From 63da9e070a6af49159ca2451a02f278176c3a549 Mon Sep 17 00:00:00 2001
From: Caitao Zhan <caitaozhan@gmail.com>
Date: Thu, 12 Sep 2024 22:08:21 -0500
Subject: [PATCH 1/9] [minor] minor fix

---
 sequence/topology/node.py          | 2 +-
 sequence/utils/config_generator.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/sequence/topology/node.py b/sequence/topology/node.py
index e28c2762..afc7de0d 100644
--- a/sequence/topology/node.py
+++ b/sequence/topology/node.py
@@ -74,7 +74,7 @@ def init(self) -> None:
     def set_seed(self, seed: int) -> None:
         self.generator = np.random.default_rng(seed)
 
-    def get_generator(self):
+    def get_generator(self) -> np.random.Generator:
         return self.generator
 
     def add_component(self, component: Entity) -> None:
diff --git a/sequence/utils/config_generator.py b/sequence/utils/config_generator.py
index 2a835db3..4c867c59 100644
--- a/sequence/utils/config_generator.py
+++ b/sequence/utils/config_generator.py
@@ -19,7 +19,7 @@ def add_default_args(parser):
     """
 
     parser.add_argument('memo_size', type=int, help='number of memories per node')
-    parser.add_argument('qc_length', type=float, help='distance between nodes (in m)')
+    parser.add_argument('qc_length', type=float, help='distance between nodes (in km)')
     parser.add_argument('qc_atten', type=float, help='quantum channel attenuation (in dB/m)')
     parser.add_argument('cc_delay', type=float, help='classical channel delay (in ms)')
     parser.add_argument('-d', '--directory', type=str, default='tmp', help='name of output directory')

From a382dd0f1fb058f5a2441d204549085d190ee45d Mon Sep 17 00:00:00 2001
From: Caitao Zhan <caitaozhan@gmail.com>
Date: Fri, 13 Sep 2024 19:53:16 -0500
Subject: [PATCH 2/9] [major] fix a bug in reservation protocol and routing
 protocol that may lead to route for src->dst being different than dst->src
 when the network has same length edges.

---
 sequence/app/request_app.py                  |  1 -
 sequence/network_management/reservation.py   | 40 +++++++++++++-------
 sequence/network_management/routing.py       | 14 +++++--
 tests/network_management/test_reservation.py |  6 +--
 4 files changed, 40 insertions(+), 21 deletions(-)

diff --git a/sequence/app/request_app.py b/sequence/app/request_app.py
index c4cfa947..941969b6 100644
--- a/sequence/app/request_app.py
+++ b/sequence/app/request_app.py
@@ -145,7 +145,6 @@ def get_other_reservation(self, reservation: "Reservation") -> None:
 
     def schedule_reservation(self, reservation: "Reservation") -> None:
         if reservation.initiator == self.node.name:
-            # NOTE: self.path will be an issue when there are multiple reservation.path at the same time
             self.path = reservation.path
 
         reservation_protocol = self.node.network_manager.protocol_stack[1]
diff --git a/sequence/network_management/reservation.py b/sequence/network_management/reservation.py
index aede8c8c..f51381bb 100644
--- a/sequence/network_management/reservation.py
+++ b/sequence/network_management/reservation.py
@@ -45,7 +45,7 @@ class ResourceReservationMessage(Message):
         receiver (str): name of destination protocol instance.
         reservation (Reservation): reservation object relayed between nodes.
         qcaps (List[QCaps]): cumulative quantum capacity object list (if `msg_type == REQUEST`)
-        path (List[str]): cumulative node list for entanglement path (if `msg_type == APPROVE`)
+        path (List[str]): cumulative node list for entanglement path (if `msg_type == APPROVE` or `msg_type == REJECT`)
     """
 
     def __init__(self, msg_type: any, receiver: str, reservation: "Reservation", **kwargs):
@@ -54,7 +54,7 @@ def __init__(self, msg_type: any, receiver: str, reservation: "Reservation", **k
         if self.msg_type is RSVPMsgType.REQUEST:
             self.qcaps = []
         elif self.msg_type is RSVPMsgType.REJECT:
-            pass
+            self.path = kwargs["path"]
         elif self.msg_type is RSVPMsgType.APPROVE:
             self.path = kwargs["path"]
         else:
@@ -365,7 +365,6 @@ def push(self, responder: str, start_time: int, end_time: int, memory_size: int,
 
     def pop(self, src: str, msg: "ResourceReservationMessage"):
         """Method to receive messages from lower protocols.
-           NOTE (caitao, 3/19/2024): argument "src" not used
         Messages may be of 3 types, causing different network manager behavior:
 
