python-workflow-definition 0.0.1__tar.gz → 0.1.2__tar.gz

python_workflow_definition-0.1.2/.condarc

@@ -0,0 +1,3 @@
+channels:
+  - conda-forge
+

python_workflow_definition-0.1.2/.github/workflows/deploy.yml

@@ -0,0 +1,35 @@
+name: Deploy
+
+on:
+  push:
+    branches: [ main ]
+
+jobs:
+  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
+    - name: Deploy 🚀
+      uses: JamesIves/github-pages-deploy-action@3.7.1
+      with:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        BRANCH: gh-pages # The branch the action should deploy to.
+        FOLDER: public_html # The folder the action should deploy.
+        CLEAN: true

python_workflow_definition-0.1.2/.github/workflows/pipeline.yml

@@ -0,0 +1,161 @@
+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: ./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 .
+        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 .
+        conda install -c conda-forge jupyter papermill
+        verdi presto --profile-name pwd
+        sudo apt-get install -y $(cat binder/apt.txt)
+    - name: Create Additional Conda Environments
+      shell: bash -l {0}
+      run: |
+        conda env create -n preprocessing -f example_workflows/nfdi/source/envs/preprocessing.yaml -y
+        conda env create -n processing -f example_workflows/nfdi/source/envs/processing.yaml -y
+        conda env create -n postprocessing -f example_workflows/nfdi/source/envs/postprocessing.yaml -y
+    - name: Tests
+      shell: bash -l {0}
+      run: |
+        cd example_workflows/nfdi/
+        papermill aiida.ipynb aiida_out.ipynb -k "python3"
+        papermill cwl.ipynb cwl_out.ipynb -k "python3"
+        papermill jobflow.ipynb jobflow_out.ipynb -k "python3"
+        papermill pyiron_base.ipynb pyiron_base_out.ipynb -k "python3"
+        papermill pyiron_workflow.ipynb pyiron_workflow_out.ipynb -k "python3"
+        papermill universal_workflow.ipynb universal_workflow_out.ipynb -k "python3"
+
+  quantumespresso:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Setup environment
+      shell: bash -l {0}
+      run: |
+        echo -e "channels:\n  - conda-forge\n" > .condarc
+        tail --lines=+4 example_workflows/quantum_espresso/environment.yml >> binder/environment.yml
+    - uses: conda-incubator/setup-miniconda@v3
+      with:
+        python-version: "3.12"
+        miniforge-version: latest
+        condarc-file: .condarc
+        environment-file: binder/environment.yml
+    - name: Installation and setup
+      shell: bash -l {0}
+      run: |
+        pip install --no-deps --no-build-isolation -e example_workflows/quantum_espresso/qe_xml_parser
+        pip install --no-deps --no-build-isolation -e .
+        conda install -c conda-forge jupyter papermill
+        verdi presto --profile-name pwd
+    - name: Tests
+      shell: bash -l {0}
+      run: |
+        export ESPRESSO_PSEUDO=$(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 pyiron_workflow.ipynb pyiron_workflow_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 .
+        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 pyiron_workflow.ipynb pyiron_workflow_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

python_workflow_definition-0.1.2/.github/workflows/pypi.yml

@@ -0,0 +1,31 @@
+name: Pypi
+
+on:
+  push:
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  release:
+    if: startsWith(github.event.ref, 'refs/tags') || github.event_name == 'release'
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/python_workflow_definition
+    permissions:
+      id-token: write
+    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: Build
+      shell: bash -l {0}
+      run: hatchling build -t sdist -t wheel
+    - name: Publish distribution 📦 to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1

