From a15a4fbf4ece3d7418de3d32c17a07f2c3993e50 Mon Sep 17 00:00:00 2001
From: Bryan Ngo <bryanngo@berkeley.edu>
Date: Fri, 2 Dec 2022 14:01:59 -0800
Subject: [PATCH 01/36] basic flowgraph implementation

---
 src/flowgraph/node.py      | 187 +++++++++++++++++++++++++++++++++++++
 src/flowgraph/node_test.py | 102 ++++++++++++++++++++
 2 files changed, 289 insertions(+)
 create mode 100644 src/flowgraph/node.py
 create mode 100644 src/flowgraph/node_test.py

diff --git a/src/flowgraph/node.py b/src/flowgraph/node.py
new file mode 100644
index 000000000..a8737c6f1
--- /dev/null
+++ b/src/flowgraph/node.py
@@ -0,0 +1,187 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+#
+#  Represents a flowgraph in HAMMER that can be run and verified.
+#  See README.config for more details.
+#
+#  See LICENSE for licence details.
+
+# pylint: disable=invalid-name
+
+import json
+import queue
+from copy import deepcopy
+from dataclasses import asdict, dataclass, field
+from enum import Enum
+from typing import Optional
+
+import networkx as nx
+
+
+class Status(Enum):
+    """Represents the status of a node in the flowgraph.
+    https://tinyurl.com/2bstth7y
+    """
+    NOT_RUN    = "NOT_RUN"
+    RUNNING    = "RUNNING"
+    INCOMPLETE = "INCOMPLETE"
+    INVALID    = "INVALID"
+    COMPLETE   = "COMPLETE"
+
+
+class StatusEncoder(json.JSONEncoder):
+    def default(self, o: Status) -> str:
+        if isinstance(o, Status):
+            return o.name
+        return super().default(o)
+
+
+def as_status(dct):
+    if "status" in dct:
+        dct["status"] = Status[dct["status"]]
+    return dct
+
+
+# make sure union of required/optional outs is superset of children required/optional inputs
+# separate required validity checking and optional validity checking
+# meta dict for tech compatibilty
+# for cycles, reduce to DAG via cloning of one of the nodes
+
+@dataclass
+class Node:
+    action:            str
+    tool:              str
+    push_dir:          str
+    pull_dir:          str
+    required_inputs:   list[str]
+    required_outputs:  list[str]
+    children:          list
+    optional_inputs:   list[str] = field(default_factory=list)
+    optional_outputs:  list[str] = field(default_factory=list)
+    status:            Status = Status.NOT_RUN
+
+    def __key(self) -> tuple:
+        """Key value for hashing.
+
+        Returns:
+            tuple: All fields concatenated.
+        """
+        return (
+            self.action,
+            self.tool,
+            self.push_dir,
+            self.pull_dir,
+            tuple(self.required_inputs),
+            tuple(self.required_outputs),
+            tuple(self.children),
+            tuple(self.optional_inputs),
+            tuple(self.optional_outputs),
+            self.status
+        )
+
+    def __hash__(self) -> int:
+        return hash(self.__key)
+
+    def to_json(self) -> dict:
+        """Writes the node to a JSON string.
+
+        Args:
+            fname (str): File name to write to.
+
+        Returns:
+            str: Node represented as a JSON.
+        """
+        return asdict(self)
+
+
+@dataclass
+class Graph:
+    root: Node
+
+    def __post_init__(self) -> None:
+        self.networkx = self.to_networkx()
+
+    def to_json(self, indent: Optional[int] = None) -> str:
+        """Writes the graph as a JSON string and saves it to a file.
+
+        Returns:
+            dict: Entire flowgraph as a JSON.
+        """
+        out_dict = asdict(self.root)
+        return json.dumps(out_dict, indent=indent, cls=StatusEncoder)
+
+    def to_networkx(self) -> nx.DiGraph:
+        """Turns our graph into an NetworkX directed graph.
+
+        Returns:
+            nx.DiGraph: NetworkX directed graph.
+        """
+        q = queue.LifoQueue()
+        explored = []
+        q.put(self.root)
+        edge_list = {}
+        while not q.empty():
+            v = q.get()
+            if v not in explored:
+                explored.append(v)
+                edge_list[v] = tuple(c for c in v.children)
+                for c in v.children:
+                    q.put(c)
+        return nx.DiGraph(edge_list)
+
+    @staticmethod
+    def from_json(dump: str) -> dict:
+        """Converts a JSON into an instance of Graph.
+
+        Args:
+            dump (str): JSON with the correct schema for a Graph.
+
+        Returns:
+            dict: Dictionary containing graph information.
+        """
+        return json.loads(dump, object_hook=as_status)
+
+    def verify(self) -> bool:
+        """Checks if a graph is valid via its inputs and outputs.
+
+        Returns:
+            bool: If graph is valid.
+        """
+        return all(self.__process(v) for v in nx.nodes(self.networkx))
+
+    def __process(self, v: Node) -> bool:
+        """Process a specific vertex of a graph.
+
+        Args:
+            v (Node): Node to check the validity of.
+
+        Returns:
+            bool: If the particular node is valid.
+        """
+        if v == self.root:
+            return True
+        parent_outs = \
+            set().union(*(set(p.required_outputs) for p in self.networkx.predecessors(v))) \
+            | set().union(*(set(p.optional_outputs) for p in self.networkx.predecessors(v)))
+        inputs = set(v.required_inputs) | set(v.optional_inputs)
+        return parent_outs >= inputs
+
+
+def convert_to_acyclic(g: Graph) -> Graph:
+    """Eliminates cycles in a flowgraph for analysis.
+
+    Args:
+        g (Graph): (presumably) cyclic graph to transform.
+
+    Returns:
+        Graph: Graph with cloned nodes.
+    """
+    g_copy = deepcopy(g)
+    cycles = nx.simple_cycles(g_copy.networkx)
+    for cycle in cycles:
+        start, end = cycle[0], cycle[1]
+        end_copy = deepcopy(end)
+        end_copy.children = []
+        start.children[start.children.index(end)] = end_copy
+        print(start.children[start.children.index(end_copy)].children)
+    return Graph(g_copy.root)
diff --git a/src/flowgraph/node_test.py b/src/flowgraph/node_test.py
new file mode 100644
index 000000000..f9a405744
--- /dev/null
+++ b/src/flowgraph/node_test.py
@@ -0,0 +1,102 @@
+import logging
+import unittest
+
+import networkx as nx
+import node
+from node import Graph, Node
+
+
+class NodeTest(unittest.TestCase):
+
+    def test_initialize_node(self) -> None:
+        """Test that we can instantiate a node."""
+        test = Node(
+            "syn", "nop", "syn_dir", "",
+            ["bryan-test.yml"],
+            ["syn-out.json"],
+            [],
+            []
+        )
+        # logging.info(test)
+        self.assertEqual(test.action, "syn")
+
+    def test_complex_graph(self) -> None:
+        """Creating a more complex graph."""
+        child1 = Node(
+            "par", "nop", "syn_dir", "par_dir",
+            ["syn-out.json"],
+            ["par-out.json"],
+            [],
+            []
+        )
+        root = Node(
+            "syn", "nop", "syn_dir", "",
+            ["bryan-test.yml"],
+            ["syn-out.json"],
+            [child1],
+            []
+        )
+        graph = Graph(root)
+        # logging.info(nx.nodes(graph.networkx))
+        self.assertTrue(graph.verify())
+        self.assertEqual(graph.root.children[0], child1)
+
+    def test_to_json(self) -> None:
+        """Test nodal JSON output."""
+        # logging.info(test.to_json())
+        child1 = Node(
+            "par", "nop", "syn_dir", "par_dir",
+            ["syn-out.json"],
+            ["par-out.json"],
+            [],
+            []
+        )
+        root = Node(
+            "syn", "nop", "syn_dir", "",
+            ["bryan-test.yml"],
+            ["syn-out.json"],
+            [child1],
+            []
+        )
+        graph = Graph(root)
+        graph_json = graph.to_json(indent=4)
+        # logging.info(graph_json)
+        # logging.info(node.Graph.from_json(graph_json))
+
+    def test_cycle_reduction(self) -> None:
+        """Test that cycles are reduced to an acyclic graph."""
+        v0 = Node(
+            "v0", "nop", "v0_dir", "v1_dir",
+            ["v0-out.json"],
+            ["v1-out.json"],
+            [],
+            []
+        )
+        v1 = Node(
+            "v1", "nop", "v1_dir", "v2_dir",
+            ["v1-out.json"],
+            ["v2-out.json"],
+            [],
+            []
+        )
+        v2 = Node(
+            "v2", "nop", "v2_dir", "v0_dir",
+            ["v2-out.json"],
+            ["v0-out.json"],
+            [],
+            []
+        )
+        v0.children.append(v1)
+        v1.children.append(v2)
+        v2.children.append(v0)
+        g = Graph(v0)
+        self.assertTrue(len(nx.find_cycle(g.networkx)) > 0)
+        g_acyclic = node.convert_to_acyclic(g)
+        logging.info(g_acyclic.networkx)
+        with self.assertRaises(nx.NetworkXNoCycle):
+            nx.find_cycle(g_acyclic.networkx)
+
+
+if __name__ == "__main__":
+    logging.basicConfig(level=logging.DEBUG)
+    unittest.main()

From 0f1f305637145f8345c3a9ed87a0ff5cb95da771 Mon Sep 17 00:00:00 2001
From: Bryan Ngo <bryanngo@berkeley.edu>
Date: Fri, 20 Jan 2023 11:40:05 -0800
Subject: [PATCH 02/36] add visualization test

---
 src/flowgraph/node_test.py | 68 ++++++++++++++++++++++++++++++++++----
 1 file changed, 62 insertions(+), 6 deletions(-)

diff --git a/src/flowgraph/node_test.py b/src/flowgraph/node_test.py
index f9a405744..83a831919 100644
--- a/src/flowgraph/node_test.py
+++ b/src/flowgraph/node_test.py
@@ -1,6 +1,7 @@
 import logging
 import unittest
 
+import matplotlib.pyplot as plt
 import networkx as nx
 import node
 from node import Graph, Node
@@ -67,24 +68,21 @@ def test_cycle_reduction(self) -> None:
         """Test that cycles are reduced to an acyclic graph."""
         v0 = Node(
             "v0", "nop", "v0_dir", "v1_dir",
+            ["v0-in.json"],
             ["v0-out.json"],
-            ["v1-out.json"],
             [],
-            []
         )
         v1 = Node(
             "v1", "nop", "v1_dir", "v2_dir",
+            ["v0-out.json"],
             ["v1-out.json"],
-            ["v2-out.json"],
             [],
-            []
         )
         v2 = Node(
             "v2", "nop", "v2_dir", "v0_dir",
+            ["v1-out.json"],
             ["v2-out.json"],
-            ["v0-out.json"],
             [],
-            []
         )
         v0.children.append(v1)
         v1.children.append(v2)
@@ -96,6 +94,64 @@ def test_cycle_reduction(self) -> None:
         with self.assertRaises(nx.NetworkXNoCycle):
             nx.find_cycle(g_acyclic.networkx)
 
+    def test_visualization(self) -> None:
+        """Test visualization of flowgraph."""
+        v0 = Node(
+            "syn", "nop", "syn_dir", "par_dir",
+            ["syn-in.json"],
+            ["syn-out.json"],
+            [],
+        )
+        v1 = Node(
+            "par", "nop", "par_dir", "drc_dir",
+            ["syn-out.json", "par-in.json", "drc-out.json"],
+            ["par-out.json"],
+            [],
+        )
+        v2 = Node(
+            "drc", "nop", "drc_dir", "par_dir",
+            ["par-out.json", "drc-in.json"],
+            ["drc-out.json"],
+            [],
+        )
+        v0.children.append(v1)
+        v1.children.append(v2)
+        v2.children.append(v1)
+        g = Graph(v0).networkx
+        g.add_edge(v0.pull_dir, v0.action)
+        g.add_edge(v0.action, v0.push_dir)
+        g.add_edge(v1.pull_dir, v1.action)
+        g.add_edge(v1.action, v1.push_dir)
+        g.add_edge(v2.pull_dir, v2.action)
+        g.add_edge(v2.action, v2.push_dir)
+        pos = nx.planar_layout(g)
+        blue = "#003262"
+        yellow = "#fdb515"
+        nx.draw_networkx_nodes(g, pos=pos,
+            nodelist=[v0.action, v1.action, v2.action], node_size=1500, node_color=blue, label="Action")
+        nx.draw_networkx_nodes(g, pos=pos,
+            nodelist=[
+                v0.pull_dir, v0.push_dir,
+                v1.pull_dir, v1.push_dir,
+                v2.pull_dir, v2.push_dir
+            ], node_size=1500, node_color=yellow, label="Push/Pull Directory")
+        nx.draw_networkx_labels(g, pos=pos, font_size=8, font_color="whitesmoke")
+        nx.draw_networkx_edges(g, pos=pos,
+            nodelist=[v0.action, v1.action, v2.action],
+            node_size=1500, arrowsize=15, connectionstyle="arc3, rad=0.2", edge_color=blue)
+        nx.draw_networkx_edges(g, pos=pos,
+            edgelist=[
+                (v0.pull_dir, v0.action),
+                (v0.action, v0.push_dir),
+                (v1.pull_dir, v1.action),
+                (v1.action, v1.push_dir),
+                (v2.pull_dir, v2.action),
+                (v2.action, v2.push_dir),
+            ], node_size=1500, arrowsize=15, connectionstyle="arc3, rad=0.2", edge_color=yellow)
+        plt.axis("off")
+        plt.legend(loc="upper left", markerscale=0.2)
+        plt.savefig("/home/bngo/Research/hammer/graph.png", bbox_inches="tight", dpi=200)
+
 
 if __name__ == "__main__":
     logging.basicConfig(level=logging.DEBUG)

From c513c7ed10b9214e3de53781ed5242e35c70296e Mon Sep 17 00:00:00 2001
From: Bryan Ngo <bryanngo@berkeley.edu>
Date: Fri, 20 Jan 2023 11:40:15 -0800
Subject: [PATCH 03/36] refactor

---
 src/flowgraph/node.py | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/src/flowgraph/node.py b/src/flowgraph/node.py
index a8737c6f1..0c0482479 100644
--- a/src/flowgraph/node.py
+++ b/src/flowgraph/node.py
@@ -14,6 +14,7 @@
 from dataclasses import asdict, dataclass, field
 from enum import Enum
 from typing import Optional
+import uuid
 
 import networkx as nx
 
@@ -51,14 +52,15 @@ def as_status(dct):
 class Node:
     action:            str
     tool:              str
-    push_dir:          str
     pull_dir:          str
+    push_dir:          str
     required_inputs:   list[str]
     required_outputs:  list[str]
     children:          list
     optional_inputs:   list[str] = field(default_factory=list)
     optional_outputs:  list[str] = field(default_factory=list)
-    status:            Status = Status.NOT_RUN
+    status:            Status    = Status.NOT_RUN
+    __uuid:            uuid.UUID = field(default_factory=uuid.uuid4)
 
     def __key(self) -> tuple:
         """Key value for hashing.
@@ -124,7 +126,7 @@ def to_networkx(self) -> nx.DiGraph:
             v = q.get()
             if v not in explored:
                 explored.append(v)
-                edge_list[v] = tuple(c for c in v.children)
+                edge_list[v.action] = tuple(c.action for c in v.children)
                 for c in v.children:
                     q.put(c)
         return nx.DiGraph(edge_list)
@@ -185,3 +187,6 @@ def convert_to_acyclic(g: Graph) -> Graph:
         start.children[start.children.index(end)] = end_copy
         print(start.children[start.children.index(end_copy)].children)
     return Graph(g_copy.root)
+
+# TODO: refresh graph
+# TODO: unique id for nodes

From 5030e1b8a5bc69b099617b38d7badd42061a8d5f Mon Sep 17 00:00:00 2001
From: Bryan Ngo <bryanngo@berkeley.edu>
Date: Fri, 27 Jan 2023 02:10:12 -0800
Subject: [PATCH 04/36] pre-branch

---
 src/flowgraph/node.py      | 24 ++++++++++++++++--------
 src/flowgraph/node_test.py |  9 +++------
 2 files changed, 19 insertions(+), 14 deletions(-)

diff --git a/src/flowgraph/node.py b/src/flowgraph/node.py
index 0c0482479..e10c4ebee 100644
--- a/src/flowgraph/node.py
+++ b/src/flowgraph/node.py
@@ -57,10 +57,10 @@ class Node:
     required_inputs:   list[str]
     required_outputs:  list[str]
     children:          list
-    optional_inputs:   list[str] = field(default_factory=list)
-    optional_outputs:  list[str] = field(default_factory=list)
     status:            Status    = Status.NOT_RUN
     __uuid:            uuid.UUID = field(default_factory=uuid.uuid4)
+    optional_inputs:   list[str] = field(default_factory=list)
+    optional_outputs:  list[str] = field(default_factory=list)
 
     def __key(self) -> tuple:
         """Key value for hashing.
@@ -126,7 +126,8 @@ def to_networkx(self) -> nx.DiGraph:
             v = q.get()
             if v not in explored:
                 explored.append(v)
-                edge_list[v.action] = tuple(c.action for c in v.children)
+                # edge_list[v.action] = tuple(c.action for c in v.children)
+                edge_list[v] = tuple(c for c in v.children)
                 for c in v.children:
                     q.put(c)
         return nx.DiGraph(edge_list)
@@ -179,14 +180,21 @@ def convert_to_acyclic(g: Graph) -> Graph:
         Graph: Graph with cloned nodes.
     """
     g_copy = deepcopy(g)
-    cycles = nx.simple_cycles(g_copy.networkx)
+    cycles = sorted(nx.simple_cycles(g_copy.networkx))
     for cycle in cycles:
         start, end = cycle[0], cycle[1]
-        end_copy = deepcopy(end)
-        end_copy.children = []
-        start.children[start.children.index(end)] = end_copy
-        print(start.children[start.children.index(end_copy)].children)
+        end_copy = Node(
+            end.action,
+            end.tool,
+            end.pull_dir, end.push_dir,
+            end.required_inputs, end.required_outputs,
+            end.status,
+            end.optional_inputs, end.optional_outputs
+        )
+        end.children = []
     return Graph(g_copy.root)
 
+# TODO: networkx backend
+# TODO: use run_main_args_parsed
 # TODO: refresh graph
 # TODO: unique id for nodes
diff --git a/src/flowgraph/node_test.py b/src/flowgraph/node_test.py
index 83a831919..40bb34ca9 100644
--- a/src/flowgraph/node_test.py
+++ b/src/flowgraph/node_test.py
@@ -16,7 +16,6 @@ def test_initialize_node(self) -> None:
             ["bryan-test.yml"],
             ["syn-out.json"],
             [],
-            []
         )
         # logging.info(test)
         self.assertEqual(test.action, "syn")
@@ -28,14 +27,12 @@ def test_complex_graph(self) -> None:
             ["syn-out.json"],
             ["par-out.json"],
             [],
-            []
         )
         root = Node(
             "syn", "nop", "syn_dir", "",
             ["bryan-test.yml"],
             ["syn-out.json"],
             [child1],
-            []
         )
         graph = Graph(root)
         # logging.info(nx.nodes(graph.networkx))
@@ -50,14 +47,12 @@ def test_to_json(self) -> None:
             ["syn-out.json"],
             ["par-out.json"],
             [],
-            []
         )
         root = Node(
             "syn", "nop", "syn_dir", "",
             ["bryan-test.yml"],
             ["syn-out.json"],
             [child1],
-            []
         )
         graph = Graph(root)
         graph_json = graph.to_json(indent=4)
@@ -87,10 +82,12 @@ def test_cycle_reduction(self) -> None:
         v0.children.append(v1)
         v1.children.append(v2)
         v2.children.append(v0)
+
         g = Graph(v0)
         self.assertTrue(len(nx.find_cycle(g.networkx)) > 0)
+
         g_acyclic = node.convert_to_acyclic(g)
-        logging.info(g_acyclic.networkx)
+        print(g_acyclic)
         with self.assertRaises(nx.NetworkXNoCycle):
             nx.find_cycle(g_acyclic.networkx)
 

From 93eeac3740db958b690f0aa094dadbd7386d09b8 Mon Sep 17 00:00:00 2001
From: Bryan Ngo <bryanngo@berkeley.edu>
Date: Fri, 27 Jan 2023 02:53:52 -0800
Subject: [PATCH 05/36] new backend

---
 src/flowgraph/node.py      | 82 ++++++++------------------------------
 src/flowgraph/node_test.py | 58 ++++++---------------------
 2 files changed, 30 insertions(+), 110 deletions(-)

diff --git a/src/flowgraph/node.py b/src/flowgraph/node.py
index e10c4ebee..396f5b4fa 100644
--- a/src/flowgraph/node.py
+++ b/src/flowgraph/node.py
@@ -9,11 +9,8 @@
 # pylint: disable=invalid-name
 
 import json
-import queue
-from copy import deepcopy
 from dataclasses import asdict, dataclass, field
 from enum import Enum
-from typing import Optional
 import uuid
 
 import networkx as nx
@@ -56,7 +53,6 @@ class Node:
     push_dir:          str
     required_inputs:   list[str]
     required_outputs:  list[str]
-    children:          list
     status:            Status    = Status.NOT_RUN
     __uuid:            uuid.UUID = field(default_factory=uuid.uuid4)
     optional_inputs:   list[str] = field(default_factory=list)
@@ -75,7 +71,6 @@ def __key(self) -> tuple:
             self.pull_dir,
             tuple(self.required_inputs),
             tuple(self.required_outputs),
-            tuple(self.children),
             tuple(self.optional_inputs),
             tuple(self.optional_outputs),
             self.status
@@ -98,51 +93,10 @@ def to_json(self) -> dict:
 
 @dataclass
 class Graph:
-    root: Node
+    edge_list: dict[Node, list[Node]]
 
     def __post_init__(self) -> None:
-        self.networkx = self.to_networkx()
-
-    def to_json(self, indent: Optional[int] = None) -> str:
-        """Writes the graph as a JSON string and saves it to a file.
-
-        Returns:
-            dict: Entire flowgraph as a JSON.
-        """
-        out_dict = asdict(self.root)
-        return json.dumps(out_dict, indent=indent, cls=StatusEncoder)
-
-    def to_networkx(self) -> nx.DiGraph:
-        """Turns our graph into an NetworkX directed graph.
-
-        Returns:
-            nx.DiGraph: NetworkX directed graph.
-        """
-        q = queue.LifoQueue()
-        explored = []
-        q.put(self.root)
-        edge_list = {}
-        while not q.empty():
-            v = q.get()
-            if v not in explored:
-                explored.append(v)
-                # edge_list[v.action] = tuple(c.action for c in v.children)
-                edge_list[v] = tuple(c for c in v.children)
-                for c in v.children:
-                    q.put(c)
-        return nx.DiGraph(edge_list)
-
-    @staticmethod
-    def from_json(dump: str) -> dict:
-        """Converts a JSON into an instance of Graph.
-
-        Args:
-            dump (str): JSON with the correct schema for a Graph.
-
-        Returns:
-            dict: Dictionary containing graph information.
-        """
-        return json.loads(dump, object_hook=as_status)
+        self.networkx = nx.DiGraph(self.edge_list)
 
     def verify(self) -> bool:
         """Checks if a graph is valid via its inputs and outputs.
@@ -161,13 +115,11 @@ def __process(self, v: Node) -> bool:
         Returns:
             bool: If the particular node is valid.
         """
-        if v == self.root:
-            return True
         parent_outs = \
             set().union(*(set(p.required_outputs) for p in self.networkx.predecessors(v))) \
             | set().union(*(set(p.optional_outputs) for p in self.networkx.predecessors(v)))
         inputs = set(v.required_inputs) | set(v.optional_inputs)
-        return parent_outs >= inputs
+        return self.networkx.in_degree(v) == 0 or parent_outs >= inputs
 
 
 def convert_to_acyclic(g: Graph) -> Graph:
@@ -179,22 +131,22 @@ def convert_to_acyclic(g: Graph) -> Graph:
     Returns:
         Graph: Graph with cloned nodes.
     """
-    g_copy = deepcopy(g)
-    cycles = sorted(nx.simple_cycles(g_copy.networkx))
+    cycles = sorted(nx.simple_cycles(g.networkx))
+    new_edge_list = g.edge_list.copy()
     for cycle in cycles:
-        start, end = cycle[0], cycle[1]
-        end_copy = Node(
-            end.action,
-            end.tool,
-            end.pull_dir, end.push_dir,
-            end.required_inputs, end.required_outputs,
-            end.status,
-            end.optional_inputs, end.optional_outputs
+        cut_start, cut_end = cycle[0], cycle[1]
+        cut_end_copy = Node(
+            cut_end.action,
+            cut_end.tool,
+            cut_end.pull_dir, cut_end.push_dir,
+            cut_end.required_inputs, cut_end.required_outputs,
+            cut_end.status,
+            cut_end.optional_inputs, cut_end.optional_outputs
         )
-        end.children = []
-    return Graph(g_copy.root)
+        cut_start_children = new_edge_list[cut_start]
+        new_edge_list[cut_start] = []
+        new_edge_list[cut_end_copy] = cut_start_children
+    return Graph(new_edge_list)
 
