From e13b66baeef569b4e80cd6b61bb5b875e14d3dc6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20Jan=C3=9Fen?= <janssen@mpie.de>
Date: Sat, 12 Apr 2025 11:07:55 +0200
Subject: [PATCH 1/3] Add plotting function

---
 .../src/python_workflow_definition/plot.py    | 36 +++++++++++++++++++
 1 file changed, 36 insertions(+)
 create mode 100644 python_workflow_definition/src/python_workflow_definition/plot.py

diff --git a/python_workflow_definition/src/python_workflow_definition/plot.py b/python_workflow_definition/src/python_workflow_definition/plot.py
new file mode 100644
index 0000000..aa106e6
--- /dev/null
+++ b/python_workflow_definition/src/python_workflow_definition/plot.py
@@ -0,0 +1,36 @@
+import json
+
+from IPython.display import SVG, display
+import networkx as nx
+
+
+from python_workflow_definition.shared import get_kwargs, convert_nodes_list_to_dict
+from python_workflow_definition.purepython import group_edges
+
+
+def plot(json_file_name):
+    with open(json_file_name, "r") as f:
+        content = json.load(f)
+
+    graph = nx.DiGraph()
+    node_dict = convert_nodes_list_to_dict(nodes_list=content["nodes"])
+    total_lst = group_edges(edges_lst=content["edges"])
+
+    for node_id, node_name in node_dict.items():
+        graph.add_node(node_id, name=str(node_name), label=str(node_name))
+
+    for edge_tuple in total_lst:
+        target_node, edge_dict = edge_tuple
+        edge_label_dict = {}
+        for k, v in edge_dict.items():
+            if v["source"] not in edge_label_dict:
+                edge_label_dict[v["source"]] = []
+            if v["sourcePort"] is None:
+                edge_label_dict[v["source"]].append(k)
+            else:
+                edge_label_dict[v["source"]].append(v["sourcePort"] + "=" + k)
+        for k, v in edge_label_dict.items():
+            graph.add_edge(str(k), str(target_node), label=", ".join(v))
+
+    svg = nx.nx_agraph.to_agraph(graph).draw(prog="dot", format="svg")
+    display(SVG(svg))

From 2ef0f010240e3956bc4cecfe1763cd021cfadf90 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20Jan=C3=9Fen?= <janssen@mpie.de>
Date: Sat, 12 Apr 2025 12:40:43 +0200
Subject: [PATCH 2/3] Plot notebooks

---
 environment.yml                               |  1 +
 .../src/python_workflow_definition/plot.py    | 31 ++++++++++++-------
 universal_workflow_nfdi.ipynb                 | 19 ++++++++++++
 universal_workflow_qe.ipynb                   | 19 ++++++++++++
 universal_workflow_simple.ipynb               | 19 ++++++++++++
 5 files changed, 77 insertions(+), 12 deletions(-)

diff --git a/environment.yml b/environment.yml
index 5f7edb0..f58de08 100644
--- a/environment.yml
+++ b/environment.yml
@@ -7,3 +7,4 @@ dependencies:
 - pygraphviz=1.14
 - aiida-workgraph=0.5.1
 - conda_subprocess =0.0.6
+- networkx=3.4.2
\ No newline at end of file
diff --git a/python_workflow_definition/src/python_workflow_definition/plot.py b/python_workflow_definition/src/python_workflow_definition/plot.py
index aa106e6..94853d5 100644
--- a/python_workflow_definition/src/python_workflow_definition/plot.py
+++ b/python_workflow_definition/src/python_workflow_definition/plot.py
@@ -4,17 +4,24 @@
 import networkx as nx
 
