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test.yaml
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name: Test
on:
push:
branches:
- master
pull_request:
branches:
- master
schedule:
- cron: "0 5 * * 1-6"
- cron: "0 5 * * 0"
workflow_dispatch:
# Cancel any in-progress runs when a new run is triggered
concurrency:
group: ${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: true
jobs:
unit-tests:
name: Unit
runs-on: ubuntu-latest
defaults:
run:
shell: bash -l {0}
steps:
- uses: actions/checkout@v6
- name: Setup Pixi
uses: prefix-dev/setup-pixi@v0.9.4
with:
pixi-version: v0.59.0
cache: true
cache-write: ${{ github.event_name == 'push' && github.ref_name == 'master' }}
- name: Run unit tests
run: |
pixi run unit-tests
# integration-tests:
# name: Integration
# runs-on: ${{ matrix.os }}-latest
# strategy:
# fail-fast: false
# matrix:
# # Run windows only on scheduled runs on Sundays, otherwise ignore
# os: ${{ github.event.schedule == '0 5 * * 0' && fromJson('["ubuntu", "macos", "windows"]') || fromJson('["ubuntu", "macos"]') }}
#
# defaults:
# run:
# shell: bash -l {0}
#
# steps:
# - uses: actions/checkout@v6
#
# - uses: dorny/paths-filter@v4
# id: filter
# with:
# filters: |
# src:
# - 'scripts/**'
# - 'rules/**'
# - 'data/**'
# - 'Snakefile'
# - 'config/**'
# - 'pixi.toml'
# - 'pixi.lock'
# - '.github/workflows/test.yaml'
#
# - name: Free up disk space
# run: |
# echo "Initial disk space"
# df -h
# echo "Free up disk space"
# sudo rm -rf /usr/share/dotnet /usr/local/lib/android /opt/ghc /opt/hostedtoolcache/CodeQL
# sudo docker image prune --all --force
# sudo docker builder prune -a --force
# echo "Final disk space"
# df -h
#
# - name: Skip - no source changes
# if: steps.filter.outputs.src != 'true' && github.event_name != 'schedule' && github.event_name != 'workflow_dispatch'
# run: echo "Skipping tests because no source code changes detected"
#
# - name: Setup Pixi
# if: steps.filter.outputs.src == 'true' || github.event_name == 'schedule' || github.event_name == 'workflow_dispatch'
# uses: prefix-dev/setup-pixi@v0.9.4
# with:
# pixi-version: v0.59.0
# cache: true
# cache-write: ${{ github.event_name == 'push' && github.ref_name == 'master' }}
#
# - name: Setup cache keys
# if: steps.filter.outputs.src == 'true' || github.event_name == 'schedule' || github.event_name == 'workflow_dispatch'
# run: |
# echo "WEEK=$(date +'%Y%U')" >> $GITHUB_ENV # data
# echo "MONTH=$(date +'%Y%m')" >> $GITHUB_ENV # cutouts
# echo "VERSIONS_HASH=${{ hashFiles('data/versions.csv') }}" >> $GITHUB_ENV
#
# - uses: actions/cache@v5
# if: steps.filter.outputs.src == 'true' || github.event_name == 'schedule' || github.event_name == 'workflow_dispatch'
# with:
# path: data
# key: data-${{ env.WEEK }}-${{ env.VERSIONS_HASH }}
#
# - uses: actions/cache@v5
# if: steps.filter.outputs.src == 'true' || github.event_name == 'schedule' || github.event_name == 'workflow_dispatch'
# with:
# path: cutouts
# key: cutouts-${{ env.MONTH }}
#
# - name: Restore git-tracked files in data/
# if: steps.filter.outputs.src == 'true' || github.event_name == 'schedule' || github.event_name == 'workflow_dispatch'
# run: git checkout HEAD -- data/
#
# - name: Run pylint check on scripts
# if: steps.filter.outputs.src == 'true' || github.event_name == 'schedule' || github.event_name == 'workflow_dispatch'
# # check for undefined variables to reuse functions across scripts
# run: |
# pixi run pylint --disable=all --enable=E0601,E0606 --output-format=parseable scripts/add_* scripts/prepare_* scripts/solve_*
#
# - name: Run snakemake test workflows
# if: steps.filter.outputs.src == 'true' || github.event_name == 'schedule' || github.event_name == 'workflow_dispatch'
# env:
# SNAKEMAKE_STORAGE_CACHED_HTTP_CACHE: ""
# SNAKEMAKE_STORAGE_CACHED_HTTP_SKIP_REMOTE_CHECKS: "1"
# run: |
# pixi run integration-tests
#
# - name: Upload artifacts
# if: always()
# uses: actions/upload-artifact@v7
# with:
# name: results-${{ matrix.os }}
# path: |
# logs
# .snakemake/log
# results
# retention-days: 3
#
# - name: Show remaining disk space
# if: always()
# run: df -h