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rename notebooks
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‎.github/workflows/pipeline.yml‎

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@@ -46,18 +46,18 @@ jobs:
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shell: bash -l {0}
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run: |
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cd example_workflows/nfdi/
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papermill aiida_nfdi.ipynb aiida_nfdi_out.ipynb -k "python3"
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papermill jobflow_nfdi.ipynb jobflow_nfdi_out.ipynb -k "python3"
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papermill pyiron_base_nfdi.ipynb pyiron_base_nfdi_out.ipynb -k "python3"
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papermill universal_workflow_nfdi.ipynb universal_workflow_nfdi_out.ipynb -k "python3"
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papermill aiida.ipynb aiida_out.ipynb -k "python3"
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papermill jobflow.ipynb jobflow_out.ipynb -k "python3"
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papermill pyiron_base.ipynb pyiron_base_out.ipynb -k "python3"
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papermill universal_workflow.ipynb universal_workflow_out.ipynb -k "python3"
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quantumespresso:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- name: Setup environment
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shell: bash -l {0}
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run: tail --lines=+4 example_workflows/quantum_espresso/environment_qe.yml >> binder/environment.yml
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run: tail --lines=+4 example_workflows/quantum_espresso/environment.yml >> binder/environment.yml
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- uses: conda-incubator/setup-miniconda@v3
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with:
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auto-update-conda: true
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export ESPRESSO_PSEUDO=$(pwd)/espresso/pseudo
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cp -r example_workflows/quantum_espresso/espresso .
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cd example_workflows/quantum_espresso
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papermill aiida_qe.ipynb aiida_qe_out.ipynb -k "python3"
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papermill jobflow_qe.ipynb jobflow_qe_out.ipynb -k "python3"
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papermill pyiron_base_qe.ipynb pyiron_base_qe_out.ipynb -k "python3"
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papermill universal_workflow_qe.ipynb universal_workflow_qe_out.ipynb -k "python3"
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papermill aiida.ipynb aiida_out.ipynb -k "python3"
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papermill jobflow.ipynb jobflow_out.ipynb -k "python3"
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papermill pyiron_base.ipynb pyiron_base_out.ipynb -k "python3"
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papermill universal_workflow.ipynb universal_workflow_out.ipynb -k "python3"
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arithmetic:
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runs-on: ubuntu-latest
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shell: bash -l {0}
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run: |
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cd example_workflows/arithmetic
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papermill aiida_arithmetic.ipynb aiida_arithmetic_out.ipynb -k "python3"
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papermill jobflow_arithmetic.ipynb jobflow_arithmetic_out.ipynb -k "python3"
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papermill pyiron_base_arithmetic.ipynb pyiron_base_arithmetic_out.ipynb -k "python3"
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papermill universal_workflow_arithmetic.ipynb universal_workflow_arithmetic_out.ipynb -k "python3"
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papermill aiida.ipynb aiida_out.ipynb -k "python3"
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papermill jobflow.ipynb jobflow_out.ipynb -k "python3"
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papermill pyiron_base.ipynb pyiron_base_out.ipynb -k "python3"
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papermill universal_workflow.ipynb universal_workflow_out.ipynb -k "python3"
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book:
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runs-on: ubuntu-latest

