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nightly.yaml
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name: Nightly
on:
push:
branches:
- '*'
pull_request:
branches:
- '*'
release:
types: [published]
schedule:
- cron: '0 0 * * *'
env:
GITHUB_USERNAME: ${{ github.actor }}
GITHUB_TOKEN: ${{ github.token }}
RUN_CMD: "./rebar"
jobs:
# ---------------------------------------------------------------------------
# Latest is a model/algorithm test, only needs the linux version compiled
compile:
uses: ./.github/workflows/compile.yaml
strategy:
fail-fast: false
matrix:
include:
# Linux
- arch: x86_64-unknown-linux-musl
os: ubuntu-latest
binary: rebar
with:
arch: ${{ matrix.arch }}
os: ${{ matrix.os }}
binary: ${{ matrix.binary }}
# ---------------------------------------------------------------------------
nightly:
needs: compile
strategy:
fail-fast: false
matrix:
include:
# Linux
- arch: x86_64-unknown-linux-musl
os: ubuntu-latest
binary: rebar
runs-on: ${{ matrix.os }}
steps:
- name: download binary from build
uses: actions/download-artifact@v3
with:
name: rebar-${{ matrix.arch }}
path: target/${{ matrix.arch }}/release
- name: install
run: |
chmod +x target/${{ matrix.arch }}/release/${{ matrix.binary }}
cp target/${{ matrix.arch }}/release/${{ matrix.binary }} .
${{ env.RUN_CMD }} --help
- name: dataset download
run: |
${{ env.RUN_CMD }} dataset download --name sars-cov-2 --tag nightly --output-dir dataset/sars-cov-2/nightly
- name: run
run: |
${{ env.RUN_CMD }} run --dataset-dir dataset/sars-cov-2/nightly --output-dir output/sars-cov-2/nightly/validate --populations "*" --threads 2
- name: plot
run: |
${{ env.RUN_CMD }} plot --annotations dataset/sars-cov-2/nightly/annotations.tsv --run-dir output/sars-cov-2/nightly/validate
- name: validate
run: |
if [[ $(grep "fail" output/sars-cov-2/nightly/validate/linelist.tsv) ]]; then exit 1; fi
- name: upload
uses: actions/upload-artifact@v3
if: always()
with:
name: validate-linelist_${{ matrix.arch }}
path: output/sars-cov-2/nightly/validate/linelist.tsv
if-no-files-found: error
retention-days: 7