         1. REQUEST: requests are evaluated, and forwarded along the path if accepted.
@@ -387,39 +386,54 @@ def pop(self, src: str, msg: "ResourceReservationMessage"):
 
         if msg.msg_type == RSVPMsgType.REQUEST:
             assert self.owner.timeline.now() < msg.reservation.start_time
-            if self.schedule(msg.reservation):
-                qcap = QCap(self.owner.name)
-                msg.qcaps.append(qcap)
+            qcap = QCap(self.owner.name)
+            msg.qcaps.append(qcap)
+            path = [qcap.node for qcap in msg.qcaps]
+            if self.schedule(msg.reservation):  # schedule success
                 if self.owner.name == msg.reservation.responder:
-                    path = [qcap.node for qcap in msg.qcaps]
                     rules = self.create_rules(path, reservation=msg.reservation)
                     self.load_rules(rules, msg.reservation)
                     msg.reservation.set_path(path)
                     new_msg = ResourceReservationMessage(RSVPMsgType.APPROVE, self.name, msg.reservation, path=path)
                     self._pop(msg=msg)
-                    self._push(dst=msg.reservation.initiator, msg=new_msg)
+                    self._push(dst=None, msg=new_msg, next_hop=src)
                 else:
                     self._push(dst=msg.reservation.responder, msg=msg)
-            else:
-                new_msg = ResourceReservationMessage(RSVPMsgType.REJECT, self.name, msg.reservation)
-                self._push(dst=msg.reservation.initiator, msg=new_msg)
+            else:                               # schedule failed
+                new_msg = ResourceReservationMessage(RSVPMsgType.REJECT, self.name, msg.reservation, path=path)
+                self._push(dst=None, msg=new_msg, next_hop=src)
         elif msg.msg_type == RSVPMsgType.REJECT:
             for card in self.timecards:
                 card.remove(msg.reservation)
             if msg.reservation.initiator == self.owner.name:
                 self._pop(msg=msg)
             else:
-                self._push(dst=msg.reservation.initiator, msg=msg)
+                next_hop = self.next_hop_when_tracing_back(msg.path)
+                self._push(dst=None, msg=msg, next_hop=next_hop)
         elif msg.msg_type == RSVPMsgType.APPROVE:
             rules = self.create_rules(msg.path, msg.reservation)
             self.load_rules(rules, msg.reservation)
             if msg.reservation.initiator == self.owner.name:
                 self._pop(msg=msg)
             else:
-                self._push(dst=msg.reservation.initiator, msg=msg)
+                next_hop = self.next_hop_when_tracing_back(msg.path)
+                self._push(dst=None, msg=msg, next_hop=next_hop)
         else:
             raise Exception("Unknown type of message", msg.msg_type)
 
+    def next_hop_when_tracing_back(self, path: List[str]) -> str:
+        '''the next hop when going back from the responder to the initiator
+
+        Args:
+            path (List[str]): a list of router names that goes from initiator to responder
+        Return:
+            str: the name of the next hop
+        '''
+        cur_index = path.index(self.owner.name)
+        assert cur_index >= 1, f'{cur_index} must be larger equal than 1'
+        next_hop = path[cur_index - 1]
+        return next_hop
+
     def schedule(self, reservation: "Reservation") -> bool:
         """Method to attempt reservation request. If attempt succeeded, return True; otherwise, return False.
 
diff --git a/sequence/network_management/routing.py b/sequence/network_management/routing.py
index 90dce917..3029cf1a 100644
--- a/sequence/network_management/routing.py
+++ b/sequence/network_management/routing.py
@@ -69,23 +69,29 @@ def update_forwarding_rule(self, dst: str, next_node: str):
 
         self.forwarding_table[dst] = next_node
 
-    def push(self, dst: str, msg: "Message"):
+    def push(self, dst: str, msg: "Message", next_hop: str = None):
         """Method to receive message from upper protocols.
 