-# TODO: networkx backend
 # TODO: use run_main_args_parsed
 # TODO: refresh graph
-# TODO: unique id for nodes
diff --git a/src/flowgraph/node_test.py b/src/flowgraph/node_test.py
index 40bb34ca9..7cb26ad62 100644
--- a/src/flowgraph/node_test.py
+++ b/src/flowgraph/node_test.py
@@ -1,7 +1,6 @@
 import logging
 import unittest
 
-import matplotlib.pyplot as plt
 import networkx as nx
 import node
 from node import Graph, Node
@@ -15,49 +14,24 @@ def test_initialize_node(self) -> None:
             "syn", "nop", "syn_dir", "",
             ["bryan-test.yml"],
             ["syn-out.json"],
-            [],
         )
         # logging.info(test)
         self.assertEqual(test.action, "syn")
 
     def test_complex_graph(self) -> None:
         """Creating a more complex graph."""
-        child1 = Node(
-            "par", "nop", "syn_dir", "par_dir",
-            ["syn-out.json"],
-            ["par-out.json"],
-            [],
-        )
         root = Node(
             "syn", "nop", "syn_dir", "",
             ["bryan-test.yml"],
             ["syn-out.json"],
-            [child1],
         )
-        graph = Graph(root)
-        # logging.info(nx.nodes(graph.networkx))
-        self.assertTrue(graph.verify())
-        self.assertEqual(graph.root.children[0], child1)
-
-    def test_to_json(self) -> None:
-        """Test nodal JSON output."""
-        # logging.info(test.to_json())
         child1 = Node(
             "par", "nop", "syn_dir", "par_dir",
             ["syn-out.json"],
             ["par-out.json"],
-            [],
         )
-        root = Node(
-            "syn", "nop", "syn_dir", "",
-            ["bryan-test.yml"],
-            ["syn-out.json"],
-            [child1],
-        )
-        graph = Graph(root)
-        graph_json = graph.to_json(indent=4)
-        # logging.info(graph_json)
-        # logging.info(node.Graph.from_json(graph_json))
+        graph = Graph({root: [child1]})
+        self.assertTrue(graph.verify())
 
     def test_cycle_reduction(self) -> None:
         """Test that cycles are reduced to an acyclic graph."""
@@ -65,56 +39,50 @@ def test_cycle_reduction(self) -> None:
             "v0", "nop", "v0_dir", "v1_dir",
             ["v0-in.json"],
             ["v0-out.json"],
-            [],
         )
         v1 = Node(
             "v1", "nop", "v1_dir", "v2_dir",
             ["v0-out.json"],
             ["v1-out.json"],
-            [],
         )
         v2 = Node(
             "v2", "nop", "v2_dir", "v0_dir",
             ["v1-out.json"],
             ["v2-out.json"],
-            [],
         )
-        v0.children.append(v1)
-        v1.children.append(v2)
-        v2.children.append(v0)
-
-        g = Graph(v0)
+        g = Graph({
+            v0: [v1],
+            v1: [v2],
+            v2: [v0],
+        })
         self.assertTrue(len(nx.find_cycle(g.networkx)) > 0)
-
         g_acyclic = node.convert_to_acyclic(g)
-        print(g_acyclic)
         with self.assertRaises(nx.NetworkXNoCycle):
             nx.find_cycle(g_acyclic.networkx)
 
     def test_visualization(self) -> None:
         """Test visualization of flowgraph."""
+        import matplotlib.pyplot as plt
         v0 = Node(
             "syn", "nop", "syn_dir", "par_dir",
             ["syn-in.json"],
             ["syn-out.json"],
-            [],
         )
         v1 = Node(
             "par", "nop", "par_dir", "drc_dir",
             ["syn-out.json", "par-in.json", "drc-out.json"],
             ["par-out.json"],
-            [],
         )
         v2 = Node(
             "drc", "nop", "drc_dir", "par_dir",
             ["par-out.json", "drc-in.json"],
             ["drc-out.json"],
-            [],
         )
-        v0.children.append(v1)
-        v1.children.append(v2)
-        v2.children.append(v1)
-        g = Graph(v0).networkx
+        g = Graph({
+            v0.action: [v1.action],
+            v1.action: [v2.action],
+            v2.action: []
+        }).networkx
         g.add_edge(v0.pull_dir, v0.action)
         g.add_edge(v0.action, v0.push_dir)
         g.add_edge(v1.pull_dir, v1.action)

From b49bf0bea6cb3e63d62f4878495ffaf5bab18ae3 Mon Sep 17 00:00:00 2001
From: Bryan Ngo <bryanngo@berkeley.edu>
Date: Fri, 27 Jan 2023 03:10:07 -0800
Subject: [PATCH 06/36] rebase master with pypi packaging

---
 {src => hammer}/flowgraph/node.py                | 0
 src/flowgraph/node_test.py => tests/test_node.py | 0
 2 files changed, 0 insertions(+), 0 deletions(-)
 rename {src => hammer}/flowgraph/node.py (100%)
 rename src/flowgraph/node_test.py => tests/test_node.py (100%)

diff --git a/src/flowgraph/node.py b/hammer/flowgraph/node.py
similarity index 100%
rename from src/flowgraph/node.py
rename to hammer/flowgraph/node.py
diff --git a/src/flowgraph/node_test.py b/tests/test_node.py
similarity index 100%
rename from src/flowgraph/node_test.py
rename to tests/test_node.py

From f8fc5c59d3c0078db7e74d33cdbfd6ff34331f6a Mon Sep 17 00:00:00 2001
From: Bryan Ngo <bryanngo@berkeley.edu>
Date: Mon, 30 Jan 2023 10:49:39 -0800
Subject: [PATCH 07/36] preliminary run graph algo

---
 hammer/flowgraph/node.py | 52 +++++++++++++++++++++++++++++++++++++---
 poetry.lock              | 21 +++++++++++++++-
 pyproject.toml           |  1 +
 tests/test_node.py       |  4 ++--
 4 files changed, 72 insertions(+), 6 deletions(-)

diff --git a/hammer/flowgraph/node.py b/hammer/flowgraph/node.py
index 396f5b4fa..bb19a6eaf 100644
--- a/hammer/flowgraph/node.py
+++ b/hammer/flowgraph/node.py
@@ -9,12 +9,15 @@
 # pylint: disable=invalid-name
 
 import json
+import os
+import uuid
 from dataclasses import asdict, dataclass, field
 from enum import Enum
-import uuid
 
 import networkx as nx
 
+from hammer.vlsi import cli_driver
+
 
 class Status(Enum):
     """Represents the status of a node in the flowgraph.
@@ -104,7 +107,7 @@ def verify(self) -> bool:
         Returns:
             bool: If graph is valid.
         """
-        return all(self.__process(v) for v in nx.nodes(self.networkx))
+        return all(self.__process(v) for v in convert_to_acyclic(self).networkx)
 
     def __process(self, v: Node) -> bool:
         """Process a specific vertex of a graph.
@@ -121,6 +124,50 @@ def __process(self, v: Node) -> bool:
         inputs = set(v.required_inputs) | set(v.optional_inputs)
         return self.networkx.in_degree(v) == 0 or parent_outs >= inputs
 
+    def run(self, start: Node) -> None:
+        """Run a HAMMER flowgraph."""
+        if not self.verify():
+            raise RuntimeError("Flowgraph is invalid")
+        if start not in self.networkx:
+            raise RuntimeError("Node not in flowgraph")
+
+        start.status = Status.RUNNING
+        arg_list = {
+            "action": start.action,
+            'environment_config': None,
+            'configs': [os.path.join(start.pull_dir, i) for i in start.required_inputs],
+            'log': None,
+            'obj_dir': start.push_dir,
+            'syn_rundir': '',
+            'par_rundir': '',
+            'drc_rundir': '',
+            'lvs_rundir': '',
+            'sim_rundir': '',
+            'power_rundir': '',
+            'formal_rundir': '',
+            'timing_rundir': '',
+            # TODO: sub-step determinations
+            'from_step': None,
+            'after_step': None,
+            'to_step': None,
+            'until_step': None,
+            'only_step': None,
+            'output': 'output.json',
+            'verilog': None,
+            'firrtl': None,
+            'top': None,
+            'cad_files': None
+        }
+
+        driver = cli_driver.CLIDriver()
+        try:
+            driver.run_main_parsed(arg_list)
+            start.status = Status.COMPLETE
+            for c in nx.neighbors(self.networkx, start):
+                self.run(c)
+        except Exception as e:
+            start.status = Status.INCOMPLETE
+            raise e
 
 def convert_to_acyclic(g: Graph) -> Graph:
     """Eliminates cycles in a flowgraph for analysis.
@@ -148,5 +195,4 @@ def convert_to_acyclic(g: Graph) -> Graph:
         new_edge_list[cut_end_copy] = cut_start_children
     return Graph(new_edge_list)
 
-# TODO: use run_main_args_parsed
 # TODO: refresh graph
diff --git a/poetry.lock b/poetry.lock
index 7ca376e95..9ebff9f13 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -666,6 +666,25 @@ linkify = ["linkify-it-py (>=1.0,<2.0)"]
 rtd = ["ipython", "sphinx-book-theme", "sphinx-design", "sphinxcontrib.mermaid (>=0.7.1,<0.8.0)", "sphinxext-opengraph (>=0.6.3,<0.7.0)", "sphinxext-rediraffe (>=0.2.7,<0.3.0)"]
 testing = ["beautifulsoup4", "coverage[toml]", "pytest (>=6,<7)", "pytest-cov", "pytest-param-files (>=0.3.4,<0.4.0)", "pytest-regressions", "sphinx (<5.2)", "sphinx-pytest"]
 
+[[package]]
+name = "networkx"
+version = "3.0"
+description = "Python package for creating and manipulating graphs and networks"
+category = "main"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "networkx-3.0-py3-none-any.whl", hash = "sha256:58058d66b1818043527244fab9d41a51fcd7dcc271748015f3c181b8a90c8e2e"},
+    {file = "networkx-3.0.tar.gz", hash = "sha256:9a9992345353618ae98339c2b63d8201c381c2944f38a2ab49cb45a4c667e412"},
+]
+
+[package.extras]
+default = ["matplotlib (>=3.4)", "numpy (>=1.20)", "pandas (>=1.3)", "scipy (>=1.8)"]
+developer = ["mypy (>=0.991)", "pre-commit (>=2.20)"]
+doc = ["nb2plots (>=0.6)", "numpydoc (>=1.5)", "pillow (>=9.2)", "pydata-sphinx-theme (>=0.11)", "sphinx (==5.2.3)", "sphinx-gallery (>=0.11)", "texext (>=0.6.7)"]
+extra = ["lxml (>=4.6)", "pydot (>=1.4.2)", "pygraphviz (>=1.10)", "sympy (>=1.10)"]
+test = ["codecov (>=2.1)", "pytest (>=7.2)", "pytest-cov (>=4.0)"]
+
 [[package]]
 name = "numpy"
 version = "1.24.1"
@@ -1412,4 +1431,4 @@ asap7-gdstk = ["gdstk"]
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.9"
-content-hash = "010b3a88ee8645e703e98c359f877f1b24bb2accc6082e9ade79bcc57a808056"
+content-hash = "67c4116b3ad38c850c787570708e14362df542402503fa53b6414f7aaa598644"
diff --git a/pyproject.toml b/pyproject.toml
index df9aac953..b630cebed 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -24,6 +24,7 @@ python = "^3.9"
 pydantic = "^1.9.2"
 PyYAML = "^6.0"
 "ruamel.yaml" = "^0.17.21"
+networkx = "^3.0"
 numpy = "^1.23.0"
 
 gdstk = { version = "^0.9.0", optional = true }
diff --git a/tests/test_node.py b/tests/test_node.py
index 7cb26ad62..5fd463eac 100644
--- a/tests/test_node.py
+++ b/tests/test_node.py
@@ -2,8 +2,8 @@
 import unittest
 
 import networkx as nx
-import node
-from node import Graph, Node
+from hammer.flowgraph import node
+from hammer.flowgraph.node import Graph, Node
 
 
 class NodeTest(unittest.TestCase):

From 05a4043614078fdc2cf1d1ff3ee09a92f4ffa2a0 Mon Sep 17 00:00:00 2001
From: Bryan Ngo <bryanngo@berkeley.edu>
Date: Tue, 31 Jan 2023 18:19:57 -0800
Subject: [PATCH 08/36] implementing graph running

---
 hammer/flowgraph/node.py | 33 +++-------------
 tests/test_node.py       | 84 +++++++++++++++++++++++++++++++++++++++-
 2 files changed, 88 insertions(+), 29 deletions(-)

diff --git a/hammer/flowgraph/node.py b/hammer/flowgraph/node.py
index bb19a6eaf..9b7299b90 100644
--- a/hammer/flowgraph/node.py
+++ b/hammer/flowgraph/node.py
@@ -8,14 +8,14 @@
 
 # pylint: disable=invalid-name
 
-import json
 import os
 import uuid
-from dataclasses import asdict, dataclass, field
+from dataclasses import dataclass, field
 from enum import Enum
 
 import networkx as nx
 
+from hammer.logging import HammerVLSILogging
 from hammer.vlsi import cli_driver
 
 
@@ -30,19 +30,6 @@ class Status(Enum):
     COMPLETE   = "COMPLETE"
 
 
-class StatusEncoder(json.JSONEncoder):
-    def default(self, o: Status) -> str:
-        if isinstance(o, Status):
-            return o.name
-        return super().default(o)
-
-
-def as_status(dct):
-    if "status" in dct:
-        dct["status"] = Status[dct["status"]]
-    return dct
-
-
 # make sure union of required/optional outs is superset of children required/optional inputs
 # separate required validity checking and optional validity checking
 # meta dict for tech compatibilty
@@ -82,18 +69,6 @@ def __key(self) -> tuple:
     def __hash__(self) -> int:
         return hash(self.__key)
 
-    def to_json(self) -> dict:
-        """Writes the node to a JSON string.
-
-        Args:
-            fname (str): File name to write to.
-
-        Returns:
-            str: Node represented as a JSON.
-        """
-        return asdict(self)
-
-
 @dataclass
 class Graph:
     edge_list: dict[Node, list[Node]]
@@ -132,6 +107,8 @@ def run(self, start: Node) -> None:
             raise RuntimeError("Node not in flowgraph")
 
         start.status = Status.RUNNING
+        ctxt = HammerVLSILogging.context()
+        ctxt.info(f"Running graph step {start.action}")
         arg_list = {
             "action": start.action,
             'environment_config': None,
@@ -152,7 +129,7 @@ def run(self, start: Node) -> None:
             'to_step': None,
             'until_step': None,
             'only_step': None,
-            'output': 'output.json',
+            'output': os.path.join(start.push_dir, start.required_outputs[0]),
             'verilog': None,
             'firrtl': None,
             'top': None,
diff --git a/tests/test_node.py b/tests/test_node.py
index 5fd463eac..8acb3f98a 100644
--- a/tests/test_node.py
+++ b/tests/test_node.py
@@ -1,7 +1,12 @@
 import logging
+import os
+import tempfile
 import unittest
 
 import networkx as nx
+import pytest
+from networkx.readwrite import json_graph
+
 from hammer.flowgraph import node
 from hammer.flowgraph.node import Graph, Node
 
@@ -15,7 +20,6 @@ def test_initialize_node(self) -> None:
             ["bryan-test.yml"],
             ["syn-out.json"],
         )
-        # logging.info(test)
         self.assertEqual(test.action, "syn")
 
     def test_complex_graph(self) -> None:
@@ -32,6 +36,8 @@ def test_complex_graph(self) -> None:
         )
         graph = Graph({root: [child1]})
         self.assertTrue(graph.verify())
+        self.assertEqual(len(graph.networkx), 2)
+        self.assertEqual(graph.networkx.number_of_edges(), 1)
 
     def test_cycle_reduction(self) -> None:
         """Test that cycles are reduced to an acyclic graph."""
@@ -59,7 +65,10 @@ def test_cycle_reduction(self) -> None:
         g_acyclic = node.convert_to_acyclic(g)
         with self.assertRaises(nx.NetworkXNoCycle):
             nx.find_cycle(g_acyclic.networkx)
+        self.assertEqual(len(g_acyclic.networkx), 4)
+        self.assertEqual(g.networkx.number_of_edges(), 3)
 
+    @pytest.mark.xfail(raises=ImportError, reason="Matplotlib currently not imported")
     def test_visualization(self) -> None:
         """Test visualization of flowgraph."""
         import matplotlib.pyplot as plt
@@ -117,6 +126,79 @@ def test_visualization(self) -> None:
         plt.legend(loc="upper left", markerscale=0.2)
         plt.savefig("/home/bngo/Research/hammer/graph.png", bbox_inches="tight", dpi=200)
 
+    def test_run_basic(self) -> None:
+        """Test a basic syn -> par -> drc flow, all with nop tools."""
+        with tempfile.TemporaryDirectory() as td:
+            os.mkdir(os.path.join(td, "syn_dir"))
+            os.mkdir(os.path.join(td, "par_dir"))
+            os.mkdir(os.path.join(td, "drc_dir"))
+
+            with open(os.path.join(td, "syn_dir", "syn-in.yml"), 'w', encoding="utf-8") as tf1:
+                tf1.write("""
+synthesis.inputs:
+    input_files: ["LICENSE", "README.md"]
+    top_module: "z1top.xdc"
+
+par.inputs:
+    input_files: ["LICENSE", "README.md"]
+    top_module: "z1top.xdc"
+
+drc.inputs:
+    input_files: ["LICENSE", "README.md"]
+    top_module: "z1top.xdc"
+
+lvs.inputs:
+    input_files: ["LICENSE", "README.md"]
+    schematic_files: ["LICENSE", "README.md"]
+    top_module: "z1top.xdc"
+    hcells_list: []
+
+pcb.inputs:
+    top_module: "z1top.xdc"
+
+formal.inputs:
+    input_files: ["LICENSE", "README.md"]
+    top_module: "z1top.xdc"
+
+sim.inputs:
+    input_files: ["LICENSE", "README.md"]
+    top_module: "z1top.xdc"
+
+vlsi:
+    core:
+        technology: "hammer.technology.nop"
+
+        synthesis_tool: "hammer.synthesis.nop"
+        par_tool: "hammer.par.nop"
+        drc_tool: "hammer.drc.nop"
+        lvs_tool: "hammer.lvs.nop"
+        power_tool: "hammer.power.nop"
+        sim_tool: "mocksim"
+""")
+
+            v0 = Node(
+                "syn-to-par", "nop", os.path.join(td, "syn_dir"), os.path.join(td, "par_dir"),
+                ["syn-in.yml"],
+                ["syn-out.json"],
+            )
+            v1 = Node(
+                "par-to-drc", "nop", os.path.join(td, "par_dir"), os.path.join(td, "drc_dir"),
+                ["syn-out.json"],
+                ["par-out.json"],
+            )
+            v2 = Node(
+                "drc", "nop", os.path.join(td, "drc_dir"), os.path.join(td, "out_dir"),
+                ["par-out.json"],
+                ["drc-out.json"],
+            )
+            g = Graph({
+                v0: [v1],
+                v1: [v2],
+                v2: []
+            })
+            g.run(v0)
+
+
 
 if __name__ == "__main__":
     logging.basicConfig(level=logging.DEBUG)

From e51170e64fd89d8caf688270bda901d8677955ed Mon Sep 17 00:00:00 2001
From: Bryan Ngo <bryanngo@berkeley.edu>
Date: Thu, 2 Feb 2023 18:02:15 -0800
Subject: [PATCH 09/36] passing basic run test

---
 hammer/flowgraph/node.py |  6 +++---
 tests/test_node.py       | 40 +++++++++++++++++++++++-----------------
 2 files changed, 26 insertions(+), 20 deletions(-)

diff --git a/hammer/flowgraph/node.py b/hammer/flowgraph/node.py
index 9b7299b90..c2ddb1bfe 100644
--- a/hammer/flowgraph/node.py
+++ b/hammer/flowgraph/node.py
@@ -107,8 +107,6 @@ def run(self, start: Node) -> None:
             raise RuntimeError("Node not in flowgraph")
 
         start.status = Status.RUNNING
-        ctxt = HammerVLSILogging.context()
-        ctxt.info(f"Running graph step {start.action}")
         arg_list = {
             "action": start.action,
             'environment_config': None,
@@ -129,7 +127,7 @@ def run(self, start: Node) -> None:
             'to_step': None,
             'until_step': None,
             'only_step': None,
-            'output': os.path.join(start.push_dir, start.required_outputs[0]),
+            'output': os.path.join(start.push_dir, start.required_outputs[0]),  # TODO: fix this
             'verilog': None,
             'firrtl': None,
             'top': None,
@@ -138,6 +136,8 @@ def run(self, start: Node) -> None:
 
         driver = cli_driver.CLIDriver()
         try:
+            ctxt = HammerVLSILogging.context(start.action)
+            # ctxt.info(f"Running graph step {start.action}")
             driver.run_main_parsed(arg_list)
             start.status = Status.COMPLETE
             for c in nx.neighbors(self.networkx, start):
diff --git a/tests/test_node.py b/tests/test_node.py
index 8acb3f98a..9e603e2c5 100644
--- a/tests/test_node.py
+++ b/tests/test_node.py
@@ -1,14 +1,13 @@
-import logging
 import os
 import tempfile
 import unittest
 
 import networkx as nx
 import pytest
-from networkx.readwrite import json_graph
 
 from hammer.flowgraph import node
-from hammer.flowgraph.node import Graph, Node
+from hammer.flowgraph.node import Graph, Node, Status
+from hammer.logging import HammerVLSILogging
 
 
 class NodeTest(unittest.TestCase):
@@ -127,7 +126,10 @@ def test_visualization(self) -> None:
         plt.savefig("/home/bngo/Research/hammer/graph.png", bbox_inches="tight", dpi=200)
 
     def test_run_basic(self) -> None:
-        """Test a basic syn -> par -> drc flow, all with nop tools."""
+        """Test a basic syn -> par flow, all with nop tools."""
+        HammerVLSILogging.clear_callbacks()
+        HammerVLSILogging.add_callback(HammerVLSILogging.callback_buffering)
+
         with tempfile.TemporaryDirectory() as td:
             os.mkdir(os.path.join(td, "syn_dir"))
             os.mkdir(os.path.join(td, "par_dir"))
@@ -176,30 +178,34 @@ def test_run_basic(self) -> None:
         sim_tool: "mocksim"
 """)
 
-            v0 = Node(
-                "syn-to-par", "nop", os.path.join(td, "syn_dir"), os.path.join(td, "par_dir"),
+            syn = Node(
+                "syn", "nop",
+                os.path.join(td, "syn_dir"), os.path.join(td, "s2p_dir"),
                 ["syn-in.yml"],
                 ["syn-out.json"],
             )
-            v1 = Node(
-                "par-to-drc", "nop", os.path.join(td, "par_dir"), os.path.join(td, "drc_dir"),
+            s2p = Node(
+                "syn-to-par", "nop",
+                os.path.join(td, "s2p_dir"), os.path.join(td, "par_dir"),
                 ["syn-out.json"],
-                ["par-out.json"],
+                ["s2p-out.json"],
             )
-            v2 = Node(
-                "drc", "nop", os.path.join(td, "drc_dir"), os.path.join(td, "out_dir"),
+            par = Node(
+                "par", "nop",
+                os.path.join(td, "par_dir"), os.path.join(td, "out_dir"),
+                ["s2p-out.json"],
                 ["par-out.json"],
-                ["drc-out.json"],
             )
             g = Graph({
-                v0: [v1],
-                v1: [v2],
-                v2: []
+                syn: [s2p],
+                s2p: [par],
+                par: []
             })
-            g.run(v0)
+            g.run(syn)
 
+        for n in g.networkx:
+            self.assertEqual(n.status, Status.COMPLETE)
 
 
 if __name__ == "__main__":
-    logging.basicConfig(level=logging.DEBUG)
     unittest.main()

From 4a41864f741c59839b0a35cc1ca948c19142c5df Mon Sep 17 00:00:00 2001
From: Bryan Ngo <bryanngo@berkeley.edu>
Date: Fri, 3 Feb 2023 11:50:20 -0800
Subject: [PATCH 10/36] more cycle reduction tests