{python_workflow_definition-0.0.1 → python_workflow_definition-0.1.2}/.gitignore

@@ -178,7 +178,7 @@ cython_debug/
 input_tmp.in
 pyiron.log
 pyiron_draw.png
-python_workflow_definition/src/python_workflow_definition/__pycache__/
+src/python_workflow_definition/__pycache__/
 test/
 mini/
 evcurve.png
@@ -199,4 +199,4 @@ jobflow_to_aiida_qe.json
 aiida_to_jobflow_qe.json
 pyiron_base_to_aiida_simple.json
 pyiron_base_to_jobflow_qe.json
-
+**/*.h5

python_workflow_definition-0.1.2/CITATION.cff

@@ -0,0 +1,40 @@
+cff-version: "1.2.0"
+authors:
+- family-names: Janssen
+  given-names: Jan
+  orcid: "https://orcid.org/0000-0001-9948-7119"
+- family-names: George
+  given-names: Janine
+  orcid: "https://orcid.org/0000-0001-8907-0336"
+- family-names: Geiger
+  given-names: Julian
+  orcid: "https://orcid.org/0000-0003-0023-1960"
+- family-names: Bercx
+  given-names: Marnik
+  orcid: "https://orcid.org/0000-0001-8470-1012"
+- family-names: Wang
+  given-names: Xing
+- family-names: Ertural
+  given-names: Christina
+  orcid: "https://orcid.org/0000-0002-7696-5824"
+- family-names: Schaarschmidt
+  given-names: Joerg
+  orcid: "https://orcid.org/0000-0002-4389-2366"
+- family-names: Ganose
+  given-names: Alex
+  orcid: "https://orcid.org/0000-0002-4486-3321"
+- family-names: Pizzi
+  given-names: Giovanni
+  orcid: "https://orcid.org/0000-0002-3583-4377"
+- family-names: Hickel
+  given-names: Tilmann
+  orcid: "https://orcid.org/0000-0003-0698-4891"
+- family-names: Neugebauer
+  given-names: Joerg
+  orcid: "https://orcid.org/0000-0002-7903-2472"
+title: "A Python workflow definition for computational materials design"
+version: 0.1.1
+doi: 10.1039/D5DD00231A
+date-released: 2025-10-25
+license: bsd-3-clause
+url: "https://github.com/pythonworkflow/python-workflow-definition"

python_workflow_definition-0.1.2/LICENSE

@@ -0,0 +1,29 @@
+BSD 3-Clause License
+
+Copyright (c) 2025, Jan Janssen
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the name of the copyright holder nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

{python_workflow_definition-0.0.1 → python_workflow_definition-0.1.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: python_workflow_definition
-Version: 0.0.1
+Version: 0.1.2
 Summary: Python Workflow Definition - workflow interoperability for aiida, jobflow and pyiron
 Author-email: Jan Janssen <janssen@mpie.de>, Janine George <janine.geogre@bam.de>, Julian Geiger <julian.geiger@psi.ch>, Xing Wang <xing.wang@psi.ch>, Marnik Bercx <marnik.bercx@psi.ch>, Christina Ertural <christina.ertural@bam.de>
 License: BSD 3-Clause License
@@ -32,11 +32,16 @@ License: BSD 3-Clause License
         CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
         OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
         OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-Requires-Dist: aiida-workgraph<=0.5.2,>=0.5.1
-Requires-Dist: jobflow<=0.1.19,>=0.1.18
-Requires-Dist: numpy<2,>=1.21
-Requires-Dist: pyiron-base<=0.11.11,>=0.11.10
+License-File: LICENSE
+Requires-Dist: numpy>=1.21
+Requires-Dist: pydantic<=2.12.4,>=2.7.0
+Provides-Extra: aiida
+Requires-Dist: aiida-workgraph<=0.7.6,>=0.5.1; extra == 'aiida'
+Provides-Extra: jobflow
+Requires-Dist: jobflow<=0.2.1,>=0.1.18; extra == 'jobflow'
 Provides-Extra: plot
-Requires-Dist: ipython<=9.0.2,>=7.33.0; extra == 'plot'
-Requires-Dist: networkx<=3.4.2,>=2.8.8; extra == 'plot'
+Requires-Dist: ipython<=9.8.0,>=7.33.0; extra == 'plot'
+Requires-Dist: networkx<=3.5,>=2.8.8; extra == 'plot'
 Requires-Dist: pygraphviz<=1.14,>=1.10; extra == 'plot'
+Provides-Extra: pyiron
+Requires-Dist: pyiron-base<=0.15.10,>=0.11.10; extra == 'pyiron'