‎README.md‎

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result = get_sum(x=tmp_dict["prod"], y=tmp_dict["div"])
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```
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For the workflow representation of these Python functions the Python functions are stored in the [arithmetic_workflow.py](example_workflows/arithmetic/arithmetic_workflow.py)
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Python module. The connection of the Python functions are stored in the [workflow_arithmetic.json](example_workflows/arithmetic/workflow_arithmetic.json)
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Python module. The connection of the Python functions are stored in the [workflow_arithmetic.json](example_workflows/arithmetic/workflow.json)
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JSON file:
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```
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{
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| Example | Explanation |
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|----------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------|
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| [aiida_arithmetic.ipynb](example_workflows/arithmetic/aiida_arithmetic.ipynb) | Define Workflow with aiida and execute it with jobflow and pyiron_base. |
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| [jobflow_arithmetic.ipynb](example_workflows/arithmetic/jobflow_arithmetic.ipynb) | Define Workflow with jobflow and execute it with aiida and pyiron_base. |
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| [pyiron_base_arithmetic.ipynb](example_workflows/arithmetic/pyiron_base_arithmetic.ipynb) | Define Workflow with pyiron_base and execute it with aiida and jobflow. |
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| [universal_workflow_arithmetic.ipynb](example_workflows/arithmetic/universal_workflow_arithmetic.ipynb) | Execute workflow defined in the Python Workflow Definition with aiida, executorlib, jobflow, pyiron_base and pure Python. |
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| [aiida_arithmetic.ipynb](example_workflows/arithmetic/aiida.ipynb) | Define Workflow with aiida and execute it with jobflow and pyiron_base. |
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| [jobflow_arithmetic.ipynb](example_workflows/arithmetic/jobflow.ipynb) | Define Workflow with jobflow and execute it with aiida and pyiron_base. |
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| [pyiron_base_arithmetic.ipynb](example_workflows/arithmetic/pyiron_base.ipynb) | Define Workflow with pyiron_base and execute it with aiida and jobflow. |
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| [universal_workflow_arithmetic.ipynb](example_workflows/arithmetic/universal_workflow.ipynb) | Execute workflow defined in the Python Workflow Definition with aiida, executorlib, jobflow, pyiron_base and pure Python. |
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### Quantum Espresso Workflow
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The second workflow example is the calculation of an energy volume curve with Quantum Espresso. In the first step the
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initial structure is relaxed, afterward it is strained and the total energy is calculated.
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* [quantum_espresso_workflow.py](example_workflows/quantum_espresso/quantum_espresso_workflow.py) Python functions
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* [workflow_qe.json](example_workflows/quantum_espresso/workflow_qe.json) Workflow definition in the Python Workflow Definition.
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* [environment_qe.yml](example_workflows/quantum_espresso/environment_qe.yml) Conda environment
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* [workflow_qe.json](example_workflows/quantum_espresso/workflow.json) Workflow definition in the Python Workflow Definition.
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* [environment_qe.yml](example_workflows/quantum_espresso/environment.yml) Conda environment
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| Example | Explanation |
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|------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------|
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| [aiida_qe.ipynb](example_workflows/quantum_espresso/aiida_qe.ipynb) | Define Workflow with aiida and execute it with jobflow and pyiron_base. |
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| [jobflow_qe.ipynb](example_workflows/quantum_espresso/jobflow_qe.ipynb) | Define Workflow with jobflow and execute it with aiida and pyiron_base. |
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| [pyiron_base_qe.ipynb](example_workflows/quantum_espresso/pyiron_base_qe.ipynb) | Define Workflow with pyiron_base and execute it with aiida and jobflow. |
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| [universal_workflow_qe.ipynb](example_workflows/quantum_espresso/universal_workflow_qe.ipynb) | Execute workflow defined in the Python Workflow Definition with aiida, executorlib, jobflow, pyiron_base and pure Python. |
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| [aiida_qe.ipynb](example_workflows/quantum_espresso/aiida.ipynb) | Define Workflow with aiida and execute it with jobflow and pyiron_base. |
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| [jobflow_qe.ipynb](example_workflows/quantum_espresso/jobflow.ipynb) | Define Workflow with jobflow and execute it with aiida and pyiron_base. |
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| [pyiron_base_qe.ipynb](example_workflows/quantum_espresso/pyiron_base.ipynb) | Define Workflow with pyiron_base and execute it with aiida and jobflow. |
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| [universal_workflow_qe.ipynb](example_workflows/quantum_espresso/universal_workflow.ipynb) | Execute workflow defined in the Python Workflow Definition with aiida, executorlib, jobflow, pyiron_base and pure Python. |
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### NFDI4Ing Scientific Workflow Requirements
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To demonstrate the compatibility of the Python Workflow Definition to file based workflows, the workflow benchmark developed as part of [NFDI4Ing](https://github.com/BAMresearch/NFDI4IngScientificWorkflowRequirements)
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is implemented for all three simulation codes based on a shared workflow definition.
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* [nfdi_ing_workflow.py](example_workflows/nfdi/nfdi_ing_workflow.py) Python functions
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* [workflow_nfdi.json](example_workflows/nfdi/workflow_nfdi.json) Workflow definition in the Python Workflow Definition.
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* [workflow_nfdi.json](example_workflows/nfdi/workflow.json) Workflow definition in the Python Workflow Definition.
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Additional source files provided with the workflow benchmark:
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* [source/envs/preprocessing.yaml](example_workflows/nfdi/source/envs/preprocessing.yaml) Conda environment for preprocessing
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| Example | Explanation |
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|----------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------|
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| [aiida_nfdi.ipynb](example_workflows/nfdi/aiida_nfdi.ipynb) | Define Workflow with aiida and execute it with jobflow and pyiron_base. |
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| [jobflow_nfdi.ipynb](example_workflows/nfdi/jobflow_nfdi.ipynb) | Define Workflow with jobflow and execute it with aiida and pyiron_base. |
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| [pyiron_base_nfdi.ipynb](example_workflows/nfdi/pyiron_base_nfdi.ipynb) | Define Workflow with pyiron_base and execute it with aiida and jobflow. |
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| [universal_workflow_nfdi.ipynb](example_workflows/nfdi/universal_workflow_nfdi.ipynb) | Execute workflow defined in the Python Workflow Definition with aiida, executorlib, jobflow, pyiron_base and pure Python. |
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| [aiida_nfdi.ipynb](example_workflows/nfdi/aiida.ipynb) | Define Workflow with aiida and execute it with jobflow and pyiron_base. |
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| [jobflow_nfdi.ipynb](example_workflows/nfdi/jobflow.ipynb) | Define Workflow with jobflow and execute it with aiida and pyiron_base. |
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| [pyiron_base_nfdi.ipynb](example_workflows/nfdi/pyiron_base.ipynb) | Define Workflow with pyiron_base and execute it with aiida and jobflow. |
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| [universal_workflow_nfdi.ipynb](example_workflows/nfdi/universal_workflow.ipynb) | Execute workflow defined in the Python Workflow Definition with aiida, executorlib, jobflow, pyiron_base and pure Python. |

