUILD=$(echo *.tar.gz)" >> $GITHUB_ENV
92+
shell: bash
93+
94+
- name: Set TESTING_DEPTH
95+
env:
96+
COMMIT_NEWEST_MESSAGE: ${{ github.event.head_commit.message }}
97+
COMMIT_OLDEST_MESSAGE: ${{ github.event.commits[0].message }}
98+
run: |
99+
cd ${{ github.event.repository.name }}
100+
# set TESTING_DEPTH for PR
101+
if [[ ! -z "${GITHUB_HEAD_REF}" ]]; then
102+
TESTING_DEPTH=3
103+
echo "TESTING_DEPTH=3" >> $GITHUB_ENV
104+
COMMIT_NEWEST_MESSAGE=$(git log --format=%B -n 1 ${{ github.event.after }})
105+
fi
106+
if [[ $COMMIT_NEWEST_MESSAGE == *"[skip tests]"* ]]; then
107+
echo "NO_TESTS=1" >> $GITHUB_ENV
108+
fi
109+
# default TESTING_DEPTH
110+
if [[ -z "${TESTING_DEPTH}" ]]; then
111+
echo "TESTING_DEPTH=1" >> $GITHUB_ENV
112+
fi
113+
shell: bash
114+
115+
- name: Print TESTING_DEPTH and NO_TESTS
116+
run: |
117+
echo "TESTING_DEPTH = $TESTING_DEPTH"
118+
echo "NO_TESTS = $NO_TESTS"
119+
120+
# TODO: if configurable then --as-cran optionally
121+
- name: Run R CMD CHECK
122+
run: |
123+
if [[ -z "${{ env.NO_TESTS }}" ]]; then
124+
R CMD check ${{ env.PKGBUILD }}
125+
else
126+
R CMD check --no-tests ${{ env.PKGBUILD }}
127+
fi
128+
shell: bash
129+
continue-on-error: true
130+
env:
131+
# TESTING_DEPTH: 1
132+
_R_CHECK_TESTS_NLINES_: 0
133+
134+
- name: Check whether JUnit XML report exists
135+
id: check_junit_xml
136+
uses: andstor/file-existence-action@v1
137+
with:
138+
files: "${{ github.event.repository.name }}.Rcheck/tests/testthat/junit-result.xml"
139+
140+
- name: Publish Unit Test Summary
141+
uses: EnricoMi/publish-unit-test-result-action@v1
142+
if: ${{ steps.check_junit_xml.outputs.files_exists == 'true' && github.event_name == 'pull_request' }}
143+
with:
144+
check_name: Unit Tests Summary
145+
files: "${{ github.event.repository.name }}.Rcheck/tests/testthat/junit-result.xml"
146+
147+
- name: Catch warnings in R CMD check output
148+
id: catch-errors
149+
run: |
150+
x <- tail(readLines("${{ github.event.repository.name }}.Rcheck/00check.log"), 1)
151+
if (!grepl("^Status", x)) stop("No status line found in R CMD check log")
152+
if (grepl("ERROR", x)) stop("R CMD check has errors")
153+
if (grepl("WARNING", x)) stop("R CMD check has warnings")
154+
shell: Rscript {0}
155+
156+
- name: Upload check results
157+
if: failure()
158+
uses: actions/upload-artifact@v2
159+
with:
160+
name: ${{ matrix.config.tag }}-results
161+
path: ${{ github.event.repository.name }}.Rcheck/00check.log
162+
163+
- name: Install R package
164+
run: R CMD INSTALL ${{ env.PKGBUILD }}
165+
shell: bash
166+
167+
- name: Upload package
168+
if: startsWith(github.ref, 'refs/tags/v')
169+
uses: actions/upload-artifact@v2
170+
with:
171+
path: ${{ env.PKGBUILD }}
172+
name: ${{ env.PKGBUILD }}
173+
174+
upload-release-assets:
175+
name: Upload build tar.gz
176+
needs: build-install-check
177+
runs-on: ubuntu-latest
178+
if: startsWith(github.ref, 'refs/tags/v')
179+
steps:
180+
- name: Checkout
181+
uses: actions/checkout@v2
182+
- name: Wait for release to succeed
183+
timeout-minutes: 2
184+
uses: lewagon/[email protected]
185+
with:
186+
ref: "${{ github.ref }}"
187+
check-name: 'Release'
188+
repo-token: ${{ secrets.REPO_GITHUB_TOKEN }}
189+
wait-interval: 10
190+
- name: Set env
191+
run: echo "RELEASE_VERSION=${GITHUB_REF#refs/*/v}" >> $GITHUB_ENV
192+
- name: Get package name
193+
run: echo "PKGBUILD=${{ github.event.repository.name }}_${{ env.RELEASE_VERSION }}.tar.gz" >> $GITHUB_ENV
194+
- name: Download artifact
195+
uses: actions/download-artifact@v2
196+
with:
197+
name: "${{ env.PKGBUILD }}"
198+
- name: Upload binaries to release
199+
uses: svenstaro/upload-release-action@v2
200+
with:
201+
repo_token: ${{ secrets.REPO_GITHUB_TOKEN }}
202+
file: "${{ env.PKGBUILD }}"
203+
asset_name: "${{ env.PKGBUILD }}"
204+
tag: "${{ github.ref }}"
205+
overwrite: false

‎.github/workflows/links.yml

+38
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,38 @@
1+
name: Check URLs
2+
3+
on:
4+
push:
5+
branches:
6+
- main
7+
- pre-release
8+
pull_request:
9+
10+
jobs:
11+
linkChecker:
12+
name: Validate Links
13+
runs-on: ubuntu-latest
14+
steps:
15+
- name: Checkout repo
16+
uses: actions/checkout@v2
17+
18+
- name: Check URLs in docs
19+
uses: lycheeverse/[email protected]
20+
with:
21+
args: >-
22+
--exclude-private
23+
--exclude "https://github.com.*.git|https://insightsengineering.github.io.*|lewagon.*|knightdave.*|.*users.noreply.github.com|lycheeverse.*"
24+
--verbose
25+
--no-progress
26+
**/*.md
27+
**/*.html
28+
**/*.Rmd
29+
**/*.yaml
30+
**/*.yml
31+
env:
32+
GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }}
33+
34+
- name: Upload lychee report
35+
uses: actions/upload-artifact@v2
36+
with:
37+
name: urls-check-report.md
38+
path: ./lychee/out.md

‎.github/workflows/linter.yaml

+32
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,32 @@
1+
name: SuperLinter
2+
3+
on:
4+
push:
5+
branches:
6+
- main
7+
- pre-release
8+
pull_request:
9+
10+
jobs:
11+
lint:
12+
name: SuperLinter
13+
runs-on: ubuntu-latest
14+
15+
steps:
16+
- name: Checkout Code
17+
uses: actions/checkout@v2
18+
with:
19+
fetch-depth: 0
20+
21+
- name: Lint Code Base
22+
uses: github/super-linter/slim@v4
23+
env:
24+
DEFAULT_BRANCH: main
25+
FILTER_REGEX_EXCLUDE: NEWS.md
26+
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
27+
VALIDATE_ALL_CODEBASE: false
28+
VALIDATE_BASH: true
29+
VALIDATE_DOCKERFILE: true
30+
VALIDATE_MARKDOWN: true
31+
VALIDATE_R: TRUE
32+
VALIDATE_YAML: true

0 commit comments

Comments
 (0)