From d72816d43938898984747c5e2266583c9a5e1e8e Mon Sep 17 00:00:00 2001
From: Jan Janssen <janssen@mpie.de>
Date: Mon, 12 Oct 2026 09:27:31 +0200
Subject: [PATCH 1/6] Add tests for jupyter notebooks

---
 .github/workflows/pipeline.yml | 83 ++++++++++++++++++++++++++++++++++
 1 file changed, 83 insertions(+)
 create mode 100644 .github/workflows/pipeline.yml

diff --git a/.github/workflows/pipeline.yml b/.github/workflows/pipeline.yml
new file mode 100644
index 0000000..1b5921d
--- /dev/null
+++ b/.github/workflows/pipeline.yml
@@ -0,0 +1,83 @@
+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
+    - 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"

From c62ba3428965e23e5693dc184e385ecce518b717 Mon Sep 17 00:00:00 2001
From: Jan Janssen <janssen@mpie.de>
Date: Mon, 12 Oct 2026 09:34:14 +0200
Subject: [PATCH 2/6] install hatchling

---
 .github/workflows/pipeline.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pipeline.yml b/.github/workflows/pipeline.yml
index 1b5921d..5699ae9 100644
--- a/.github/workflows/pipeline.yml
+++ b/.github/workflows/pipeline.yml
@@ -50,8 +50,8 @@ jobs:
     - name: Installation and setup
       shell: bash -l {0}
       run: |
+        conda install -c conda-forge jupyter papermill hatchling
         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: |

From 772a17b29a8d5f670f521cb8847a4672799a6bcd Mon Sep 17 00:00:00 2001
From: Jan Janssen <janssen@mpie.de>
Date: Mon, 12 Oct 2026 09:34:26 +0200
Subject: [PATCH 3/6] Use JSON files from official repo

---
 arithmetic/workflow.json       |  80 +---
 nfdi/workflow.json             | 175 ++-------
 quantum_espresso/workflow.json | 645 +++++----------------------------
 3 files changed, 131 insertions(+), 769 deletions(-)

