Update version to 0.1.0 (#3)

* Update version to 0.1.0

* fixes

* Update environment.yml

* Update pipeline.yml

* Update environment.yml

* Update processing.yaml

Author: jan-janssen

.github/workflows/pipeline.yml

@@ -21,6 +21,7 @@ jobs:
     - name: Test
       shell: bash -l {0}
       run: |
+        conda install -c conda-forge -y aiida-workgraph=0.5.2
         sudo apt-get install -y $(cat apt.txt)
         conda env create -n preprocessing -f source/envs/preprocessing.yaml -y
         conda env create -n processing -f source/envs/processing.yaml -y
@@ -44,6 +45,7 @@ jobs:
     - name: Test
       shell: bash -l {0}
       run: |
+        conda install -c conda-forge -y jobflow=0.1.19
         sudo apt-get install -y $(cat apt.txt)
         conda env create -n preprocessing -f source/envs/preprocessing.yaml -y
         conda env create -n processing -f source/envs/processing.yaml -y
@@ -66,9 +68,34 @@ jobs:
     - name: Test
       shell: bash -l {0}
       run: |
+        conda install -c conda-forge -y pyiron_base=0.11.11
         sudo apt-get install -y $(cat apt.txt)
         conda env create -n preprocessing -f source/envs/preprocessing.yaml -y
         conda env create -n processing -f source/envs/processing.yaml -y
         conda env create -n postprocessing -f source/envs/postprocessing.yaml -y
         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-22.04
+    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: |
+        conda install -c conda-forge -y cwltool=3.1.20250110105449
+        sudo apt-get install -y $(cat apt.txt)
+        conda env create -n preprocessing -f source/envs/preprocessing.yaml -y
+        conda env create -n processing -f source/envs/processing.yaml -y
+        conda env create -n postprocessing -f source/envs/postprocessing.yaml -y
+        echo -e 'import os\nimport json\nfrom python_workflow_definition.cwl import write_workflow\n\n\nif __name__ == "__main__":\n    with open("workflow.json") as f:\n        content = json.load(f)\n    node_lst = []\n    for n in content["nodes"]:\n        if "name" in n and n["name"] == "source_directory":\n            n["value"] = os.path.abspath(n["value"])\n        node_lst.append(n)\n    content["nodes"] = node_lst\n    with open("workflow.json", "w") as f:\n        json.dump(content, f)\n    write_workflow(file_name="workflow.json")' > test_with_cwl.py
+        python test_with_cwl.py
+        cwltool --preserve-environment=CONDA_EXE workflow.cwl workflow.yml

environment.yml

@@ -2,5 +2,5 @@ channels:
 - conda-forge
 dependencies:
 - python =3.12
-- python-workflow-definition =0.0.1
+- python-workflow-definition =0.1.0
 - conda_subprocess =0.0.6

source/envs/processing.yaml

@@ -1,5 +1,5 @@
 channels:
   - conda-forge
-  - defaults
 dependencies:
   - fenics=2019.1.0=py39hf3d152e_26
+  - sympy=1.13.3

workflow.json

@@ -1,24 +1,33 @@
 {
+  "version": "0.1.0",
   "nodes": [
-    {"id": 0, "function": "workflow.generate_mesh"},
-    {"id": 1, "function": "workflow.convert_to_xdmf"},
-    {"id": 2, "function": "workflow.poisson"},
-    {"id": 3, "function": "workflow.plot_over_line"},
-    {"id": 4, "function": "workflow.substitute_macros"},
-    {"id": 5, "function": "workflow.compile_paper"},
-    {"id": 6, "value": 2.0}
+    {"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": 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": "plot_file", "source": 3, "sourcePort": null},
+    {"target": 5, "targetPort": "source_directory", "source": 7, "sourcePort": null},
+    {"target": 8, "targetPort": null, "source": 5, "sourcePort": null}
   ]
 }

workflow.py

@@ -2,15 +2,13 @@
 from conda_subprocess import check_output
 import shutil
 
-source_directory = os.path.join(os.path.dirname(os.path.abspath(__file__)), "source")
 
-
-def generate_mesh(domain_size: float = 2.0) -> str:
+def generate_mesh(domain_size: float, source_directory: str) -> str:
     stage_name = "preprocessing"
     gmsh_output_file_name = "square.msh"
     source_file_name ="unit_square.geo"
     os.makedirs(stage_name, exist_ok=True)
-    _copy_file_from_source(stage_name=stage_name, source_file_name=source_file_name)
+    _copy_file_from_source(stage_name=stage_name, source_file_name=source_file_name, source_directory=source_directory)
     _ = check_output(
         [
             "gmsh", "-2", "-setnumber", "domain_size", str(domain_size),
@@ -40,13 +38,13 @@ def convert_to_xdmf(gmsh_output_file : str) -> dict:
     }
 