 
-from python_workflow_definition.shared import get_kwargs, convert_nodes_list_to_dict
 from python_workflow_definition.purepython import group_edges
-
-
-def plot(json_file_name):
-    with open(json_file_name, "r") as f:
+from python_workflow_definition.shared import (
+    get_kwargs,
+    convert_nodes_list_to_dict,
+    NODES_LABEL,
+    EDGES_LABEL,
+    SOURCE_LABEL,
+    SOURCE_PORT_LABEL,
+)
+
+
+def plot(file_name):
+    with open(file_name, "r") as f:
         content = json.load(f)
 
     graph = nx.DiGraph()
-    node_dict = convert_nodes_list_to_dict(nodes_list=content["nodes"])
-    total_lst = group_edges(edges_lst=content["edges"])
+    node_dict = convert_nodes_list_to_dict(nodes_list=content[NODES_LABEL])
+    total_lst = group_edges(edges_lst=content[EDGES_LABEL])
 
     for node_id, node_name in node_dict.items():
         graph.add_node(node_id, name=str(node_name), label=str(node_name))
@@ -23,12 +30,12 @@ def plot(json_file_name):
         target_node, edge_dict = edge_tuple
         edge_label_dict = {}
         for k, v in edge_dict.items():
-            if v["source"] not in edge_label_dict:
-                edge_label_dict[v["source"]] = []
-            if v["sourcePort"] is None:
-                edge_label_dict[v["source"]].append(k)
+            if v[SOURCE_LABEL] not in edge_label_dict:
+                edge_label_dict[v[SOURCE_LABEL]] = []
+            if v[SOURCE_PORT_LABEL] is None:
+                edge_label_dict[v[SOURCE_LABEL]].append(k)
             else:
-                edge_label_dict[v["source"]].append(v["sourcePort"] + "=" + k)
+                edge_label_dict[v[SOURCE_LABEL]].append(v[SOURCE_PORT_LABEL] + "=" + k)
         for k, v in edge_label_dict.items():
             graph.add_edge(str(k), str(target_node), label=", ".join(v))
 
diff --git a/universal_workflow_nfdi.ipynb b/universal_workflow_nfdi.ipynb
index 2ae6836..894bb02 100644
--- a/universal_workflow_nfdi.ipynb
+++ b/universal_workflow_nfdi.ipynb
@@ -7,6 +7,25 @@
     "# Load Simple Workflow"
    ]
   },
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": "## Plot"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": "from python_workflow_definition.plot import plot"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": "plot(file_name='workflow_nfdi.json')"
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
diff --git a/universal_workflow_qe.ipynb b/universal_workflow_qe.ipynb
index b0fde02..182229d 100644
--- a/universal_workflow_qe.ipynb
+++ b/universal_workflow_qe.ipynb
@@ -7,6 +7,25 @@
     "# Load Quantum Espresso Energy Volume Curve Workflow"
    ]
   },
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": "## Plot"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": "from python_workflow_definition.plot import plot"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": "plot(file_name='workflow_qe.json')"
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
diff --git a/universal_workflow_simple.ipynb b/universal_workflow_simple.ipynb
index 5e011c3..aaf8d2e 100644
--- a/universal_workflow_simple.ipynb
+++ b/universal_workflow_simple.ipynb
@@ -7,6 +7,25 @@
     "# Load Simple Workflow"
    ]
   },
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": "## Plot"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": "from python_workflow_definition.plot import plot"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": "plot(file_name='workflow_simple.json')"
+  },
   {
    "cell_type": "markdown",
    "metadata": {},

From 28a000e713c47fce0629f439ec840f51d0da61bf Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20Jan=C3=9Fen?= <janssen@mpie.de>
Date: Sat, 12 Apr 2025 12:44:16 +0200
Subject: [PATCH 3/3] add empty line at the end of environment

---
 environment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/environment.yml b/environment.yml
index f58de08..ee30024 100644
--- a/environment.yml
+++ b/environment.yml
@@ -7,4 +7,4 @@ dependencies:
 - pygraphviz=1.14
 - aiida-workgraph=0.5.1
 - conda_subprocess =0.0.6
-- networkx=3.4.2
\ No newline at end of file
+- networkx=3.4.2