Merge remote-tracking branch 'origin/main' into pyiron_workflow

# Conflicts:
#	src/python_workflow_definition/pyiron_workflow.py

Author: jan-janssen

.github/workflows/pipeline.yml

@@ -13,7 +13,7 @@ jobs:
     - uses: psf/black@stable
       with:
         options: "--check --diff"
-        src: ./python_workflow_definition/src/python_workflow_definition
+        src: ./src/python_workflow_definition
     - uses: psf/black@stable
       with:
         options: "--check --diff"
@@ -35,7 +35,7 @@ jobs:
     - name: Pip check
       shell: bash -l {0}
       run: |
-        pip install --no-deps --no-build-isolation -e python_workflow_definition
+        pip install --no-deps --no-build-isolation -e .
         pip check
 
   nfdi4ing:
@@ -53,7 +53,7 @@ jobs:
     - name: Installation and setup
       shell: bash -l {0}
       run: |
-        pip install --no-deps --no-build-isolation -e python_workflow_definition
+        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)
@@ -93,7 +93,7 @@ jobs:
       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 python_workflow_definition
+        pip install --no-deps --no-build-isolation -e .
         conda install -c conda-forge jupyter papermill
         verdi presto --profile-name pwd
     - name: Tests
@@ -124,7 +124,7 @@ jobs:
     - name: Installation and setup
       shell: bash -l {0}
       run: |
-        pip install --no-deps --no-build-isolation -e python_workflow_definition
+        pip install --no-deps --no-build-isolation -e .
         conda install -c conda-forge jupyter papermill
         verdi presto --profile-name pwd
     - name: Tests

.github/workflows/pypi.yml

@@ -26,9 +26,7 @@ jobs:
         environment-file: binder/environment.yml
     - name: Build
       shell: bash -l {0}
-      run: |
-        cd python_workflow_definition
-        hatch build -t sdist -t wheel
+      run: hatch build -t sdist -t wheel
     - name: Publish distribution 📦 to PyPI
       uses: pypa/gh-action-pypi-publish@release/v1
       with:

.gitignore

@@ -178,7 +178,7 @@ cython_debug/
 input_tmp.in
 pyiron.log
 pyiron_draw.png
-python_workflow_definition/src/python_workflow_definition/__pycache__/
+src/python_workflow_definition/__pycache__/
 test/
 mini/
 evcurve.png

CITATION.cff

@@ -0,0 +1,40 @@
+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: 10.5281/zenodo.15516180
+date-released: 2025-05-26
+license: bsd-3-clause
+url: "https://github.com/pythonworkflow/python-workflow-definition"

README.md

@@ -1,6 +1,8 @@
 # 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)
+[![arXiv](https://img.shields.io/badge/arXiv-2505.20366-b31b1b.svg)](https://arxiv.org/abs/2505.20366)
+[![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 

binder/environment.yml

@@ -2,11 +2,12 @@ channels:
 - conda-forge
 dependencies:
 - python =3.12
+- click =8.1.8
 - pydantic =2.11.4
 - hatch =1.14.1
 - hatchling =1.27.0
 - httpcore =1.0.7
-- jobflow =0.1.19
+- jobflow =0.2.0
 - pyiron_base =0.12.0
 - pyiron_workflow =0.13.0
 - pygraphviz =1.14

example_workflows/quantum_espresso/environment.yml

@@ -5,5 +5,5 @@ dependencies:
 - matplotlib=3.10.1
 - xmlschema=3.4.3
 - optimade=1.2.3
-- qe=7.2
-- qe-tools=2.0.0
+- qe=7.4
+- qe-tools=2.0.0

example_workflows/quantum_espresso/qe_xml_parser/src/qe_xml_parser/schemas/qes_230310.xsd