python_workflow_definition-0.1.2/README.md

@@ -0,0 +1,119 @@
+# Python Workflow Definition
+[![Pipeline](https://github.com/pythonworkflow/python-workflow-definition/actions/workflows/pipeline.yml/badge.svg)](https://github.com/pythonworkflow/python-workflow-definition/actions/workflows/pipeline.yml)
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/pythonworkflow/python-workflow-definition/HEAD)
+[![DOI](https://zenodo.org/badge/945869529.svg)](https://doi.org/10.5281/zenodo.15516179)
+
+## Definition
+In the Python Workflow Definition (PWD) each node represents a Python function, with the edges defining the connection 
+between input and output of the different Python functions. 
+
+Published in: [J. Janssen, J. George, J. Geiger, M. Bercx, X. Wang, C. Ertural, J. Schaarschmidt, A.M. Ganose, G. Pizzi, T. Hickel and J. Neugebauer. A python workflow definition for computational materials design. Digital Discovery, 2025](https://doi.org/10.1039/D5DD00231A)
+
+## Format
+Each workflow consists of three files, a Python module which defines the individual Pythons, a JSON file which defines
+the connections between the different Python functions and a conda environment file to define the software dependencies.
+The files are not intended to be human readable, but rather interact as a machine readable exchange format between the 
+different workflow engines to enable interoperability. 
+
+## Installation
+The Python Workflow Definition can either be installed via pypi or via conda. For the [pypi installation](https://pypi.org/project/python-workflow-definition/) use:
+```
+pip install python-workflow-definition
+```
+For the conda installation via the [conda-forge community channel](https://anaconda.org/conda-forge/python-workflow-definition) use: 
+```
+conda install conda-forge::python-workflow-definition
+```
+
+## Examples
+### Simple Example 
+As a first example we define two Python functions which add multiple inputs: 
+```python
+def get_sum(x, y):
+    return x + y
+    
+def get_prod_and_div(x: float, y: float) -> dict:
+    return {"prod": x * y, "div": x / y}
+```
+These two Python functions are combined in the following example workflow:
+```python
+def combined_workflow(x=1, y=2):
+    tmp_dict = get_prod_and_div(x=x, y=y)
+    return get_sum(x=tmp_dict["prod"], y=tmp_dict["div"])
+```
+For the workflow representation of these Python functions the Python functions are stored in the [example_workflows/arithmetic/workflow.py](example_workflows/arithmetic/workflow.py)
+Python module. The connection of the Python functions are stored in the [example_workflows/arithmetic/workflow.json](example_workflows/arithmetic/workflow.json) 
+JSON file:
+```JSON
+{
+  "nodes": [
+    {"id": 0, "type": "function", "value": "workflow.get_prod_and_div"},
+    {"id": 1, "type": "function", "value": "workflow.get_sum"},
+    {"id": 2, "type": "input", "value": 1, "name": "x"},
+    {"id": 3, "type": "input", "value": 2, "name": "y"},
+    {"id": 4, "type": "output", "name": "result"}
+  ],
+  "edges": [
+    {"target": 0, "targetPort": "x", "source": 2, "sourcePort": null},
+    {"target": 0, "targetPort": "y", "source": 3, "sourcePort": null},
+    {"target": 1, "targetPort": "x", "source": 0, "sourcePort": "prod"},
+    {"target": 1, "targetPort": "y", "source": 0, "sourcePort": "div"},
+    {"target": 4, "targetPort": null, "source": 1, "sourcePort": null}
+  ]
+}
+```
+The abbreviations in the definition of the edges are:
+* `target` - target node 
+* `targetPort` - target port - for a node with multiple input parameters the target port specifies which input parameter to use.
+* `source` - source node 
+* `sourcePort` - source port - for a node with multiple output parameters the source port specifies which output parameter to use.
+
+As the workflow does not require any additional resources, as it is only using built-in functionality of the Python standard 
+library.
+
+The corresponding Jupyter notebooks demonstrate this functionality:
+
+| Example                                                                                                        | Explanation                                                                                                               | 
+|----------------------------------------------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------|
+| [example_workflows/arithmetic/aiida.ipynb](example_workflows/arithmetic/aiida.ipynb)                           | Define Workflow with aiida and execute it with jobflow and pyiron_base.                                                   |
+| [example_workflows/arithmetic/jobflow.ipynb](example_workflows/arithmetic/jobflow.ipynb)                       | Define Workflow with jobflow and execute it with aiida and pyiron_base.                                                   |
+| [example_workflows/arithmetic/pyiron_base.ipynb](example_workflows/arithmetic/pyiron_base.ipynb)               | Define Workflow with pyiron_base and execute it with aiida and jobflow.                                                   |