         Routing packages the message and forwards it to the next node in the optimal path (determined by the forwarding table).
 
         Args:
-            dst (str): name of destination node.
+            dst (str): name of destination node. If not None, resort to the forwarding table to ger the next hop
             msg (Message): message to relay.
+            next_hop (str): name of next hop. If dst is None, next_hop shouldn't be None. next_hop directly tells the next_hop
 
         Side Effects:
             Will invoke `push` method of lower protocol or network manager.
         """
 
         assert dst != self.owner.name
-        dst = self.forwarding_table[dst]
         new_msg = StaticRoutingMessage(Enum, self.name, msg)
-        self._push(dst=dst, msg=new_msg)
+        if dst:                                     # if dst is not None, use the forwarding table
+            next_hop = self.forwarding_table[dst]
+            self._push(dst=next_hop, msg=new_msg)
+        elif next_hop:                              # if next_hop is not None, use next_hop
+            self._push(dst=next_hop, msg=new_msg)  
+        else:
+            raise Exception(f'Both dst and next_hop are None!')
 
     def pop(self, src: str, msg: "StaticRoutingMessage"):
         """Message to receive reservation messages.
diff --git a/tests/network_management/test_reservation.py b/tests/network_management/test_reservation.py
index 0b1d049d..e67d5437 100644
--- a/tests/network_management/test_reservation.py
+++ b/tests/network_management/test_reservation.py
@@ -131,7 +131,7 @@ def reset(node):
     msg.qcaps.append(QCap("n0"))
     n1.rsvp.pop("n0", msg)
     assert len(n1.pop_log) == 1 and len(n1.push_log) == 1
-    assert n1.push_log[0]["dst"] == "n0"
+    assert n1.push_log[0]["next_hop"] == "n0"
     assert n1.push_log[0]["msg"].msg_type == RSVPMsgType.APPROVE
     assert len(n1.push_log[0]["msg"].path) == 2
     for card in n1.rsvp.timecards:
@@ -144,7 +144,7 @@ def reset(node):
     msg.qcaps.append(QCap("n0"))
     n1.rsvp.pop("n0", msg)
     assert len(n1.pop_log) == 0 and len(n1.push_log) == 1
-    assert n1.push_log[0]["dst"] == "n0"
+    assert n1.push_log[0]["next_hop"] == "n0"
     assert n1.push_log[0]["msg"].msg_type == RSVPMsgType.REJECT
     for card in n1.rsvp.timecards:
         assert len(card.reservations) == 0
@@ -193,7 +193,7 @@ def reset(node):
     msg = ResourceReservationMessage(RSVPMsgType.APPROVE, n1.rsvp.name, reservation, path=["n0", "n1", "n2"])
     n1.rsvp.pop("n2", msg)
     assert len(n1.pop_log) == 0 and len(n1.push_log) == 1
-    assert n1.push_log[0]["dst"] == "n0" and n1.push_log[0]["msg"].msg_type == RSVPMsgType.APPROVE
+    assert n1.push_log[0]["next_hop"] == "n0" and n1.push_log[0]["msg"].msg_type == RSVPMsgType.APPROVE
     reset(n1)
 
 

From 0d3da3a7f907961e8779f6190afa10ee8c69cde6 Mon Sep 17 00:00:00 2001
From: Caitao Zhan <caitaozhan@gmail.com>
Date: Fri, 13 Sep 2024 19:56:51 -0500
Subject: [PATCH 3/9] [minor] typo

---
 sequence/network_management/routing.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sequence/network_management/routing.py b/sequence/network_management/routing.py
index 3029cf1a..c85c0ae4 100644
--- a/sequence/network_management/routing.py
+++ b/sequence/network_management/routing.py
@@ -75,9 +75,9 @@ def push(self, dst: str, msg: "Message", next_hop: str = None):
         Routing packages the message and forwards it to the next node in the optimal path (determined by the forwarding table).
 
