Add pure python interface (#15)

* Add pure python interface

* fix CI

Author: jan-janssen

.github/workflows/python.yml

@@ -0,0 +1,29 @@
+name: python
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - uses: conda-incubator/setup-miniconda@v3
+      with:
+        auto-update-conda: true
+        python-version: "3.12"
+        environment-file: environment.yml
+        auto-activate-base: false
+    - name: Tests
+      shell: bash -l {0}
+      run: |
+        pip install -e adis_tools
+        pip install -e python_workflow_definition
+        conda install -c conda-forge jupyter papermill
+        export ESPRESSO_PSEUDO=$(pwd)/espresso/pseudo
+        papermill universal_simple_to_python.ipynb universal_simple_to_python_out.ipynb -k "python3"
+        papermill universal_qe_to_python.ipynb universal_qe_to_python_out.ipynb -k "python3"

python_workflow_definition/src/python_workflow_definition/purepython.py

@@ -0,0 +1,105 @@
+import json
+from importlib import import_module
+from inspect import isfunction
+
+
+def get_dict(**kwargs):
+    return {k: v for k, v in kwargs.items()}
+
+
+def get_list(**kwargs):
+    return list(kwargs.values())
+
+
+def get_kwargs(lst):
+    return {t['targetHandle']: {'source': t['source'], 'sourceHandle': t['sourceHandle']} for t in lst}
+
+
+def resort_total_lst(total_lst, nodes_dict):
+    nodes_with_dep_lst = list(sorted([v[0] for v in total_lst]))
+    nodes_without_dep_lst = [k for k in nodes_dict.keys() if k not in nodes_with_dep_lst]
+    ordered_lst, total_new_lst = [], []
+    while len(total_new_lst) < len(total_lst):
+        for ind, connect in total_lst:
+            if ind not in ordered_lst:
+                source_lst = [sd["source"] for sd in connect.values()]
+                if all([s in ordered_lst or s in nodes_without_dep_lst for s in source_lst]):
+                    ordered_lst.append(ind)
+                    total_new_lst.append([ind, connect])
+    return total_new_lst
+
+
+def group_edges(edges_lst):
+    edges_sorted_lst = sorted(edges_lst, key=lambda x: x['target'], reverse=True)
+    total_lst, tmp_lst = [], []
+    target_id = edges_sorted_lst[0]['target']
+    for ed in edges_sorted_lst:
+        if target_id == ed["target"]:
+            tmp_lst.append(ed)
+        else:
+            total_lst.append((target_id, get_kwargs(lst=tmp_lst)))
+            target_id = ed["target"]
+            tmp_lst = [ed]
+    total_lst.append((target_id, get_kwargs(lst=tmp_lst)))
+    return total_lst
+
+
+def get_source_handles(edges_lst):
+    source_handle_dict = {}
+    for ed in edges_lst:
+        if ed['source'] not in source_handle_dict.keys():
+            source_handle_dict[ed['source']] = [ed['sourceHandle']]
+        else:
+            source_handle_dict[ed['source']].append(ed['sourceHandle'])
+    return {
+        k: list(range(len(v))) if len(v) > 1 and all([el is None for el in v]) else v
+        for k, v in source_handle_dict.items()
+    }
+
+
+def get_value(result_dict, nodes_new_dict, link_dict):
+    source, source_handle = link_dict["source"], link_dict["sourceHandle"]
+    if source in result_dict.keys():
+        result = result_dict[source]
+    elif source in nodes_new_dict.keys():
+        result = nodes_new_dict[source]
+    else:
+        raise KeyError()
+    if source_handle is None:
+        return result
+    else:
+        return result[source_handle]
+
+
+def load_workflow_json(file_name):
+    with open(file_name, "r") as f:
+        content = json.load(f)
+
+    edges_new_lst = content["edges"]
+    nodes_new_dict = {}
+    for k, v in content["nodes"].items():
+        if isinstance(v, str) and "." in v:
+            p, m = v.rsplit('.', 1)
+            if p == "python_workflow_definition.pyiron_base":
+                p = "python_workflow_definition.purepython"
+            mod = import_module(p)
+            nodes_new_dict[int(k)] = getattr(mod, m)
+        else:
+            nodes_new_dict[int(k)] = v
+
+    total_lst = group_edges(edges_new_lst)
+    total_new_lst = resort_total_lst(total_lst=total_lst, nodes_dict=nodes_new_dict)
+
+    result_dict = {}
+    last_key = None
+    for lst in total_new_lst:
+        node = nodes_new_dict[lst[0]]
+        if isfunction(node):
+            kwargs = {
+                k: get_value(result_dict=result_dict, nodes_new_dict=nodes_new_dict, link_dict=v)
+                for k, v in lst[1].items()
+            }
+            result_dict[lst[0]] = node(**kwargs)
+            last_key = lst[0]
+
+    return result_dict[last_key]

universal_qe_to_python.ipynb

@@ -0,0 +1,45 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "b0f920a2-c646-485b-af0f-48251e061163",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from python_workflow_definition.purepython import load_workflow_json"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "46559120-d58a-492f-b734-db27424b5659",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "load_workflow_json(file_name=\"workflow_qe.json\")"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.5"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

universal_simple_to_python.ipynb

@@ -0,0 +1,45 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "b0f920a2-c646-485b-af0f-48251e061163",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from python_workflow_definition.purepython import load_workflow_json"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "46559120-d58a-492f-b734-db27424b5659",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "load_workflow_json(file_name=\"workflow_simple.json\")"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.5"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}