+| [example_workflows/arithmetic/universal_workflow.ipynb](example_workflows/arithmetic/universal_workflow.ipynb) | Execute workflow defined in the Python Workflow Definition with aiida, executorlib, jobflow, pyiron_base and pure Python. |
+
+### Quantum Espresso Workflow
+The second workflow example is the calculation of an energy volume curve with Quantum Espresso. In the first step the 
+initial structure is relaxed, afterward it is strained and the total energy is calculated. 
+* [example_workflows/quantum_espresso/workflow.py](example_workflows/quantum_espresso/workflow.py) Python functions 
+* [example_workflows/quantum_espresso/workflow.json](example_workflows/quantum_espresso/workflow.json) Workflow definition in the Python Workflow Definition.
+* [example_workflows/quantum_espresso/environment.yml](example_workflows/quantum_espresso/environment.yml) Conda environment
+
+| Example                                                                                                                    | Explanation                                                                                                               | 
+|----------------------------------------------------------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------|
+| [example_workflows/quantum_espresso/aiida.ipynb](example_workflows/quantum_espresso/aiida.ipynb)                           | Define Workflow with aiida and execute it with jobflow and pyiron_base.                                                   |
+| [example_workflows/quantum_espresso/jobflow.ipynb](example_workflows/quantum_espresso/jobflow.ipynb)                       | Define Workflow with jobflow and execute it with aiida and pyiron_base.                                                   |
+| [example_workflows/quantum_espresso/pyiron_base.ipynb](example_workflows/quantum_espresso/pyiron_base.ipynb)               | Define Workflow with pyiron_base and execute it with aiida and jobflow.                                                   |
+| [example_workflows/quantum_espresso/universal_workflow.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. |
+
+### NFDI4Ing Scientific Workflow Requirements
+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)
+is implemented for all three simulation codes based on a shared workflow definition. 
+* [example_workflows/nfdi/workflow.py](example_workflows/nfdi/workflow.py) Python functions 
+* [example_workflows/nfdi/workflow.json](example_workflows/nfdi/workflow.json) Workflow definition in the Python Workflow Definition.
+
+Additional source files provided with the workflow benchmark:
+* [example_workflows/nfdi/source/envs/preprocessing.yaml](example_workflows/nfdi/source/envs/preprocessing.yaml) Conda environment for preprocessing
+* [example_workflows/nfdi/source/envs/processing.yaml](example_workflows/nfdi/source/envs/processing.yaml) Conda environment for processing
+* [example_workflows/nfdi/source/envs/postprocessing.yaml](example_workflows/nfdi/source/envs/postprocessing.yaml) Conda environment for postprocessing
+* [example_workflows/nfdi/source/macros.tex.template](example_workflows/nfdi/source/macros.tex.template) LaTeX module template 
+* [example_workflows/nfdi/source/paper.tex](example_workflows/nfdi/source/paper.tex) LaTeX paper template 
+* [example_workflows/nfdi/source/poisson.py](example_workflows/nfdi/source/poisson.py) Poisson Python script 
+* [example_workflows/nfdi/source/postprocessing.py](example_workflows/nfdi/source/postprocessing.py) Postprocessing Python script
+* [example_workflows/nfdi/source/prepare_paper_macros.py](example_workflows/nfdi/source/prepare_paper_macros.py) LaTeX preprocessing Python script
+* [example_workflows/nfdi/source/unit_square.geo](example_workflows/nfdi/source/unit_square.geo) Input structure 
+
+| Example                                                                                            | Explanation                                                                                                               | 
+|----------------------------------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------|
+| [example_workflows/nfdi/aiida.ipynb](example_workflows/nfdi/aiida.ipynb)                           | Define Workflow with aiida and execute it with jobflow and pyiron_base.                                                   |
+| [example_workflows/nfdi/jobflow.ipynb](example_workflows/nfdi/jobflow.ipynb)                       | Define Workflow with jobflow and execute it with aiida and pyiron_base.                                                   |
+| [example_workflows/nfdi/pyiron_base.ipynb](example_workflows/nfdi/pyiron_base.ipynb)               | Define Workflow with pyiron_base and execute it with aiida and jobflow.                                                   |
+| [example_workflows/nfdi/universal_workflow.ipynb](example_workflows/nfdi/universal_workflow.ipynb) | Execute workflow defined in the Python Workflow Definition with aiida, executorlib, jobflow, pyiron_base and pure Python. |

