update Readme and enforce strict channel priority in github ci #286
Workflow file for this run
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: CI | |
| on: | |
| push: | |
| pull_request: | |
| branches: [ main ] | |
| # Allows you to run this workflow manually from the Actions tab | |
| workflow_dispatch: | |
| # Runs the workflow once per day at 3:15am | |
| schedule: | |
| - cron: '3 16 * * *' | |
| env: | |
| CACHE_NUMBER: 1 # increase to reset cache manually | |
| jobs: | |
| tests: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: checkout repo content | |
| uses: actions/checkout@v2 | |
| - name: Setup Mambaforge | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniforge-version: latest | |
| activate-environment: model-validation | |
| use-mamba: true | |
| - name: Set strict channel priority | |
| run: conda config --set channel_priority strict | |
| - name: Update environment | |
| run: mamba env update -n model-validation -f environment_benchmarks.yml | |
| - name: run-linear-elastic-plate-with-hole-benchmarks | |
| shell: bash -l {0} | |
| run: | | |
| cd $GITHUB_WORKSPACE/benchmarks/linear-elastic-plate-with-hole/ | |
| python generate_config.py | |
| snakemake --use-conda --force --cores 'all' | |
| snakemake --use-conda --force --cores 'all' --reporter metadata4ing | |
| - name: run-fenics-nextflow-benchmark | |
| shell: bash -l {0} | |
| run: | | |
| cd $GITHUB_WORKSPACE/benchmarks/linear-elastic-plate-with-hole/FEniCS_nextflow/ | |
| nextflow run main.nf -plugins nf-prov@1.4.0 | |
| - name: Archive Linear Elastic plate with a hole benchmark data from snakemake | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: linear-elastic-plate-with-hole_snakemake | |
| path: | | |
| benchmarks/linear-elastic-plate-with-hole/snakemake_results/ | |
| - name: Archive Linear Elastic plate with a hole benchmark data from snakemake provenance | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: linear-elastic-plate-with-hole_snakemake_provenance | |
| path: | | |
| benchmarks/linear-elastic-plate-with-hole/*.zip | |
| - name: Archive fenics nextflow data | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: fenics-nextflow-output | |
| path: | | |
| benchmarks/linear-elastic-plate-with-hole/FEniCS_nextflow/work/** | |
| !benchmarks/linear-elastic-plate-with-hole/FEniCS_nextflow/work/conda/** | |
| - name: Archive fenics nextflow provenance | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: fenics-nextflow-provenance | |
| path: | | |
| benchmarks/linear-elastic-plate-with-hole/FEniCS_nextflow/provenance.json |