Skip to content

Update links to markdown files #78

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 1 commit into from
Apr 23, 2025
Merged

Update links to markdown files #78

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
68 changes: 34 additions & 34 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -27,8 +27,8 @@ These two Python functions are combined in the following example workflow:
tmp_dict = get_prod_and_div(x=1, y=2)
result = 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 [arithmetic_workflow.py](example_workflows/arithmetic/workflow.py)
Python module. The connection of the Python functions are stored in the [workflow_arithmetic.json](example_workflows/arithmetic/workflow.json)
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:
```
{
Expand Down Expand Up @@ -57,47 +57,47 @@ library.

The corresponding Jupyter notebooks demonstrate this functionality:

| Example | Explanation |
|----------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------|
| [aiida_arithmetic.ipynb](example_workflows/arithmetic/aiida.ipynb) | Define Workflow with aiida and execute it with jobflow and pyiron_base. |
| [jobflow_arithmetic.ipynb](example_workflows/arithmetic/jobflow.ipynb) | Define Workflow with jobflow and execute it with aiida and pyiron_base. |
| [pyiron_base_arithmetic.ipynb](example_workflows/arithmetic/pyiron_base.ipynb) | Define Workflow with pyiron_base and execute it with aiida and jobflow. |
| [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. |
| 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.
* [quantum_espresso_workflow.py](example_workflows/quantum_espresso/workflow.py) Python functions
* [workflow_qe.json](example_workflows/quantum_espresso/workflow.json) Workflow definition in the Python Workflow Definition.
* [environment_qe.yml](example_workflows/quantum_espresso/environment.yml) Conda environment
* [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 |
|------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------|
| [aiida_qe.ipynb](example_workflows/quantum_espresso/aiida.ipynb) | Define Workflow with aiida and execute it with jobflow and pyiron_base. |
| [jobflow_qe.ipynb](example_workflows/quantum_espresso/jobflow.ipynb) | Define Workflow with jobflow and execute it with aiida and pyiron_base. |
| [pyiron_base_qe.ipynb](example_workflows/quantum_espresso/pyiron_base.ipynb) | Define Workflow with pyiron_base and execute it with aiida and jobflow. |
| [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. |
| 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.
* [nfdi_ing_workflow.py](example_workflows/nfdi/workflow.py) Python functions
* [workflow_nfdi.json](example_workflows/nfdi/workflow.json) Workflow definition in the Python 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:
* [source/envs/preprocessing.yaml](example_workflows/nfdi/source/envs/preprocessing.yaml) Conda environment for preprocessing
* [source/envs/processing.yaml](example_workflows/nfdi/source/envs/processing.yaml) Conda environment for processing
* [source/envs/postprocessing.yaml](example_workflows/nfdi/source/envs/postprocessing.yaml) Conda environment for postprocessing
* [source/macros.tex.template](example_workflows/nfdi/source/macros.tex.template) LaTeX module template
* [source/paper.tex](example_workflows/nfdi/source/paper.tex) LaTeX paper template
* [source/poisson.py](example_workflows/nfdi/source/poisson.py) Poisson Python script
* [source/postprocessing.py](example_workflows/nfdi/source/postprocessing.py) Postprocessing Python script
* [source/prepare_paper_macros.py](example_workflows/nfdi/source/prepare_paper_macros.py) LaTeX preprocessing Python script
* [source/unit_square.geo](example_workflows/nfdi/source/unit_square.geo) Input structure
* [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 |
|----------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------|
| [aiida_nfdi.ipynb](example_workflows/nfdi/aiida.ipynb) | Define Workflow with aiida and execute it with jobflow and pyiron_base. |
| [jobflow_nfdi.ipynb](example_workflows/nfdi/jobflow.ipynb) | Define Workflow with jobflow and execute it with aiida and pyiron_base. |
| [pyiron_base_nfdi.ipynb](example_workflows/nfdi/pyiron_base.ipynb) | Define Workflow with pyiron_base and execute it with aiida and jobflow. |
| [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. |
| 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. |
8 changes: 4 additions & 4 deletions documentation/arithmetic.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -12,14 +12,14 @@ These two Python functions are combined in the following example workflow:
tmp_dict = get_prod_and_div(x=1, y=2)
result = 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 [arithmetic_workflow.py](example_workflows/arithmetic/arithmetic_workflow.py)
Python module. The connection of the Python functions are stored in the [workflow_arithmetic.json](example_workflows/arithmetic/workflow_arithmetic.json)
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, "function": "arithmetic_workflow.get_prod_and_div"},
{"id": 1, "function": "arithmetic_workflow.get_sum"},
{"id": 0, "function": "workflow.get_prod_and_div"},
{"id": 1, "function": "workflow.get_sum"},
{"id": 2, "value": 1},
{"id": 3, "value": 2}
],
Expand Down
2 changes: 1 addition & 1 deletion documentation/intro.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -17,5 +17,5 @@ Currently supported workflow engines:
## Example Workflows
Three workflows are implemented:
* Simple workflow coupling two python functions
* Calculation of an energy volume curve with quantum espresso
* 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/)
Loading