diff --git a/arithmetic/workflow.json b/arithmetic/workflow.json
index 24b1d52..7aa94a8 100644
--- a/arithmetic/workflow.json
+++ b/arithmetic/workflow.json
@@ -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}
   ]
 }
\ No newline at end of file
diff --git a/nfdi/workflow.json b/nfdi/workflow.json
index 8803901..b9135dc 100644
--- a/nfdi/workflow.json
+++ b/nfdi/workflow.json
@@ -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}
   ]
 }
\ No newline at end of file
diff --git a/quantum_espresso/workflow.json b/quantum_espresso/workflow.json
index 078d9e7..e653d59 100644
--- a/quantum_espresso/workflow.json
+++ b/quantum_espresso/workflow.json
@@ -1,559 +1,100 @@
 {
   "version": "0.1.0",
   "nodes": [
-    {
-      "id": 0,
-      "type": "function",
-      "value": "workflow.get_bulk_structure"
-    },
-    {
-      "id": 1,
-      "type": "function",
-      "value": "python_workflow_definition.shared.get_dict"
-    },
-    {
-      "id": 2,
-      "type": "function",
-      "value": "workflow.calculate_qe"
-    },
-    {
-      "id": 3,
-      "type": "function",
-      "value": "workflow.generate_structures"
-    },
-    {
-      "id": 4,
-      "type": "function",
-      "value": "python_workflow_definition.shared.get_dict"
-    },
-    {
-      "id": 5,
-      "type": "function",
-      "value": "workflow.calculate_qe"
-    },
-    {
-      "id": 6,
-      "type": "function",
-      "value": "python_workflow_definition.shared.get_dict"
-    },
-    {
-      "id": 7,
-      "type": "function",
-      "value": "workflow.calculate_qe"
-    },
-    {
-      "id": 8,
-      "type": "function",
-      "value": "python_workflow_definition.shared.get_dict"
-    },
-    {
-      "id": 9,
-      "type": "function",
-      "value": "workflow.calculate_qe"
-    },
-    {
-      "id": 10,
-      "type": "function",
-      "value": "python_workflow_definition.shared.get_dict"
-    },
-    {
-      "id": 11,
-      "type": "function",
-      "value": "workflow.calculate_qe"
-    },
-    {
-      "id": 12,
-      "type": "function",
-      "value": "python_workflow_definition.shared.get_dict"
-    },
-    {
-      "id": 13,
-      "type": "function",
-      "value": "workflow.calculate_qe"
-    },
-    {
-      "id": 14,
-      "type": "function",
-      "value": "python_workflow_definition.shared.get_list"
-    },
-    {
-      "id": 15,
-      "type": "function",
-      "value": "python_workflow_definition.shared.get_list"
-    },
-    {
-      "id": 16,
-      "type": "function",
-      "value": "workflow.plot_energy_volume_curve"
-    },
-    {
-      "id": 17,
-      "type": "input",
-      "name": "element",
-      "value": "Al"
-    },
-    {
-      "id": 18,
-      "type": "input",
-      "name": "a",
-      "value": 4.04
-    },
-    {
-      "id": 19,
-      "type": "input",
-      "name": "cubic",
-      "value": true
-    },
-    {
-      "id": 20,
-      "type": "input",
-      "name": "pseudopotentials",
-      "value": {
-        "Al": "Al.pbe-n-kjpaw_psl.1.0.0.UPF"
-      }
-    },
-    {
-      "id": 21,
-      "type": "input",
-      "name": "kpts",
-      "value": [
-        3,
-        3,
-        3
-      ]
-    },
-    {
-      "id": 22,
-      "type": "input",
-      "name": "calculation_0",
-      "value": "vc-relax"
-    },
-    {
-      "id": 23,
-      "type": "input",
-      "name": "smearing",
-      "value": 0.02
-    },
-    {
-      "id": 24,
-      "type": "input",
-      "name": "working_directory_0",
-      "value": "mini"
-    },
-    {
-      "id": 25,
-      "type": "input",
-      "name": "strain_lst",
-      "value": [
-        0.9,
-        0.9500000000000001,
-        1.0,
-        1.05,
-        1.1
-      ]
-    },
-    {
-      "id": 26,
-      "type": "input",
-      "name": "calculation_1",
-      "value": "scf"
-    },
-    {
-      "id": 27,
-      "type": "input",
-      "name": "working_directory_1",
-      "value": "strain_0"
-    },
-    {
-      "id": 28,
-      "type": "input",
-      "name": "working_directory_2",
-      "value": "strain_1"
-    },
-    {
-      "id": 29,
-      "type": "input",
-      "name": "working_directory_3",
-      "value": "strain_2"
-    },
-    {
-      "id": 30,
-      "type": "input",
-      "name": "working_directory_4",
-      "value": "strain_3"
-    },
-    {
-      "id": 31,
-      "type": "input",
-      "name": "working_directory_5",
-      "value": "strain_4"
-    },
-    {
-      "id": 32,
-      "type": "output",
-      "name": "result"
-    }
+    {"id": 0, "type": "function", "value": "workflow.get_bulk_structure"},
+    {"id": 1, "type": "function", "value": "workflow.calculate_qe"},
+    {"id": 2, "type": "function", "value": "workflow.generate_structures"},
+    {"id": 3, "type": "function", "value": "workflow.calculate_qe"},