---
 tests/test_node.py | 277 +++++++++++++++++++++++++++++++++++++--------
 1 file changed, 232 insertions(+), 45 deletions(-)

diff --git a/tests/test_node.py b/tests/test_node.py
index 9e603e2c5..3be15a9d9 100644
--- a/tests/test_node.py
+++ b/tests/test_node.py
@@ -1,6 +1,7 @@
 import os
 import tempfile
 import unittest
+from textwrap import dedent
 
 import networkx as nx
 import pytest
@@ -16,7 +17,7 @@ def test_initialize_node(self) -> None:
         """Test that we can instantiate a node."""
         test = Node(
             "syn", "nop", "syn_dir", "",
-            ["bryan-test.yml"],
+            ["foo.yml"],
             ["syn-out.json"],
         )
         self.assertEqual(test.action, "syn")
@@ -25,7 +26,7 @@ def test_complex_graph(self) -> None:
         """Creating a more complex graph."""
         root = Node(
             "syn", "nop", "syn_dir", "",
-            ["bryan-test.yml"],
+            ["foo.yml"],
             ["syn-out.json"],
         )
         child1 = Node(
@@ -34,9 +35,24 @@ def test_complex_graph(self) -> None:
             ["par-out.json"],
         )
         graph = Graph({root: [child1]})
-        self.assertTrue(graph.verify())
         self.assertEqual(len(graph.networkx), 2)
         self.assertEqual(graph.networkx.number_of_edges(), 1)
+        self.assertTrue(graph.verify())
+
+    def test_invalid_graph(self) -> None:
+        """Test that invalid flowgraphs are detected."""
+        root = Node(
+            "syn", "nop", "syn_dir", "",
+            ["foo.yml"],
+            ["syn-out.json"],
+        )
+        child1 = Node(
+            "par", "nop", "syn_dir", "par_dir",
+            ["syn-in.json"],
+            ["par-out.json"],
+        )
+        graph = Graph({root: [child1]})
+        self.assertFalse(graph.verify())
 
     def test_cycle_reduction(self) -> None:
         """Test that cycles are reduced to an acyclic graph."""
@@ -67,6 +83,86 @@ def test_cycle_reduction(self) -> None:
         self.assertEqual(len(g_acyclic.networkx), 4)
         self.assertEqual(g.networkx.number_of_edges(), 3)
 
+    def test_big_cycle_reduction(self) -> None:
+        """Test that larger cycles are reduced to an acyclic graph."""
+        v0 = Node(
+            "v0", "nop", "v0_dir", "v1_dir",
+            ["v0-in.json"],
+            ["v0-out.json"],
+        )
+        v1 = Node(
+            "v1", "nop", "v1_dir", "v2_dir",
+            ["v0-out.json"],
+            ["v1-out.json"],
+        )
+        v2 = Node(
+            "v2", "nop", "v2_dir", "v3_dir",
+            ["v1-out.json"],
+            ["v2-out.json"],
+        )
+        v3 = Node(
+            "v3", "nop", "v3_dir", "v0_dir",
+            ["v2-out.json"],
+            ["v3-out.json"],
+        )
+        g = Graph({
+            v0: [v1],
+            v1: [v2],
+            v2: [v3],
+            v3: [v0]
+        })
+        self.assertTrue(len(nx.find_cycle(g.networkx)) > 0)
+        g_acyclic = node.convert_to_acyclic(g)
+        with self.assertRaises(nx.NetworkXNoCycle):
+            nx.find_cycle(g_acyclic.networkx)
+        self.assertEqual(len(g_acyclic.networkx), 5)
+        self.assertEqual(g.networkx.number_of_edges(), 4)
+
+    def test_multi_cycle_reduction(self) -> None:
+        """Test that multiple cycles are reduced to an acyclic graph."""
+        v0 = Node(
+            "v0", "nop", "v0_dir", "v1_dir",
+            ["v0-in.json"],
+            ["v0-out.json"],
+        )
+        v1 = Node(
+            "v1", "nop", "v1_dir", "v2_dir",
+            ["v0-out.json"],
+            ["v1-out.json"],
+        )
+        v2 = Node(
+            "v2", "nop", "v2_dir", "v0_dir",
+            ["v1-out.json"],
+            ["v2-out.json"],
+        )
+        v3 = Node(
+            "v3", "nop", "v3_dir", "v4_dir",
+            ["v2-out.json"],
+            ["v3-out.json"],
+        )
+        v4 = Node(
+            "v4", "nop", "v4_dir", "v5_dir",
+            ["v3-out.json"],
+            ["v4-out.json"],
+        )
+        v5 = Node(
+            "v5", "nop", "v5_dir", "v3_dir",
+            ["v4-out.json"],
+            ["v3-out.json"],
+        )
+        g = Graph({
+            v0: [v1],
+            v1: [v2],
+            v2: [v0, v3],
+            v3: [v4, v2],
+            v4: [v5],
+            v5: [v3]
+        })
+        self.assertTrue(len(nx.find_cycle(g.networkx)) > 0)
+        g_acyclic = node.convert_to_acyclic(g)
+        with self.assertRaises(nx.NetworkXNoCycle):
+            nx.find_cycle(g_acyclic.networkx)
+
     @pytest.mark.xfail(raises=ImportError, reason="Matplotlib currently not imported")
     def test_visualization(self) -> None:
         """Test visualization of flowgraph."""
@@ -130,53 +226,54 @@ def test_run_basic(self) -> None:
         HammerVLSILogging.clear_callbacks()
         HammerVLSILogging.add_callback(HammerVLSILogging.callback_buffering)
 
+        cfg = dedent("""
+            synthesis.inputs:
+                input_files: ["LICENSE", "README.md"]
+                top_module: "z1top.xdc"
+
+            par.inputs:
+                input_files: ["LICENSE", "README.md"]
+                top_module: "z1top.xdc"
+
+            drc.inputs:
+                input_files: ["LICENSE", "README.md"]
+                top_module: "z1top.xdc"
+
+            lvs.inputs:
+                input_files: ["LICENSE", "README.md"]
+                schematic_files: ["LICENSE", "README.md"]
+                top_module: "z1top.xdc"
+                hcells_list: []
+
+            pcb.inputs:
+                top_module: "z1top.xdc"
+
+            formal.inputs:
+                input_files: ["LICENSE", "README.md"]
+                top_module: "z1top.xdc"
+
+            sim.inputs:
+                input_files: ["LICENSE", "README.md"]
+                top_module: "z1top.xdc"
+
+            vlsi:
+                core:
+                    technology: "hammer.technology.nop"
+
+                    synthesis_tool: "hammer.synthesis.nop"
+                    par_tool: "hammer.par.nop"
+                    drc_tool: "hammer.drc.nop"
+                    lvs_tool: "hammer.lvs.nop"
+                    power_tool: "hammer.power.nop"
+                    sim_tool: "mocksim"
+        """)
+
         with tempfile.TemporaryDirectory() as td:
             os.mkdir(os.path.join(td, "syn_dir"))
             os.mkdir(os.path.join(td, "par_dir"))
-            os.mkdir(os.path.join(td, "drc_dir"))
 
             with open(os.path.join(td, "syn_dir", "syn-in.yml"), 'w', encoding="utf-8") as tf1:
-                tf1.write("""
-synthesis.inputs:
-    input_files: ["LICENSE", "README.md"]
-    top_module: "z1top.xdc"
-
-par.inputs:
-    input_files: ["LICENSE", "README.md"]
-    top_module: "z1top.xdc"
-
-drc.inputs:
-    input_files: ["LICENSE", "README.md"]
-    top_module: "z1top.xdc"
-
-lvs.inputs:
-    input_files: ["LICENSE", "README.md"]
-    schematic_files: ["LICENSE", "README.md"]
-    top_module: "z1top.xdc"
-    hcells_list: []
-
-pcb.inputs:
-    top_module: "z1top.xdc"
-
-formal.inputs:
-    input_files: ["LICENSE", "README.md"]
-    top_module: "z1top.xdc"
-
-sim.inputs:
-    input_files: ["LICENSE", "README.md"]
-    top_module: "z1top.xdc"
-
-vlsi:
-    core:
-        technology: "hammer.technology.nop"
-
-        synthesis_tool: "hammer.synthesis.nop"
-        par_tool: "hammer.par.nop"
-        drc_tool: "hammer.drc.nop"
-        lvs_tool: "hammer.lvs.nop"
-        power_tool: "hammer.power.nop"
-        sim_tool: "mocksim"
-""")
+                tf1.write(cfg)
 
             syn = Node(
                 "syn", "nop",
@@ -206,6 +303,96 @@ def test_run_basic(self) -> None:
         for n in g.networkx:
             self.assertEqual(n.status, Status.COMPLETE)
 
+    def test_invalid_run(self) -> None:
+        """
+        Test that a failing run should not run
+        other steps and exit gracefully.
+        """
+        HammerVLSILogging.clear_callbacks()
+        HammerVLSILogging.add_callback(HammerVLSILogging.callback_buffering)
+
+        cfg = dedent("""
+            synthesis.inputs:
+                input_files: ["LICENSE", "README.md"]
+                top_module: "z1top.xdc"
+
+            par.inputs:
+                input_files: ["LICENSE", "README.md"]
+                top_module: "z1top.xdc"
+
+            drc.inputs:
+                input_files: ["LICENSE", "README.md"]
+                top_module: "z1top.xdc"
+
+            lvs.inputs:
+                input_files: ["LICENSE", "README.md"]
+                schematic_files: ["LICENSE", "README.md"]
+                top_module: "z1top.xdc"
+                hcells_list: []
+
+            pcb.inputs:
+                top_module: "z1top.xdc"
+
+            formal.inputs:
+                input_files: ["LICENSE", "README.md"]
+                top_module: "z1top.xdc"
+
+            sim.inputs:
+                input_files: ["LICENSE", "README.md"]
+                top_module: "z1top.xdc"
+
+            vlsi:
+                core:
+                    technology: "hammer.technology.nop"
+
+                    synthesis_tool: "hammer.synthesis.nop"
+                    par_tool: "hammer.par.nop"
+                    drc_tool: "hammer.drc.nop"
+                    lvs_tool: "hammer.lvs.nop"
+                    power_tool: "hammer.power.nop"
+                    sim_tool: "mocksim"
+        """)
+
+        with tempfile.TemporaryDirectory() as td:
+            os.mkdir(os.path.join(td, "syn_dir"))
+            os.mkdir(os.path.join(td, "par_dir"))
+
+            with open(os.path.join(td, "syn_dir", "syn-in.yml"), 'w', encoding="utf-8") as tf1:
+                tf1.write(cfg)
+
+            syn = Node(
+                "syn", "nop",
+                os.path.join(td, "syn_dir"), os.path.join(td, "s2p_dir"),
+                ["syn-in.yml"],
+                ["syn-out.json"],
+            )
+            s2p_bad = Node(
+                "blah", "nop",
+                os.path.join(td, "s2p_dir"), os.path.join(td, "par_dir"),
+                ["syn-out.json"],
+                ["s2p-out.json"],
+            )
+            par = Node(
+                "par", "nop",
+                os.path.join(td, "par_dir"), os.path.join(td, "out_dir"),
+                ["s2p-out.json"],
+                ["par-out.json"],
+            )
+            g = Graph({
+                syn: [s2p_bad],
+                s2p_bad: [par],
+                par: []
+            })
+            with pytest.raises(Exception):
+                g.run(syn)
+
+            print(syn.status)
+            print(s2p_bad.status)
+            print(par.status)
+            self.assertEqual(syn.status, Status.COMPLETE)
+            self.assertEqual(s2p_bad.status, Status.INCOMPLETE)
+            self.assertEqual(par.status, Status.NOT_RUN)
+
 
 if __name__ == "__main__":
     unittest.main()

From e81c1a0869bfb70a21ff42840b63c90f54b7fbc8 Mon Sep 17 00:00:00 2001
From: Bryan Ngo <bryanngo@berkeley.edu>
Date: Fri, 3 Feb 2023 11:50:37 -0800
Subject: [PATCH 11/36] better capture of errors

---
 hammer/flowgraph/node.py | 23 ++++++++++-------------
 1 file changed, 10 insertions(+), 13 deletions(-)

diff --git a/hammer/flowgraph/node.py b/hammer/flowgraph/node.py
index c2ddb1bfe..ca8d6c518 100644
--- a/hammer/flowgraph/node.py
+++ b/hammer/flowgraph/node.py
@@ -30,10 +30,8 @@ class Status(Enum):
     COMPLETE   = "COMPLETE"
 
 
-# make sure union of required/optional outs is superset of children required/optional inputs
 # separate required validity checking and optional validity checking
 # meta dict for tech compatibilty
-# for cycles, reduce to DAG via cloning of one of the nodes
 
 @dataclass
 class Node:
@@ -134,17 +132,18 @@ def run(self, start: Node) -> None:
             'cad_files': None
         }
 
+        ctxt = HammerVLSILogging.context(start.action)
+        ctxt.info(f"Running graph step {start.action}")
         driver = cli_driver.CLIDriver()
-        try:
-            ctxt = HammerVLSILogging.context(start.action)
-            # ctxt.info(f"Running graph step {start.action}")
-            driver.run_main_parsed(arg_list)
+        code = driver.run_main_parsed(arg_list)
+        if code == 0:
             start.status = Status.COMPLETE
-            for c in nx.neighbors(self.networkx, start):
-                self.run(c)
-        except Exception as e:
+        else:
             start.status = Status.INCOMPLETE
-            raise e
+            raise RuntimeError(f"Step {start.action} failed")
+
+        for c in nx.neighbors(self.networkx, start):
+            self.run(c)
 
 def convert_to_acyclic(g: Graph) -> Graph:
     """Eliminates cycles in a flowgraph for analysis.
@@ -155,7 +154,7 @@ def convert_to_acyclic(g: Graph) -> Graph:
     Returns:
         Graph: Graph with cloned nodes.
     """
-    cycles = sorted(nx.simple_cycles(g.networkx))
+    cycles = nx.simple_cycles(g.networkx)
     new_edge_list = g.edge_list.copy()
     for cycle in cycles:
         cut_start, cut_end = cycle[0], cycle[1]
@@ -171,5 +170,3 @@ def convert_to_acyclic(g: Graph) -> Graph:
         new_edge_list[cut_start] = []
         new_edge_list[cut_end_copy] = cut_start_children
     return Graph(new_edge_list)
-
-# TODO: refresh graph

From f6219f593c35fdfd6b6042916fadd8a2a6bf1a45 Mon Sep 17 00:00:00 2001
From: Bryan Ngo <bryanngo@berkeley.edu>
Date: Fri, 3 Mar 2023 11:17:28 -0800
Subject: [PATCH 12/36] add serialization test

---
 tests/test_node.py | 90 +++++++++++++++++++++++++++++++++++++++++++---
 1 file changed, 86 insertions(+), 4 deletions(-)

diff --git a/tests/test_node.py b/tests/test_node.py
index 3be15a9d9..1d29600c1 100644
--- a/tests/test_node.py
+++ b/tests/test_node.py
@@ -1,3 +1,4 @@
+import json
 import os
 import tempfile
 import unittest
@@ -5,13 +6,14 @@
 
 import networkx as nx
 import pytest
+from networkx.readwrite import json_graph
 
 from hammer.flowgraph import node
 from hammer.flowgraph.node import Graph, Node, Status
 from hammer.logging import HammerVLSILogging
 
 
-class NodeTest(unittest.TestCase):
+class TestNode(unittest.TestCase):
 
     def test_initialize_node(self) -> None:
         """Test that we can instantiate a node."""
@@ -386,13 +388,93 @@ def test_invalid_run(self) -> None:
             with pytest.raises(Exception):
                 g.run(syn)
 
-            print(syn.status)
-            print(s2p_bad.status)
-            print(par.status)
             self.assertEqual(syn.status, Status.COMPLETE)
             self.assertEqual(s2p_bad.status, Status.INCOMPLETE)
             self.assertEqual(par.status, Status.NOT_RUN)
 
+    def test_encode_decode(self) -> None:
+        """
+        Test that a flowgraph can be encoded and decoded.
+        """
+        HammerVLSILogging.clear_callbacks()
+        HammerVLSILogging.add_callback(HammerVLSILogging.callback_buffering)
+
+        cfg = dedent("""
+            synthesis.inputs:
+                input_files: ["LICENSE", "README.md"]
+                top_module: "z1top.xdc"
+
+            par.inputs:
+                input_files: ["LICENSE", "README.md"]
+                top_module: "z1top.xdc"
+
+            drc.inputs:
+                input_files: ["LICENSE", "README.md"]
+                top_module: "z1top.xdc"
+
+            lvs.inputs:
+                input_files: ["LICENSE", "README.md"]
+                schematic_files: ["LICENSE", "README.md"]
+                top_module: "z1top.xdc"
+                hcells_list: []
+
+            pcb.inputs:
+                top_module: "z1top.xdc"
+
+            formal.inputs:
+                input_files: ["LICENSE", "README.md"]
+                top_module: "z1top.xdc"
+
+            sim.inputs:
+                input_files: ["LICENSE", "README.md"]
+                top_module: "z1top.xdc"
+
+            vlsi:
+                core:
+                    technology: "hammer.technology.nop"
+
+                    synthesis_tool: "hammer.synthesis.nop"
+                    par_tool: "hammer.par.nop"
+                    drc_tool: "hammer.drc.nop"
+                    lvs_tool: "hammer.lvs.nop"
+                    power_tool: "hammer.power.nop"
+                    sim_tool: "mocksim"
+        """)
+
+        with tempfile.TemporaryDirectory() as td:
+            os.mkdir(os.path.join(td, "syn_dir"))
+            os.mkdir(os.path.join(td, "par_dir"))
+
+            with open(os.path.join(td, "syn_dir", "syn-in.yml"), 'w', encoding="utf-8") as tf1:
+                tf1.write(cfg)
+            syn = Node(
+                "syn", "nop",
+                os.path.join(td, "syn_dir"), os.path.join(td, "s2p_dir"),
+                ["syn-in.yml"],
+                ["syn-out.json"],
+            )
+            s2p = Node(
+                "syn-to-par", "nop",
+                os.path.join(td, "s2p_dir"), os.path.join(td, "par_dir"),
+                ["syn-out.json"],
+                ["s2p-out.json"],
+            )
+            par = Node(
+                "par", "nop",
+                os.path.join(td, "par_dir"), os.path.join(td, "out_dir"),
+                ["s2p-out.json"],
+                ["par-out.json"],
+            )
+            g = Graph({
+                syn: [s2p],
+                s2p: [par],
+                par: []
+            })
+
+            out = json.dumps(g.to_json(), cls=node.NodeEncoder)
+            g_dec = json.loads(out, object_hook=node.as_node)
+            # print(g.to_json())
+            print(json_graph.node_link_graph(g_dec).nodes)
 
 if __name__ == "__main__":
     unittest.main()

From cbede149e6758a6e8869b7f3d8779c98be6712b4 Mon Sep 17 00:00:00 2001
From: Bryan Ngo <bryanngo@berkeley.edu>
Date: Fri, 3 Mar 2023 11:17:57 -0800
Subject: [PATCH 13/36] using property decorators

---
 hammer/config/config_src.py | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/hammer/config/config_src.py b/hammer/config/config_src.py
index 99a3fadb9..a7b437d3a 100644
--- a/hammer/config/config_src.py
+++ b/hammer/config/config_src.py
@@ -717,6 +717,7 @@ def get_config(self) -> dict:
             self.__config_cache_dirty = False
         return self.__config_cache
 
+    @property
     def get_config_types(self) -> dict:
         """
         Get the types for the configuration of a database.
@@ -818,9 +819,9 @@ def get_setting_type(self, key: str, nullvalue: Any = None) -> Any:
         :param nullvalue: Value to return for nulls.
         :return: Data type of key.
         """
-        if key not in self.get_config_types():
+        if key not in self.get_config_types:
             raise KeyError(f"Key type {key} is missing")
-        value = self.get_config_types()[key]
+        value = self.get_config_types[key]
         return nullvalue if value is None else value
 
     def set_setting_type(self, key: str, value: Any) -> None:
@@ -840,7 +841,7 @@ def has_setting_type(self, key: str) -> bool:
         :param key: Desired key.
         :return: True if the given setting exists.
         """
-        return key in self.get_config_types()
+        return key in self.get_config_types
 
     def check_setting(self, key: str, cfg: Optional[dict] = None) -> bool:
         """
@@ -852,11 +853,11 @@ def check_setting(self, key: str, cfg: Optional[dict] = None) -> bool:
 
         if cfg is None:
             cfg = self.get_config()
-        if key not in self.get_config_types():
+        if key not in self.get_config_types:
             self.logger.warning(f"Key {key} is not associated with a type")
             return True
         try:
-            exp_value_type = parse_setting_type(self.get_config_types()[key])
+            exp_value_type = parse_setting_type(self.get_config_types[key])
         except ValueError as ve:
             raise ValueError(f'Key {key} has an invalid outer type: perhaps you have "List" instead of "list" or "Dict" instead of "dict"?') from ve
 

From 62b262df8b015eccc7eb6677b85ba0a6eaee5bae Mon Sep 17 00:00:00 2001
From: Bryan Ngo <bryanngo@berkeley.edu>
Date: Fri, 10 Mar 2023 02:16:48 -0800
Subject: [PATCH 14/36] add step control and custom driver

---
 hammer/flowgraph/node.py | 146 ++++++++++++++++++++++++++++++++++-----
 1 file changed, 130 insertions(+), 16 deletions(-)

diff --git a/hammer/flowgraph/node.py b/hammer/flowgraph/node.py
index ca8d6c518..c179f5cac 100644
--- a/hammer/flowgraph/node.py
+++ b/hammer/flowgraph/node.py
@@ -8,12 +8,16 @@
 
 # pylint: disable=invalid-name
 
+import importlib
+import json
 import os
 import uuid
-from dataclasses import dataclass, field
+from dataclasses import dataclass, field, asdict
 from enum import Enum
+from typing import Any, Union
 
 import networkx as nx
+from networkx.readwrite import json_graph
 
 from hammer.logging import HammerVLSILogging
 from hammer.vlsi import cli_driver
@@ -35,6 +39,11 @@ class Status(Enum):
 
 @dataclass
 class Node:
+    """Defines a node for an action in a flowgraph.
+
+    Returns:
+        Node: Complete description of an action.
+    """
     action:            str
     tool:              str
     pull_dir:          str
@@ -42,9 +51,17 @@ class Node:
     required_inputs:   list[str]
     required_outputs:  list[str]
     status:            Status    = Status.NOT_RUN
-    __uuid:            uuid.UUID = field(default_factory=uuid.uuid4)
+    # __uuid:            uuid.UUID = field(default_factory=uuid.uuid4)
+    driver:            str       = ""
     optional_inputs:   list[str] = field(default_factory=list)
     optional_outputs:  list[str] = field(default_factory=list)
+    step_controls:     dict[str, str] = field(default_factory=lambda: {
+        "from_step": "",
+        "after_step": "",
+        "to_step": "",
+        "until_step": "",
+        "only_step": "",
+    })
 
     def __key(self) -> tuple:
         """Key value for hashing.
@@ -61,15 +78,69 @@ def __key(self) -> tuple:
             tuple(self.required_outputs),
             tuple(self.optional_inputs),
             tuple(self.optional_outputs),
-            self.status
+            self.status,
+            tuple(self.step_controls.items())
         )
 
     def __hash__(self) -> int:
+        """Dunder method for uniquely hashing a `Node` object.
+
+        Returns:
+            int: Hash of a `Node`.
+        """
         return hash(self.__key)
 
+    def __is_privileged(self) -> bool:
+        """Private method for checking if
+        step control is applied to a `Node`.
+
+        Returns:
+            bool: If the node is allowed to be the starting point of a flow.
+        """
+        return any(i != "" for i in self.step_controls.values())
+
+    @property
+    def privileged(self) -> bool:
+        """Property for determining node privilege.
+
+        Returns:
+            bool: If the node is allowed to be the starting point of a flow.
+        """
+        return self.__is_privileged()
+
+class NodeEncoder(json.JSONEncoder):
+    def default(self, o: Any) -> Any:
+        if isinstance(o, Node):
+            return asdict(o)
+        elif isinstance(o, Status):
+            return o.value
+        return super().default(o)
+
+def as_node(dct: dict) -> Union[Node, dict]:
+    if "action" in dct:
+        return Node(
+            dct["action"],
+            dct["tool"],
+            dct["pull_dir"],
+            dct["push_dir"],
+            dct["required_inputs"],
+            dct["required_outputs"],
+            Status(dct["status"]),
+            dct["optional_inputs"],
+            dct["optional_outputs"],
+        )
+    return dct
+
 @dataclass
 class Graph:
+    """Defines a flowgraph.
+
+    Returns:
+        Graph: HAMMER flowgraph.
+    """
     edge_list: dict[Node, list[Node]]
+    driver: str = ""
+    # driver: cli_driver.CLIDriver = field(default_factory=cli_driver.CLIDriver)
 
     def __post_init__(self) -> None:
         self.networkx = nx.DiGraph(self.edge_list)
@@ -97,14 +168,32 @@ def __process(self, v: Node) -> bool:
         inputs = set(v.required_inputs) | set(v.optional_inputs)
         return self.networkx.in_degree(v) == 0 or parent_outs >= inputs
 
-    def run(self, start: Node) -> None:
-        """Run a HAMMER flowgraph."""
+    def run(self, start: Node) -> Any:
+        """Runs a flowgraph.
+
+        Args:
+            start (Node): Node to start the run on.
+
+        Raises:
+            RuntimeError: If the flowgraph is invalid.
+            RuntimeError: If the starting node is not in the flowgraph.
+        """
         if not self.verify():
-            raise RuntimeError("Flowgraph is invalid")
+            raise RuntimeError("Flowgraph is invalid. Please check your flow's inputs and outputs.")
         if start not in self.networkx:
-            raise RuntimeError("Node not in flowgraph")
+            raise RuntimeError("Node not in flowgraph. Did you construct the graph correctly?")
+        if not start.privileged and any(i.privileged for i in self.networkx):
+            raise RuntimeError("Attempting to run non-privileged node in privileged flow. Please complete your stepped flow first.")
+
+        if start.driver != "":
+            driver_pkg_path, driver_module = self.driver.rsplit('.', 1)
+            driver_pkg = importlib.import_module(driver_pkg_path)
+            driver = getattr(driver_pkg, driver_module)()
+            if not isinstance(driver, cli_driver.CLIDriver):
+                raise TypeError(f"Driver {driver} does not extend CLIDriver, cannot run a flow.")
+        else:
+            driver = cli_driver.CLIDriver()
 
-        start.status = Status.RUNNING
         arg_list = {
             "action": start.action,
             'environment_config': None,
@@ -120,31 +209,47 @@ def run(self, start: Node) -> None:
             'formal_rundir': '',
             'timing_rundir': '',
             # TODO: sub-step determinations
-            'from_step': None,
-            'after_step': None,
-            'to_step': None,
-            'until_step': None,
-            'only_step': None,
+            'from_step': start.step_controls["from_step"],
+            'after_step': start.step_controls["after_step"],
+            'to_step': start.step_controls["to_step"],
+            'until_step': start.step_controls["until_step"],
+            'only_step': start.step_controls["only_step"],
             'output': os.path.join(start.push_dir, start.required_outputs[0]),  # TODO: fix this
             'verilog': None,
             'firrtl': None,
             'top': None,
-            'cad_files': None
+            'cad_files': None,
+            'dump_history': False
         }
 
+        start.status = Status.RUNNING
         ctxt = HammerVLSILogging.context(start.action)
         ctxt.info(f"Running graph step {start.action}")
-        driver = cli_driver.CLIDriver()
         code = driver.run_main_parsed(arg_list)
         if code == 0:
             start.status = Status.COMPLETE
         else:
             start.status = Status.INCOMPLETE
-            raise RuntimeError(f"Step {start.action} failed")
+            ctxt.fatal(f"Step {start.action} failed")
+            return self
 
         for c in nx.neighbors(self.networkx, start):
             self.run(c)
 
+        return self
+
+    def to_json(self) -> dict:
+        """Encodes a graph as a JSON string.
+
+        Returns:
+            str: JSON dump of a flowgraph.
+        """
+        return json_graph.node_link_data(self.networkx)
+
+    def visualize(self) -> Any:
+        raise NotImplementedError()
+
+
 def convert_to_acyclic(g: Graph) -> Graph:
     """Eliminates cycles in a flowgraph for analysis.
 
