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

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)
@@ -71,6 +71,7 @@ jobs:
         papermill cwl.ipynb cwl_out.ipynb -k "python3"
         papermill jobflow.ipynb jobflow_out.ipynb -k "python3"
         papermill pyiron_base.ipynb pyiron_base_out.ipynb -k "python3"
+        papermill pyiron_workflow.ipynb pyiron_workflow_out.ipynb -k "python3"
         papermill universal_workflow.ipynb universal_workflow_out.ipynb -k "python3"
 
   quantumespresso:
@@ -92,7 +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
@@ -105,6 +106,7 @@ jobs:
         papermill cwl.ipynb cwl_out.ipynb -k "python3"
         papermill jobflow.ipynb jobflow_out.ipynb -k "python3"
         papermill pyiron_base.ipynb pyiron_base_out.ipynb -k "python3"
+        papermill pyiron_workflow.ipynb pyiron_workflow_out.ipynb -k "python3"
         papermill universal_workflow.ipynb universal_workflow_out.ipynb -k "python3"
 
   arithmetic:
@@ -122,7 +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
@@ -133,6 +135,7 @@ jobs:
         papermill cwl.ipynb cwl_out.ipynb -k "python3"
         papermill jobflow.ipynb jobflow_out.ipynb -k "python3"
         papermill pyiron_base.ipynb pyiron_base_out.ipynb -k "python3"
+        papermill pyiron_workflow.ipynb pyiron_workflow_out.ipynb -k "python3"
         papermill universal_workflow.ipynb universal_workflow_out.ipynb -k "python3"
 
   documentation:

.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

binder/environment.yml

@@ -2,12 +2,14 @@ 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
 - aiida-workgraph =0.5.2
 - conda_subprocess =0.0.7

example_workflows/arithmetic/aiida.ipynb

@@ -232,6 +232,39 @@
     }
    ],
    "execution_count": 15
+  },
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": "## Load Workflow with pyiron_workflow"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": "from python_workflow_definition.pyiron_workflow import load_workflow_json"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": "wf = load_workflow_json(file_name=workflow_json_filename)"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": "wf.draw(size=(10,10))"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": "wf.run()"
   }
  ]
 }

example_workflows/arithmetic/jobflow.ipynb

@@ -369,18 +369,42 @@
    }
   },
   {
-   "id": "c199b28f3c0399cc",
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": "## Load Workflow with pyiron_workflow",
+   "id": "7da4733bfeffee63"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": "from python_workflow_definition.pyiron_workflow import load_workflow_json",
+   "id": "6c87661996ff840b"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": "wf = load_workflow_json(file_name=workflow_json_filename)",
+   "id": "33b1e9408924f9c0"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": "wf.draw(size=(10,10))",
+   "id": "df63b2963a0d90a5"
+  },
+  {
+   "metadata": {},
    "cell_type": "code",
-   "source": "",
-   "metadata": {
-    "collapsed": false,
-    "jupyter": {
-     "outputs_hidden": false
-    },
-    "trusted": true
-   },
    "outputs": [],
-   "execution_count": null
+   "execution_count": null,
+   "source": "wf.run()",
+   "id": "bf110395454bd694"
   }
  ]
 }

example_workflows/arithmetic/pyiron_base.ipynb

@@ -274,15 +274,49 @@
    ],
    "execution_count": 18
   },
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": "## Load Workflow with pyiron_workflow",
+   "id": "406fd07dd4bd8006"
+  },
   {
    "id": "cf76f305-24de-45a7-be8e-cfe45cd6458e",
    "cell_type": "code",
-   "source": "",
+   "source": "from python_workflow_definition.pyiron_workflow import load_workflow_json",
    "metadata": {
-    "trusted": true
+    "trusted": true,
+    "ExecuteTime": {
+     "end_time": "2025-05-24T08:25:33.797570Z",
+     "start_time": "2025-05-24T08:25:33.771214Z"
+    }
    },
    "outputs": [],
    "execution_count": null
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": "wf = load_workflow_json(file_name=workflow_json_filename)",
+   "id": "5b442611457aa5a8"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": "wf.draw(size=(10,10))",
+   "id": "2ca33c8590a54866"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": "wf.run()",
+   "id": "d36522a1c315b7f5"
   }
  ]
 }