python_workflow_definition-0.1.2/binder/apt.txt

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+libgl1-mesa-glx
+libegl1-mesa

python_workflow_definition-0.1.2/binder/environment.yml

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+channels:
+- conda-forge
+dependencies:
+- python =3.12
+- click =8.1.8
+- pydantic =2.12.4
+- hatchling =1.27.0
+- httpcore =1.0.7
+- jobflow =0.2.1
+- pyiron_base =0.15.10
+- pyiron_workflow =0.15.4
+- pygraphviz =1.14
+- aiida-workgraph =0.7.6
+- plumpy =0.25.0
+- conda_subprocess =0.0.10
+- networkx =3.4.2
+- cwltool =3.1.20251031082601

python_workflow_definition-0.1.2/binder/postBuild

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+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
+conda env update --name base --file example_workflows/quantum_espresso/environment.yml
+pip install -e example_workflows/quantum_espresso/qe_xml_parser
+pip install -e python_workflow_definition
+verdi presto --profile-name pwd
+mv example_workflows/quantum_espresso/espresso ~

python_workflow_definition-0.1.2/binder/setup-miniconda-patched-environment.yml

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+channels:
+  - conda-forge
+dependencies:
+  - python =3.12
+  - click =8.1.8
+  - pydantic =2.12.4
+  - hatchling =1.27.0
+  - httpcore =1.0.7
+  - jobflow =0.2.1
+  - pyiron_base =0.15.10
+  - pyiron_workflow =0.15.4
+  - pygraphviz =1.14
+  - aiida-workgraph =0.7.6
+  - plumpy =0.25.0
+  - conda_subprocess =0.0.10
+  - networkx =3.4.2
+  - cwltool =3.1.20251031082601
+  - python=3.12

python_workflow_definition-0.1.2/documentation/_config.yml

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+title: Python Workflow Definition
+author: Jan Janssen
+
+execute:
+  execute_notebooks           : off
+
+repository:
+    url                       : https://github.com/pythonworkflow/python-workflow-definition
+    path_to_book              : ""
+
+launch_buttons:
+  notebook_interface          : jupyterlab
+  binderhub_url               : https://mybinder.org

python_workflow_definition-0.1.2/documentation/_toc.yml

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+format: jb-book
+root: README
+chapters:
+- file: intro.md
+- file: arithmetic.md
+  sections:
+    - file: example_workflows/arithmetic/aiida.ipynb
+    - file: example_workflows/arithmetic/jobflow.ipynb
+    - file: example_workflows/arithmetic/pyiron_base.ipynb
+- file: evcurve.md
+  sections:
+    - file: example_workflows/quantum_espresso/aiida.ipynb
+    - file: example_workflows/quantum_espresso/jobflow.ipynb
+    - file: example_workflows/quantum_espresso/pyiron_base.ipynb
+- file: nfdi.md
+  sections:
+    - file: example_workflows/nfdi/aiida.ipynb
+    - file: example_workflows/nfdi/jobflow.ipynb
+    - file: example_workflows/nfdi/pyiron_base.ipynb
+- file: conclusion.md