@@ -170,3 +275,12 @@ def convert_to_acyclic(g: Graph) -> Graph:
         new_edge_list[cut_start] = []
         new_edge_list[cut_end_copy] = cut_start_children
     return Graph(new_edge_list)
+
+
+# TODO: serialization format
+# TODO: cycles are conditional on user input
+# TODO: put x-to-y actions between connections
+# TODO: hooks into nodes
+# TODO: stopping/starting flows
+# TODO: d2 stuff
+# TODO: write tests for hooks/steps

From 36553c40625fd4bf27b2fb64e71b865ccdcfa2b5 Mon Sep 17 00:00:00 2001
From: Bryan Ngo <bryanngo@berkeley.edu>
Date: Fri, 10 Mar 2023 02:17:08 -0800
Subject: [PATCH 15/36] small linting fix

---
 hammer/vlsi/cli_driver.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/hammer/vlsi/cli_driver.py b/hammer/vlsi/cli_driver.py
index cd91f7c9f..aaf89ca33 100644
--- a/hammer/vlsi/cli_driver.py
+++ b/hammer/vlsi/cli_driver.py
@@ -322,8 +322,8 @@ def info_action(driver: HammerDriver, append_error_func: Callable[[str], None])
                     if "_meta" not in k:
                         print(k)
                 while True:
+                    key = input("Select from the current level of keys: ")
                     try:
-                        key = input("Select from the current level of keys: ")
                         next_level = curr_level[key]
                         break
                     except KeyError:

From 9465d20b8a817b87bcd65f640a56839cdde72622 Mon Sep 17 00:00:00 2001
From: Bryan Ngo <bryanngo@berkeley.edu>
Date: Fri, 10 Mar 2023 02:17:30 -0800
Subject: [PATCH 16/36] graph runner should not raise exception

---
 tests/test_node.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/tests/test_node.py b/tests/test_node.py
index 1d29600c1..a0e165650 100644
--- a/tests/test_node.py
+++ b/tests/test_node.py
@@ -385,8 +385,7 @@ def test_invalid_run(self) -> None:
                 s2p_bad: [par],
                 par: []
             })
-            with pytest.raises(Exception):
-                g.run(syn)
+            g.run(syn)
 
             self.assertEqual(syn.status, Status.COMPLETE)
             self.assertEqual(s2p_bad.status, Status.INCOMPLETE)

From 74685bdb0b252eafc9ba29c3874e8f4def82616f Mon Sep 17 00:00:00 2001
From: Bryan Ngo <bryanngo@berkeley.edu>
Date: Fri, 10 Mar 2023 03:19:35 -0800
Subject: [PATCH 17/36] add mermaid support

---
 hammer/flowgraph/node.py | 17 ++++++++++++++---
 1 file changed, 14 insertions(+), 3 deletions(-)

diff --git a/hammer/flowgraph/node.py b/hammer/flowgraph/node.py
index c179f5cac..bb8f1fe9f 100644
--- a/hammer/flowgraph/node.py
+++ b/hammer/flowgraph/node.py
@@ -246,9 +246,22 @@ def to_json(self) -> dict:
         """
         return json_graph.node_link_data(self.networkx)
 
-    def visualize(self) -> Any:
+    def to_d2(self) -> Any:
         raise NotImplementedError()
 
+    def to_mermaid(self, fname: str) -> None:
+        """Converts the flowgraph into Mermaid format for visualization.
+
+        Args:
+            fname (str): Output file name.
+        """
+        with open(fname, 'w', encoding="utf-8") as f:
+            f.write("stateDiagram-v2\n")
+            for start in self.networkx:
+                f.writelines(
+                    f"    {start.action} --> {child.action}\n"
+                    for child in nx.neighbors(self.networkx, start)
+                )
 
 def convert_to_acyclic(g: Graph) -> Graph:
     """Eliminates cycles in a flowgraph for analysis.
@@ -280,7 +293,5 @@ def convert_to_acyclic(g: Graph) -> Graph:
 # TODO: serialization format
 # TODO: cycles are conditional on user input
 # TODO: put x-to-y actions between connections
-# TODO: hooks into nodes
-# TODO: stopping/starting flows
 # TODO: d2 stuff
 # TODO: write tests for hooks/steps

From 13c9f006286c70b3c3e8d1914b6ad7ae1bdf3868 Mon Sep 17 00:00:00 2001
From: Bryan Ngo <bryanngo@berkeley.edu>
Date: Fri, 10 Mar 2023 03:19:41 -0800
Subject: [PATCH 18/36] add test for mermaid

---
 tests/test_node.py | 127 +++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 127 insertions(+)

diff --git a/tests/test_node.py b/tests/test_node.py
index a0e165650..803e8a023 100644
--- a/tests/test_node.py
+++ b/tests/test_node.py
@@ -391,6 +391,133 @@ def test_invalid_run(self) -> None:
             self.assertEqual(s2p_bad.status, Status.INCOMPLETE)
             self.assertEqual(par.status, Status.NOT_RUN)
 
+    def test_resume_graph(self) -> None:
+        """
+        Test that a user can stop and start a flow if needed.
+        """
+        HammerVLSILogging.clear_callbacks()
+        HammerVLSILogging.add_callback(HammerVLSILogging.callback_buffering)
+
+        cfg = dedent("""
+            synthesis.inputs:
+                input_files: ["LICENSE", "README.md"]
+                top_module: "z1top.xdc"
+
+            par.inputs:
+                input_files: ["LICENSE", "README.md"]
+                top_module: "z1top.xdc"
+
+            drc.inputs:
+                input_files: ["LICENSE", "README.md"]
+                top_module: "z1top.xdc"
+
+            lvs.inputs:
+                input_files: ["LICENSE", "README.md"]
+                schematic_files: ["LICENSE", "README.md"]
+                top_module: "z1top.xdc"
+                hcells_list: []
+
+            pcb.inputs:
+                top_module: "z1top.xdc"
+
+            formal.inputs:
+                input_files: ["LICENSE", "README.md"]
+                top_module: "z1top.xdc"
+
+            sim.inputs:
+                input_files: ["LICENSE", "README.md"]
+                top_module: "z1top.xdc"
+
+            vlsi:
+                core:
+                    technology: "hammer.technology.nop"
+
+                    synthesis_tool: "hammer.synthesis.nop"
+                    par_tool: "hammer.par.nop"
+                    drc_tool: "hammer.drc.nop"
+                    lvs_tool: "hammer.lvs.nop"
+                    power_tool: "hammer.power.nop"
+                    sim_tool: "mocksim"
+        """)
+
+        with tempfile.TemporaryDirectory() as td:
+            os.mkdir(os.path.join(td, "syn_dir"))
+            os.mkdir(os.path.join(td, "par_dir"))
+
+            with open(os.path.join(td, "syn_dir", "syn-in.yml"), 'w', encoding="utf-8") as tf1:
+                tf1.write(cfg)
+
+            syn = Node(
+                "syn", "nop",
+                os.path.join(td, "syn_dir"), os.path.join(td, "s2p_dir"),
+                ["syn-in.yml"],
+                ["syn-out.json"],
+            )
+            s2p_bad = Node(
+                "blah", "nop",
+                os.path.join(td, "s2p_dir"), os.path.join(td, "par_dir"),
+                ["syn-out.json"],
+                ["s2p-out.json"],
+            )
+            par = Node(
+                "par", "nop",
+                os.path.join(td, "par_dir"), os.path.join(td, "out_dir"),
+                ["s2p-out.json"],
+                ["par-out.json"],
+            )
+            g = Graph({
+                syn: [s2p_bad],
+                s2p_bad: [par],
+                par: []
+            })
+            g_failed_run = g.run(syn)
+
+            self.assertEqual(syn.status, Status.COMPLETE)
+            self.assertEqual(s2p_bad.status, Status.INCOMPLETE)
+            self.assertEqual(par.status, Status.NOT_RUN)
+
+            s2p_bad.action = "syn-to-par"
+            g_good = g_failed_run.run(s2p_bad)
+            for n in g_good.networkx:
+                self.assertEqual(n.status, Status.COMPLETE)
+
+    def test_mermaid(self) -> None:
+        """
+        Test that Mermaid visualization works.
+        """
+        with tempfile.TemporaryDirectory() as td:
+            os.mkdir(os.path.join(td, "syn_dir"))
+            os.mkdir(os.path.join(td, "par_dir"))
+
+            syn = Node(
+                "syn", "nop",
+                os.path.join(td, "syn_dir"), os.path.join(td, "s2p_dir"),
+                ["syn-in.yml"],
+                ["syn-out.json"],
+            )
+            s2p = Node(
+                "syn-to-par", "nop",
+                os.path.join(td, "s2p_dir"), os.path.join(td, "par_dir"),
+                ["syn-out.json"],
+                ["s2p-out.json"],
+            )
+            par = Node(
+                "par", "nop",
+                os.path.join(td, "par_dir"), os.path.join(td, "out_dir"),
+                ["s2p-out.json"],
+                ["par-out.json"],
+            )
+            g = Graph({
+                syn: [s2p],
+                s2p: [par],
+                par: []
+            })
+
+            g.to_mermaid(os.path.join(td, "mermaid.txt"))
+            with open(os.path.join(td, "mermaid.txt"), 'r', encoding="utf-8") as f:
+                s = f.readlines()
+                self.assertListEqual(s, ["stateDiagram-v2\n", "    syn --> syn-to-par\n", "    syn-to-par --> par\n"])
+
     def test_encode_decode(self) -> None:
         """
         Test that a flowgraph can be encoded and decoded.

From 51bf5ea86db0e70b7956d25a21043f5b2fea23a5 Mon Sep 17 00:00:00 2001
From: Bryan Ngo <bryanngo@berkeley.edu>
Date: Thu, 23 Mar 2023 16:48:18 -0700
Subject: [PATCH 19/36] implement and test auto-insertion of aux actions

---
 hammer/flowgraph/node.py |  74 +++++++++++++++--
 tests/test_node.py       | 174 ++++++++++++++++++++++-----------------
 2 files changed, 166 insertions(+), 82 deletions(-)

diff --git a/hammer/flowgraph/node.py b/hammer/flowgraph/node.py
index bb8f1fe9f..9c03d6dad 100644
--- a/hammer/flowgraph/node.py
+++ b/hammer/flowgraph/node.py
@@ -139,11 +139,10 @@ class Graph:
         Graph: HAMMER flowgraph.
     """
     edge_list: dict[Node, list[Node]]
-    driver: str = ""
-    # driver: cli_driver.CLIDriver = field(default_factory=cli_driver.CLIDriver)
+    auto_auxiliary: bool = True
 
     def __post_init__(self) -> None:
-        self.networkx = nx.DiGraph(self.edge_list)
+        self.networkx = nx.DiGraph(Graph.insert_auxiliary_actions(self.edge_list) if self.auto_auxiliary else self.edge_list)
 
     def verify(self) -> bool:
         """Checks if a graph is valid via its inputs and outputs.
@@ -168,6 +167,69 @@ def __process(self, v: Node) -> bool:
         inputs = set(v.required_inputs) | set(v.optional_inputs)
         return self.networkx.in_degree(v) == 0 or parent_outs >= inputs
 
+    @staticmethod
+    def insert_auxiliary_actions(edge_list: dict[Node, list[Node]]) -> dict[Node, list[Node]]:
+        """Inserts x-to-y actions between two semantically related actions (e.g. if syn and par are connected, then we have to insert a syn-to-par node here).
+
+        Args:
+            edge_list (dict[Node, list[Node]]): Edge list without auxiliary actions.
+
+        Returns:
+            dict[Node, list[Node]]: Transformed edge list with auxiliary actions.
+        """
+        valid_auxiliary_actions = [
+            ("synthesis", "par"),
+            ("syn", "par"),
+            ("heir-par", "syn"),
+            ("heir_par", "syn"),
+            ("par", "drc"),
+            ("par", "lvs"),
+            ("synthesis", "sim"),
+            ("syn", "sim"),
+            ("par", "sim"),
+            ("syn", "power"),
+            ("par", "power"),
+            ("sim", "power"),
+            ("synthesis", "formal"),
+            ("syn", "formal"),
+            ("par", "formal"),
+            ("synthesis", "timing"),
+            ("syn", "timing"),
+            ("par", "timing"),
+        ]
+
+        changes = []
+        edge_list_copy = edge_list.copy()
+        for parent_idx, (parent, children) in enumerate(edge_list.items()):
+            for child_idx, child in enumerate(children):
+                if (parent.action, child.action) in valid_auxiliary_actions:
+                    aux_action = f"{parent.action}-to-{child.action}"
+                    aux_node = Node(
+                        aux_action,
+                        parent.tool,
+                        os.path.join(os.path.dirname(parent.pull_dir), f"{aux_action}-dir"),
+                        child.pull_dir,
+                        parent.required_outputs,
+                        [f"{aux_action}-out.json"],
+                    )
+                    changes.append((parent_idx, child_idx, aux_node))
+
+        for parent_idx, child_idx, aux_node in changes:
+            parent, children = list(edge_list_copy.items())[parent_idx]
+            parent.push_dir = os.path.join(
+                os.path.dirname(parent.pull_dir),
+                f"{aux_node.action}-dir")
+
+            child = children[child_idx]
+            child.required_inputs = aux_node.required_outputs
+
+            children[child_idx] = aux_node
+            if aux_node not in edge_list_copy:
+                edge_list_copy[aux_node] = []
+            edge_list_copy[aux_node].append(child)
+        return edge_list_copy
+
+
     def run(self, start: Node) -> Any:
         """Runs a flowgraph.
 
@@ -186,7 +248,7 @@ def run(self, start: Node) -> Any:
             raise RuntimeError("Attempting to run non-privileged node in privileged flow. Please complete your stepped flow first.")
 
         if start.driver != "":
-            driver_pkg_path, driver_module = self.driver.rsplit('.', 1)
+            driver_pkg_path, driver_module = start.driver.rsplit('.', 1)
             driver_pkg = importlib.import_module(driver_pkg_path)
             driver = getattr(driver_pkg, driver_module)()
             if not isinstance(driver, cli_driver.CLIDriver):
@@ -208,7 +270,6 @@ def run(self, start: Node) -> Any:
             'power_rundir': '',
             'formal_rundir': '',
             'timing_rundir': '',
-            # TODO: sub-step determinations
             'from_step': start.step_controls["from_step"],
             'after_step': start.step_controls["after_step"],
             'to_step': start.step_controls["to_step"],
@@ -292,6 +353,5 @@ def convert_to_acyclic(g: Graph) -> Graph:
 
 # TODO: serialization format
 # TODO: cycles are conditional on user input
-# TODO: put x-to-y actions between connections
-# TODO: d2 stuff
 # TODO: write tests for hooks/steps
+# TODO: make custom driver and tech for steps
diff --git a/tests/test_node.py b/tests/test_node.py
index 803e8a023..d8956e883 100644
--- a/tests/test_node.py
+++ b/tests/test_node.py
@@ -27,14 +27,14 @@ def test_initialize_node(self) -> None:
     def test_complex_graph(self) -> None:
         """Creating a more complex graph."""
         root = Node(
-            "syn", "nop", "syn_dir", "",
+            "foo", "nop", "foo_dir", "",
             ["foo.yml"],
-            ["syn-out.json"],
+            ["foo-out.json"],
         )
         child1 = Node(
-            "par", "nop", "syn_dir", "par_dir",
-            ["syn-out.json"],
-            ["par-out.json"],
+            "bar", "nop", "foo_dir", "bar_dir",
+            ["foo-out.json"],
+            ["bar-out.json"],
         )
         graph = Graph({root: [child1]})
         self.assertEqual(len(graph.networkx), 2)
@@ -44,14 +44,14 @@ def test_complex_graph(self) -> None:
     def test_invalid_graph(self) -> None:
         """Test that invalid flowgraphs are detected."""
         root = Node(
-            "syn", "nop", "syn_dir", "",
+            "foo", "nop", "foo_dir", "",
             ["foo.yml"],
-            ["syn-out.json"],
+            ["foo-out.json"],
         )
         child1 = Node(
-            "par", "nop", "syn_dir", "par_dir",
-            ["syn-in.json"],
-            ["par-out.json"],
+            "bar", "nop", "foo_dir", "bar_dir",
+            ["foo-in.json"],
+            ["bar-out.json"],
         )
         graph = Graph({root: [child1]})
         self.assertFalse(graph.verify())
@@ -165,64 +165,6 @@ def test_multi_cycle_reduction(self) -> None:
         with self.assertRaises(nx.NetworkXNoCycle):
             nx.find_cycle(g_acyclic.networkx)
 
-    @pytest.mark.xfail(raises=ImportError, reason="Matplotlib currently not imported")
-    def test_visualization(self) -> None:
-        """Test visualization of flowgraph."""
-        import matplotlib.pyplot as plt
-        v0 = Node(
-            "syn", "nop", "syn_dir", "par_dir",
-            ["syn-in.json"],
-            ["syn-out.json"],
-        )
-        v1 = Node(
-            "par", "nop", "par_dir", "drc_dir",
-            ["syn-out.json", "par-in.json", "drc-out.json"],
-            ["par-out.json"],
-        )
-        v2 = Node(
-            "drc", "nop", "drc_dir", "par_dir",
-            ["par-out.json", "drc-in.json"],
-            ["drc-out.json"],
-        )
-        g = Graph({
-            v0.action: [v1.action],
-            v1.action: [v2.action],
-            v2.action: []
-        }).networkx
-        g.add_edge(v0.pull_dir, v0.action)
-        g.add_edge(v0.action, v0.push_dir)
-        g.add_edge(v1.pull_dir, v1.action)
-        g.add_edge(v1.action, v1.push_dir)
-        g.add_edge(v2.pull_dir, v2.action)
-        g.add_edge(v2.action, v2.push_dir)
-        pos = nx.planar_layout(g)
-        blue = "#003262"
-        yellow = "#fdb515"
-        nx.draw_networkx_nodes(g, pos=pos,
-            nodelist=[v0.action, v1.action, v2.action], node_size=1500, node_color=blue, label="Action")
-        nx.draw_networkx_nodes(g, pos=pos,
-            nodelist=[
-                v0.pull_dir, v0.push_dir,
-                v1.pull_dir, v1.push_dir,
-                v2.pull_dir, v2.push_dir
-            ], node_size=1500, node_color=yellow, label="Push/Pull Directory")
-        nx.draw_networkx_labels(g, pos=pos, font_size=8, font_color="whitesmoke")
-        nx.draw_networkx_edges(g, pos=pos,
-            nodelist=[v0.action, v1.action, v2.action],
-            node_size=1500, arrowsize=15, connectionstyle="arc3, rad=0.2", edge_color=blue)
-        nx.draw_networkx_edges(g, pos=pos,
-            edgelist=[
-                (v0.pull_dir, v0.action),
-                (v0.action, v0.push_dir),
-                (v1.pull_dir, v1.action),
-                (v1.action, v1.push_dir),
-                (v2.pull_dir, v2.action),
-                (v2.action, v2.push_dir),
-            ], node_size=1500, arrowsize=15, connectionstyle="arc3, rad=0.2", edge_color=yellow)
-        plt.axis("off")
-        plt.legend(loc="upper left", markerscale=0.2)
-        plt.savefig("/home/bngo/Research/hammer/graph.png", bbox_inches="tight", dpi=200)
-
     def test_run_basic(self) -> None:
         """Test a basic syn -> par flow, all with nop tools."""
         HammerVLSILogging.clear_callbacks()
@@ -299,7 +241,7 @@ def test_run_basic(self) -> None:
                 syn: [s2p],
                 s2p: [par],
                 par: []
-            })
+            }, auto_auxiliary=False)
             g.run(syn)
 
         for n in g.networkx:
@@ -384,7 +326,7 @@ def test_invalid_run(self) -> None:
                 syn: [s2p_bad],
                 s2p_bad: [par],
                 par: []
-            })
+            }, auto_auxiliary=False)
             g.run(syn)
 
             self.assertEqual(syn.status, Status.COMPLETE)
@@ -469,7 +411,7 @@ def test_resume_graph(self) -> None:
                 syn: [s2p_bad],
                 s2p_bad: [par],
                 par: []
-            })
+            }, auto_auxiliary=False)
             g_failed_run = g.run(syn)
 
             self.assertEqual(syn.status, Status.COMPLETE)
@@ -511,12 +453,94 @@ def test_mermaid(self) -> None:
                 syn: [s2p],
                 s2p: [par],
                 par: []
-            })
+            }, auto_auxiliary=False)
 
