Update to pyiron_base 0.9.7 with delayed execution #328
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| name: run-exemplary-workflow | |
| on: | |
| push: | |
| branches: [ main ] | |
| pull_request: | |
| branches: [ main ] | |
| # Allows you to run this workflow manually from the Actions tab | |
| workflow_dispatch: | |
| jobs: | |
| run-pydoit: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: checkout-repository | |
| uses: actions/checkout@v2 | |
| - name: install-basic-deps | |
| uses: ./.github/actions/install-basic-deps | |
| - name: setup-conda-environment | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| environment-file: exemplary_workflow/source/envs/default_env.yaml | |
| miniforge-version: latest | |
| activate-environment: exemplary_workflow | |
| - name: run-workflow | |
| shell: bash -l {0} | |
| run: | | |
| conda install --channel conda-forge doit=0.33.1 | |
| cd $GITHUB_WORKSPACE/exemplary_workflow/pydoit | |
| doit | |
| - name: upload-paper-artifact | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: paper | |
| path: ./exemplary_workflow/pydoit/paper.pdf | |
| retention-days: 1 | |
| if-no-files-found: error | |
| run-cwl: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: checkout-repository | |
| uses: actions/checkout@v2 | |
| - name: install-basic-deps | |
| uses: ./.github/actions/install-basic-deps | |
| - name: setup-conda-environment | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| environment-file: exemplary_workflow/source/envs/default_env.yaml | |
| miniforge-version: latest | |
| activate-environment: exemplary_workflow | |
| - name: run-workflow | |
| shell: bash -l {0} | |
| run: | | |
| conda install --channel conda-forge cwltool | |
| cd $GITHUB_WORKSPACE/exemplary_workflow/cwl | |
| cwltool wf_run_exemplary_wf.cwl | |
| - name: upload-paper-artifact | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: paper | |
| path: ./exemplary_workflow/cwl/paper.pdf | |
| retention-days: 1 | |
| if-no-files-found: error | |
| run-nextflow: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: checkout-repository | |
| uses: actions/checkout@v2 | |
| - name: install-basic-deps | |
| uses: ./.github/actions/install-basic-deps | |
| - name: setup-conda-environment | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| miniforge-version: latest | |
| activate-environment: exemplary_workflow | |
| - name: run-workflow | |
| shell: bash -l {0} | |
| run: | | |
| conda install --channel bioconda nextflow=21.04.0 | |
| cd $GITHUB_WORKSPACE/exemplary_workflow/nextflow | |
| nextflow run exemplarywf.nf | |
| - name: upload-paper-artifact | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: paper | |
| path: ./exemplary_workflow/nextflow/paper.pdf | |
| retention-days: 1 | |
| if-no-files-found: error | |
| run-snakemake: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: checkout-repository | |
| uses: actions/checkout@v2 | |
| - name: install-basic-deps | |
| uses: ./.github/actions/install-basic-deps | |
| - name: setup-conda-environment | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| miniforge-version: latest | |
| activate-environment: exemplary_workflow | |
| channels: conda-forge,bioconda | |
| channel-priority: strict | |
| - name: run-workflow | |
| shell: bash -l {0} | |
| run: | | |
| conda install snakemake | |
| cd $GITHUB_WORKSPACE/exemplary_workflow/snakemake | |
| snakemake --cores 1 --use-conda --conda-frontend conda ./paper.pdf | |
| - name: upload-paper-artifact | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: paper | |
| path: ./exemplary_workflow/snakemake/paper.pdf | |
| retention-days: 1 | |
| if-no-files-found: error | |
| run-kadistudio: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: checkout-repository | |
| uses: actions/checkout@v2 | |
| - name: install-basic-deps | |
| uses: ./.github/actions/install-basic-deps | |
| - name: setup-conda-environment | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| environment-file: exemplary_workflow/source/envs/default_env.yaml | |
| miniforge-version: latest | |
| activate-environment: exemplary_workflow | |
