try again with .sh file fix #28
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# Get ss3 releases and run test model with estimation and hessian | |
name: run-releases-with-test-model | |
on: | |
workflow_dispatch: | |
push: | |
schedule: | |
- cron: '0 15 * * 2' # every Tuesday at 3pm UTC (= 1 0am EST or 11am EDT Eastern time) | |
# Run fast running SS3 test models with estimation | |
jobs: | |
run-releases-with-test-model: | |
runs-on: ${{ matrix.config.os }} | |
name: ${{ matrix.config.os }} | |
strategy: | |
fail-fast: false | |
matrix: | |
config: | |
- {os: windows-latest} | |
- {os: macos-13} | |
- {os: macos-latest} | |
- {os: ubuntu-latest} | |
env: | |
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
R_KEEP_PKG_SOURCE: yes | |
steps: | |
- name: Checkout models repo | |
uses: actions/checkout@v4 | |
with: | |
repository: 'nmfs-ost/ss3-test-models' | |
path: test-models-repo | |
- name: Update Ubuntu packages | |
if: matrix.config.os == 'ubuntu-latest' | |
run: | | |
sudo add-apt-repository ppa:ubuntu-toolchain-r/test | |
sudo apt-get update | |
sudo apt-get install --only-upgrade libstdc++6 | |
sudo apt install libc6 | |
sudo apt-get install -y libcurl4-openssl-dev | |
sudo apt install libfontconfig1-dev | |
- name: Setup R | |
uses: r-lib/actions/setup-r@v2 | |
- name: Install r4ss and run test model on two_morph_seas_areas model | |
run: | | |
install.packages(c("remotes", "svglite", "systemfonts"), dependencies = TRUE) | |
remotes::install_github("r4ss/r4ss") | |
library(r4ss) | |
dir <- file.path(getwd(), "test-models-repo", "models", "two_morph_seas_areas") | |
r4ss::get_ss3_exe(dir = dir) | |
r4ss::run(dir = dir) | |
r4ss::SS_output(dir, verbose = TRUE) | |
shell: Rscript {0} | |