-            g.to_mermaid(os.path.join(td, "mermaid.txt"))
-            with open(os.path.join(td, "mermaid.txt"), 'r', encoding="utf-8") as f:
+            g.to_mermaid(os.path.join(td, "mermaid.md"))
+            with open(os.path.join(td, "mermaid.md"), 'r', encoding="utf-8") as f:
                 s = f.readlines()
-                self.assertListEqual(s, ["stateDiagram-v2\n", "    syn --> syn-to-par\n", "    syn-to-par --> par\n"])
+                self.assertListEqual(s,
+                                     ["stateDiagram-v2\n",
+                                      "    syn --> syn-to-par\n",
+                                      "    syn-to-par --> par\n"])
+
+    def test_auto_auxiliary(self) -> None:
+        """
+        Test that auxiliary actions are automatically inserted.
+        """
+        HammerVLSILogging.clear_callbacks()
+        HammerVLSILogging.add_callback(HammerVLSILogging.callback_buffering)
+
+        cfg = dedent("""
+            synthesis.inputs:
+                input_files: ["LICENSE", "README.md"]
+                top_module: "z1top.xdc"
+
+            par.inputs:
+                input_files: ["LICENSE", "README.md"]
+                top_module: "z1top.xdc"
+
+            drc.inputs:
+                input_files: ["LICENSE", "README.md"]
+                top_module: "z1top.xdc"
+
+            lvs.inputs:
+                input_files: ["LICENSE", "README.md"]
+                schematic_files: ["LICENSE", "README.md"]
+                top_module: "z1top.xdc"
+                hcells_list: []
+
+            pcb.inputs:
+                top_module: "z1top.xdc"
+
+            formal.inputs:
+                input_files: ["LICENSE", "README.md"]
+                top_module: "z1top.xdc"
+
+            sim.inputs:
+                input_files: ["LICENSE", "README.md"]
+                top_module: "z1top.xdc"
+
+            vlsi:
+                core:
+                    technology: "hammer.technology.nop"
+
+                    synthesis_tool: "hammer.synthesis.nop"
+                    par_tool: "hammer.par.nop"
+                    drc_tool: "hammer.drc.nop"
+                    lvs_tool: "hammer.lvs.nop"
+                    power_tool: "hammer.power.nop"
+                    sim_tool: "mocksim"
+        """)
+
+        with tempfile.TemporaryDirectory() as td:
+            os.mkdir(os.path.join(td, "syn_dir"))
+            os.mkdir(os.path.join(td, "par_dir"))
+
+            with open(os.path.join(td, "syn_dir", "syn-in.yml"), 'w', encoding="utf-8") as tf1:
+                tf1.write(cfg)
+
+            syn = Node(
+                "syn", "nop",
+                os.path.join(td, "syn_dir"), os.path.join(td, "par_dir"),
+                ["syn-in.yml"],
+                ["syn-out.json"],
+            )
+            par = Node(
+                "par", "nop",
+                os.path.join(td, "par_dir"), os.path.join(td, "out_dir"),
+                ["syn-out.json"],
+                ["par-out.json"],
+            )
+            g = Graph({
+                syn: [par],
+                par: []
+            })
+            self.assertEqual(len(g.networkx), 3)  # check that there are three nodes
+            self.assertEqual(len(g.networkx.edges), 2)  # check that there are two edge connections
+            g.run(syn)
+
+        for n in g.networkx:
+            self.assertEqual(n.status, Status.COMPLETE)
 
     def test_encode_decode(self) -> None:
         """

From 3d1be77e3edfad784ec89d5f73316adfb2d145b0 Mon Sep 17 00:00:00 2001
From: Bryan Ngo <bryanngo@berkeley.edu>
Date: Thu, 23 Mar 2023 17:02:08 -0700
Subject: [PATCH 20/36] update poetry.lock

---
 poetry.lock | 700 ++++++++++++++++++++++++++--------------------------
 1 file changed, 354 insertions(+), 346 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 9ebff9f13..8cfb05fba 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -14,14 +14,14 @@ files = [
 
 [[package]]
 name = "astroid"
-version = "2.13.3"
+version = "2.15.0"
 description = "An abstract syntax tree for Python with inference support."
 category = "dev"
 optional = false
 python-versions = ">=3.7.2"
 files = [
-    {file = "astroid-2.13.3-py3-none-any.whl", hash = "sha256:14c1603c41cc61aae731cad1884a073c4645e26f126d13ac8346113c95577f3b"},
-    {file = "astroid-2.13.3.tar.gz", hash = "sha256:6afc22718a48a689ca24a97981ad377ba7fb78c133f40335dfd16772f29bcfb1"},
+    {file = "astroid-2.15.0-py3-none-any.whl", hash = "sha256:e3e4d0ffc2d15d954065579689c36aac57a339a4679a679579af6401db4d3fdb"},
+    {file = "astroid-2.15.0.tar.gz", hash = "sha256:525f126d5dc1b8b0b6ee398b33159105615d92dc4a17f2cd064125d57f6186fa"},
 ]
 
 [package.dependencies]
@@ -53,19 +53,16 @@ tests-no-zope = ["cloudpickle", "cloudpickle", "hypothesis", "hypothesis", "mypy
 
 [[package]]
 name = "babel"
-version = "2.11.0"
+version = "2.12.1"
 description = "Internationalization utilities"
 category = "dev"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 files = [
-    {file = "Babel-2.11.0-py3-none-any.whl", hash = "sha256:1ad3eca1c885218f6dce2ab67291178944f810a10a9b5f3cb8382a5a232b64fe"},
-    {file = "Babel-2.11.0.tar.gz", hash = "sha256:5ef4b3226b0180dedded4229651c8b0e1a3a6a2837d45a073272f313e4cf97f6"},
+    {file = "Babel-2.12.1-py3-none-any.whl", hash = "sha256:b4246fb7677d3b98f501a39d43396d3cafdc8eadb045f4a31be01863f655c610"},
+    {file = "Babel-2.12.1.tar.gz", hash = "sha256:cc2d99999cd01d44420ae725a21c9e3711b3aadc7976d6147f622d8581963455"},
 ]
 
-[package.dependencies]
-pytz = ">=2015.7"
-
 [[package]]
 name = "certifi"
 version = "2022.12.7"
@@ -80,100 +77,87 @@ files = [
 
 [[package]]
 name = "charset-normalizer"
-version = "3.0.1"
+version = "3.1.0"
 description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
 category = "dev"
 optional = false
-python-versions = "*"
+python-versions = ">=3.7.0"
 files = [
-    {file = "charset-normalizer-3.0.1.tar.gz", hash = "sha256:ebea339af930f8ca5d7a699b921106c6e29c617fe9606fa7baa043c1cdae326f"},
-    {file = "charset_normalizer-3.0.1-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:88600c72ef7587fe1708fd242b385b6ed4b8904976d5da0893e31df8b3480cb6"},
-    {file = "charset_normalizer-3.0.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:c75ffc45f25324e68ab238cb4b5c0a38cd1c3d7f1fb1f72b5541de469e2247db"},
-    {file = "charset_normalizer-3.0.1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:db72b07027db150f468fbada4d85b3b2729a3db39178abf5c543b784c1254539"},
-    {file = "charset_normalizer-3.0.1-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:62595ab75873d50d57323a91dd03e6966eb79c41fa834b7a1661ed043b2d404d"},
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 [[package]]
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 category = "dev"
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 python-versions = ">=3.7"
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 [package.extras]
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 name = "gdspy"
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 [package.dependencies]
@@ -335,14 +328,14 @@ files = [
 
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-version = "6.0.0"
+version = "6.1.0"
 description = "Read metadata from Python packages"
 category = "dev"
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 python-versions = ">=3.7"
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@@ -367,19 +360,19 @@ files = [
 
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+version = "5.12.0"
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-pipfile-deprecated-finder = ["pipreqs", "requirementslib"]
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 plugins = ["setuptools"]
 requirements-deprecated-finder = ["pip-api", "pipreqs"]
 
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 profiling = ["gprof2dot"]
 rtd = ["attrs", "myst-parser", "pyyaml", "sphinx", "sphinx-copybutton", "sphinx-design", "sphinx_book_theme"]
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 name = "pluggy"
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 [package.dependencies]
@@ -849,18 +842,18 @@ plugins = ["importlib-metadata"]
 
 [[package]]
 name = "pylint"
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+version = "2.17.1"
 description = "python code static checker"
 category = "dev"
 optional = false
 python-versions = ">=3.7.2"
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 [package.dependencies]
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 colorama = {version = ">=0.4.5", markers = "sys_platform == \"win32\""}
 dill = [
     {version = ">=0.2", markers = "python_version < \"3.11\""},
@@ -879,14 +872,14 @@ testutils = ["gitpython (>3)"]
 
 [[package]]
 name = "pytest"
-version = "7.2.1"
+version = "7.2.2"
 description = "pytest: simple powerful testing with Python"
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
@@ -901,18 +894,6 @@ tomli = {version = ">=1.0.0", markers = "python_version < \"3.11\""}
 [package.extras]
 testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "xmlschema"]
 
-[[package]]
-name = "pytz"
-version = "2022.7.1"
-description = "World timezone definitions, modern and historical"
-category = "dev"
-optional = false
-python-versions = "*"
-files = [
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-]
-
 [[package]]
 name = "pyyaml"
 version = "6.0"
@@ -1110,19 +1091,20 @@ test = ["cython", "html5lib", "pytest (>=4.6)", "typed_ast"]
 
 [[package]]
 name = "sphinx-rtd-theme"
-version = "1.1.1"
+version = "1.2.0"
 description = "Read the Docs theme for Sphinx"
 category = "dev"
 optional = false
-python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,>=2.7"
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7"
 files = [
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 ]
 
 [package.dependencies]
-docutils = "<0.18"
-sphinx = ">=1.6,<6"
+docutils = "<0.19"
+sphinx = ">=1.6,<7"
+sphinxcontrib-jquery = {version = ">=2.0.0,<3.0.0 || >3.0.0", markers = "python_version > \"3\""}
 
 [package.extras]
 dev = ["bump2version", "sphinxcontrib-httpdomain", "transifex-client", "wheel"]
@@ -1161,20 +1143,35 @@ test = ["pytest"]
 
 [[package]]
 name = "sphinxcontrib-htmlhelp"
-version = "2.0.0"
+version = "2.0.1"
 description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files"
 category = "dev"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [package.extras]
 lint = ["docutils-stubs", "flake8", "mypy"]
 test = ["html5lib", "pytest"]
 
+[[package]]
+name = "sphinxcontrib-jquery"
+version = "4.1"
+description = "Extension to include jQuery on newer Sphinx releases"
+category = "dev"
+optional = false
+python-versions = ">=2.7"
+files = [
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+
+[package.dependencies]
+Sphinx = ">=1.8"
+
 [[package]]
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 version = "1.0.1"
@@ -1274,38 +1271,38 @@ testing = ["flaky (>=3.4.0)", "freezegun (>=0.3.11)", "pathlib2 (>=2.3.3)", "psu
 
 [[package]]
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+version = "6.0.12.8"
 description = "Typing stubs for PyYAML"
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 [[package]]
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+version = "4.5.0"
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 python-versions = ">=3.7"
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 [[package]]
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 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
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 [package.extras]
@@ -1315,114 +1312,125 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
 
 [[package]]
 name = "virtualenv"
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+version = "20.21.0"
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 [package.dependencies]
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 filelock = ">=3.4.1,<4"
-platformdirs = ">=2.4,<3"
+platformdirs = ">=2.4,<4"
 
 [package.extras]
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+    {file = "wrapt-1.15.0-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:7dc0713bf81287a00516ef43137273b23ee414fe41a3c14be10dd95ed98a2df9"},
+    {file = "wrapt-1.15.0-cp39-cp39-win32.whl", hash = "sha256:46ed616d5fb42f98630ed70c3529541408166c22cdfd4540b88d5f21006b0eff"},
+    {file = "wrapt-1.15.0-cp39-cp39-win_amd64.whl", hash = "sha256:eef4d64c650f33347c1f9266fa5ae001440b232ad9b98f1f43dfe7a79435c0a6"},
+    {file = "wrapt-1.15.0-py3-none-any.whl", hash = "sha256:64b1df0f83706b4ef4cfb4fb0e4c2669100fd7ecacfb59e091fad300d4e04640"},
+    {file = "wrapt-1.15.0.tar.gz", hash = "sha256:d06730c6aed78cee4126234cf2d071e01b44b915e725a6cb439a879ec9754a3a"},
 ]
 
 [[package]]
 name = "zipp"
-version = "3.11.0"
+version = "3.15.0"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "zipp-3.11.0-py3-none-any.whl", hash = "sha256:83a28fcb75844b5c0cdaf5aa4003c2d728c77e05f5aeabe8e95e56727005fbaa"},
-    {file = "zipp-3.11.0.tar.gz", hash = "sha256:a7a22e05929290a67401440b39690ae6563279bced5f314609d9d03798f56766"},
+    {file = "zipp-3.15.0-py3-none-any.whl", hash = "sha256:48904fc76a60e542af151aded95726c1a5c34ed43ab4134b597665c86d7ad556"},
+    {file = "zipp-3.15.0.tar.gz", hash = "sha256:112929ad649da941c23de50f356a2b5570c954b65150642bccdd66bf194d224b"},
 ]
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)"]
-testing = ["flake8 (<5)", "func-timeout", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"]
+docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"]
 
 [extras]
 asap7 = ["gdspy"]

From 02d0cf2bbce064669bc2caf8a0ac393266622369 Mon Sep 17 00:00:00 2001
From: Bryan Ngo <bryanngo@berkeley.edu>
Date: Thu, 23 Mar 2023 17:21:11 -0700
Subject: [PATCH 21/36] mermaid generator automatically writes to file

---
 hammer/flowgraph/node.py | 11 +++++++++--
 tests/test_node.py       | 16 +++++++++-------
 2 files changed, 18 insertions(+), 9 deletions(-)

diff --git a/hammer/flowgraph/node.py b/hammer/flowgraph/node.py
index 9c03d6dad..c5b936cfb 100644
--- a/hammer/flowgraph/node.py
+++ b/hammer/flowgraph/node.py
@@ -310,19 +310,26 @@ def to_json(self) -> dict:
     def to_d2(self) -> Any:
         raise NotImplementedError()
 
-    def to_mermaid(self, fname: str) -> None:
+    def to_mermaid(self) -> str:
         """Converts the flowgraph into Mermaid format for visualization.
 
         Args:
             fname (str): Output file name.
+
+        Returns:
+            str: Path to Mermaid Markdown file.
         """
+        folder = os.path.dirname(list(self.networkx.nodes)[0].pull_dir)
+        fname = os.path.join(folder, "graph_viz.md")
         with open(fname, 'w', encoding="utf-8") as f:
-            f.write("stateDiagram-v2\n")
+            f.write("```mermaid\nstateDiagram-v2\n")
             for start in self.networkx:
                 f.writelines(
                     f"    {start.action} --> {child.action}\n"
                     for child in nx.neighbors(self.networkx, start)
                 )
+            f.write("```\n")
+        return fname
 
 def convert_to_acyclic(g: Graph) -> Graph:
     """Eliminates cycles in a flowgraph for analysis.
diff --git a/tests/test_node.py b/tests/test_node.py
index d8956e883..ca53569cd 100644
--- a/tests/test_node.py
+++ b/tests/test_node.py
@@ -455,13 +455,15 @@ def test_mermaid(self) -> None:
                 par: []
             }, auto_auxiliary=False)
 
-            g.to_mermaid(os.path.join(td, "mermaid.md"))
-            with open(os.path.join(td, "mermaid.md"), 'r', encoding="utf-8") as f:
+            fname = g.to_mermaid()
+            with open(fname, 'r', encoding="utf-8") as f:
                 s = f.readlines()
                 self.assertListEqual(s,
-                                     ["stateDiagram-v2\n",
+                                     ["```mermaid\n",
+                                      "stateDiagram-v2\n",
                                       "    syn --> syn-to-par\n",
-                                      "    syn-to-par --> par\n"])
+                                      "    syn-to-par --> par\n",
+                                      "```\n"])
 
     def test_auto_auxiliary(self) -> None:
         """
@@ -535,8 +537,8 @@ def test_auto_auxiliary(self) -> None:
                 syn: [par],
                 par: []
             })
-            self.assertEqual(len(g.networkx), 3)  # check that there are three nodes
-            self.assertEqual(len(g.networkx.edges), 2)  # check that there are two edge connections
+            self.assertEqual(g.networkx.number_of_nodes(), 3)  # check that there are three nodes
+            self.assertEqual(g.networkx.number_of_edges(), 2)  # check that there are two edge connections
             g.run(syn)
 
         for n in g.networkx:
@@ -624,7 +626,7 @@ def test_encode_decode(self) -> None:
             out = json.dumps(g.to_json(), cls=node.NodeEncoder)
             g_dec = json.loads(out, object_hook=node.as_node)
             # print(g.to_json())
-            print(json_graph.node_link_graph(g_dec).nodes)
+            # print(json_graph.node_link_graph(g_dec).nodes)
 
 if __name__ == "__main__":
     unittest.main()

From f8ae7e2f6dd8c257c8f4f1b483a6e1abec8c6e40 Mon Sep 17 00:00:00 2001
From: Bryan Ngo <bryanngo@berkeley.edu>
Date: Fri, 24 Mar 2023 12:13:48 -0700
Subject: [PATCH 22/36] implement hook test and direct imports

---
 hammer/flowgraph/node.py |  25 ++--
 tests/test_node.py       | 315 +++++++++++++--------------------------
 2 files changed, 117 insertions(+), 223 deletions(-)

diff --git a/hammer/flowgraph/node.py b/hammer/flowgraph/node.py
index c5b936cfb..cc196252a 100644
--- a/hammer/flowgraph/node.py
+++ b/hammer/flowgraph/node.py
@@ -20,7 +20,7 @@
 from networkx.readwrite import json_graph
 
 from hammer.logging import HammerVLSILogging
-from hammer.vlsi import cli_driver
+from hammer.vlsi.cli_driver import CLIDriver
 
 
 class Status(Enum):
@@ -52,7 +52,7 @@ class Node:
     required_outputs:  list[str]
     status:            Status    = Status.NOT_RUN
     # __uuid:            uuid.UUID = field(default_factory=uuid.uuid4)
-    driver:            str       = ""
+    driver:            CLIDriver = field(default_factory=CLIDriver)
     optional_inputs:   list[str] = field(default_factory=list)
     optional_outputs:  list[str] = field(default_factory=list)
     step_controls:     dict[str, str] = field(default_factory=lambda: {
@@ -247,14 +247,16 @@ def run(self, start: Node) -> Any:
         if not start.privileged and any(i.privileged for i in self.networkx):
             raise RuntimeError("Attempting to run non-privileged node in privileged flow. Please complete your stepped flow first.")
 
-        if start.driver != "":
-            driver_pkg_path, driver_module = start.driver.rsplit('.', 1)
-            driver_pkg = importlib.import_module(driver_pkg_path)
-            driver = getattr(driver_pkg, driver_module)()
-            if not isinstance(driver, cli_driver.CLIDriver):
-                raise TypeError(f"Driver {driver} does not extend CLIDriver, cannot run a flow.")
-        else:
-            driver = cli_driver.CLIDriver()
+        # if start.driver != "":
+        #     driver_pkg_path, driver_module = start.driver.rsplit('.', 1)
+        #     driver_pkg = importlib.import_module(driver_pkg_path)
+        #     driver = getattr(driver_pkg, driver_module)()
+        #     if not isinstance(driver, cli_driver.CLIDriver):
+        #         raise TypeError(f"Driver {driver} does not extend CLIDriver, cannot run a flow.")
+        # else:
+        #     driver = cli_driver.CLIDriver()
+
+        driver = start.driver
 
         arg_list = {
             "action": start.action,
@@ -307,9 +309,6 @@ def to_json(self) -> dict:
         """
         return json_graph.node_link_data(self.networkx)
 
-    def to_d2(self) -> Any:
-        raise NotImplementedError()
-
     def to_mermaid(self) -> str:
         """Converts the flowgraph into Mermaid format for visualization.
 
diff --git a/tests/test_node.py b/tests/test_node.py
index ca53569cd..9e8807048 100644
--- a/tests/test_node.py
+++ b/tests/test_node.py
@@ -8,11 +8,59 @@
 import pytest
 from networkx.readwrite import json_graph
 
+from hammer.vlsi.cli_driver import (
+    CLIDriver,
+    HammerTool,
+    HammerToolHookAction
+)
 from hammer.flowgraph import node
 from hammer.flowgraph.node import Graph, Node, Status
 from hammer.logging import HammerVLSILogging
+from hammer.vlsi import HammerTool
 
 
+MOCK_CFG = dedent("""
+synthesis.inputs:
+    input_files: ["LICENSE", "README.md"]
+    top_module: "z1top.xdc"
+
+par.inputs:
+    input_files: ["LICENSE", "README.md"]
+    top_module: "z1top.xdc"
+
+drc.inputs:
+    input_files: ["LICENSE", "README.md"]
+    top_module: "z1top.xdc"
+
+lvs.inputs:
+    input_files: ["LICENSE", "README.md"]
+    schematic_files: ["LICENSE", "README.md"]
+    top_module: "z1top.xdc"
+    hcells_list: []
+
+pcb.inputs:
+    top_module: "z1top.xdc"
+
+formal.inputs:
+    input_files: ["LICENSE", "README.md"]
+    top_module: "z1top.xdc"
+
+sim.inputs:
+    input_files: ["LICENSE", "README.md"]
+    top_module: "z1top.xdc"
+
+vlsi:
+    core:
+        technology: "hammer.technology.nop"
+
+        synthesis_tool: "hammer.synthesis.nop"
+        par_tool: "hammer.par.nop"
+        drc_tool: "hammer.drc.nop"
+        lvs_tool: "hammer.lvs.nop"
+        power_tool: "hammer.power.nop"
+        sim_tool: "mocksim"
+""")
+
 class TestNode(unittest.TestCase):
 
     def test_initialize_node(self) -> None:
@@ -170,54 +218,12 @@ def test_run_basic(self) -> None:
         HammerVLSILogging.clear_callbacks()
         HammerVLSILogging.add_callback(HammerVLSILogging.callback_buffering)
 
-        cfg = dedent("""
-            synthesis.inputs:
-                input_files: ["LICENSE", "README.md"]
-                top_module: "z1top.xdc"
-
-            par.inputs:
-                input_files: ["LICENSE", "README.md"]
-                top_module: "z1top.xdc"
-
-            drc.inputs:
-                input_files: ["LICENSE", "README.md"]
-                top_module: "z1top.xdc"
-
-            lvs.inputs:
-                input_files: ["LICENSE", "README.md"]
-                schematic_files: ["LICENSE", "README.md"]
-                top_module: "z1top.xdc"
-                hcells_list: []
-
-            pcb.inputs:
-                top_module: "z1top.xdc"
-
-            formal.inputs:
-                input_files: ["LICENSE", "README.md"]
-                top_module: "z1top.xdc"
-
-            sim.inputs:
-                input_files: ["LICENSE", "README.md"]
-                top_module: "z1top.xdc"
-
-            vlsi:
-                core:
-                    technology: "hammer.technology.nop"
-
-                    synthesis_tool: "hammer.synthesis.nop"
-                    par_tool: "hammer.par.nop"
-                    drc_tool: "hammer.drc.nop"
-                    lvs_tool: "hammer.lvs.nop"
-                    power_tool: "hammer.power.nop"
-                    sim_tool: "mocksim"
-        """)
-
         with tempfile.TemporaryDirectory() as td:
             os.mkdir(os.path.join(td, "syn_dir"))
             os.mkdir(os.path.join(td, "par_dir"))
 
             with open(os.path.join(td, "syn_dir", "syn-in.yml"), 'w', encoding="utf-8") as tf1:
-                tf1.write(cfg)
+                tf1.write(MOCK_CFG)
 
             syn = Node(
                 "syn", "nop",
@@ -255,54 +261,12 @@ def test_invalid_run(self) -> None:
         HammerVLSILogging.clear_callbacks()
         HammerVLSILogging.add_callback(HammerVLSILogging.callback_buffering)
 
-        cfg = dedent("""
-            synthesis.inputs:
-                input_files: ["LICENSE", "README.md"]
-                top_module: "z1top.xdc"
-
-            par.inputs:
-                input_files: ["LICENSE", "README.md"]
-                top_module: "z1top.xdc"
-
-            drc.inputs:
-                input_files: ["LICENSE", "README.md"]
-                top_module: "z1top.xdc"
-
-            lvs.inputs:
-                input_files: ["LICENSE", "README.md"]
-                schematic_files: ["LICENSE", "README.md"]
-                top_module: "z1top.xdc"
-                hcells_list: []
-
-            pcb.inputs:
-                top_module: "z1top.xdc"
-
-            formal.inputs:
-                input_files: ["LICENSE", "README.md"]
-                top_module: "z1top.xdc"
-
-            sim.inputs:
-                input_files: ["LICENSE", "README.md"]
-                top_module: "z1top.xdc"
-
-            vlsi:
-                core:
-                    technology: "hammer.technology.nop"
-
-                    synthesis_tool: "hammer.synthesis.nop"
-                    par_tool: "hammer.par.nop"
-                    drc_tool: "hammer.drc.nop"
-                    lvs_tool: "hammer.lvs.nop"
-                    power_tool: "hammer.power.nop"
-                    sim_tool: "mocksim"
-        """)
-
         with tempfile.TemporaryDirectory() as td:
             os.mkdir(os.path.join(td, "syn_dir"))
             os.mkdir(os.path.join(td, "par_dir"))
 
             with open(os.path.join(td, "syn_dir", "syn-in.yml"), 'w', encoding="utf-8") as tf1:
-                tf1.write(cfg)
+                tf1.write(MOCK_CFG)
 
             syn = Node(
                 "syn", "nop",
@@ -340,54 +304,12 @@ def test_resume_graph(self) -> None:
         HammerVLSILogging.clear_callbacks()
         HammerVLSILogging.add_callback(HammerVLSILogging.callback_buffering)
 