‎binder/postBuild‎

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conda env create -n preprocessing -f example_workflows/nfdi/source/envs/preprocessing.yaml -y
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conda env create -n processing -f example_workflows/nfdi/source/envs/processing.yaml -y
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conda env create -n postprocessing -f example_workflows/nfdi/source/envs/postprocessing.yaml -y
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conda env update --name base --file example_workflows/quantum_espresso/environment_qe.yml
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conda env update --name base --file example_workflows/quantum_espresso/environment.yml
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pip install -e example_workflows/quantum_espresso/qe_xml_parser
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pip install -e python_workflow_definition
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verdi presto --profile-name pwd

‎book/_toc.yml‎

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- file: intro.md
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- file: arithmetic.md
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sections:
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- file: example_workflows/arithmetic/aiida_arithmetic.ipynb
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- file: example_workflows/arithmetic/jobflow_arithmetic.ipynb
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- file: example_workflows/arithmetic/pyiron_base_arithmetic.ipynb
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- file: example_workflows/arithmetic/aiida.ipynb
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- file: example_workflows/arithmetic/jobflow.ipynb
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- file: example_workflows/arithmetic/pyiron_base.ipynb
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- file: evcurve.md
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sections:
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- file: example_workflows/quantum_espresso/aiida_qe.ipynb
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- file: example_workflows/quantum_espresso/jobflow_qe.ipynb
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- file: example_workflows/quantum_espresso/pyiron_base_qe.ipynb
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- file: example_workflows/quantum_espresso/aiida.ipynb
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- file: example_workflows/quantum_espresso/jobflow.ipynb
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- file: example_workflows/quantum_espresso/pyiron_base.ipynb
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- file: nfdi.md
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sections:
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- file: example_workflows/nfdi/aiida_nfdi.ipynb
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- file: example_workflows/nfdi/jobflow_nfdi.ipynb
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- file: example_workflows/nfdi/pyiron_base_nfdi.ipynb
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- file: example_workflows/nfdi/aiida.ipynb
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- file: example_workflows/nfdi/jobflow.ipynb
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- file: example_workflows/nfdi/pyiron_base.ipynb
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- file: conclusion.md

example_workflows/arithmetic/aiida_arithmetic.ipynb renamed to example_workflows/arithmetic/aiida.ipynb

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example_workflows/arithmetic/jobflow_arithmetic.ipynb renamed to example_workflows/arithmetic/jobflow.ipynb

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example_workflows/arithmetic/pyiron_base_arithmetic.ipynb renamed to example_workflows/arithmetic/pyiron_base.ipynb

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