Update to Version 0.1.0 (#3)

Author: jan-janssen

.github/workflows/pipeline.yml

@@ -22,6 +22,7 @@ jobs:
       shell: bash -l {0}
       run: |
         export ESPRESSO_PSEUDO=$(pwd)/espresso/pseudo
+        conda install -c conda-forge -y aiida-workgraph=0.5.2
         pip install --no-deps --no-build-isolation -e qe_xml_parser
         verdi presto --profile-name pwd
         echo -e 'from aiida import load_profile\nload_profile()\n\nfrom python_workflow_definition.aiida import load_workflow_json\n\n\nif __name__ == "__main__":\n    workgraph = load_workflow_json(file_name="workflow.json")\n    workgraph.run()' > test_with_aiida.py
@@ -43,6 +44,7 @@ jobs:
       shell: bash -l {0}
       run: |
         export ESPRESSO_PSEUDO=$(pwd)/espresso/pseudo
+        conda install -c conda-forge -y jobflow=0.1.19
         pip install --no-deps --no-build-isolation -e qe_xml_parser
         echo -e 'from jobflow.managers.local import run_locally\nfrom python_workflow_definition.jobflow import load_workflow_json\n\n\nif __name__ == "__main__":\n    flow = load_workflow_json(file_name="workflow.json")\n    print(run_locally(flow))' > test_with_jobflow.py
         python test_with_jobflow.py
@@ -63,6 +65,29 @@ jobs:
       shell: bash -l {0}
       run: |
         export ESPRESSO_PSEUDO=$(pwd)/espresso/pseudo
+        conda install -c conda-forge -y pyiron_base=0.11.11
         pip install --no-deps --no-build-isolation -e qe_xml_parser
         echo -e 'from python_workflow_definition.pyiron_base import load_workflow_json\n\n\nif __name__ == "__main__":\n    delayed_object_lst = load_workflow_json(file_name="workflow.json")\n    print(delayed_object_lst[-1].pull())' > test_with_pyiron.py
         python test_with_pyiron.py
+
+  cwl:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Conda config
+      run: echo -e "channels:\n  - conda-forge\n" > .condarc
+    - uses: conda-incubator/setup-miniconda@v3
+      with:
+        python-version: "3.12"
+        miniforge-version: latest
+        condarc-file: .condarc
+        environment-file: environment.yml
+    - name: Test
+      shell: bash -l {0}
+      run: |
+        export ESPRESSO_PSEUDO=$(pwd)/espresso/pseudo
+        conda install -c conda-forge -y cwltool=3.1.20250110105449
+        pip install --no-deps --no-build-isolation -e qe_xml_parser
+        echo -e 'from python_workflow_definition.cwl import write_workflow\n\n\nif __name__ == "__main__":\n    write_workflow(file_name="workflow.json")' > test_with_cwl.py
+        python test_with_cwl.py
+        cwltool --preserve-environment=ESPRESSO_PSEUDO workflow.cwl workflow.yml

environment.yml

@@ -2,7 +2,7 @@ channels:
 - conda-forge
 dependencies:
 - python =3.12
-- python-workflow-definition =0.0.1
+- python-workflow-definition =0.1.0
 - ase=3.24.0
 - hatchling =1.27.0
 - matplotlib=3.10.1

workflow.json

@@ -1,37 +1,39 @@
 {
+  "version": "0.1.0",
   "nodes": [
-    {"id": 0, "function": "workflow.get_bulk_structure"},
-    {"id": 1, "function": "workflow.calculate_qe"},
-    {"id": 2, "function": "workflow.generate_structures"},
-    {"id": 3, "function": "workflow.calculate_qe"},
-    {"id": 4, "function": "workflow.calculate_qe"},
-    {"id": 5, "function": "workflow.calculate_qe"},
-    {"id": 6, "function": "workflow.calculate_qe"},
-    {"id": 7, "function": "workflow.calculate_qe"},
-    {"id": 8, "function": "workflow.plot_energy_volume_curve"},
-    {"id": 9, "value": "Al"},
-    {"id": 10, "value": 4.05},
-    {"id": 11, "value": true},
-    {"id": 12, "value": "mini"},
-    {"id": 13, "function": "python_workflow_definition.shared.get_dict"},
-    {"id": 14, "value": {"Al": "Al.pbe-n-kjpaw_psl.1.0.0.UPF"}},
-    {"id": 15, "value": [3, 3, 3]},
-    {"id": 16, "value": "vc-relax"},
-    {"id": 17, "value": 0.02},
-    {"id": 18, "value": [0.9, 0.95, 1.0, 1.05, 1.1]},
-    {"id": 19, "value": "strain_0"},
-    {"id": 20, "function": "python_workflow_definition.shared.get_dict"},
-    {"id": 21, "value": "scf"},
-    {"id": 22, "value": "strain_1"},
-    {"id": 23, "function": "python_workflow_definition.shared.get_dict"},
-    {"id": 24, "value": "strain_2"},
-    {"id": 25, "function": "python_workflow_definition.shared.get_dict"},
-    {"id": 26, "value": "strain_3"},
-    {"id": 27, "function": "python_workflow_definition.shared.get_dict"},
-    {"id": 28, "value": "strain_4"},
-    {"id": 29, "function": "python_workflow_definition.shared.get_dict"},
-    {"id": 30, "function": "python_workflow_definition.shared.get_list"},
-    {"id": 31, "function": "python_workflow_definition.shared.get_list"}
+    {"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": 0, "targetPort": "element", "source": 9, "sourcePort": null},
@@ -92,6 +94,7 @@
     {"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": 8, "targetPort": "energy_lst", "source": 31, "sourcePort": null},
+    {"target": 32, "targetPort": null, "source": 8, "sourcePort": null}
   ]
 }