python_workflow_definition-0.1.2/documentation/arithmetic.md

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+# Arithmetic Workflow
+As a first example we define two Python functions which add multiple inputs: 
+```python
+def get_sum(x, y):
+    return x + y
+    
+def get_prod_and_div(x: float, y: float) -> dict:
+    return {"prod": x * y, "div": x / y}
+```
+These two Python functions are combined in the following example workflow:
+```python
+def combined_workflow(x=1, y=2):
+    tmp_dict = get_prod_and_div(x=x, y=y)
+    return get_sum(x=tmp_dict["prod"], y=tmp_dict["div"])
+```
+For the workflow representation of these Python functions the Python functions are stored in the [workflow.py](example_workflows/arithmetic/workflow.py)
+Python module. The connection of the Python functions are stored in the [workflow.json](example_workflows/arithmetic/workflow.json) 
+JSON file:
+```
+{
+  "nodes": [
+    {"id": 0, "type": "function", "value": "workflow.get_prod_and_div"},
+    {"id": 1, "type": "function", "value": "workflow.get_sum"},
+    {"id": 2, "type": "input", "value": 1, "name": "x"},
+    {"id": 3, "type": "input", "value": 2, "name": "y"},
+    {"id": 4, "type": "output", "name": "result"}
+  ],
+  "edges": [
+    {"target": 0, "targetPort": "x", "source": 2, "sourcePort": null},
+    {"target": 0, "targetPort": "y", "source": 3, "sourcePort": null},
+    {"target": 1, "targetPort": "x", "source": 0, "sourcePort": "prod"},
+    {"target": 1, "targetPort": "y", "source": 0, "sourcePort": "div"},
+    {"target": 4, "targetPort": null, "source": 1, "sourcePort": null}
+  ]
+}
+```
+The abbreviations in the definition of the edges are:
+* `target` - target node 
+* `targetPort` - target port - for a node with multiple input parameters the target port specifies which input parameter to use.
+* `source` - source node 
+* `sourcePort` - source port - for a node with multiple output parameters the source port specifies which output parameter to use.
+
+As the workflow does not require any additional resources, as it is only using built-in functionality of the Python standard 
+library.

python_workflow_definition-0.1.2/documentation/conclusion.md

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+# Conclusion 
+Based on the Python Workflow Definition three rather different workflows were implemented in rather different workflow 
+engines. This demonstrates the interoperability achieved with the Python Workflow Definition. 

python_workflow_definition-0.1.2/documentation/environment.yml

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+channels:
+- conda-forge
+dependencies:
+- jupyter-book <2

python_workflow_definition-0.1.2/documentation/evcurve.md

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+# Energy Volume Curve
+Based on [previous work](https://materialdigital.github.io/ADIS2023/README.html) from the [ADIS 2023 workshop](https://www.mpie.de/4902385/adis2023)
+the calculation of an energy volume curve with the [quantum espresso](https://www.quantum-espresso.org) density 
+functional theory (DFT) simulation code is implemented in the Python Workflow Definition.

python_workflow_definition-0.1.2/documentation/intro.md

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+# Definition
+In the Python Workflow Definition (PWD) each node represents a Python function, with the edges defining the connection 
+between input and output of the different Python functions. 
+
+## Format
+Each workflow consists of three files, a Python module which defines the individual Pythons, a JSON file which defines
+the connections between the different Python functions and a conda environment file to define the software dependencies.
+The files are not intended to be human readable, but rather interact as a machine readable exchange format between the 
+different workflow engines to enable interoperability. 
+
+## Workflow Engines
+Currently supported workflow engines: 
+* [aiida-workgraph](https://github.com/aiidateam/aiida-workgraph)
+* [jobflow](https://github.com/materialsproject/jobflow)
+* [pyiron_base](https://github.com/pyiron/pyiron_base)
+
+## Example Workflows
+Three workflows are implemented:
+* Simple workflow coupling two python functions
+* Calculation of an [energy volume curve with quantum espresso](https://materialdigital.github.io/ADIS2023/)
+* File based workflow benchmark from [NFDI4Ing](https://www.inggrid.org/article/id/3726/)

python_workflow_definition-0.1.2/documentation/nfdi.md

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+# NFDI4Ing Benchmark
+To demonstrate the compatibility of the Python Workflow Definition to file based workflows, the workflow benchmark 
+developed as part of [NFDI4Ing](https://www.inggrid.org/article/id/3726/) is implemented for all three simulation codes 
+based on the Python Workflow Definition.