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Merged
jan-janssen merged 6 commits into from
Oct 12, 2026
Merged

Add tests for jupyter notebooks #1

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d72816d
Add tests for jupyter notebooks
jan-janssen Oct 12, 2026
c62ba34
install hatchling
jan-janssen Oct 12, 2026
772a17b
Use JSON files from official repo
jan-janssen Oct 12, 2026
ae1fd27
Add hatchling to central environment
jan-janssen Oct 12, 2026
27043fe
Install NFDI4Ing libGL dependency via apt
jan-janssen Oct 12, 2026
4794d44
add postbuild script for mybinder
jan-janssen Oct 12, 2026
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84 changes: 84 additions & 0 deletions .github/workflows/pipeline.yml
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name: Pipeline

on:
push:
branches: [ main ]
pull_request:

jobs:
nfdi4ing:
runs-on: ubuntu-22.04
steps:
- uses: actions/checkout@v6
- name: Conda config
run: echo -e "channels:\n - conda-forge\n" > .condarc
- uses: conda-incubator/setup-miniconda@v4
with:
python-version: "3.12"
miniforge-version: latest
condarc-file: .condarc
environment-file: environment.yml
- name: Installation and setup
shell: bash -l {0}
run: |
conda install -c conda-forge jupyter papermill
sudo apt-get install -y $(cat apt.txt)
- name: Create Additional Conda Environments
shell: bash -l {0}
run: |
conda env create -n preprocessing -f nfdi/source/envs/preprocessing.yaml -y
conda env create -n processing -f nfdi/source/envs/processing.yaml -y
conda env create -n postprocessing -f nfdi/source/envs/postprocessing.yaml -y
- name: Tests
shell: bash -l {0}
run: |
cd nfdi/
papermill pyironflow.ipynb pyironflow_out.ipynb -k "python3"

quantumespresso:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v6
- name: Setup environment
shell: bash -l {0}
run: echo -e "channels:\n - conda-forge\n" > .condarc
- uses: conda-incubator/setup-miniconda@v4
with:
python-version: "3.12"
miniforge-version: latest
condarc-file: .condarc
environment-file: environment.yml
- name: Installation and setup
shell: bash -l {0}
run: |
pip install --no-deps --no-build-isolation -e quantum_espresso/qe_xml_parser
conda install -c conda-forge jupyter papermill
- name: Tests
shell: bash -l {0}
run: |
export ESPRESSO_PSEUDO=$(pwd)/espresso/pseudo
cp -r quantum_espresso/espresso .
cd quantum_espresso
papermill pyironflow.ipynb pyironflow_out.ipynb -k "python3"