         Args:
-            dst (str): name of destination node. If not None, resort to the forwarding table to ger the next hop
+            dst (str): name of destination node. If not None, resort to the forwarding table to get the next hop.
             msg (Message): message to relay.
-            next_hop (str): name of next hop. If dst is None, next_hop shouldn't be None. next_hop directly tells the next_hop
+            next_hop (str): name of next hop. If dst is None, next_hop shouldn't be None. next_hop directly tells the next hop.
 
         Side Effects:
             Will invoke `push` method of lower protocol or network manager.

From 2bd529d92461949dbfc87b48ef7bc43842de6c81 Mon Sep 17 00:00:00 2001
From: SagarPatange <sagarpatangev@gmail.com>
Date: Thu, 19 Sep 2024 16:00:32 -0500
Subject: [PATCH 4/9] [minor] fixed comments (db/km) and own-> owner

---
 example/ANTS_demos_2023/GUI_and_code_demo.ipynb        | 2 +-
 example/ANTS_demos_2023/GUI_and_code_demo_filled.ipynb | 2 +-
 example/QCE_demos_2022/GUI_and_code_demo.ipynb         | 2 +-
 example/QCE_demos_2022/Teleport_demo.ipynb             | 2 +-
 example/QCE_demos_2022/Teleport_demo_filled.ipynb      | 2 +-
 example/QCE_demos_2023/GUI_and_code_demo.ipynb         | 2 +-
 example/QCE_demos_2023/GUI_and_code_demo_filled.ipynb  | 2 +-
 example/qkd.ipynb                                      | 2 +-
 example/random_request_network.ipynb                   | 2 +-
 example/random_request_network_mod.ipynb               | 2 +-
 example/three_node_eg_ep_es.ipynb                      | 2 +-
 example/two_node_eg.ipynb                              | 2 +-
 sequence/qkd/BB84.py                                   | 4 ++--
 13 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/example/ANTS_demos_2023/GUI_and_code_demo.ipynb b/example/ANTS_demos_2023/GUI_and_code_demo.ipynb
index b1cc1794..2cd246c5 100644
--- a/example/ANTS_demos_2023/GUI_and_code_demo.ipynb
+++ b/example/ANTS_demos_2023/GUI_and_code_demo.ipynb
@@ -162,7 +162,7 @@
     "def test(sim_time=1.5, qc_atten=1e-5):\n",
     "    \"\"\"\n",
     "    sim_time: duration of simulation time (s)\n",
-    "    qc_atten: quantum channel attenuation (dB/km)\n",
+    "    qc_atten: quantum channel attenuation (dB/m)\n",
     "    \"\"\"\n",
     "    \n",
     "    network_config = \"star_network.json\"\n",
diff --git a/example/ANTS_demos_2023/GUI_and_code_demo_filled.ipynb b/example/ANTS_demos_2023/GUI_and_code_demo_filled.ipynb
index cf460475..43a7dc0c 100644
--- a/example/ANTS_demos_2023/GUI_and_code_demo_filled.ipynb
+++ b/example/ANTS_demos_2023/GUI_and_code_demo_filled.ipynb
@@ -164,7 +164,7 @@
     "def test(sim_time=1.5, qc_atten=1e-5):\n",
     "    \"\"\"\n",
     "    sim_time: duration of simulation time (s)\n",
-    "    qc_atten: quantum channel attenuation (dB/km)\n",
+    "    qc_atten: quantum channel attenuation (dB/m)\n",
     "    \"\"\"\n",
     "    \n",
     "    network_config = \"star_network.json\"\n",
diff --git a/example/QCE_demos_2022/GUI_and_code_demo.ipynb b/example/QCE_demos_2022/GUI_and_code_demo.ipynb
index cf460475..43a7dc0c 100644
--- a/example/QCE_demos_2022/GUI_and_code_demo.ipynb
+++ b/example/QCE_demos_2022/GUI_and_code_demo.ipynb
@@ -164,7 +164,7 @@
     "def test(sim_time=1.5, qc_atten=1e-5):\n",