| - name: run-workflow | |
| shell: bash -l -i {0} | |
| run: | | |
| bash $GITHUB_WORKSPACE/exemplary_workflow/kadistudio/install_components.sh | |
| mkdir $GITHUB_WORKSPACE/run | |
| process_engine run $GITHUB_WORKSPACE/exemplary_workflow/kadistudio/exemplary_workflow.flow -p $GITHUB_WORKSPACE/run | |
| - name: upload-paper-artifact | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: paper | |
| path: ./exemplary_workflow/kadistudio/paper.pdf | |
| retention-days: 1 | |
| if-no-files-found: error | |
| run-aiida: | |
| runs-on: ubuntu-latest | |
| services: | |
| postgres: | |
| image: postgres:10 | |
| env: | |
| POSTGRES_DB: test_aiida | |
| POSTGRES_PASSWORD: '' | |
| POSTGRES_HOST_AUTH_METHOD: trust | |
| options: >- | |
| --health-cmd pg_isready | |
| --health-interval 10s | |
| --health-timeout 5s | |
| --health-retries 5 | |
| ports: | |
| - 5432:5432 | |
| rabbitmq: | |
| image: rabbitmq:3.8.14 | |
| ports: | |
| - 5672:5672 | |
| slurm: | |
| image: xenonmiddleware/slurm:17 | |
| ports: | |
| - 5001:22 | |
| steps: | |
| - name: checkout-repository | |
| uses: actions/checkout@v2 | |
| - name: install-basic-deps | |
| uses: ./.github/actions/install-basic-deps | |
| - name: install-system-dependencies | |
| run: | | |
| sudo apt update | |
| sudo apt install postgresql graphviz | |
| - name: setup-conda-environment | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| environment-file: exemplary_workflow/source/envs/default_env.yaml | |
| miniforge-version: latest | |
| activate-environment: exemplary_workflow | |
| - name: install-aiida-shell | |
| # the shell directive is necessary to properly activate the shell | |
| # see https://github.com/marketplace/actions/setup-miniconda | |
| shell: bash -l {0} | |
| run: | | |
| pip install "aiida-core>=2.0,<2.1" "aiida-shell==0.2.0" | |
| - name: setup-aiida-profile | |
| shell: bash -l {0} | |
| run: | | |
| verdi quicksetup --non-interactive --profile default --email aiida@localhost --first-name Giuseppe --last-name Verdi --institution Khedivial --db-backend psql_dos | |
| - name: run-workflow | |
| working-directory: exemplary_workflow/aiida | |
| shell: bash -l {0} | |
| run: | |
| ./exemplary_workflow.py | |
| - name: upload-paper-artifact | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: paper | |
| path: ./exemplary_workflow/aiida/paper.pdf | |
| retention-days: 1 | |
| if-no-files-found: error | |
| run-gwl: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Install Guix | |
| id: install-guix | |
| uses: PromyLOPh/guix-install-action@v1 | |
| with: | |
| channels: |- | |
| (list (channel | |
| (name 'guix) | |
| (url "https://git.savannah.gnu.org/git/guix.git") | |
| (branch "master") | |
| (commit | |
| "8e54584d4448d37ddf8ae995bb545a181ba2493c"))) | |
| - name: Install Guix Workflow Language | |
| run: | | |
| guix install gwl | |
| echo "GUIX_EXTENSIONS_PATH=$HOME/.guix-profile/share/guix/extensions" >> $GITHUB_ENV | |
| - name: checkout-repository | |
| uses: actions/checkout@v2 | |
| - name: run-workflow | |
| run: | | |
| cd exemplary_workflow/gwl | |
| guix workflow run workflow.w | |
| - name: upload-paper-artifact | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: paper | |
| path: exemplary_workflow/gwl/paper.pdf | |
| run-pyiron: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: checkout-repository | |
| uses: actions/checkout@v2 | |
| - name: install-basic-deps | |
| uses: ./.github/actions/install-basic-deps | |
| - name: setup-conda-environment | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| miniforge-version: latest | |
| activate-environment: exemplary_workflow | |
| channels: conda-forge | |
| channel-priority: strict | |
| - name: run-workflow | |
| shell: bash -l {0} | |
| run: | | |
| conda install conda_subprocess=0.0.4 pyiron_base=0.9.6 | |
| cd $GITHUB_WORKSPACE/exemplary_workflow/pyiron | |
| python workflow.py | |
| - name: upload-paper-artifact | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: paper | |
| path: ./exemplary_workflow/pyiron/workflow/tectonic_hdf5/tectonic/paper.pdf | |
| retention-days: 1 | |
| if-no-files-found: error |