 
-def poisson(meshio_output_xdmf: str, meshio_output_h5: str) -> dict:
+def poisson(meshio_output_xdmf: str, meshio_output_h5: str, source_directory: str) -> dict:
     stage_name = "processing"
     poisson_output_pvd_file_name = "poisson.pvd"
     poisson_output_numdofs_file_name = "numdofs.txt"
     source_file_name = "poisson.py"
     os.makedirs(stage_name, exist_ok=True)
-    _copy_file_from_source(stage_name=stage_name, source_file_name=source_file_name)
+    _copy_file_from_source(stage_name=stage_name, source_file_name=source_file_name, source_directory=source_directory)
     _copy_file(stage_name=stage_name, source_file=meshio_output_xdmf)
     _copy_file(stage_name=stage_name, source_file=meshio_output_h5)
     _ = check_output(
@@ -65,12 +63,12 @@ def poisson(meshio_output_xdmf: str, meshio_output_h5: str) -> dict:
     }
 
 
-def plot_over_line(poisson_output_pvd_file: str, poisson_output_vtu_file: str) -> str:
+def plot_over_line(poisson_output_pvd_file: str, poisson_output_vtu_file: str, source_directory: str) -> str:
     stage_name = "postprocessing"
     pvbatch_output_file_name = "plotoverline.csv"
     source_file_name = "postprocessing.py"
     os.makedirs(stage_name, exist_ok=True)
-    _copy_file_from_source(stage_name=stage_name, source_file_name=source_file_name)
+    _copy_file_from_source(stage_name=stage_name, source_file_name=source_file_name, source_directory=source_directory)
     _copy_file(stage_name=stage_name, source_file=poisson_output_pvd_file)
     _copy_file(stage_name=stage_name, source_file=poisson_output_vtu_file)
     _ = check_output(
@@ -82,14 +80,14 @@ def plot_over_line(poisson_output_pvd_file: str, poisson_output_vtu_file: str) -
     return os.path.abspath(os.path.join("postprocessing", pvbatch_output_file_name))
 
 
-def substitute_macros(pvbatch_output_file: str, ndofs: int, domain_size: float = 2.0) -> str:
+def substitute_macros(pvbatch_output_file: str, ndofs: int, domain_size: float, source_directory: str) -> str:
     stage_name = "postprocessing"
     source_file_name = "prepare_paper_macros.py"
     template_file_name = "macros.tex.template"
     macros_output_file_name = "macros.tex"
     os.makedirs(stage_name, exist_ok=True)
-    _copy_file_from_source(stage_name=stage_name, source_file_name=source_file_name)
-    _copy_file_from_source(stage_name=stage_name, source_file_name=template_file_name)
+    _copy_file_from_source(stage_name=stage_name, source_file_name=source_file_name, source_directory=source_directory)
+    _copy_file_from_source(stage_name=stage_name, source_file_name=template_file_name, source_directory=source_directory)
     _copy_file(stage_name=stage_name, source_file=pvbatch_output_file)
     _ = check_output(
         [
@@ -104,12 +102,12 @@ def substitute_macros(pvbatch_output_file: str, ndofs: int, domain_size: float =
     return os.path.abspath(os.path.join(stage_name, macros_output_file_name))
 
 
-def compile_paper(macros_tex: str, plot_file: str) -> str:
+def compile_paper(macros_tex: str, plot_file: str, source_directory: str) -> str:
     stage_name = "postprocessing"
     paper_output = "paper.pdf"
     source_file_name = "paper.tex"
     os.makedirs(stage_name, exist_ok=True)
-    _copy_file_from_source(stage_name=stage_name, source_file_name=source_file_name)
+    _copy_file_from_source(stage_name=stage_name, source_file_name=source_file_name, source_directory=source_directory)
     _copy_file(stage_name=stage_name, source_file=macros_tex)
     _copy_file(stage_name=stage_name, source_file=plot_file)
     _ = check_output(
@@ -126,12 +124,12 @@ def _poisson_collect_output(numdofs_file: str) -> int:
         return int(f.read())
 
 
-def _copy_file(stage_name, source_file):
+def _copy_file(stage_name: str, source_file: str):
     input_file = os.path.join(os.path.abspath(stage_name), os.path.basename(source_file))
     if input_file != source_file:
         shutil.copyfile(source_file, input_file)
 
 
-def _copy_file_from_source(stage_name, source_file_name):
+def _copy_file_from_source(stage_name: str, source_file_name: str, source_directory: str):
     source_file = os.path.join(source_directory, source_file_name)
     shutil.copyfile(source_file, os.path.join(stage_name, source_file_name))