     "    \"\"\"\n",
     "    sim_time: duration of simulation time (s)\n",
-    "    qc_atten: quantum channel attenuation (dB/km)\n",
+    "    qc_atten: quantum channel attenuation (dB/m)\n",
     "    \"\"\"\n",
     "    \n",
     "    network_config = \"star_network.json\"\n",
diff --git a/example/QCE_demos_2022/Teleport_demo.ipynb b/example/QCE_demos_2022/Teleport_demo.ipynb
index 68bd9e1c..1cc2c5bf 100644
--- a/example/QCE_demos_2022/Teleport_demo.ipynb
+++ b/example/QCE_demos_2022/Teleport_demo.ipynb
@@ -263,7 +263,7 @@
     "def test(sim_time=1.5, qc_atten=1e-5):\n",
     "    \"\"\"\n",
     "    sim_time: duration of simulation time (ms)\n",
-    "    qc_atten: quantum channel attenuation (dB/km)\n",
+    "    qc_atten: quantum channel attenuation (dB/m)\n",
     "    \"\"\"\n",
     "    \n",
     "    network_config = \"star_network.json\"\n",
diff --git a/example/QCE_demos_2022/Teleport_demo_filled.ipynb b/example/QCE_demos_2022/Teleport_demo_filled.ipynb
index acadf7c1..c92d2d22 100644
--- a/example/QCE_demos_2022/Teleport_demo_filled.ipynb
+++ b/example/QCE_demos_2022/Teleport_demo_filled.ipynb
@@ -249,7 +249,7 @@
     "def test(sim_time=1.5, qc_atten=1e-5):\n",
     "    \"\"\"\n",
     "    sim_time: duration of simulation time (ms)\n",
-    "    qc_atten: quantum channel attenuation (dB/km)\n",
+    "    qc_atten: quantum channel attenuation (dB/m)\n",
     "    \"\"\"\n",
     "    \n",
     "    network_config = \"star_network.json\"\n",
diff --git a/example/QCE_demos_2023/GUI_and_code_demo.ipynb b/example/QCE_demos_2023/GUI_and_code_demo.ipynb
index b1cc1794..2cd246c5 100644
--- a/example/QCE_demos_2023/GUI_and_code_demo.ipynb
+++ b/example/QCE_demos_2023/GUI_and_code_demo.ipynb
@@ -162,7 +162,7 @@
     "def test(sim_time=1.5, qc_atten=1e-5):\n",
     "    \"\"\"\n",
     "    sim_time: duration of simulation time (s)\n",
-    "    qc_atten: quantum channel attenuation (dB/km)\n",
+    "    qc_atten: quantum channel attenuation (dB/m)\n",
     "    \"\"\"\n",
     "    \n",
     "    network_config = \"star_network.json\"\n",
diff --git a/example/QCE_demos_2023/GUI_and_code_demo_filled.ipynb b/example/QCE_demos_2023/GUI_and_code_demo_filled.ipynb
index cf460475..43a7dc0c 100644
--- a/example/QCE_demos_2023/GUI_and_code_demo_filled.ipynb
+++ b/example/QCE_demos_2023/GUI_and_code_demo_filled.ipynb
@@ -164,7 +164,7 @@
     "def test(sim_time=1.5, qc_atten=1e-5):\n",
     "    \"\"\"\n",
     "    sim_time: duration of simulation time (s)\n",
-    "    qc_atten: quantum channel attenuation (dB/km)\n",
+    "    qc_atten: quantum channel attenuation (dB/m)\n",
     "    \"\"\"\n",
     "    \n",
     "    network_config = \"star_network.json\"\n",
diff --git a/example/qkd.ipynb b/example/qkd.ipynb
index ca6770cc..bc4ec525 100644
--- a/example/qkd.ipynb
+++ b/example/qkd.ipynb
@@ -133,7 +133,7 @@
     "    cc0.set_ends(n1, n2.name)\n",
     "    cc1.set_ends(n2, n1.name)\n",
     "    # construct a quantum communication channel\n",
-    "    # (with arguments for the channel name, timeline, attenuation (in dB/km), and distance (in m))\n",
+    "    # (with arguments for the channel name, timeline, attenuation (in db/m), and distance (in m))\n",
     "    qc0 = QuantumChannel(\"qc_n1_n2\", tl, attenuation=1e-5, distance=1e3,\n",