+    {"id": 4, "type": "function", "value": "workflow.calculate_qe"},
+    {"id": 5, "type": "function", "value": "workflow.calculate_qe"},
+    {"id": 6, "type": "function", "value": "workflow.calculate_qe"},
+    {"id": 7, "type": "function", "value": "workflow.calculate_qe"},
+    {"id": 8, "type": "function", "value": "workflow.plot_energy_volume_curve"},
+    {"id": 9, "type": "input", "value": "Al", "name": "element"},
+    {"id": 10, "type": "input", "value": 4.05, "name": "a"},
+    {"id": 11, "type": "input", "value": true, "name": "cubic"},
+    {"id": 12, "type": "input", "value": "mini", "name": "working_directory_0"},
+    {"id": 13, "type": "function", "value": "python_workflow_definition.shared.get_dict"},
+    {"id": 14, "type": "input", "value": {"Al": "Al.pbe-n-kjpaw_psl.1.0.0.UPF"}, "name": "pseudopotentials"},
+    {"id": 15, "type": "input", "value": [3, 3, 3], "name": "kpts"},
+    {"id": 16, "type": "input", "value": "vc-relax", "name": "calculation_0"},
+    {"id": 17, "type": "input", "value": 0.02, "name": "smearing"},
+    {"id": 18, "type": "input", "value": [0.9, 0.95, 1.0, 1.05, 1.1], "name": "strain_lst"},
+    {"id": 19, "type": "input", "value": "strain_0", "name": "working_directory_1"},
+    {"id": 20, "type": "function", "value": "python_workflow_definition.shared.get_dict"},
+    {"id": 21, "type": "input", "value": "scf", "name": "calculation_1"},
+    {"id": 22, "type": "input", "value": "strain_1", "name": "working_directory_2"},
+    {"id": 23, "type": "function", "value": "python_workflow_definition.shared.get_dict"},
+    {"id": 24, "type": "input", "value": "strain_2", "name": "working_directory_3"},
+    {"id": 25, "type": "function", "value": "python_workflow_definition.shared.get_dict"},
+    {"id": 26, "type": "input", "value": "strain_3", "name": "working_directory_4"},
+    {"id": 27, "type": "function", "value": "python_workflow_definition.shared.get_dict"},
+    {"id": 28, "type": "input", "value": "strain_4", "name": "working_directory_5"},
+    {"id": 29, "type": "function", "value": "python_workflow_definition.shared.get_dict"},
+    {"id": 30, "type": "function", "value": "python_workflow_definition.shared.get_list"},
+    {"id": 31, "type": "function", "value": "python_workflow_definition.shared.get_list"},
+    {"id": 32, "type": "output", "name": "result"}
   ],
   "edges": [
-    {
-      "target": 3,
-      "targetPort": "structure",
-      "source": 2,
-      "sourcePort": "structure"
-    },
-    {
-      "target": 12,
-      "targetPort": "structure",
-      "source": 3,
-      "sourcePort": "s_4"
-    },
-    {
-      "target": 10,
-      "targetPort": "structure",
-      "source": 3,
-      "sourcePort": "s_3"
-    },
-    {
-      "target": 8,
-      "targetPort": "structure",
-      "source": 3,
-      "sourcePort": "s_2"
-    },
-    {
-      "target": 6,
-      "targetPort": "structure",
-      "source": 3,
-      "sourcePort": "s_1"
-    },
-    {
-      "target": 4,
-      "targetPort": "structure",
-      "source": 3,
-      "sourcePort": "s_0"
-    },
-    {
-      "target": 15,
-      "targetPort": "0",
-      "source": 5,
-      "sourcePort": "energy"
-    },
-    {
-      "target": 14,
-      "targetPort": "0",
-      "source": 5,
-      "sourcePort": "volume"
-    },
-    {
-      "target": 15,
-      "targetPort": "1",
-      "source": 7,
-      "sourcePort": "energy"
-    },
-    {
-      "target": 14,
-      "targetPort": "1",
-      "source": 7,
-      "sourcePort": "volume"
-    },
-    {
-      "target": 15,
-      "targetPort": "2",
-      "source": 9,
-      "sourcePort": "energy"
-    },
-    {
-      "target": 14,
-      "targetPort": "2",
-      "source": 9,
-      "sourcePort": "volume"
-    },
-    {
-      "target": 15,
-      "targetPort": "3",
-      "source": 11,
-      "sourcePort": "energy"
-    },
-    {
-      "target": 14,
-      "targetPort": "3",
-      "source": 11,
-      "sourcePort": "volume"
-    },
-    {
-      "target": 15,
-      "targetPort": "4",
-      "source": 13,
-      "sourcePort": "energy"
-    },
-    {
-      "target": 14,
-      "targetPort": "4",
-      "source": 13,
-      "sourcePort": "volume"
-    },
-    {
-      "target": 1,
-      "targetPort": "structure",
-      "source": 0,
-      "sourcePort": null
-    },
-    {
-      "target": 2,
-      "targetPort": "input_dict",
-      "source": 1,
-      "sourcePort": null
-    },
-    {
-      "target": 5,
-      "targetPort": "input_dict",
-      "source": 4,
-      "sourcePort": null
-    },
-    {
-      "target": 7,
-      "targetPort": "input_dict",
-      "source": 6,
-      "sourcePort": null
-    },
-    {
-      "target": 9,
-      "targetPort": "input_dict",
-      "source": 8,
