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Adding functions and scripts for downloading, extracting, and processing observations, initial conditions, land cover types, ERA5 drivers for anchor sites within NA. #5546

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Adding functions and scripts for downloading, extracting, and processing observations, initial conditions, land cover types, ERA5 drivers for anchor sites within NA.

Adding functions and scripts for downloading, extracting, and processing observations, initial conditions, land cover types, ERA5 drivers for anchor sites within NA. #5546

Workflow file for this run

.github/workflows/ci.yml at d11887c
name: CI
on:
push:
branches:
- master
- develop
tags:
- '*'
pull_request:
merge_group:
issue_comment:
types:
- created
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: ${{ secrets.GITHUB_TOKEN }}
strategy:
fail-fast: false
matrix:
R:
- "4.2"
- "4.1"
services:
postgres:
image: mdillon/postgis:9.5
options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5
container:
image: pecan/depends:R${{ 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- name: check for out-of-date dependencies files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- name: check for out-of-date files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:
package: [check_base, check_modules, check_models]
R:
- "4.2"
- "4.1"
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 "$GITHUB_WORKSPACE"
- uses: actions/checkout@v4
with:
set-safe-directory: false
# Forbid spaces in names. Yes, *we* know it's not 1980 anymore, but Make doesn't.
- name: check for filenames that would confuse Make
run: |
SPACENAMES=`find . -name '* *'`
if [ -n "$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 ${{ matrix.package }}
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: ${{ secrets.GITHUB_TOKEN }}
strategy:
fail-fast: false
matrix:
R:
- "4.2"
- "4.1"
services:
postgres:
image: mdillon/postgis:9.5
options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5
container:
image: pecan/depends:R${{ 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