-        cfg = dedent("""
-            synthesis.inputs:
-                input_files: ["LICENSE", "README.md"]
-                top_module: "z1top.xdc"
-
-            par.inputs:
-                input_files: ["LICENSE", "README.md"]
-                top_module: "z1top.xdc"
-
-            drc.inputs:
-                input_files: ["LICENSE", "README.md"]
-                top_module: "z1top.xdc"
-
-            lvs.inputs:
-                input_files: ["LICENSE", "README.md"]
-                schematic_files: ["LICENSE", "README.md"]
-                top_module: "z1top.xdc"
-                hcells_list: []
-
-            pcb.inputs:
-                top_module: "z1top.xdc"
-
-            formal.inputs:
-                input_files: ["LICENSE", "README.md"]
-                top_module: "z1top.xdc"
-
-            sim.inputs:
-                input_files: ["LICENSE", "README.md"]
-                top_module: "z1top.xdc"
-
-            vlsi:
-                core:
-                    technology: "hammer.technology.nop"
-
-                    synthesis_tool: "hammer.synthesis.nop"
-                    par_tool: "hammer.par.nop"
-                    drc_tool: "hammer.drc.nop"
-                    lvs_tool: "hammer.lvs.nop"
-                    power_tool: "hammer.power.nop"
-                    sim_tool: "mocksim"
-        """)
-
         with tempfile.TemporaryDirectory() as td:
             os.mkdir(os.path.join(td, "syn_dir"))
             os.mkdir(os.path.join(td, "par_dir"))
 
             with open(os.path.join(td, "syn_dir", "syn-in.yml"), 'w', encoding="utf-8") as tf1:
-                tf1.write(cfg)
+                tf1.write(MOCK_CFG)
 
             syn = Node(
                 "syn", "nop",
@@ -472,54 +394,13 @@ def test_auto_auxiliary(self) -> None:
         HammerVLSILogging.clear_callbacks()
         HammerVLSILogging.add_callback(HammerVLSILogging.callback_buffering)
 
-        cfg = dedent("""
-            synthesis.inputs:
-                input_files: ["LICENSE", "README.md"]
-                top_module: "z1top.xdc"
-
-            par.inputs:
-                input_files: ["LICENSE", "README.md"]
-                top_module: "z1top.xdc"
-
-            drc.inputs:
-                input_files: ["LICENSE", "README.md"]
-                top_module: "z1top.xdc"
-
-            lvs.inputs:
-                input_files: ["LICENSE", "README.md"]
-                schematic_files: ["LICENSE", "README.md"]
-                top_module: "z1top.xdc"
-                hcells_list: []
-
-            pcb.inputs:
-                top_module: "z1top.xdc"
-
-            formal.inputs:
-                input_files: ["LICENSE", "README.md"]
-                top_module: "z1top.xdc"
-
-            sim.inputs:
-                input_files: ["LICENSE", "README.md"]
-                top_module: "z1top.xdc"
-
-            vlsi:
-                core:
-                    technology: "hammer.technology.nop"
-
-                    synthesis_tool: "hammer.synthesis.nop"
-                    par_tool: "hammer.par.nop"
-                    drc_tool: "hammer.drc.nop"
-                    lvs_tool: "hammer.lvs.nop"
-                    power_tool: "hammer.power.nop"
-                    sim_tool: "mocksim"
-        """)
 
         with tempfile.TemporaryDirectory() as td:
             os.mkdir(os.path.join(td, "syn_dir"))
             os.mkdir(os.path.join(td, "par_dir"))
 
             with open(os.path.join(td, "syn_dir", "syn-in.yml"), 'w', encoding="utf-8") as tf1:
-                tf1.write(cfg)
+                tf1.write(MOCK_CFG)
 
             syn = Node(
                 "syn", "nop",
@@ -544,61 +425,66 @@ def test_auto_auxiliary(self) -> None:
         for n in g.networkx:
             self.assertEqual(n.status, Status.COMPLETE)
 
-    def test_encode_decode(self) -> None:
+    def test_flowgraph_hooks(self) -> None:
         """
-        Test that a flowgraph can be encoded and decoded.
+        Test that hooks can be used in flowgraphs.
         """
-        HammerVLSILogging.clear_callbacks()
-        HammerVLSILogging.add_callback(HammerVLSILogging.callback_buffering)
-
-        cfg = dedent("""
-            synthesis.inputs:
-                input_files: ["LICENSE", "README.md"]
-                top_module: "z1top.xdc"
+        with tempfile.TemporaryDirectory() as td:
+            syn_dir = os.path.join(td, "syn_dir")
+            out_dir = os.path.join(td, "out_dir")
+            os.mkdir(syn_dir)
+            os.mkdir(out_dir)
 
-            par.inputs:
-                input_files: ["LICENSE", "README.md"]
-                top_module: "z1top.xdc"
+            cfg = dedent(f"""
+                vlsi.core:
+                    synthesis_tool: hammer.synthesis.mocksynth
+                    technology: hammer.technology.nop
 
-            drc.inputs:
-                input_files: ["LICENSE", "README.md"]
-                top_module: "z1top.xdc"
+                synthesis.inputs:
+                    top_module: dummy
+                    input_files: ["/dev/null"]
 
-            lvs.inputs:
-                input_files: ["LICENSE", "README.md"]
-                schematic_files: ["LICENSE", "README.md"]
-                top_module: "z1top.xdc"
-                hcells_list: []
+                synthesis.mocksynth.temp_folder: {out_dir}
+            """)
 
-            pcb.inputs:
-                top_module: "z1top.xdc"
+            with open(os.path.join(syn_dir, "syn-in.yml"), 'w', encoding="utf-8") as tf1:
+                tf1.write(cfg)
 
-            formal.inputs:
-                input_files: ["LICENSE", "README.md"]
-                top_module: "z1top.xdc"
+            syn = Node(
+                "syn", "mocksynth",
+                syn_dir, out_dir,
+                ["syn-in.yml"],
+                ["syn-out.json"],
+                driver=NodeDummyDriver()
+            )
 
-            sim.inputs:
-                input_files: ["LICENSE", "README.md"]
-                top_module: "z1top.xdc"
+            g = Graph({
+                syn: []
+            })
+            g.run(syn)
 
-            vlsi:
-                core:
-                    technology: "hammer.technology.nop"
+            for i in range(1, 5):
+                file = os.path.join(out_dir, f"step{i}.txt")
+                if i in (2, 4):
+                    self.assertFalse(os.path.exists(file))
+                else:
+                    self.assertTrue(os.path.exists(file))
 
-                    synthesis_tool: "hammer.synthesis.nop"
-                    par_tool: "hammer.par.nop"
-                    drc_tool: "hammer.drc.nop"
-                    lvs_tool: "hammer.lvs.nop"
-                    power_tool: "hammer.power.nop"
-                    sim_tool: "mocksim"
-        """)
+    @pytest.mark.skip
+    def test_encode_decode(self) -> None:
+        """
+        Test that a flowgraph can be encoded and decoded.
+        """
+        HammerVLSILogging.clear_callbacks()
+        HammerVLSILogging.add_callback(HammerVLSILogging.callback_buffering)
 
         with tempfile.TemporaryDirectory() as td:
             os.mkdir(os.path.join(td, "syn_dir"))
             os.mkdir(os.path.join(td, "par_dir"))
 
             with open(os.path.join(td, "syn_dir", "syn-in.yml"), 'w', encoding="utf-8") as tf1:
-                tf1.write(cfg)
+                tf1.write(MOCK_CFG)
+                
             syn = Node(
                 "syn", "nop",
                 os.path.join(td, "syn_dir"), os.path.join(td, "s2p_dir"),
@@ -628,5 +514,14 @@ def test_encode_decode(self) -> None:
             # print(g.to_json())
             # print(json_graph.node_link_graph(g_dec).nodes)
 
+class NodeDummyDriver(CLIDriver):
+    def get_extra_synthesis_hooks(self) -> list[HammerToolHookAction]:
+        extra_hooks = [
+            HammerTool.make_removal_hook("step2"),
+            HammerTool.make_removal_hook("step4"),
+        ]
+        return extra_hooks
+
+
 if __name__ == "__main__":
     unittest.main()

From 117516348bc66aa4e636b8ba1717d78190e53cc1 Mon Sep 17 00:00:00 2001
From: Bryan Ngo <bryanngo@berkeley.edu>
Date: Mon, 27 Mar 2023 21:14:05 -0700
Subject: [PATCH 23/36] change runner to iteratively run nodes via BFS

---
 hammer/flowgraph/node.py | 67 +++++++++++++++++++++-------------------
 1 file changed, 36 insertions(+), 31 deletions(-)

diff --git a/hammer/flowgraph/node.py b/hammer/flowgraph/node.py
index cc196252a..1854c4d29 100644
--- a/hammer/flowgraph/node.py
+++ b/hammer/flowgraph/node.py
@@ -8,7 +8,6 @@
 
 # pylint: disable=invalid-name
 
-import importlib
 import json
 import os
 import uuid
@@ -247,23 +246,34 @@ def run(self, start: Node) -> Any:
         if not start.privileged and any(i.privileged for i in self.networkx):
             raise RuntimeError("Attempting to run non-privileged node in privileged flow. Please complete your stepped flow first.")
 
-        # if start.driver != "":
-        #     driver_pkg_path, driver_module = start.driver.rsplit('.', 1)
-        #     driver_pkg = importlib.import_module(driver_pkg_path)
-        #     driver = getattr(driver_pkg, driver_module)()
-        #     if not isinstance(driver, cli_driver.CLIDriver):
-        #         raise TypeError(f"Driver {driver} does not extend CLIDriver, cannot run a flow.")
-        # else:
-        #     driver = cli_driver.CLIDriver()
+        start_code = Graph.__run_single(start)
+        if start_code != 0:
+            return self
+        else:
+            for _, c in nx.bfs_edges(self.networkx, start):
+                code = Graph.__run_single(c)
+                if code != 0:
+                    break
+        return self
 
-        driver = start.driver
+    @staticmethod
+    def __run_single(node: Node) -> int:
+        """Helper function to run a HAMMER node.
+
+        Args:
+            node (Node): Node to run action on.
+
+        Returns:
+            int: Status code.
+        """
+        driver = node.driver
 
         arg_list = {
-            "action": start.action,
+            "action": node.action,
             'environment_config': None,
-            'configs': [os.path.join(start.pull_dir, i) for i in start.required_inputs],
+            'configs': [os.path.join(node.pull_dir, i) for i in node.required_inputs],
             'log': None,
-            'obj_dir': start.push_dir,
+            'obj_dir': node.push_dir,
             'syn_rundir': '',
             'par_rundir': '',
             'drc_rundir': '',
@@ -272,12 +282,12 @@ def run(self, start: Node) -> Any:
             'power_rundir': '',
             'formal_rundir': '',
             'timing_rundir': '',
-            'from_step': start.step_controls["from_step"],
-            'after_step': start.step_controls["after_step"],
-            'to_step': start.step_controls["to_step"],
-            'until_step': start.step_controls["until_step"],
-            'only_step': start.step_controls["only_step"],
-            'output': os.path.join(start.push_dir, start.required_outputs[0]),  # TODO: fix this
+            'from_step': node.step_controls["from_step"],
+            'after_step': node.step_controls["after_step"],
+            'to_step': node.step_controls["to_step"],
+            'until_step': node.step_controls["until_step"],
+            'only_step': node.step_controls["only_step"],
+            'output': os.path.join(node.push_dir, node.required_outputs[0]),  # TODO: fix this
             'verilog': None,
             'firrtl': None,
             'top': None,
@@ -285,21 +295,16 @@ def run(self, start: Node) -> Any:
             'dump_history': False
         }
 
-        start.status = Status.RUNNING
-        ctxt = HammerVLSILogging.context(start.action)
-        ctxt.info(f"Running graph step {start.action}")
+        node.status = Status.RUNNING
+        ctxt = HammerVLSILogging.context(node.action)
+        ctxt.info(f"Running graph step {node.action}")
         code = driver.run_main_parsed(arg_list)
         if code == 0:
-            start.status = Status.COMPLETE
+            node.status = Status.COMPLETE
         else:
-            start.status = Status.INCOMPLETE
-            ctxt.fatal(f"Step {start.action} failed")
-            return self
-
-        for c in nx.neighbors(self.networkx, start):
-            self.run(c)
-
-        return self
+            node.status = Status.INCOMPLETE
+            ctxt.fatal(f"Step {node.action} failed")
+        return code
 
     def to_json(self) -> dict:
         """Encodes a graph as a JSON string.

From 812b763950f71ef88a2af5f5c3aac6a55f26b8b5 Mon Sep 17 00:00:00 2001
From: Bryan Ngo <bryanngo@berkeley.edu>
Date: Mon, 27 Mar 2023 21:33:32 -0700
Subject: [PATCH 24/36] add mermaid support to docs

---
 doc/conf.py    |  3 ++-
 poetry.lock    | 50 +++++++++++++++++++++++++++++++-------------------
 pyproject.toml |  1 +
 3 files changed, 34 insertions(+), 20 deletions(-)

diff --git a/doc/conf.py b/doc/conf.py
index 443fa8815..afbd1f5aa 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -31,7 +31,8 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    "myst_parser"
+    "myst_parser",
+    "sphinxcontrib.mermaid"
 ]
 
 # Add any paths that contain templates here, relative to this directory.
diff --git a/poetry.lock b/poetry.lock
index 8cfb05fba..3f0e7997b 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -14,14 +14,14 @@ files = [
 
 [[package]]
 name = "astroid"
-version = "2.15.0"
+version = "2.15.1"
 description = "An abstract syntax tree for Python with inference support."
 category = "dev"
 optional = false
 python-versions = ">=3.7.2"
 files = [
-    {file = "astroid-2.15.0-py3-none-any.whl", hash = "sha256:e3e4d0ffc2d15d954065579689c36aac57a339a4679a679579af6401db4d3fdb"},
-    {file = "astroid-2.15.0.tar.gz", hash = "sha256:525f126d5dc1b8b0b6ee398b33159105615d92dc4a17f2cd064125d57f6186fa"},
+    {file = "astroid-2.15.1-py3-none-any.whl", hash = "sha256:89860bda98fe2bbd1f5d262229be7629d778ce280de68d95d4a73d1f592ad268"},
+    {file = "astroid-2.15.1.tar.gz", hash = "sha256:af4e0aff46e2868218502789898269ed95b663fba49e65d91c1e09c966266c34"},
 ]
 
 [package.dependencies]
@@ -228,19 +228,19 @@ test = ["pytest (>=6)"]
 
 [[package]]
 name = "filelock"
-version = "3.10.3"
+version = "3.10.7"
 description = "A platform independent file lock."
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "filelock-3.10.3-py3-none-any.whl", hash = "sha256:99d6282f732410d44242ca02aa49835cf5473e2dd4d6734a2a785c8889dc191e"},
-    {file = "filelock-3.10.3.tar.gz", hash = "sha256:a26bfa34d26293e04886dff13fa8dd0c8c6e1a786b723c689755fe8939297410"},
+    {file = "filelock-3.10.7-py3-none-any.whl", hash = "sha256:bde48477b15fde2c7e5a0713cbe72721cb5a5ad32ee0b8f419907960b9d75536"},
+    {file = "filelock-3.10.7.tar.gz", hash = "sha256:892be14aa8efc01673b5ed6589dbccb95f9a8596f0507e232626155495c18105"},
 ]
 
 [package.extras]
 docs = ["furo (>=2022.12.7)", "sphinx (>=6.1.3)", "sphinx-autodoc-typehints (>=1.22,!=1.23.4)"]
-testing = ["covdefaults (>=2.3)", "coverage (>=7.2.2)", "pytest (>=7.2.2)", "pytest-cov (>=4)", "pytest-timeout (>=2.1)"]
+testing = ["covdefaults (>=2.3)", "coverage (>=7.2.2)", "diff-cover (>=7.5)", "pytest (>=7.2.2)", "pytest-cov (>=4)", "pytest-mock (>=3.10)", "pytest-timeout (>=2.1)"]
 
 [[package]]
 name = "gdspy"
@@ -730,19 +730,19 @@ files = [
 
 [[package]]
 name = "platformdirs"
-version = "3.1.1"
+version = "3.2.0"
 description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "platformdirs-3.1.1-py3-none-any.whl", hash = "sha256:e5986afb596e4bb5bde29a79ac9061aa955b94fca2399b7aaac4090860920dd8"},
-    {file = "platformdirs-3.1.1.tar.gz", hash = "sha256:024996549ee88ec1a9aa99ff7f8fc819bb59e2c3477b410d90a16d32d6e707aa"},
+    {file = "platformdirs-3.2.0-py3-none-any.whl", hash = "sha256:ebe11c0d7a805086e99506aa331612429a72ca7cd52a1f0d277dc4adc20cb10e"},
+    {file = "platformdirs-3.2.0.tar.gz", hash = "sha256:d5b638ca397f25f979350ff789db335903d7ea010ab28903f57b27e1b16c2b08"},
 ]
 
 [package.extras]
 docs = ["furo (>=2022.12.7)", "proselint (>=0.13)", "sphinx (>=6.1.3)", "sphinx-autodoc-typehints (>=1.22,!=1.23.4)"]
-test = ["appdirs (==1.4.4)", "covdefaults (>=2.2.2)", "pytest (>=7.2.1)", "pytest-cov (>=4)", "pytest-mock (>=3.10)"]
+test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.2.2)", "pytest-cov (>=4)", "pytest-mock (>=3.10)"]
 
 [[package]]
 name = "pluggy"
@@ -1187,6 +1187,18 @@ files = [
 [package.extras]
 test = ["flake8", "mypy", "pytest"]
 
+[[package]]
+name = "sphinxcontrib-mermaid"
+version = "0.8.1"
+description = "Mermaid diagrams in yours Sphinx powered docs"
+category = "main"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "sphinxcontrib-mermaid-0.8.1.tar.gz", hash = "sha256:fa3e5325d4ba395336e6137d113f55026b1a03ccd115dc54113d1d871a580466"},
+    {file = "sphinxcontrib_mermaid-0.8.1-py3-none-any.whl", hash = "sha256:15491c24ec78cf1626b1e79e797a9ce87cb7959cf38f955eb72dd5512aeb6ce9"},
+]
+
 [[package]]
 name = "sphinxcontrib-qthelp"
 version = "1.0.3"
@@ -1233,14 +1245,14 @@ files = [
 
 [[package]]
 name = "tomlkit"
-version = "0.11.6"
+version = "0.11.7"
 description = "Style preserving TOML library"
 category = "dev"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 files = [
-    {file = "tomlkit-0.11.6-py3-none-any.whl", hash = "sha256:07de26b0d8cfc18f871aec595fda24d95b08fef89d147caa861939f37230bf4b"},
-    {file = "tomlkit-0.11.6.tar.gz", hash = "sha256:71b952e5721688937fb02cf9d354dbcf0785066149d2855e44531ebdd2b65d73"},
+    {file = "tomlkit-0.11.7-py3-none-any.whl", hash = "sha256:5325463a7da2ef0c6bbfefb62a3dc883aebe679984709aee32a317907d0a8d3c"},
+    {file = "tomlkit-0.11.7.tar.gz", hash = "sha256:f392ef70ad87a672f02519f99967d28a4d3047133e2d1df936511465fbb3791d"},
 ]
 
 [[package]]
@@ -1271,14 +1283,14 @@ testing = ["flaky (>=3.4.0)", "freezegun (>=0.3.11)", "pathlib2 (>=2.3.3)", "psu
 
 [[package]]
 name = "types-pyyaml"
-version = "6.0.12.8"
+version = "6.0.12.9"
 description = "Typing stubs for PyYAML"
 category = "dev"
 optional = false
 python-versions = "*"
 files = [
-    {file = "types-PyYAML-6.0.12.8.tar.gz", hash = "sha256:19304869a89d49af00be681e7b267414df213f4eb89634c4495fa62e8f942b9f"},
-    {file = "types_PyYAML-6.0.12.8-py3-none-any.whl", hash = "sha256:5314a4b2580999b2ea06b2e5f9a7763d860d6e09cdf21c0e9561daa9cbd60178"},
+    {file = "types-PyYAML-6.0.12.9.tar.gz", hash = "sha256:c51b1bd6d99ddf0aa2884a7a328810ebf70a4262c292195d3f4f9a0005f9eeb6"},
+    {file = "types_PyYAML-6.0.12.9-py3-none-any.whl", hash = "sha256:5aed5aa66bd2d2e158f75dda22b059570ede988559f030cf294871d3b647e3e8"},
 ]
 
 [[package]]
@@ -1439,4 +1451,4 @@ asap7-gdstk = ["gdstk"]
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.9"
-content-hash = "67c4116b3ad38c850c787570708e14362df542402503fa53b6414f7aaa598644"
+content-hash = "905376dcbe86ee41ff3fc09b22e3cf3cd05e40e2cf66a327f5412816e01c3c24"
diff --git a/pyproject.toml b/pyproject.toml
index b630cebed..9f5d8a08c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -26,6 +26,7 @@ PyYAML = "^6.0"
 "ruamel.yaml" = "^0.17.21"
 networkx = "^3.0"
 numpy = "^1.23.0"
+sphinxcontrib-mermaid = "^0.8.1"
 
 gdstk = { version = "^0.9.0", optional = true }
 gdspy = { version = "1.4", optional = true }

From 673adfaf04ca7ec60da6d25321f23349fb25e2a2 Mon Sep 17 00:00:00 2001
From: Bryan Ngo <bryanngo@berkeley.edu>
Date: Mon, 27 Mar 2023 21:46:52 -0700
Subject: [PATCH 25/36] simplify module imports

---
 hammer/flowgraph/__init__.py               |  5 +++++
 hammer/flowgraph/{node.py => flowgraph.py} |  5 -----
 tests/test_node.py                         | 17 ++++++++---------
 3 files changed, 13 insertions(+), 14 deletions(-)
 create mode 100644 hammer/flowgraph/__init__.py
 rename hammer/flowgraph/{node.py => flowgraph.py} (98%)

diff --git a/hammer/flowgraph/__init__.py b/hammer/flowgraph/__init__.py
new file mode 100644
index 000000000..38b16ffff
--- /dev/null
+++ b/hammer/flowgraph/__init__.py
@@ -0,0 +1,5 @@
+#  Hammer logging code.
+#
+#  See LICENSE for licence details.
+
+from .flowgraph import *
diff --git a/hammer/flowgraph/node.py b/hammer/flowgraph/flowgraph.py
similarity index 98%
rename from hammer/flowgraph/node.py
rename to hammer/flowgraph/flowgraph.py
index 1854c4d29..6a49401c9 100644
--- a/hammer/flowgraph/node.py
+++ b/hammer/flowgraph/flowgraph.py
@@ -33,9 +33,6 @@ class Status(Enum):
     COMPLETE   = "COMPLETE"
 
 
-# separate required validity checking and optional validity checking
-# meta dict for tech compatibilty
-
 @dataclass
 class Node:
     """Defines a node for an action in a flowgraph.
@@ -364,5 +361,3 @@ def convert_to_acyclic(g: Graph) -> Graph:
 
 # TODO: serialization format
 # TODO: cycles are conditional on user input
-# TODO: write tests for hooks/steps
-# TODO: make custom driver and tech for steps
diff --git a/tests/test_node.py b/tests/test_node.py
index 9e8807048..2faff83ad 100644
--- a/tests/test_node.py
+++ b/tests/test_node.py
@@ -6,17 +6,16 @@
 
 import networkx as nx
 import pytest
-from networkx.readwrite import json_graph
 
 from hammer.vlsi.cli_driver import (
     CLIDriver,
     HammerTool,
     HammerToolHookAction
 )
-from hammer.flowgraph import node
-from hammer.flowgraph.node import Graph, Node, Status
+
+from hammer import flowgraph
+from hammer.flowgraph import convert_to_acyclic, Graph, Node, Status
 from hammer.logging import HammerVLSILogging
-from hammer.vlsi import HammerTool
 
 
 MOCK_CFG = dedent("""
@@ -127,7 +126,7 @@ def test_cycle_reduction(self) -> None:
             v2: [v0],
         })
         self.assertTrue(len(nx.find_cycle(g.networkx)) > 0)
-        g_acyclic = node.convert_to_acyclic(g)
+        g_acyclic = convert_to_acyclic(g)
         with self.assertRaises(nx.NetworkXNoCycle):
             nx.find_cycle(g_acyclic.networkx)
         self.assertEqual(len(g_acyclic.networkx), 4)
@@ -162,7 +161,7 @@ def test_big_cycle_reduction(self) -> None:
             v3: [v0]
         })
         self.assertTrue(len(nx.find_cycle(g.networkx)) > 0)
-        g_acyclic = node.convert_to_acyclic(g)
+        g_acyclic = convert_to_acyclic(g)
         with self.assertRaises(nx.NetworkXNoCycle):
             nx.find_cycle(g_acyclic.networkx)
         self.assertEqual(len(g_acyclic.networkx), 5)
@@ -209,7 +208,7 @@ def test_multi_cycle_reduction(self) -> None:
             v5: [v3]
         })
         self.assertTrue(len(nx.find_cycle(g.networkx)) > 0)
-        g_acyclic = node.convert_to_acyclic(g)
+        g_acyclic = convert_to_acyclic(g)
         with self.assertRaises(nx.NetworkXNoCycle):
             nx.find_cycle(g_acyclic.networkx)
 
@@ -509,8 +508,8 @@ def test_encode_decode(self) -> None:
                 par: []
             })
 
-            out = json.dumps(g.to_json(), cls=node.NodeEncoder)
-            g_dec = json.loads(out, object_hook=node.as_node)
+            out = json.dumps(g.to_json(), cls=flowgraph.NodeEncoder)
+            g_dec = json.loads(out, object_hook=flowgraph.as_node)
             # print(g.to_json())
             # print(json_graph.node_link_graph(g_dec).nodes)
 

From 4fcb13d4d5d7bfb6f123037488e2a4702e3f97bf Mon Sep 17 00:00:00 2001
From: Bryan Ngo <bryanngo@berkeley.edu>
Date: Mon, 27 Mar 2023 22:24:16 -0700
Subject: [PATCH 26/36] rename test

---
 tests/{test_node.py => test_flowgraph.py} | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)
 rename tests/{test_node.py => test_flowgraph.py} (99%)

diff --git a/tests/test_node.py b/tests/test_flowgraph.py
similarity index 99%
rename from tests/test_node.py
rename to tests/test_flowgraph.py
index 2faff83ad..ce9f50fdb 100644
--- a/tests/test_node.py
+++ b/tests/test_flowgraph.py
@@ -60,7 +60,7 @@
         sim_tool: "mocksim"
 """)
 
-class TestNode(unittest.TestCase):
+class TestFlowgraph(unittest.TestCase):
 
     def test_initialize_node(self) -> None:
         """Test that we can instantiate a node."""

