python-workflow-definition 0.1.2__tar.gz → 0.1.3__tar.gz

{python_workflow_definition-0.1.2 → python_workflow_definition-0.1.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: python_workflow_definition
-Version: 0.1.2
+Version: 0.1.3
 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
@@ -44,4 +44,4 @@ 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'
+Requires-Dist: pyiron-base<=0.15.12,>=0.11.10; extra == 'pyiron'

{python_workflow_definition-0.1.2 → python_workflow_definition-0.1.3}/pyproject.toml

@@ -4,7 +4,6 @@ build-backend = "hatchling.build"
 
 [project]
 name = "python_workflow_definition"
-version = "0.1.2"
 description = "Python Workflow Definition - workflow interoperability for aiida, jobflow and pyiron"
 authors = [
   { name = "Jan Janssen", email = "janssen@mpie.de" },
@@ -19,6 +18,7 @@ dependencies = [
     "numpy>=1.21",
     "pydantic>=2.7.0,<=2.12.4",
 ]
+dynamic = ["version"]
 
 [project.optional-dependencies]
 aiida = [
@@ -28,10 +28,36 @@ jobflow = [
     "jobflow>=0.1.18,<=0.2.1",
 ]
 pyiron = [
-    "pyiron_base>=0.11.10,<=0.15.10",
+    "pyiron_base>=0.11.10,<=0.15.12",
 ]
 plot = [
     "pygraphviz>=1.10,<=1.14",
     "networkx>=2.8.8,<=3.5",
     "ipython>=7.33.0,<=9.8.0",
 ]
+
+[tool.hatch.build]
+include = [
+    "src/python_workflow_definition"
+]
+
+[tool.hatch.build.hooks.vcs]
+version-file = "src/python_workflow_definition/_version.py"
+
+[tool.hatch.build.targets.sdist]
+include = [
+    "src/python_workflow_definition"
+]
+
+[tool.hatch.build.targets.wheel]
+packages = [
+    "src/python_workflow_definition"
+]
+
+[tool.hatch.version]
+source = "vcs"
+path = "src/python_workflow_definition/_version.py"
+
+[tool.coverage.run]
+source = ["python_workflow_definition"]
+command_line = "-m unittest discover tests"

python_workflow_definition-0.1.3/src/python_workflow_definition/__init__.py

@@ -0,0 +1,3 @@
+import python_workflow_definition._version
+
+__version__ = python_workflow_definition._version.__version__

python_workflow_definition-0.1.3/src/python_workflow_definition/_version.py

@@ -0,0 +1,34 @@
+# file generated by setuptools-scm
+# don't change, don't track in version control
+
+__all__ = [
+    "__version__",
+    "__version_tuple__",
+    "version",
+    "version_tuple",
+    "__commit_id__",
+    "commit_id",
+]
+
+TYPE_CHECKING = False
+if TYPE_CHECKING:
+    from typing import Tuple
+    from typing import Union
+
+    VERSION_TUPLE = Tuple[Union[int, str], ...]
+    COMMIT_ID = Union[str, None]
+else:
+    VERSION_TUPLE = object
+    COMMIT_ID = object
+
+version: str
+__version__: str
+__version_tuple__: VERSION_TUPLE
+version_tuple: VERSION_TUPLE
+commit_id: COMMIT_ID
+__commit_id__: COMMIT_ID
+
+__version__ = version = '0.1.3'
+__version_tuple__ = version_tuple = (0, 1, 3)
+
+__commit_id__ = commit_id = None

{python_workflow_definition-0.1.2 → python_workflow_definition-0.1.3}/src/python_workflow_definition/models.py

@@ -1,5 +1,15 @@
 from pathlib import Path
-from typing import List, Union, Optional, Literal, Any, Annotated, Type, TypeVar
+from typing import (
+    List,
+    Union,
+    Optional,
+    Literal,
+    Any,
+    Annotated,
+    Type,
+    TypeVar,
+)
+from typing_extensions import TypeAliasType
 from pydantic import BaseModel, Field, field_validator, field_serializer
 from pydantic import ValidationError
 import json
@@ -19,6 +29,13 @@ __all__ = (
 )
 
 
+JsonPrimitive = Union[str, int, float, bool, None]
+AllowableDefaults = TypeAliasType(
+    "AllowableDefaults",
+    "Union[JsonPrimitive, dict[str, AllowableDefaults], list[AllowableDefaults]]",
+)
+
+
 class PythonWorkflowDefinitionBaseNode(BaseModel):
     """Base model for all node types, containing common fields."""
 
@@ -33,7 +50,7 @@ class PythonWorkflowDefinitionInputNode(PythonWorkflowDefinitionBaseNode):
 
     type: Literal["input"]
     name: str
-    value: Optional[Any] = None
+    value: Optional[AllowableDefaults] = None
 
 
 class PythonWorkflowDefinitionOutputNode(PythonWorkflowDefinitionBaseNode):

{python_workflow_definition-0.1.2 → python_workflow_definition-0.1.3}/src/python_workflow_definition/pyiron_base.py

@@ -285,18 +285,32 @@ def write_workflow_json(
     )
 
     nodes_store_lst = []
-    for k, v in nodes_new_dict.items():
+    translate_dict = {}
+    for i, k in enumerate(list(nodes_new_dict.keys())[::-1]):
+        v = nodes_new_dict[k]
+        translate_dict[k] = i
         if isfunction(v):
             mod = v.__module__
             if mod == "python_workflow_definition.pyiron_base":
                 mod = "python_workflow_definition.shared"
             nodes_store_lst.append(
-                {"id": k, "type": "function", "value": mod + "." + v.__name__}
+                {"id": i, "type": "function", "value": mod + "." + v.__name__}
             )
         elif isinstance(v, np.ndarray):
-            nodes_store_lst.append({"id": k, "type": "input", "value": v.tolist()})
+            nodes_store_lst.append({"id": i, "type": "input", "value": v.tolist()})
         else:
-            nodes_store_lst.append({"id": k, "type": "input", "value": v})
+            nodes_store_lst.append({"id": i, "type": "input", "value": v})
+
+    print(translate_dict)
+    edges_store_lst = [
+        {
+            TARGET_LABEL: translate_dict[edge[TARGET_LABEL]],
+            TARGET_PORT_LABEL: edge[TARGET_PORT_LABEL],
+            SOURCE_LABEL: translate_dict[edge[SOURCE_LABEL]],
+            SOURCE_PORT_LABEL: edge[SOURCE_PORT_LABEL],
+        }
+        for edge in edges_new_lst
+    ]
 
     PythonWorkflowDefinitionWorkflow(
         **set_result_node(
@@ -304,7 +318,7 @@ def write_workflow_json(
                 workflow_dict={
                     VERSION_LABEL: VERSION_NUMBER,
                     NODES_LABEL: nodes_store_lst,
-                    EDGES_LABEL: edges_new_lst,
+                    EDGES_LABEL: edges_store_lst,
                 }
             )
         )

python_workflow_definition-0.1.2/.condarc

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

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

@@ -1,35 +0,0 @@
-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

@@ -1,161 +0,0 @@
-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

@@ -1,31 +0,0 @@
-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-0.1.2/CITATION.cff

@@ -1,40 +0,0 @@
-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/README.md

@@ -1,119 +0,0 @@
-# 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

@@ -1,2 +0,0 @@
-libgl1-mesa-glx
-libegl1-mesa

python_workflow_definition-0.1.2/binder/environment.yml

@@ -1,17 +0,0 @@
-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

@@ -1,8 +0,0 @@
-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

@@ -1,18 +0,0 @@
-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

@@ -1,13 +0,0 @@
-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