-      "sourcePort": null
-    },
-    {
-      "target": 11,
-      "targetPort": "input_dict",
-      "source": 10,
-      "sourcePort": null
-    },
-    {
-      "target": 13,
-      "targetPort": "input_dict",
-      "source": 12,
-      "sourcePort": null
-    },
-    {
-      "target": 16,
-      "targetPort": "volume_lst",
-      "source": 14,
-      "sourcePort": null
-    },
-    {
-      "target": 16,
-      "targetPort": "energy_lst",
-      "source": 15,
-      "sourcePort": null
-    },
-    {
-      "target": 0,
-      "targetPort": "element",
-      "source": 17,
-      "sourcePort": null
-    },
-    {
-      "target": 0,
-      "targetPort": "a",
-      "source": 18,
-      "sourcePort": null
-    },
-    {
-      "target": 0,
-      "targetPort": "cubic",
-      "source": 19,
-      "sourcePort": null
-    },
-    {
-      "target": 1,
-      "targetPort": "pseudopotentials",
-      "source": 20,
-      "sourcePort": null
-    },
-    {
-      "target": 1,
-      "targetPort": "kpts",
-      "source": 21,
-      "sourcePort": null
-    },
-    {
-      "target": 1,
-      "targetPort": "calculation",
-      "source": 22,
-      "sourcePort": null
-    },
-    {
-      "target": 1,
-      "targetPort": "smearing",
-      "source": 23,
-      "sourcePort": null
-    },
-    {
-      "target": 2,
-      "targetPort": "working_directory",
-      "source": 24,
-      "sourcePort": null
-    },
-    {
-      "target": 3,
-      "targetPort": "strain_lst",
-      "source": 25,
-      "sourcePort": null
-    },
-    {
-      "target": 4,
-      "targetPort": "pseudopotentials",
-      "source": 20,
-      "sourcePort": null
-    },
-    {
-      "target": 4,
-      "targetPort": "kpts",
-      "source": 21,
-      "sourcePort": null
-    },
-    {
-      "target": 4,
-      "targetPort": "calculation",
-      "source": 26,
-      "sourcePort": null
-    },
-    {
-      "target": 4,
-      "targetPort": "smearing",
-      "source": 23,
-      "sourcePort": null
-    },
-    {
-      "target": 5,
-      "targetPort": "working_directory",
-      "source": 27,
-      "sourcePort": null
-    },
-    {
-      "target": 6,
-      "targetPort": "pseudopotentials",
-      "source": 20,
-      "sourcePort": null
-    },
-    {
-      "target": 6,
-      "targetPort": "kpts",
-      "source": 21,
-      "sourcePort": null
-    },
-    {
-      "target": 6,
-      "targetPort": "calculation",
-      "source": 26,
-      "sourcePort": null
-    },
-    {
-      "target": 6,
-      "targetPort": "smearing",
-      "source": 23,
-      "sourcePort": null
-    },
-    {
-      "target": 7,
-      "targetPort": "working_directory",
-      "source": 28,
-      "sourcePort": null
-    },
-    {
-      "target": 8,
-      "targetPort": "pseudopotentials",
-      "source": 20,
-      "sourcePort": null
-    },
-    {
-      "target": 8,
-      "targetPort": "kpts",
-      "source": 21,
-      "sourcePort": null
-    },
-    {
-      "target": 8,
-      "targetPort": "calculation",
-      "source": 26,
-      "sourcePort": null
-    },
-    {
-      "target": 8,
-      "targetPort": "smearing",
-      "source": 23,
-      "sourcePort": null
-    },
-    {
-      "target": 9,
-      "targetPort": "working_directory",
-      "source": 29,
-      "sourcePort": null
-    },
-    {
-      "target": 10,
-      "targetPort": "pseudopotentials",
-      "source": 20,
-      "sourcePort": null
-    },
-    {
-      "target": 10,
-      "targetPort": "kpts",
-      "source": 21,
-      "sourcePort": null
-    },
-    {
-      "target": 10,
-      "targetPort": "calculation",
-      "source": 26,
-      "sourcePort": null
-    },
-    {
-      "target": 10,
-      "targetPort": "smearing",
-      "source": 23,
-      "sourcePort": null
-    },
-    {
-      "target": 11,
-      "targetPort": "working_directory",
-      "source": 30,
-      "sourcePort": null
-    },
-    {
-      "target": 12,
-      "targetPort": "pseudopotentials",
-      "source": 20,
-      "sourcePort": null
-    },
-    {
-      "target": 12,
-      "targetPort": "kpts",
-      "source": 21,
-      "sourcePort": null
-    },
-    {
-      "target": 12,
-      "targetPort": "calculation",
-      "source": 26,
-      "sourcePort": null
-    },
-    {
-      "target": 12,
-      "targetPort": "smearing",
-      "source": 23,
-      "sourcePort": null
-    },
-    {
-      "target": 13,
-      "targetPort": "working_directory",
-      "source": 31,
-      "sourcePort": null
-    },
-    {
-      "target": 32,
-      "targetPort": null,
-      "source": 16,
-      "sourcePort": null
-    }
+    {"target": 0, "targetPort": "element", "source": 9, "sourcePort": null},
+    {"target": 0, "targetPort": "a", "source": 10, "sourcePort": null},