@@ -73,6 +73,7 @@ datecode 220603
       <element type="qes:ekin_functionalType" name="ekin_functional" minOccurs="0" />
       <element type="qes:matrixType" name="external_atomic_forces" minOccurs="0" />
       <element type="qes:integerMatrixType" name="free_positions" minOccurs="0" />
+      <element type="qes:twochemType" name="twoch_" minOccurs="0" />
       <element type="qes:matrixType" name="starting_atomic_velocities" minOccurs="0" />
       <element type="qes:electric_fieldType" name="electric_field" minOccurs="0" />
       <element type="qes:atomic_constraintsType" name="atomic_constraints" minOccurs="0" />
@@ -235,6 +236,7 @@ datecode 220603
       <element type="qes:cellType" name="cell"/>
     </sequence>
     <attribute type="positiveInteger" name="nat" />
+    <attribute type="positiveInteger" name="num_of_atomic_wfc" />
     <attribute type="double" name="alat" use="optional"/>
     <attribute type="positiveInteger" name="bravais_index" use="optional"/>
       <attribute type="string" name="alternative_axes" use="optional" />
@@ -908,6 +910,15 @@ datecode 220603
      </simpleContent>
   </complexType>
 
+  <complexType name="twochemType">
+    <sequence>
+      <element type="boolean" name="twochem" minOccurs="0"/>
+      <element type="integer" name="nbnd_cond" minOccurs="0"/>
+      <element type="double" name="degauss_cond" minOccurs="0"/>
+      <element type="double" name="nelec_cond" minOccurs="0"/>
+    </sequence>  
+  </complexType>
+
   <!-- OUTPUT TYPE -->
 
   <complexType name="outputElectricFieldType">
@@ -997,6 +1008,7 @@ datecode 220603
     <sequence>
       <element type="qes:scf_convType" name="scf_conv"/>
       <element type="qes:opt_convType" name="opt_conv" minOccurs="0"/>
+      <element type="boolean" name="wf_collected" minOccurs="0"/>
     </sequence>
   </complexType>
   <complexType name="scf_convType">
@@ -1024,6 +1036,7 @@ datecode 220603
   <complexType name="symmetriesType">
     <sequence>
       <element type="unsignedByte" name="nsym"/>
+      <element type="unsignedByte" name="colin_mag"/>
       <element type="unsignedByte" name="nrot"/>
       <element type="unsignedByte" name="space_group"/>
       <element type="qes:symmetryType" name="symmetry" maxOccurs="48" minOccurs="1"/>
@@ -1101,8 +1114,9 @@ datecode 220603
       <element type="nonNegativeInteger" name="nbnd_up" minOccurs="0" />
       <element type="nonNegativeInteger" name="nbnd_dw" minOccurs="0" />
       <element type="double" name="nelec"/>
+      <element type="double" name="fermi_energy"/>
       <element type="integer" name = "num_of_atomic_wfc" minOccurs = "0"/>
-      <element type="boolean" name = "wf_collected" />
+      <element type="boolean" name = "wf_collected" minOccurs = "0"/>
       <element type="double" name="fermi_energy" minOccurs="0" />
       <element type="double" name="highestOccupiedLevel" minOccurs ="0"/>
       <element type="double" name="lowestUnoccupiedLevel" minOccurs="0"/>
@@ -1367,4 +1381,4 @@ datecode 220603
       <element type="double"  name="left_buffer_v"  minOccurs="0"/>
     </sequence>
   </complexType>
-</schema>
+</schema>

python_workflow_definition/pyproject.toml renamed to pyproject.toml

@@ -14,7 +14,7 @@ authors = [
   { name = "Marnik Bercx", email = "marnik.bercx@psi.ch" },
   { name = "Christina Ertural", email = "christina.ertural@bam.de" },
 ]
-license = { file = "../LICENSE" }
+license = { file = "LICENSE" }
 dependencies = [
     "numpy>=1.21,<2",
     "pydantic>=2.7.0,<=2.11.4",
@@ -25,7 +25,7 @@ aiida = [
     "aiida-workgraph>=0.5.1,<=0.5.2",
 ]
 jobflow = [
-    "jobflow>=0.1.18,<=0.1.19",
+    "jobflow>=0.1.18,<=0.2.0",
 ]
 pyiron = [
     "pyiron_base>=0.11.10,<=0.12.0",