Update pyiron_base to 0.12.0 (#108) #214
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| name: Pipeline | |
| on: | |
| push: | |
| branches: [ main ] | |
| pull_request: | |
| jobs: | |
| black: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: psf/black@stable | |
| with: | |
| options: "--check --diff" | |
| src: ./python_workflow_definition/src/python_workflow_definition | |
| - uses: psf/black@stable | |
| with: | |
| options: "--check --diff" | |
| src: ./example_workflows/quantum_espresso/qe_xml_parser/src/qe_xml_parser | |
| pip_check: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Conda config | |
| run: echo -e "channels:\n - conda-forge\n" > .condarc | |
| - name: Setup Mambaforge | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| python-version: "3.12" | |
| miniforge-version: latest | |
| condarc-file: .condarc | |
| environment-file: binder/environment.yml | |
| - name: Pip check | |
| shell: bash -l {0} | |
| run: | | |
| pip install --no-deps --no-build-isolation -e python_workflow_definition | |
| pip check | |
| nfdi4ing: | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Conda config | |
| run: echo -e "channels:\n - conda-forge\n" > .condarc | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| python-version: "3.12" | |
| miniforge-version: latest | |
| condarc-file: .condarc | |
| environment-file: binder/environment.yml | |
| - name: Installation and setup | |
| shell: bash -l {0} | |
| run: | | |
| pip install --no-deps --no-build-isolation -e python_workflow_definition | |
| conda install -c conda-forge jupyter papermill | |
| verdi presto --profile-name pwd | |
| sudo apt-get install -y $(cat binder/apt.txt) | |
| - name: Create Additional Conda Environments | |
| shell: bash -l {0} | |
| run: | | |
| conda env create -n preprocessing -f example_workflows/nfdi/source/envs/preprocessing.yaml -y | |
| conda env create -n processing -f example_workflows/nfdi/source/envs/processing.yaml -y | |
| conda env create -n postprocessing -f example_workflows/nfdi/source/envs/postprocessing.yaml -y | |
| - name: Tests | |
| shell: bash -l {0} | |
| run: | | |
| cd example_workflows/nfdi/ | |
| papermill aiida.ipynb aiida_out.ipynb -k "python3" | |
| papermill cwl.ipynb cwl_out.ipynb -k "python3" | |
| papermill jobflow.ipynb jobflow_out.ipynb -k "python3" | |
| papermill pyiron_base.ipynb pyiron_base_out.ipynb -k "python3" | |
| papermill universal_workflow.ipynb universal_workflow_out.ipynb -k "python3" | |
| quantumespresso: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Setup environment | |
| shell: bash -l {0} | |
| run: | | |
| echo -e "channels:\n - conda-forge\n" > .condarc | |
| tail --lines=+4 example_workflows/quantum_espresso/environment.yml >> binder/environment.yml | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| python-version: "3.12" | |
| miniforge-version: latest | |
| condarc-file: .condarc | |
| environment-file: binder/environment.yml | |
| - name: Installation and setup | |
| shell: bash -l {0} | |
| run: | | |
| pip install --no-deps --no-build-isolation -e example_workflows/quantum_espresso/qe_xml_parser | |
| pip install --no-deps --no-build-isolation -e python_workflow_definition | |
| conda install -c conda-forge jupyter papermill | |
| verdi presto --profile-name pwd | |
| - name: Tests | |
| shell: bash -l {0} | |
| run: | | |
| export ESPRESSO_PSEUDO=$(pwd)/espresso/pseudo | |
| cp -r example_workflows/quantum_espresso/espresso . | |
| cd example_workflows/quantum_espresso | |
| papermill aiida.ipynb aiida_out.ipynb -k "python3" | |
| papermill cwl.ipynb cwl_out.ipynb -k "python3" | |
| papermill jobflow.ipynb jobflow_out.ipynb -k "python3" | |
| papermill pyiron_base.ipynb pyiron_base_out.ipynb -k "python3" | |
| papermill universal_workflow.ipynb universal_workflow_out.ipynb -k "python3" | |
| arithmetic: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Conda config | |
| run: echo -e "channels:\n - conda-forge\n" > .condarc | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| python-version: "3.12" | |
| miniforge-version: latest | |
| condarc-file: .condarc | |
| environment-file: binder/environment.yml | |
| - name: Installation and setup | |
| shell: bash -l {0} | |
| run: | | |
| pip install --no-deps --no-build-isolation -e python_workflow_definition | |
| conda install -c conda-forge jupyter papermill | |
| verdi presto --profile-name pwd | |
| - name: Tests | |
| shell: bash -l {0} | |
| run: | | |
| cd example_workflows/arithmetic | |
| papermill aiida.ipynb aiida_out.ipynb -k "python3" | |
| papermill cwl.ipynb cwl_out.ipynb -k "python3" | |
| papermill jobflow.ipynb jobflow_out.ipynb -k "python3" | |
| papermill pyiron_base.ipynb pyiron_base_out.ipynb -k "python3" | |
| papermill universal_workflow.ipynb universal_workflow_out.ipynb -k "python3" | |
| documentation: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Conda config | |
| run: echo -e "channels:\n - conda-forge\n" > .condarc | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| python-version: "3.12" | |
| miniforge-version: latest | |
| condarc-file: .condarc | |
| environment-file: documentation/environment.yml | |
| - name: Install Jupyterbook | |
| shell: bash -l {0} | |
| run: | | |
| cp documentation/_config.yml . | |
| cp documentation/_toc.yml . | |
| cp documentation/*.md . | |
| jupyter-book build . --path-output public | |
| mv public/_build/html public_html | |
| touch public_html/.nojekyll |