From 1cbdcddef590107a6aa80fc6040e765d26e524d7 Mon Sep 17 00:00:00 2001
From: Bryan Ngo <bryanngo@berkeley.edu>
Date: Tue, 28 Mar 2023 15:05:29 -0700
Subject: [PATCH 27/36] start documentation

---
 doc/Hammer-Use/Flowgraphs.rst | 156 ++++++++++++++++++++++++++++++++++
 doc/Hammer-Use/index.rst      |   1 +
 hammer/flowgraph/flowgraph.py |   7 +-
 tests/test_flowgraph.py       |   4 +-
 4 files changed, 162 insertions(+), 6 deletions(-)
 create mode 100644 doc/Hammer-Use/Flowgraphs.rst

diff --git a/doc/Hammer-Use/Flowgraphs.rst b/doc/Hammer-Use/Flowgraphs.rst
new file mode 100644
index 000000000..b394a579d
--- /dev/null
+++ b/doc/Hammer-Use/Flowgraphs.rst
@@ -0,0 +1,156 @@
+.. _flowgraphs:
+
+Flowgraphs
+==========
+
+Hammer has **experimental** support for flowgraph constructions, similar to tools like `mflowgen <https://github.com/mflowgen/mflowgen>`_.
+Their intention is to simplify the way flows are constructed and ran in Hammer.
+They can be imported via the ``hammer.flowgraph`` module.
+
+Construction
+------------
+
+Flowgraphs are nothing more than a collection of ``Node`` instances linked together via a ``Graph`` instance.
+Each ``Node`` "pulls" from a directory to feed in inputs and "pushes" output files to another directory to be used by other nodes.
+``Node`` instances are roughly equivalent to a single call to the ``hammer-vlsi`` CLI, so they take in similar attributes:
+
+* The action being called
+* The tool used to perform the action
+* The pull and push directories
+* Any *required* input/output files
+* Any *optional* input/output files
+* A driver to run the node with; this enables backwards compatibility with :ref:`hooks <hooks>`.
+* Options to specify steps within an action; this enables backwards compatibility with :ref:`flow control <flow-control>`.
+
+    * ``from_step``
+    * ``after_step``
+    * ``to_step``
+    * ``until_step``
+    * ``only_step``
+
+A minimal example of a ``Node``:
+
+.. code-block:: python
+    
+    from hammer.flowgraph import Node
+
+    test = Node(
+        action="foo",
+        tool="nop",
+        pull_dir="foo_dir",
+        push_dir="/dev/null",
+        required_inputs=["foo.yml"],
+        required_outputs=["foo-out.json"],
+    )
+
+Each ``Node`` has the ability to be "privileged", meaning that a flow *must* start with this node.
+This only occurs when a flow is being controlled using any of the steps.
+
+Running a Flowgraph
+-------------------
+
+``Node`` instances are linked together using an `adjacency list <https://en.wikipedia.org/wiki/Adjacency_list>`_.
+This list can be used to instantiate a ``Graph``:
+
+.. code-block:: python
+
+    from hammer.flowgraph import Graph, Node
+
+    root = Node(
+        "foo", "nop", "foo_dir", "",
+        ["foo.yml"],
+        ["foo-out.json"],
+    )
+    child1 = Node(
+        "bar", "nop", "foo_dir", "bar_dir",
+        ["foo-out.json"],
+        ["bar-out.json"],
+    )
+    graph = Graph({root: [child1]})
+
+``Graph`` instances by default *automatically* insert auxiliary actions.
+This means that actions such as ``syn-to-par`` or ``par-to-drc`` no longer need to be specified in a flow; the nodes are inserted by the flowgraph tool.
+This feature can be disabled by setting ``auto_auxiliary=False``.
+
+A ``Graph`` can be run by calling the ``run`` method and passing in a starting node.
+When running a flow, each ``Node`` keeps an internal status based on the status of the action being run:
+
+* ``NOT_RUN``: The action has yet to be run.
+* ``RUNNING``: The action is currently running.
+* ``COMPLETE``: The action has finished.
+* ``INCOMPLETE``: The action ran into an error while being run.
+* ``INVALID``: The action's outputs have been invalidated (e.g. inputs or attributes have changed).
+
+The interactions between the statuses are described in the diagram:
+
+.. mermaid::
+
+    stateDiagram-v2
+        [*] --> NOT_RUN
+        NOT_RUN --> RUNNING
+        RUNNING --> INCOMPLETE
+        RUNNING --> COMPLETE
+        INCOMPLETE --> NOT_RUN
+        COMPLETE --> INVALID
+        INVALID --> NOT_RUN
+
+Regardless of whether a flow completes with or without errors, the graph at the time of completion or error is returned, allowing for a graph to be "resumed" once any errors have been fixed.
+
+Visualization
+-------------
+
+A flowgraph can be visualized in Markdown files via the `Mermaid <https://mermaid.js.org/>`_ tool.
+Calling a ``Graph`` instance's ``to_mermaid`` method outputs a file named ``graph-viz.md``.
+The file can be viewed in a site like `Mermaid's live editor <https://mermaid.live/>`_ or using Github's native support.
+
+The flowgraph below would appear like this:
+
+.. code-block:: python
+
+    from hammer.flowgraph import Graph, Node
+
+    syn = Node(
+        "syn", "nop",
+        os.path.join(td, "syn_dir"), os.path.join(td, "s2p_dir"),
+        ["syn-in.yml"],
+        ["syn-out.json"],
+    )
+    s2p = Node(
+        "syn-to-par", "nop",
+        os.path.join(td, "s2p_dir"), os.path.join(td, "par_dir"),
+        ["syn-out.json"],
+        ["s2p-out.json"],
+    )
+    par = Node(
+        "par", "nop",
+        os.path.join(td, "par_dir"), os.path.join(td, "out_dir"),
+        ["s2p-out.json"],
+        ["par-out.json"],
+    )
+    g = Graph({
+        syn: [s2p],
+        s2p: [par],
+        par: []
+    })
+
+
+Here are the contents of ``graph-viz.md`` after calling ``g.to_mermaid()``:
+
+.. code-block:: markdown
+
+    ```mermaid
+    
+    stateDiagram-v2
+        syn --> syn_to_par
+        syn_to_par --> par
+    ```
+
+Which would render like this:
+
+.. mermaid::
+
+    stateDiagram-v2
+        syn --> syn_to_par
+        syn_to_par --> par
+
+Note that the separators have been changed to comply with Mermaid syntax.
diff --git a/doc/Hammer-Use/index.rst b/doc/Hammer-Use/index.rst
index 2e29006e4..b608c0969 100644
--- a/doc/Hammer-Use/index.rst
+++ b/doc/Hammer-Use/index.rst
@@ -13,3 +13,4 @@ This documentation will walk through more advanced features of the Hammer infras
    Hooks
    Buildfile
    Hierarchical
+   Flowgraphs
diff --git a/hammer/flowgraph/flowgraph.py b/hammer/flowgraph/flowgraph.py
index 6a49401c9..415d495d7 100644
--- a/hammer/flowgraph/flowgraph.py
+++ b/hammer/flowgraph/flowgraph.py
@@ -24,7 +24,6 @@
 
 class Status(Enum):
     """Represents the status of a node in the flowgraph.
-    https://tinyurl.com/2bstth7y
     """
     NOT_RUN    = "NOT_RUN"
     RUNNING    = "RUNNING"
@@ -195,7 +194,6 @@ def insert_auxiliary_actions(edge_list: dict[Node, list[Node]]) -> dict[Node, li
         ]
 
         changes = []
-        edge_list_copy = edge_list.copy()
         for parent_idx, (parent, children) in enumerate(edge_list.items()):
             for child_idx, child in enumerate(children):
                 if (parent.action, child.action) in valid_auxiliary_actions:
@@ -210,6 +208,7 @@ def insert_auxiliary_actions(edge_list: dict[Node, list[Node]]) -> dict[Node, li
                     )
                     changes.append((parent_idx, child_idx, aux_node))
 
+        edge_list_copy = edge_list.copy()
         for parent_idx, child_idx, aux_node in changes:
             parent, children = list(edge_list_copy.items())[parent_idx]
             parent.push_dir = os.path.join(
@@ -321,12 +320,12 @@ def to_mermaid(self) -> str:
             str: Path to Mermaid Markdown file.
         """
         folder = os.path.dirname(list(self.networkx.nodes)[0].pull_dir)
-        fname = os.path.join(folder, "graph_viz.md")
+        fname = os.path.join(folder, "graph-viz.md")
         with open(fname, 'w', encoding="utf-8") as f:
             f.write("```mermaid\nstateDiagram-v2\n")
             for start in self.networkx:
                 f.writelines(
-                    f"    {start.action} --> {child.action}\n"
+                    f"    {start.action.replace('-', '_')} --> {child.action.replace('-', '_')}\n"
                     for child in nx.neighbors(self.networkx, start)
                 )
             f.write("```\n")
diff --git a/tests/test_flowgraph.py b/tests/test_flowgraph.py
index ce9f50fdb..a39f0361f 100644
--- a/tests/test_flowgraph.py
+++ b/tests/test_flowgraph.py
@@ -382,8 +382,8 @@ def test_mermaid(self) -> None:
                 self.assertListEqual(s,
                                      ["```mermaid\n",
                                       "stateDiagram-v2\n",
-                                      "    syn --> syn-to-par\n",
-                                      "    syn-to-par --> par\n",
+                                      "    syn --> syn_to_par\n",
+                                      "    syn_to_par --> par\n",
                                       "```\n"])
 
     def test_auto_auxiliary(self) -> None:

From 689a88a8ee9e61e0dd8b303f1d9c0483dc539207 Mon Sep 17 00:00:00 2001
From: Bryan Ngo <bryanngo@berkeley.edu>
Date: Fri, 7 Apr 2023 15:37:42 -0700
Subject: [PATCH 28/36] fix wording

---
 doc/Hammer-Use/Flowgraphs.rst | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/doc/Hammer-Use/Flowgraphs.rst b/doc/Hammer-Use/Flowgraphs.rst
index b394a579d..d798ed932 100644
--- a/doc/Hammer-Use/Flowgraphs.rst
+++ b/doc/Hammer-Use/Flowgraphs.rst
@@ -68,8 +68,9 @@ This list can be used to instantiate a ``Graph``:
     )
     graph = Graph({root: [child1]})
 
-``Graph`` instances by default *automatically* insert auxiliary actions.
-This means that actions such as ``syn-to-par`` or ``par-to-drc`` no longer need to be specified in a flow; the nodes are inserted by the flowgraph tool.
+Using the Hammer CLI tool, separate actions are manually linked via an *auxiliary* action, such as ``syn-to-par``.
+By using a flowgraph, ``Graph`` instances by default *automatically* insert auxiliary actions.
+This means that actions no longer need to be specified in a flow; the necessary nodes are inserted by the flowgraph tool.
 This feature can be disabled by setting ``auto_auxiliary=False``.
 
 A ``Graph`` can be run by calling the ``run`` method and passing in a starting node.

From 2159e636f37715e6a8dd8cab031403aee822923e Mon Sep 17 00:00:00 2001
From: Bryan Ngo <bryanngo@berkeley.edu>
Date: Thu, 11 May 2023 11:01:31 -0700
Subject: [PATCH 29/36] bump packages

---
 doc/conf.py |  24 +++--
 poetry.lock | 282 +++++++++++++++++++++++++---------------------------
 2 files changed, 146 insertions(+), 160 deletions(-)

diff --git a/doc/conf.py b/doc/conf.py
index afbd1f5aa..8d154b6ce 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -17,12 +17,12 @@
 
 # -- Project information -----------------------------------------------------
 
-project = 'Hammer'
-copyright = '2023, Berkeley Architecture Research'
-author = 'Berkeley Architecture Research'
+project = "Hammer"
+copyright = "2023, Berkeley Architecture Research"
+author = "Berkeley Architecture Research"
 
 # The full version, including alpha/beta/rc tags
-release = '1.0.0'
+release = "1.0.0"
 
 
 # -- General configuration ---------------------------------------------------
@@ -32,30 +32,32 @@
 # ones.
 extensions = [
     "myst_parser",
-    "sphinxcontrib.mermaid"
+    "sphinx-jsonschema",
+    "sphinx_rtd_size",
+    "sphinxcontrib.mermaid",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
-source_suffix = '.rst'
+source_suffix = ".rst"
 
-master_doc = 'index'
+master_doc = "index"
 
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'sphinx_rtd_theme'
+html_theme = "sphinx_rtd_theme"
 
 html_theme_options = {
-    'collapse_navigation': False,
+    "collapse_navigation": False,
 }
 
 # Add any paths that contain custom static files (such as style sheets) here,
diff --git a/poetry.lock b/poetry.lock
index 3f0e7997b..c19b1dc5d 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.4.2 and should not be changed by hand.
 
 [[package]]
 name = "alabaster"
@@ -14,14 +14,14 @@ files = [
 
 [[package]]
 name = "astroid"
-version = "2.15.1"
+version = "2.15.4"
 description = "An abstract syntax tree for Python with inference support."
 category = "dev"
 optional = false
 python-versions = ">=3.7.2"
 files = [
-    {file = "astroid-2.15.1-py3-none-any.whl", hash = "sha256:89860bda98fe2bbd1f5d262229be7629d778ce280de68d95d4a73d1f592ad268"},
-    {file = "astroid-2.15.1.tar.gz", hash = "sha256:af4e0aff46e2868218502789898269ed95b663fba49e65d91c1e09c966266c34"},
+    {file = "astroid-2.15.4-py3-none-any.whl", hash = "sha256:a1b8543ef9d36ea777194bc9b17f5f8678d2c56ee6a45b2c2f17eec96f242347"},
+    {file = "astroid-2.15.4.tar.gz", hash = "sha256:c81e1c7fbac615037744d067a9bb5f9aeb655edf59b63ee8b59585475d6f80d8"},
 ]
 
 [package.dependencies]
@@ -32,25 +32,6 @@ wrapt = [
     {version = ">=1.14,<2", markers = "python_version >= \"3.11\""},
 ]
 
-[[package]]
-name = "attrs"
-version = "22.2.0"
-description = "Classes Without Boilerplate"
-category = "dev"
-optional = false
-python-versions = ">=3.6"
-files = [
-    {file = "attrs-22.2.0-py3-none-any.whl", hash = "sha256:29e95c7f6778868dbd49170f98f8818f78f3dc5e0e37c0b1f474e3561b240836"},
-    {file = "attrs-22.2.0.tar.gz", hash = "sha256:c9227bfc2f01993c03f68db37d1d15c9690188323c067c641f1a35ca58185f99"},
-]
-
-[package.extras]
-cov = ["attrs[tests]", "coverage-enable-subprocess", "coverage[toml] (>=5.3)"]
-dev = ["attrs[docs,tests]"]
-docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope.interface"]
-tests = ["attrs[tests-no-zope]", "zope.interface"]
-tests-no-zope = ["cloudpickle", "cloudpickle", "hypothesis", "hypothesis", "mypy (>=0.971,<0.990)", "mypy (>=0.971,<0.990)", "pympler", "pympler", "pytest (>=4.3.0)", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-mypy-plugins", "pytest-xdist[psutil]", "pytest-xdist[psutil]"]
-
 [[package]]
 name = "babel"
 version = "2.12.1"
@@ -65,14 +46,14 @@ files = [
 
 [[package]]
 name = "certifi"
-version = "2022.12.7"
+version = "2023.5.7"
 description = "Python package for providing Mozilla's CA Bundle."
 category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "certifi-2022.12.7-py3-none-any.whl", hash = "sha256:4ad3232f5e926d6718ec31cfc1fcadfde020920e278684144551c91769c7bc18"},
-    {file = "certifi-2022.12.7.tar.gz", hash = "sha256:35824b4c3a97115964b408844d64aa14db1cc518f6562e8d7261699d1350a9e3"},
+    {file = "certifi-2023.5.7-py3-none-any.whl", hash = "sha256:c6c2e98f5c7869efca1f8916fed228dd91539f9f1b444c314c06eef02980c716"},
+    {file = "certifi-2023.5.7.tar.gz", hash = "sha256:0f0d56dc5a6ad56fd4ba36484d6cc34451e1c6548c61daad8c320169f91eddc7"},
 ]
 
 [[package]]
@@ -228,19 +209,19 @@ test = ["pytest (>=6)"]
 
 [[package]]
 name = "filelock"
-version = "3.10.7"
+version = "3.12.0"
 description = "A platform independent file lock."
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "filelock-3.10.7-py3-none-any.whl", hash = "sha256:bde48477b15fde2c7e5a0713cbe72721cb5a5ad32ee0b8f419907960b9d75536"},
-    {file = "filelock-3.10.7.tar.gz", hash = "sha256:892be14aa8efc01673b5ed6589dbccb95f9a8596f0507e232626155495c18105"},
+    {file = "filelock-3.12.0-py3-none-any.whl", hash = "sha256:ad98852315c2ab702aeb628412cbf7e95b7ce8c3bf9565670b4eaecf1db370a9"},
+    {file = "filelock-3.12.0.tar.gz", hash = "sha256:fc03ae43288c013d2ea83c8597001b1129db351aad9c57fe2409327916b8e718"},
 ]
 
 [package.extras]
-docs = ["furo (>=2022.12.7)", "sphinx (>=6.1.3)", "sphinx-autodoc-typehints (>=1.22,!=1.23.4)"]
-testing = ["covdefaults (>=2.3)", "coverage (>=7.2.2)", "diff-cover (>=7.5)", "pytest (>=7.2.2)", "pytest-cov (>=4)", "pytest-mock (>=3.10)", "pytest-timeout (>=2.1)"]
+docs = ["furo (>=2023.3.27)", "sphinx (>=6.1.3)", "sphinx-autodoc-typehints (>=1.23,!=1.23.4)"]
+testing = ["covdefaults (>=2.3)", "coverage (>=7.2.3)", "diff-cover (>=7.5)", "pytest (>=7.3.1)", "pytest-cov (>=4)", "pytest-mock (>=3.10)", "pytest-timeout (>=2.1)"]
 
 [[package]]
 name = "gdspy"
@@ -258,45 +239,46 @@ numpy = "*"
 
 [[package]]
 name = "gdstk"
-version = "0.9.37"
+version = "0.9.40"
 description = "Python module for creation and manipulation of GDSII files."
 category = "main"
 optional = true
 python-versions = "*"
 files = [
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+    {file = "numpy-1.24.3-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:4749e053a29364d3452c034827102ee100986903263e89884922ef01a0a6fd2f"},
+    {file = "numpy-1.24.3-cp38-cp38-win32.whl", hash = "sha256:d933fabd8f6a319e8530d0de4fcc2e6a61917e0b0c271fded460032db42a0fe4"},
+    {file = "numpy-1.24.3-cp38-cp38-win_amd64.whl", hash = "sha256:56e48aec79ae238f6e4395886b5eaed058abb7231fb3361ddd7bfdf4eed54289"},
+    {file = "numpy-1.24.3-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:4719d5aefb5189f50887773699eaf94e7d1e02bf36c1a9d353d9f46703758ca4"},
+    {file = "numpy-1.24.3-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:0ec87a7084caa559c36e0a2309e4ecb1baa03b687201d0a847c8b0ed476a7187"},
+    {file = "numpy-1.24.3-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:ea8282b9bcfe2b5e7d491d0bf7f3e2da29700cec05b49e64d6246923329f2b02"},
+    {file = "numpy-1.24.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:210461d87fb02a84ef243cac5e814aad2b7f4be953b32cb53327bb49fd77fbb4"},
+    {file = "numpy-1.24.3-cp39-cp39-win32.whl", hash = "sha256:784c6da1a07818491b0ffd63c6bbe5a33deaa0e25a20e1b3ea20cf0e43f8046c"},
+    {file = "numpy-1.24.3-cp39-cp39-win_amd64.whl", hash = "sha256:d5036197ecae68d7f491fcdb4df90082b0d4960ca6599ba2659957aafced7c17"},
+    {file = "numpy-1.24.3-pp38-pypy38_pp73-macosx_10_9_x86_64.whl", hash = "sha256:352ee00c7f8387b44d19f4cada524586f07379c0d49270f87233983bc5087ca0"},
+    {file = "numpy-1.24.3-pp38-pypy38_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:1a7d6acc2e7524c9955e5c903160aa4ea083736fde7e91276b0e5d98e6332812"},
+    {file = "numpy-1.24.3-pp38-pypy38_pp73-win_amd64.whl", hash = "sha256:35400e6a8d102fd07c71ed7dcadd9eb62ee9a6e84ec159bd48c28235bbb0f8e4"},
+    {file = "numpy-1.24.3.tar.gz", hash = "sha256:ab344f1bf21f140adab8e47fdbc7c35a477dc01408791f8ba00d018dd0bc5155"},
 ]
 
 [[package]]
 name = "packaging"
-version = "23.0"
+version = "23.1"
 description = "Core utilities for Python packages"
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "packaging-23.0-py3-none-any.whl", hash = "sha256:714ac14496c3e68c99c29b00845f7a2b85f3bb6f1078fd9f72fd20f0570002b2"},
-    {file = "packaging-23.0.tar.gz", hash = "sha256:b6ad297f8907de0fa2fe1ccbd26fdaf387f5f47c7275fedf8cce89f99446cf97"},
+    {file = "packaging-23.1-py3-none-any.whl", hash = "sha256:994793af429502c4ea2ebf6bf664629d07c1a9fe974af92966e4b8d2df7edc61"},
+    {file = "packaging-23.1.tar.gz", hash = "sha256:a392980d2b6cffa644431898be54b0045151319d1e7ec34f0cfed48767dd334f"},
 ]
 
 [[package]]
 name = "platformdirs"
-version = "3.2.0"
+version = "3.5.0"
 description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "platformdirs-3.2.0-py3-none-any.whl", hash = "sha256:ebe11c0d7a805086e99506aa331612429a72ca7cd52a1f0d277dc4adc20cb10e"},
-    {file = "platformdirs-3.2.0.tar.gz", hash = "sha256:d5b638ca397f25f979350ff789db335903d7ea010ab28903f57b27e1b16c2b08"},
+    {file = "platformdirs-3.5.0-py3-none-any.whl", hash = "sha256:47692bc24c1958e8b0f13dd727307cff1db103fca36399f457da8e05f222fdc4"},
+    {file = "platformdirs-3.5.0.tar.gz", hash = "sha256:7954a68d0ba23558d753f73437c55f89027cf8f5108c19844d4b82e5af396335"},
 ]
 
 [package.extras]
-docs = ["furo (>=2022.12.7)", "proselint (>=0.13)", "sphinx (>=6.1.3)", "sphinx-autodoc-typehints (>=1.22,!=1.23.4)"]
-test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.2.2)", "pytest-cov (>=4)", "pytest-mock (>=3.10)"]
+docs = ["furo (>=2023.3.27)", "proselint (>=0.13)", "sphinx (>=6.1.3)", "sphinx-autodoc-typehints (>=1.23,!=1.23.4)"]
+test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.3.1)", "pytest-cov (>=4)", "pytest-mock (>=3.10)"]
 
 [[package]]
 name = "pluggy"
@@ -827,14 +809,14 @@ email = ["email-validator (>=1.0.3)"]
 
