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Merge pull request #3285 from infotroph/reusable-action-workflows
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Reusable action workflows
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@infotroph
infotroph committed May 10, 2024
2 parents 4e61876 + 40436d1 commit c59fe91
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69 changes: 69 additions & 0 deletions .github/workflows/check.yml
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name: check

on:
workflow_call:
inputs:
R-version:
required: true
type: string
make-grouping:
required: true
type: string

env:
R_LIBS_USER: /usr/local/lib/R/site-library
LC_ALL: en_US.UTF-8
NCPUS: 2
PGHOST: postgres
CI: true

jobs:
check:
runs-on: ubuntu-latest

env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
_R_CHECK_LENGTH_1_CONDITION_: true
_R_CHECK_LENGTH_1_LOGIC2_: true
# Avoid compilation check warnings that come from the system Makevars
# See https://stat.ethz.ch/pipermail/r-package-devel/2019q2/003898.html
_R_CHECK_COMPILATION_FLAGS_KNOWN_: -Wformat -Werror=format-security -Wdate-time
# Keep R checks from trying to consult the very flaky worldclockapi.com
_R_CHECK_SYSTEM_CLOCK_: 0

container:
image: pecan/depends:R${{ inputs.R-version }}

steps:
# checkout source code
- name: work around https://github.com/actions/checkout/issues/766
run: git config --global --add safe.directory "$GITHUB_WORKSPACE"
- uses: actions/checkout@v4
with:
set-safe-directory: false

# Forbid spaces in names. Yes, *we* know it's not 1980 anymore, but Make doesn't.
- name: check for filenames that would confuse Make
run: |
SPACENAMES=`find . -name '* *'`
if [ -n "$SPACENAMES" ]; then
echo "::error file=${SPACENAMES}::Spaces in filename(s): ${SPACENAMES}. Please rename these files by converting spaces to underscores."
exit 1
fi
# install additional tools needed
- name: install utils
run: apt-get update && apt-get install -y postgresql-client qpdf
- name: install new dependencies
run: Rscript scripts/generate_dependencies.R && cd docker/depends && Rscript pecan.depends.R

# run PEcAn checks
# The package names of base, modules, and models are passed as matrix variables to avoid repeatability of code
- name: check
run: make -j1 ${{ inputs.make-grouping }}
env:
REBUILD_DOCS: "FALSE"
RUN_TESTS: "FALSE"

- name: check for out-of-date files
uses: infotroph/tree-is-clean@v1
166 changes: 13 additions & 153 deletions .github/workflows/ci-weekly.yml
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schedule:
- cron: '30 4 * * 1'

env:
R_LIBS_USER: /usr/local/lib/R/site-library
LC_ALL: en_US.UTF-8
NCPUS: 2
PGHOST: postgres
CI: true

jobs:
# ----------------------------------------------------------------------
# R TEST
# ----------------------------------------------------------------------
test:
if: github.event_name != 'issue_comment' || startsWith(github.event.comment.body, '/build')
runs-on: ubuntu-latest
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

strategy:
fail-fast: false
matrix:
R:
- "devel"
uses: ./.github/workflows/test.yml
with:
R-version: ${{ matrix.R }}
secrets: inherit

services:
postgres:
image: mdillon/postgis:9.5
options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5

container:
image: pecan/depends:R${{ matrix.R }}

steps:
# checkout source code
- name: work around https://github.com/actions/checkout/issues/766
run: git config --global --add safe.directory "$GITHUB_WORKSPACE"
- uses: actions/checkout@v4
with:
set-safe-directory: false

# install additional tools needed
- name: install utils
run: apt-get update && apt-get install -y postgresql-client qpdf
- name: update dependency lists
run: Rscript scripts/generate_dependencies.R
- name: check for out-of-date dependencies files
uses: infotroph/tree-is-clean@v1
- name: install newly-added dependencies
working-directory: docker/depends
run: Rscript pecan.depends.R

# initialize database
- name: db setup
uses: docker://pecan/db:ci
- name: add models to db
run: ./scripts/add.models.sh

# run PEcAn tests
- name: test
run: make -j1 test
- name: check for out-of-date files
uses: infotroph/tree-is-clean@v1

# ----------------------------------------------------------------------
# R CHECK
# ----------------------------------------------------------------------
check:
if: github.event_name != 'issue_comment' || startsWith(github.event.comment.body, '/build')
runs-on: ubuntu-latest

strategy:
fail-fast: false
matrix:
R:
- "devel"
uses: ./.github/workflows/check.yml
with:
R-version: ${{ matrix.R }}
make-grouping: "check"
secrets: inherit

env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
_R_CHECK_LENGTH_1_CONDITION_: true
_R_CHECK_LENGTH_1_LOGIC2_: true
# Avoid compilation check warnings that come from the system Makevars
# See https://stat.ethz.ch/pipermail/r-package-devel/2019q2/003898.html
_R_CHECK_COMPILATION_FLAGS_KNOWN_: -Wformat -Werror=format-security -Wdate-time
# Keep R checks from trying to consult the very flaky worldclockapi.com
_R_CHECK_SYSTEM_CLOCK_: 0

container:
image: pecan/depends:R${{ matrix.R }}

steps:
# checkout source code
- name: work around https://github.com/actions/checkout/issues/766
run: git config --global --add safe.directory "$GITHUB_WORKSPACE"
- uses: actions/checkout@v4
with:
set-safe-directory: false

# install additional tools needed
- name: install utils
run: apt-get update && apt-get install -y postgresql-client qpdf
- name: install new dependencies
run: Rscript scripts/generate_dependencies.R && cd docker/depends && Rscript pecan.depends.R

# run PEcAn checks
- name: check
run: make -j1 check
env:
REBUILD_DOCS: "FALSE"
RUN_TESTS: "FALSE"
- name: check for out-of-date files
uses: infotroph/tree-is-clean@v1


# ----------------------------------------------------------------------
# SIPNET TESTS
# ----------------------------------------------------------------------
sipnet:
if: github.event_name != 'issue_comment' || startsWith(github.event.comment.body, '/build')
runs-on: ubuntu-latest
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

strategy:
fail-fast: false
matrix:
R:
- "devel"

services:
postgres:
image: mdillon/postgis:9.5
options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5

container:
image: pecan/depends:R${{ matrix.R }}

steps:
# checkout source code
- name: work around https://github.com/actions/checkout/issues/766
run: git config --global --add safe.directory "$GITHUB_WORKSPACE"
- uses: actions/checkout@v4
with:
set-safe-directory: false

# install additional tools needed
- name: install utils
run: apt-get update && apt-get install -y postgresql-client qpdf
- name: install new dependencies
run: Rscript scripts/generate_dependencies.R && cd docker/depends && Rscript pecan.depends.R

# initialize database
- name: db setup
uses: docker://pecan/db:ci
- name: add models to db
run: ./scripts/add.models.sh

# install sipnet
- name: Check out SIPNET
uses: actions/checkout@v4
with:
repository: PecanProject/sipnet
path: sipnet
set-safe-directory: false
- name: install sipnet
run: |
cd ${GITHUB_WORKSPACE}/sipnet
make
# compile PEcAn code
- name: build
run: make -j1

# run SIPNET test
- name: integration test
run: ./tests/integration.sh ghaction
uses: ./.github/workflows/sipnet.yml
with:
R-version: ${{ matrix.R }}
secrets: inherit

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