+    {"target": 0, "targetPort": "cubic", "source": 11, "sourcePort": null},
+    {"target": 1, "targetPort": "working_directory", "source": 12, "sourcePort": null},
+    {"target": 13, "targetPort": "structure", "source": 0, "sourcePort": null},
+    {"target": 13, "targetPort": "pseudopotentials", "source": 14, "sourcePort": null},
+    {"target": 13, "targetPort": "kpts", "source": 15, "sourcePort": null},
+    {"target": 13, "targetPort": "calculation", "source": 16, "sourcePort": null},
+    {"target": 13, "targetPort": "smearing", "source": 17, "sourcePort": null},
+    {"target": 1, "targetPort": "input_dict", "source": 13, "sourcePort": null},
+    {"target": 2, "targetPort": "structure", "source": 1, "sourcePort": "structure"},
+    {"target": 2, "targetPort": "strain_lst", "source": 18, "sourcePort": null},
+    {"target": 3, "targetPort": "working_directory", "source": 19, "sourcePort": null},
+    {"target": 20, "targetPort": "structure", "source": 2, "sourcePort": "s_0"},
+    {"target": 20, "targetPort": "pseudopotentials", "source": 14, "sourcePort": null},
+    {"target": 20, "targetPort": "kpts", "source": 15, "sourcePort": null},
+    {"target": 20, "targetPort": "calculation", "source": 21, "sourcePort": null},
+    {"target": 20, "targetPort": "smearing", "source": 17, "sourcePort": null},
+    {"target": 3, "targetPort": "input_dict", "source": 20, "sourcePort": null},
+    {"target": 4, "targetPort": "working_directory", "source": 22, "sourcePort": null},
+    {"target": 23, "targetPort": "structure", "source": 2, "sourcePort": "s_1"},
+    {"target": 23, "targetPort": "pseudopotentials", "source": 14, "sourcePort": null},
+    {"target": 23, "targetPort": "kpts", "source": 15, "sourcePort": null},
+    {"target": 23, "targetPort": "calculation", "source": 21, "sourcePort": null},
+    {"target": 23, "targetPort": "smearing", "source": 17, "sourcePort": null},
+    {"target": 4, "targetPort": "input_dict", "source": 23, "sourcePort": null},
+    {"target": 5, "targetPort": "working_directory", "source": 24, "sourcePort": null},
+    {"target": 25, "targetPort": "structure", "source": 2, "sourcePort": "s_2"},
+    {"target": 25, "targetPort": "pseudopotentials", "source": 14, "sourcePort": null},
+    {"target": 25, "targetPort": "kpts", "source": 15, "sourcePort": null},
+    {"target": 25, "targetPort": "calculation", "source": 21, "sourcePort": null},
+    {"target": 25, "targetPort": "smearing", "source": 17, "sourcePort": null},
+    {"target": 5, "targetPort": "input_dict", "source": 25, "sourcePort": null},
+    {"target": 6, "targetPort": "working_directory", "source": 26, "sourcePort": null},
+    {"target": 27, "targetPort": "structure", "source": 2, "sourcePort": "s_3"},
+    {"target": 27, "targetPort": "pseudopotentials", "source": 14, "sourcePort": null},
+    {"target": 27, "targetPort": "kpts", "source": 15, "sourcePort": null},
+    {"target": 27, "targetPort": "calculation", "source": 21, "sourcePort": null},
+    {"target": 27, "targetPort": "smearing", "source": 17, "sourcePort": null},
+    {"target": 6, "targetPort": "input_dict", "source": 27, "sourcePort": null},
+    {"target": 7, "targetPort": "working_directory", "source": 28, "sourcePort": null},
+    {"target": 29, "targetPort": "structure", "source": 2, "sourcePort": "s_4"},
+    {"target": 29, "targetPort": "pseudopotentials", "source": 14, "sourcePort": null},
+    {"target": 29, "targetPort": "kpts", "source": 15, "sourcePort": null},
+    {"target": 29, "targetPort": "calculation", "source": 21, "sourcePort": null},
+    {"target": 29, "targetPort": "smearing", "source": 17, "sourcePort": null},
+    {"target": 7, "targetPort": "input_dict", "source": 29, "sourcePort": null},
+    {"target": 30, "targetPort": "0", "source": 3, "sourcePort": "volume"},
+    {"target": 30, "targetPort": "1", "source": 4, "sourcePort": "volume"},
+    {"target": 30, "targetPort": "2", "source": 5, "sourcePort": "volume"},
+    {"target": 30, "targetPort": "3", "source": 6, "sourcePort": "volume"},
+    {"target": 30, "targetPort": "4", "source": 7, "sourcePort": "volume"},
+    {"target": 8, "targetPort": "volume_lst", "source": 30, "sourcePort": null},
+    {"target": 31, "targetPort": "0", "source": 3, "sourcePort": "energy"},
+    {"target": 31, "targetPort": "1", "source": 4, "sourcePort": "energy"},
+    {"target": 31, "targetPort": "2", "source": 5, "sourcePort": "energy"},
+    {"target": 31, "targetPort": "3", "source": 6, "sourcePort": "energy"},
+    {"target": 31, "targetPort": "4", "source": 7, "sourcePort": "energy"},
+    {"target": 8, "targetPort": "energy_lst", "source": 31, "sourcePort": null},
+    {"target": 32, "targetPort": null, "source": 8, "sourcePort": null}
   ]
 }
\ No newline at end of file