 [[package]]
 name = "pygments"
-version = "2.14.0"
+version = "2.15.1"
 description = "Pygments is a syntax highlighting package written in Python."
 category = "dev"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 files = [
-    {file = "Pygments-2.14.0-py3-none-any.whl", hash = "sha256:fa7bd7bd2771287c0de303af8bfdfc731f51bd2c6a47ab69d117138893b82717"},
-    {file = "Pygments-2.14.0.tar.gz", hash = "sha256:b3ed06a9e8ac9a9aae5a6f5dbe78a8a58655d17b43b93c078f094ddc476ae297"},
+    {file = "Pygments-2.15.1-py3-none-any.whl", hash = "sha256:db2db3deb4b4179f399a09054b023b6a586b76499d36965813c71aa8ed7b5fd1"},
+    {file = "Pygments-2.15.1.tar.gz", hash = "sha256:8ace4d3c1dd481894b2005f560ead0f9f19ee64fe983366be1a21e171d12775c"},
 ]
 
 [package.extras]
@@ -842,18 +824,18 @@ plugins = ["importlib-metadata"]
 
 [[package]]
 name = "pylint"
-version = "2.17.1"
+version = "2.17.4"
 description = "python code static checker"
 category = "dev"
 optional = false
 python-versions = ">=3.7.2"
 files = [
-    {file = "pylint-2.17.1-py3-none-any.whl", hash = "sha256:8660a54e3f696243d644fca98f79013a959c03f979992c1ab59c24d3f4ec2700"},
-    {file = "pylint-2.17.1.tar.gz", hash = "sha256:d4d009b0116e16845533bc2163493d6681846ac725eab8ca8014afb520178ddd"},
+    {file = "pylint-2.17.4-py3-none-any.whl", hash = "sha256:7a1145fb08c251bdb5cca11739722ce64a63db479283d10ce718b2460e54123c"},
+    {file = "pylint-2.17.4.tar.gz", hash = "sha256:5dcf1d9e19f41f38e4e85d10f511e5b9c35e1aa74251bf95cdd8cb23584e2db1"},
 ]
 
 [package.dependencies]
-astroid = ">=2.15.0,<=2.17.0-dev0"
+astroid = ">=2.15.4,<=2.17.0-dev0"
 colorama = {version = ">=0.4.5", markers = "sys_platform == \"win32\""}
 dill = [
     {version = ">=0.2", markers = "python_version < \"3.11\""},
@@ -872,18 +854,17 @@ testutils = ["gitpython (>3)"]
 
 [[package]]
 name = "pytest"
-version = "7.2.2"
+version = "7.3.1"
 description = "pytest: simple powerful testing with Python"
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "pytest-7.2.2-py3-none-any.whl", hash = "sha256:130328f552dcfac0b1cec75c12e3f005619dc5f874f0a06e8ff7263f0ee6225e"},
-    {file = "pytest-7.2.2.tar.gz", hash = "sha256:c99ab0c73aceb050f68929bc93af19ab6db0558791c6a0715723abe9d0ade9d4"},
+    {file = "pytest-7.3.1-py3-none-any.whl", hash = "sha256:3799fa815351fea3a5e96ac7e503a96fa51cc9942c3753cda7651b93c1cfa362"},
+    {file = "pytest-7.3.1.tar.gz", hash = "sha256:434afafd78b1d78ed0addf160ad2b77a30d35d4bdf8af234fe621919d9ed15e3"},
 ]
 
 [package.dependencies]
-attrs = ">=19.2.0"
 colorama = {version = "*", markers = "sys_platform == \"win32\""}
 exceptiongroup = {version = ">=1.0.0rc8", markers = "python_version < \"3.11\""}
 iniconfig = "*"
@@ -892,7 +873,7 @@ pluggy = ">=0.12,<2.0"
 tomli = {version = ">=1.0.0", markers = "python_version < \"3.11\""}
 
 [package.extras]
-testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "xmlschema"]
+testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "xmlschema"]
 
 [[package]]
 name = "pyyaml"
@@ -946,21 +927,21 @@ files = [
 
 [[package]]
 name = "requests"
-version = "2.28.2"
+version = "2.30.0"
 description = "Python HTTP for Humans."
 category = "dev"
 optional = false
-python-versions = ">=3.7, <4"
+python-versions = ">=3.7"
 files = [
-    {file = "requests-2.28.2-py3-none-any.whl", hash = "sha256:64299f4909223da747622c030b781c0d7811e359c37124b4bd368fb8c6518baa"},
-    {file = "requests-2.28.2.tar.gz", hash = "sha256:98b1b2782e3c6c4904938b84c0eb932721069dfdb9134313beff7c83c2df24bf"},
+    {file = "requests-2.30.0-py3-none-any.whl", hash = "sha256:10e94cc4f3121ee6da529d358cdaeaff2f1c409cd377dbc72b825852f2f7e294"},
+    {file = "requests-2.30.0.tar.gz", hash = "sha256:239d7d4458afcb28a692cdd298d87542235f4ca8d36d03a15bfc128a6559a2f4"},
 ]
 
 [package.dependencies]
 certifi = ">=2017.4.17"
 charset-normalizer = ">=2,<4"
 idna = ">=2.5,<4"
-urllib3 = ">=1.21.1,<1.27"
+urllib3 = ">=1.21.1,<3"
 
 [package.extras]
 socks = ["PySocks (>=1.5.6,!=1.5.7)"]
@@ -968,18 +949,18 @@ use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
 
 [[package]]
 name = "ruamel-yaml"
-version = "0.17.21"
+version = "0.17.26"
 description = "ruamel.yaml is a YAML parser/emitter that supports roundtrip preservation of comments, seq/map flow style, and map key order"
 category = "main"
 optional = false
 python-versions = ">=3"
 files = [
-    {file = "ruamel.yaml-0.17.21-py3-none-any.whl", hash = "sha256:742b35d3d665023981bd6d16b3d24248ce5df75fdb4e2924e93a05c1f8b61ca7"},
-    {file = "ruamel.yaml-0.17.21.tar.gz", hash = "sha256:8b7ce697a2f212752a35c1ac414471dc16c424c9573be4926b56ff3f5d23b7af"},
+    {file = "ruamel.yaml-0.17.26-py3-none-any.whl", hash = "sha256:25d0ee82a0a9a6f44683dcf8c282340def4074a4562f3a24f55695bb254c1693"},
+    {file = "ruamel.yaml-0.17.26.tar.gz", hash = "sha256:baa2d0a5aad2034826c439ce61c142c07082b76f4791d54145e131206e998059"},
 ]
 
 [package.dependencies]
-"ruamel.yaml.clib" = {version = ">=0.2.6", markers = "platform_python_implementation == \"CPython\" and python_version < \"3.11\""}
+"ruamel.yaml.clib" = {version = ">=0.2.7", markers = "platform_python_implementation == \"CPython\" and python_version < \"3.12\""}
 
 [package.extras]
 docs = ["ryd"]
@@ -1002,6 +983,8 @@ files = [
     {file = "ruamel.yaml.clib-0.2.7-cp311-cp311-macosx_10_9_universal2.whl", hash = "sha256:045e0626baf1c52e5527bd5db361bc83180faaba2ff586e763d3d5982a876a9e"},
     {file = "ruamel.yaml.clib-0.2.7-cp311-cp311-macosx_12_6_arm64.whl", hash = "sha256:721bc4ba4525f53f6a611ec0967bdcee61b31df5a56801281027a3a6d1c2daf5"},
     {file = "ruamel.yaml.clib-0.2.7-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl", hash = "sha256:41d0f1fa4c6830176eef5b276af04c89320ea616655d01327d5ce65e50575c94"},
+    {file = "ruamel.yaml.clib-0.2.7-cp311-cp311-win32.whl", hash = "sha256:f6d3d39611ac2e4f62c3128a9eed45f19a6608670c5a2f4f07f24e8de3441d38"},
+    {file = "ruamel.yaml.clib-0.2.7-cp311-cp311-win_amd64.whl", hash = "sha256:da538167284de58a52109a9b89b8f6a53ff8437dd6dc26d33b57bf6699153122"},
     {file = "ruamel.yaml.clib-0.2.7-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:4b3a93bb9bc662fc1f99c5c3ea8e623d8b23ad22f861eb6fce9377ac07ad6072"},
     {file = "ruamel.yaml.clib-0.2.7-cp36-cp36m-macosx_12_0_arm64.whl", hash = "sha256:a234a20ae07e8469da311e182e70ef6b199d0fbeb6c6cc2901204dd87fb867e8"},
     {file = "ruamel.yaml.clib-0.2.7-cp36-cp36m-manylinux2014_aarch64.whl", hash = "sha256:15910ef4f3e537eea7fe45f8a5d19997479940d9196f357152a09031c5be59f3"},
@@ -1245,14 +1228,14 @@ files = [
 
 [[package]]
 name = "tomlkit"
-version = "0.11.7"
+version = "0.11.8"
 description = "Style preserving TOML library"
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "tomlkit-0.11.7-py3-none-any.whl", hash = "sha256:5325463a7da2ef0c6bbfefb62a3dc883aebe679984709aee32a317907d0a8d3c"},
-    {file = "tomlkit-0.11.7.tar.gz", hash = "sha256:f392ef70ad87a672f02519f99967d28a4d3047133e2d1df936511465fbb3791d"},
+    {file = "tomlkit-0.11.8-py3-none-any.whl", hash = "sha256:8c726c4c202bdb148667835f68d68780b9a003a9ec34167b6c673b38eff2a171"},
+    {file = "tomlkit-0.11.8.tar.gz", hash = "sha256:9330fc7faa1db67b541b28e62018c17d20be733177d290a13b24c62d1614e0c3"},
 ]
 
 [[package]]
@@ -1307,41 +1290,42 @@ files = [
 
 [[package]]
 name = "urllib3"
-version = "1.26.15"
+version = "2.0.2"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 category = "dev"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
+python-versions = ">=3.7"
 files = [
-    {file = "urllib3-1.26.15-py2.py3-none-any.whl", hash = "sha256:aa751d169e23c7479ce47a0cb0da579e3ede798f994f5816a74e4f4500dcea42"},
-    {file = "urllib3-1.26.15.tar.gz", hash = "sha256:8a388717b9476f934a21484e8c8e61875ab60644d29b9b39e11e4b9dc1c6b305"},
+    {file = "urllib3-2.0.2-py3-none-any.whl", hash = "sha256:d055c2f9d38dc53c808f6fdc8eab7360b6fdbbde02340ed25cfbcd817c62469e"},
+    {file = "urllib3-2.0.2.tar.gz", hash = "sha256:61717a1095d7e155cdb737ac7bb2f4324a858a1e2e6466f6d03ff630ca68d3cc"},
 ]
 
 [package.extras]
-brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)", "brotlipy (>=0.6.0)"]
-secure = ["certifi", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "ipaddress", "pyOpenSSL (>=0.14)", "urllib3-secure-extra"]
-socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
+brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"]
+secure = ["certifi", "cryptography (>=1.9)", "idna (>=2.0.0)", "pyopenssl (>=17.1.0)", "urllib3-secure-extra"]
+socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"]
+zstd = ["zstandard (>=0.18.0)"]
 
 [[package]]
 name = "virtualenv"
-version = "20.21.0"
+version = "20.23.0"
 description = "Virtual Python Environment builder"
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "virtualenv-20.21.0-py3-none-any.whl", hash = "sha256:31712f8f2a17bd06234fa97fdf19609e789dd4e3e4bf108c3da71d710651adbc"},
-    {file = "virtualenv-20.21.0.tar.gz", hash = "sha256:f50e3e60f990a0757c9b68333c9fdaa72d7188caa417f96af9e52407831a3b68"},
+    {file = "virtualenv-20.23.0-py3-none-any.whl", hash = "sha256:6abec7670e5802a528357fdc75b26b9f57d5d92f29c5462ba0fbe45feacc685e"},
+    {file = "virtualenv-20.23.0.tar.gz", hash = "sha256:a85caa554ced0c0afbd0d638e7e2d7b5f92d23478d05d17a76daeac8f279f924"},
 ]
 
 [package.dependencies]
 distlib = ">=0.3.6,<1"
-filelock = ">=3.4.1,<4"
-platformdirs = ">=2.4,<4"
+filelock = ">=3.11,<4"
+platformdirs = ">=3.2,<4"
 
 [package.extras]
-docs = ["furo (>=2022.12.7)", "proselint (>=0.13)", "sphinx (>=6.1.3)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=22.12)"]
-test = ["covdefaults (>=2.2.2)", "coverage (>=7.1)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23)", "pytest (>=7.2.1)", "pytest-env (>=0.8.1)", "pytest-freezegun (>=0.4.2)", "pytest-mock (>=3.10)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)"]
+docs = ["furo (>=2023.3.27)", "proselint (>=0.13)", "sphinx (>=6.1.3)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=22.12)"]
+test = ["covdefaults (>=2.3)", "coverage (>=7.2.3)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.3.1)", "pytest-env (>=0.8.1)", "pytest-freezegun (>=0.4.2)", "pytest-mock (>=3.10)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=67.7.1)", "time-machine (>=2.9)"]
 
 [[package]]
 name = "wrapt"

From cf8c55000b92056b640652d4434e6edc0518380b Mon Sep 17 00:00:00 2001
From: Bryan Ngo <bryanngo@berkeley.edu>
Date: Thu, 11 May 2023 11:30:29 -0700
Subject: [PATCH 30/36] bump lock file, add typing marker

---
 hammer/flowgraph/py.typed |  0
 poetry.lock               | 80 +++++++++++++++++----------------------
 2 files changed, 35 insertions(+), 45 deletions(-)
 create mode 100644 hammer/flowgraph/py.typed

diff --git a/hammer/flowgraph/py.typed b/hammer/flowgraph/py.typed
new file mode 100644
index 000000000..e69de29bb
diff --git a/poetry.lock b/poetry.lock
index 0fa8db890..fc6c8e67a 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -565,38 +565,38 @@ files = [
 
 [[package]]
 name = "mypy"
-version = "1.1.1"
+version = "1.3.0"
 description = "Optional static typing for Python"
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
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+    {file = "mypy-1.3.0-cp39-cp39-win_amd64.whl", hash = "sha256:95d8d31a7713510685b05fbb18d6ac287a56c8f6554d88c19e73f724a445448a"},
+    {file = "mypy-1.3.0-py3-none-any.whl", hash = "sha256:a8763e72d5d9574d45ce5881962bc8e9046bf7b375b0abf031f3e6811732a897"},
+    {file = "mypy-1.3.0.tar.gz", hash = "sha256:e1f4d16e296f5135624b34e8fb741eb0eadedca90862405b1f1fde2040b9bd11"},
 ]
 
 [package.dependencies]
@@ -898,6 +898,13 @@ files = [
     {file = "PyYAML-6.0-cp310-cp310-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl", hash = "sha256:f84fbc98b019fef2ee9a1cb3ce93e3187a6df0b2538a651bfb890254ba9f90b5"},
     {file = "PyYAML-6.0-cp310-cp310-win32.whl", hash = "sha256:2cd5df3de48857ed0544b34e2d40e9fac445930039f3cfe4bcc592a1f836d513"},
     {file = "PyYAML-6.0-cp310-cp310-win_amd64.whl", hash = "sha256:daf496c58a8c52083df09b80c860005194014c3698698d1a57cbcfa182142a3a"},
+    {file = "PyYAML-6.0-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:d4b0ba9512519522b118090257be113b9468d804b19d63c71dbcf4a48fa32358"},
+    {file = "PyYAML-6.0-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:81957921f441d50af23654aa6c5e5eaf9b06aba7f0a19c18a538dc7ef291c5a1"},
+    {file = "PyYAML-6.0-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:afa17f5bc4d1b10afd4466fd3a44dc0e245382deca5b3c353d8b757f9e3ecb8d"},
+    {file = "PyYAML-6.0-cp311-cp311-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:dbad0e9d368bb989f4515da330b88a057617d16b6a8245084f1b05400f24609f"},
+    {file = "PyYAML-6.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:432557aa2c09802be39460360ddffd48156e30721f5e8d917f01d31694216782"},
+    {file = "PyYAML-6.0-cp311-cp311-win32.whl", hash = "sha256:bfaef573a63ba8923503d27530362590ff4f576c626d86a9fed95822a8255fd7"},
+    {file = "PyYAML-6.0-cp311-cp311-win_amd64.whl", hash = "sha256:01b45c0191e6d66c470b6cf1b9531a771a83c1c4208272ead47a3ae4f2f603bf"},
     {file = "PyYAML-6.0-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:897b80890765f037df3403d22bab41627ca8811ae55e9a722fd0392850ec4d86"},
     {file = "PyYAML-6.0-cp36-cp36m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:50602afada6d6cbfad699b0c7bb50d5ccffa7e46a3d738092afddc1f9758427f"},
     {file = "PyYAML-6.0-cp36-cp36m-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:48c346915c114f5fdb3ead70312bd042a953a8ce5c7106d5bfb1a5254e47da92"},
@@ -1013,23 +1020,6 @@ files = [
     {file = "ruamel.yaml.clib-0.2.7.tar.gz", hash = "sha256:1f08fd5a2bea9c4180db71678e850b995d2a5f4537be0e94557668cf0f5f9497"},
 ]
 
-[[package]]
-name = "setuptools"
-version = "67.6.0"
-description = "Easily download, build, install, upgrade, and uninstall Python packages"
-category = "dev"
-optional = false
-python-versions = ">=3.7"
-files = [
-    {file = "setuptools-67.6.0-py3-none-any.whl", hash = "sha256:b78aaa36f6b90a074c1fa651168723acbf45d14cb1196b6f02c0fd07f17623b2"},
-    {file = "setuptools-67.6.0.tar.gz", hash = "sha256:2ee892cd5f29f3373097f5a814697e397cf3ce313616df0af11231e2ad118077"},
-]
-
-[package.extras]
-docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-hoverxref (<2)", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (==0.8.3)", "sphinx-reredirects", "sphinxcontrib-towncrier"]
-testing = ["build[virtualenv]", "filelock (>=3.4.0)", "flake8 (<5)", "flake8-2020", "ini2toml[lite] (>=0.9)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pip (>=19.1)", "pip-run (>=8.8)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)", "pytest-perf", "pytest-timeout", "pytest-xdist", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
-testing-integration = ["build[virtualenv]", "filelock (>=3.4.0)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"]
-
 [[package]]
 name = "six"
 version = "1.16.0"
@@ -1485,4 +1475,4 @@ asap7-gdstk = ["gdstk"]
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.9"
-content-hash = "905376dcbe86ee41ff3fc09b22e3cf3cd05e40e2cf66a327f5412816e01c3c24"
+content-hash = "909500729bedc90acb89cc4a4b5c8efa663af9213e0d95ff85341b3c2f0f255c"

From d32621171bc08f9bfede65956544c035b6ee49d2 Mon Sep 17 00:00:00 2001
From: Bryan Ngo <bryanngo@berkeley.edu>
Date: Thu, 11 May 2023 11:37:28 -0700
Subject: [PATCH 31/36] fix type-checking for networkx

---
 .github/workflows/pr.yml  | 1 +
 hammer/flowgraph/py.typed | 0
 2 files changed, 1 insertion(+)
 delete mode 100644 hammer/flowgraph/py.typed

diff --git a/.github/workflows/pr.yml b/.github/workflows/pr.yml
index 338a95ca3..405a67f40 100644
--- a/.github/workflows/pr.yml
+++ b/.github/workflows/pr.yml
@@ -60,4 +60,5 @@ jobs:
         id: type-checks
         run: |
           touch .venv/lib/python${{ matrix.python-version }}/site-packages/ruamel/py.typed
+          touch .venv/lib/python${{ matrix.python-version }}/site-packages/networkx/py.typed
           poetry run mypy --namespace-packages -p hammer
diff --git a/hammer/flowgraph/py.typed b/hammer/flowgraph/py.typed
deleted file mode 100644
index e69de29bb..000000000

From 8dce117bda8801fa7ea4e529b96df62a8633cb94 Mon Sep 17 00:00:00 2001
From: Bryan Ngo <bryanngo@berkeley.edu>
Date: Fri, 1 Dec 2023 13:29:22 -0800
Subject: [PATCH 32/36] fix CI pipeline

---
 hammer/config/config_src.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/hammer/config/config_src.py b/hammer/config/config_src.py
index 98d7d2032..80493940d 100644
--- a/hammer/config/config_src.py
+++ b/hammer/config/config_src.py
@@ -941,7 +941,7 @@ def check_setting(self, key: str, cfg: Optional[dict] = None) -> bool:
 
         if cfg is None:
             cfg = self.get_config()
-        if key not in self.get_config_types():
+        if key not in self.get_config_types:
             #TODO: compile this at the beginning instead of emitting every instance
             #self.logger.warning(f"Key {key} is not associated with a type")
             return True

From 842346ffbaa278df49cfb8a5937ec3cb16b0fb91 Mon Sep 17 00:00:00 2001
From: Bryan Ngo <bryanngo@berkeley.edu>
Date: Thu, 4 Jan 2024 14:04:29 -0800
Subject: [PATCH 33/36] migrate to current step control names

---
 hammer/flowgraph/flowgraph.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/hammer/flowgraph/flowgraph.py b/hammer/flowgraph/flowgraph.py
index 415d495d7..c56fafcf2 100644
--- a/hammer/flowgraph/flowgraph.py
+++ b/hammer/flowgraph/flowgraph.py
@@ -51,10 +51,10 @@ class Node:
     optional_inputs:   list[str] = field(default_factory=list)
     optional_outputs:  list[str] = field(default_factory=list)
     step_controls:     dict[str, str] = field(default_factory=lambda: {
-        "from_step": "",
-        "after_step": "",
-        "to_step": "",
-        "until_step": "",
+        "start_before_step": "",
+        "start_after_step": "",
+        "stop_before_step": "",
+        "stop_after_step": "",
         "only_step": "",
     })
 

From bbb047fc72da89c2358244331e0efb34c3067162 Mon Sep 17 00:00:00 2001
From: Bryan Ngo <bryanngo@berkeley.edu>
Date: Thu, 4 Jan 2024 14:05:52 -0800
Subject: [PATCH 34/36] reorder sections

---
 doc/Hammer-Use/index.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/Hammer-Use/index.rst b/doc/Hammer-Use/index.rst
index b608c0969..de3649b04 100644
--- a/doc/Hammer-Use/index.rst
+++ b/doc/Hammer-Use/index.rst
@@ -11,6 +11,6 @@ This documentation will walk through more advanced features of the Hammer infras
    Hammer-APIs
    Flow-Control
    Hooks
+   Flowgraphs
    Buildfile
    Hierarchical
-   Flowgraphs

From 6ca70a599b3fb0bd714464fe3f84b56d580669b2 Mon Sep 17 00:00:00 2001
From: Bryan Ngo <bryanngo@berkeley.edu>
Date: Thu, 4 Jan 2024 14:32:26 -0800
Subject: [PATCH 35/36] make docs consistent

---
 doc/Hammer-Use/Flowgraphs.rst | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/doc/Hammer-Use/Flowgraphs.rst b/doc/Hammer-Use/Flowgraphs.rst
index d798ed932..bfd0e3a32 100644
--- a/doc/Hammer-Use/Flowgraphs.rst
+++ b/doc/Hammer-Use/Flowgraphs.rst
@@ -22,10 +22,10 @@ Each ``Node`` "pulls" from a directory to feed in inputs and "pushes" output fil
 * A driver to run the node with; this enables backwards compatibility with :ref:`hooks <hooks>`.
 * Options to specify steps within an action; this enables backwards compatibility with :ref:`flow control <flow-control>`.
 
-    * ``from_step``
-    * ``after_step``
-    * ``to_step``
-    * ``until_step``
+    * ``start_before_step``
+    * ``start_after_step``
+    * ``stop_before_step``
+    * ``stop_after_step``
     * ``only_step``
 
 A minimal example of a ``Node``:

From 4b2a1aeca7d8c60bf0093a91d1c562bafaef7741 Mon Sep 17 00:00:00 2001
From: Bryan Ngo <bryanngo@berkeley.edu>
Date: Thu, 4 Jan 2024 14:34:26 -0800
Subject: [PATCH 36/36] convert back to legacy names for plugging into backend

---
 hammer/flowgraph/flowgraph.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/hammer/flowgraph/flowgraph.py b/hammer/flowgraph/flowgraph.py
index c56fafcf2..000ec81bc 100644
--- a/hammer/flowgraph/flowgraph.py
+++ b/hammer/flowgraph/flowgraph.py
@@ -278,10 +278,10 @@ def __run_single(node: Node) -> int:
             'power_rundir': '',
             'formal_rundir': '',
             'timing_rundir': '',
-            'from_step': node.step_controls["from_step"],
-            'after_step': node.step_controls["after_step"],
-            'to_step': node.step_controls["to_step"],
-            'until_step': node.step_controls["until_step"],
+            "from_step": node.step_controls["start_before_step"],
+            "after_step": node.step_controls["start_after_step"],
+            "to_step": node.step_controls["stop_before_step"],
+            "until_step": node.step_controls["stop_after_step"],
             'only_step': node.step_controls["only_step"],
             'output': os.path.join(node.push_dir, node.required_outputs[0]),  # TODO: fix this
             'verilog': None,