arithmetic:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v6
- name: Conda config
run: echo -e "channels:\n - conda-forge\n" > .condarc
- uses: conda-incubator/setup-miniconda@v4
with:
python-version: "3.12"
miniforge-version: latest
condarc-file: .condarc
environment-file: environment.yml
- name: Installation and setup
shell: bash -l {0}
run: |
conda install -c conda-forge jupyter papermill
- name: Tests
shell: bash -l {0}
run: |
cd arithmetic
papermill pyironflow.ipynb pyironflow_out.ipynb -k "python3"
2 changes: 2 additions & 0 deletions apt.txt
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@@ -0,0 +1,2 @@
libgl1-mesa-glx
libegl1-mesa
80 changes: 12 additions & 68 deletions arithmetic/workflow.json
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@@ -1,75 +1,19 @@
{
"version": "0.1.0",
"nodes": [
{
"id": 0,
"type": "function",
"value": "workflow.get_prod_and_div"
},
{
"id": 1,
"type": "function",
"value": "workflow.get_sum"
},
{
"id": 2,
"type": "function",
"value": "workflow.get_square"
},
{
"id": 3,
"type": "input",
"name": "x",
"value": 1
},
{
"id": 4,
"type": "input",
"name": "y",
"value": 2
},
{
"id": 5,
"type": "output",
"name": "result"
}
{"id": 0, "type": "function", "value": "workflow.get_prod_and_div"},
{"id": 1, "type": "function", "value": "workflow.get_sum"},
{"id": 2, "type": "function", "value": "workflow.get_square"},
{"id": 3, "type": "input", "value": 1, "name": "x"},
{"id": 4, "type": "input", "value": 2, "name": "y"},
{"id": 5, "type": "output", "name": "result"}
],
"edges": [
{
"target": 1,
"targetPort": "y",
"source": 0,
"sourcePort": "div"
},
{
"target": 1,
"targetPort": "x",
"source": 0,
"sourcePort": "prod"
},
{
"target": 2,
"targetPort": "x",
"source": 1,
"sourcePort": null
},
{
"target": 0,
"targetPort": "x",
"source": 3,
"sourcePort": null
},
{
"target": 0,
"targetPort": "y",
"source": 4,
"sourcePort": null
},
{
"target": 5,
"targetPort": null,
"source": 2,
"sourcePort": null
}
{"target": 0, "targetPort": "x", "source": 3, "sourcePort": null},
{"target": 0, "targetPort": "y", "source": 4, "sourcePort": null},
{"target": 1, "targetPort": "x", "source": 0, "sourcePort": "prod"},
{"target": 1, "targetPort": "y", "source": 0, "sourcePort": "div"},
{"target": 2, "targetPort": "x", "source": 1, "sourcePort": null},
{"target": 5, "targetPort": null, "source": 2, "sourcePort": null}
]
}
1 change: 1 addition & 0 deletions environment.yml
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Expand Up @@ -2,6 +2,7 @@ channels:
- conda-forge
dependencies:
- python =3.12
- hatchling =1.32.4
- pyiron_workflow =0.17.0
- pyironflow =0.0.24
- python-workflow-definition =0.1.5
Expand Down
175 changes: 26 additions & 149 deletions nfdi/workflow.json
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@@ -1,156 +1,33 @@
{
"version": "0.1.0",
"nodes": [
{
"id": 0,
"type": "function",
"value": "workflow.generate_mesh"
},
{
"id": 1,
"type": "function",
"value": "workflow.convert_to_xdmf"
},
{
"id": 2,
"type": "function",
"value": "workflow.poisson"
},
{
"id": 3,
"type": "function",
"value": "workflow.plot_over_line"
},
{
"id": 4,
"type": "function",
"value": "workflow.substitute_macros"
},
{
"id": 5,
"type": "function",
"value": "workflow.compile_paper"
},
{
"id": 6,
"type": "input",
"name": "domain_size",
"value": 2.0
},
{
"id": 7,
"type": "input",
"name": "source_directory",
"value": "/home/jan/Desktop/visual-programming-with-pyironflow/nfdi/source"
},
{
"id": 8,
"type": "output",
"name": "result"
}
{"id": 0, "type": "function", "value": "workflow.generate_mesh"},
{"id": 1, "type": "function", "value": "workflow.convert_to_xdmf"},
{"id": 2, "type": "function", "value": "workflow.poisson"},
{"id": 3, "type": "function", "value": "workflow.plot_over_line"},
{"id": 4, "type": "function", "value": "workflow.substitute_macros"},
{"id": 5, "type": "function", "value": "workflow.compile_paper"},
{"id": 6, "type": "input", "value": 2.0, "name": "domain_size"},
{"id": 7, "type": "input", "value": "source", "name": "source_directory"},
{"id": 8, "type": "output", "name": "result"}
],
"edges": [
{
"target": 2,
"targetPort": "meshio_output_h5",
"source": 1,
"sourcePort": "h5_file"
},
{
"target": 2,
"targetPort": "meshio_output_xdmf",
"source": 1,
"sourcePort": "xdmf_file"
},
{
"target": 4,
"targetPort": "ndofs",
"source": 2,
"sourcePort": "numdofs"
},
{
"target": 3,
"targetPort": "poisson_output_vtu_file",
"source": 2,
"sourcePort": "vtu_file"
},
{
"target": 3,
"targetPort": "poisson_output_pvd_file",
"source": 2,
"sourcePort": "pvd_file"
},
{
"target": 1,
"targetPort": "gmsh_output_file",
"source": 0,
"sourcePort": null
},
{
"target": 5,
"targetPort": "plot_file",
"source": 3,
"sourcePort": null
},
{
"target": 4,
"targetPort": "pvbatch_output_file",
"source": 3,
"sourcePort": null
},
{
"target": 5,
"targetPort": "macros_tex",
"source": 4,
"sourcePort": null
},
{
"target": 0,
"targetPort": "domain_size",
"source": 6,
"sourcePort": null
},
{
"target": 0,
"targetPort": "source_directory",
"source": 7,
"sourcePort": null
},
{
"target": 2,
"targetPort": "source_directory",
"source": 7,
"sourcePort": null
},
{
"target": 3,
"targetPort": "source_directory",
"source": 7,
"sourcePort": null
},
{
"target": 4,
"targetPort": "domain_size",
"source": 6,
"sourcePort": null
},
{
"target": 4,
"targetPort": "source_directory",
"source": 7,
"sourcePort": null
},
{
"target": 5,
"targetPort": "source_directory",
"source": 7,
"sourcePort": null
},
{
"target": 8,
"targetPort": null,
"source": 5,
"sourcePort": null
}
{"target": 0, "targetPort": "domain_size", "source": 6, "sourcePort": null},
{"target": 0, "targetPort": "source_directory", "source": 7, "sourcePort": null},
{"target": 1, "targetPort": "gmsh_output_file", "source": 0, "sourcePort": null},
{"target": 2, "targetPort": "meshio_output_xdmf", "source": 1, "sourcePort": "xdmf_file"},
{"target": 2, "targetPort": "meshio_output_h5", "source": 1, "sourcePort": "h5_file"},
{"target": 2, "targetPort": "source_directory", "source": 7, "sourcePort": null},
{"target": 3, "targetPort": "poisson_output_pvd_file", "source": 2, "sourcePort": "pvd_file"},
{"target": 3, "targetPort": "poisson_output_vtu_file", "source": 2, "sourcePort": "vtu_file"},
{"target": 3, "targetPort": "source_directory", "source": 7, "sourcePort": null},
{"target": 4, "targetPort": "pvbatch_output_file", "source": 3, "sourcePort": null},
{"target": 4, "targetPort": "ndofs", "source": 2, "sourcePort": "numdofs"},
{"target": 4, "targetPort": "domain_size", "source": 6, "sourcePort": null},
{"target": 4, "targetPort": "source_directory", "source": 7, "sourcePort": null},
{"target": 5, "targetPort": "macros_tex", "source": 4, "sourcePort": null},
{"target": 5, "targetPort": "plot_file", "source": 3, "sourcePort": null},
{"target": 5, "targetPort": "source_directory", "source": 7, "sourcePort": null},
{"target": 8, "targetPort": null, "source": 5, "sourcePort": null}
]
}
5 changes: 5 additions & 0 deletions postBuild
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conda env create -n preprocessing -f nfdi/source/envs/preprocessing.yaml -y
conda env create -n processing -f nfdi/source/envs/processing.yaml -y
conda env create -n postprocessing -f nfdi/source/envs/postprocessing.yaml -y
pip install -e quantum_espresso/qe_xml_parser
mv quantum_espresso/espresso ~
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