From ae1fd27cbabf746e5c1cf9197be1f91605bf8d83 Mon Sep 17 00:00:00 2001
From: Jan Janssen <janssen@mpie.de>
Date: Mon, 12 Oct 2026 09:43:57 +0200
Subject: [PATCH 4/6] Add hatchling to central environment

---
 environment.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/environment.yml b/environment.yml
index f7b95fb..47967b5 100644
--- a/environment.yml
+++ b/environment.yml
@@ -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

From 27043fe164ef5c70ed620c78917cba2838ba6c72 Mon Sep 17 00:00:00 2001
From: Jan Janssen <janssen@mpie.de>
Date: Mon, 12 Oct 2026 09:44:15 +0200
Subject: [PATCH 5/6] Install NFDI4Ing libGL dependency via apt

---
 .github/workflows/pipeline.yml | 3 ++-
 apt.txt                        | 2 ++
 2 files changed, 4 insertions(+), 1 deletion(-)
 create mode 100644 apt.txt

diff --git a/.github/workflows/pipeline.yml b/.github/workflows/pipeline.yml
index 5699ae9..af911fd 100644
--- a/.github/workflows/pipeline.yml
+++ b/.github/workflows/pipeline.yml
@@ -22,6 +22,7 @@ jobs:
       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: |
@@ -50,8 +51,8 @@ jobs:
     - name: Installation and setup
       shell: bash -l {0}
       run: |
-        conda install -c conda-forge jupyter papermill hatchling
         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: |
diff --git a/apt.txt b/apt.txt
new file mode 100644
index 0000000..c91b950
--- /dev/null
+++ b/apt.txt
@@ -0,0 +1,2 @@
+libgl1-mesa-glx
+libegl1-mesa
\ No newline at end of file

From 4794d449fdb82b27237d8047be48d3b25ce5ae8a Mon Sep 17 00:00:00 2001
From: Jan Janssen <janssen@mpie.de>
Date: Mon, 12 Oct 2026 09:44:26 +0200
Subject: [PATCH 6/6] add postbuild script for mybinder

---
 postBuild | 5 +++++
 1 file changed, 5 insertions(+)
 create mode 100644 postBuild

diff --git a/postBuild b/postBuild
new file mode 100644
index 0000000..6680e1f
--- /dev/null
+++ b/postBuild
@@ -0,0 +1,5 @@
+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 ~
\ No newline at end of file