     "                         polarization_fidelity=0.97)\n",
     "    qc1 = QuantumChannel(\"qc_n2_n1\", tl, attenuation=1e-5, distance=1e3,\n",
diff --git a/example/random_request_network.ipynb b/example/random_request_network.ipynb
index 38ed1a5f..313a2381 100644
--- a/example/random_request_network.ipynb
+++ b/example/random_request_network.ipynb
@@ -85,7 +85,7 @@
     "def test(sim_time, qc_atten):\n",
     "    \"\"\"\n",
     "    sim_time: duration of simulation time (ms)\n",
-    "    qc_atten: quantum channel attenuation (dB/km)\n",
+    "    qc_atten: quantum channel attenuation (dB/m)\n",
     "    \"\"\"\n",
     "    network_config = \"star_network.json\"\n",
     "\n",
diff --git a/example/random_request_network_mod.ipynb b/example/random_request_network_mod.ipynb
index 2966650e..c427a398 100644
--- a/example/random_request_network_mod.ipynb
+++ b/example/random_request_network_mod.ipynb
@@ -87,7 +87,7 @@
     "def test(sim_time, qc_atten):\n",
     "    \"\"\"\n",
     "    sim_time: duration of simulation time (ms)\n",
-    "    qc_atten: quantum channel attenuation (dB/km)\n",
+    "    qc_atten: quantum channel attenuation (db/m)\n",
     "    \"\"\"\n",
     "    \n",
     "    network_config = \"star_network.json\"\n",
diff --git a/example/three_node_eg_ep_es.ipynb b/example/three_node_eg_ep_es.ipynb
index 72189e0f..a9ad7179 100644
--- a/example/three_node_eg_ep_es.ipynb
+++ b/example/three_node_eg_ep_es.ipynb
@@ -145,7 +145,7 @@
     "            cc.set_ends(node1, node2.name)\n",
     "            \n",
     "    # create quantum channels linking r1 and r2 to m1\n",
-    "    # (with arguments for the channel name, timeline, attenuation (in dB/km), and distance (in m))\n",
+    "    # (with arguments for the channel name, timeline, attenuation (in dB/m), and distance (in m))\n",
     "    qc0 = QuantumChannel(\"qc_r1_m1\", tl, qc_atten, qc_dist)\n",
     "    qc1 = QuantumChannel(\"qc_r2_m1\", tl, qc_atten, qc_dist)\n",
     "    qc0.set_ends(r1, m1.name)\n",
diff --git a/example/two_node_eg.ipynb b/example/two_node_eg.ipynb
index ad592b9c..110569fa 100644
--- a/example/two_node_eg.ipynb
+++ b/example/two_node_eg.ipynb
@@ -186,7 +186,7 @@
     "    \n",
     "    # create linear quantum network between routers and middle node\n",
     "    # for this, we create quantum channels\n",
-    "    # (with arguments for the channel name, timeline, attenuation (in dB/km), and distance (in m))\n",
+    "    # (with arguments for the channel name, timeline, attenuation (in dB/m), and distance (in m))\n",
     "    qc1 = QuantumChannel(\"qc_r1_m1\", tl, qc_atten, qc_dist)\n",
     "    qc1.set_ends(r1, m1.name)\n",
     "    qc2 = QuantumChannel(\"qc_r2_m1\", tl, qc_atten, qc_dist)\n",
diff --git a/sequence/qkd/BB84.py b/sequence/qkd/BB84.py
index af839df9..e9d637b9 100644
--- a/sequence/qkd/BB84.py
+++ b/sequence/qkd/BB84.py
@@ -85,7 +85,7 @@ class BB84(StackProtocol):
     The BB84 protocol uses photons to create a secure key between two QKD Nodes.
 
     Attributes:
-        own (QKDNode): node that protocol instance is attached to.
+        owner (QKDNode): node that protocol instance is attached to.
         name (str): label for protocol instance.
         role (int): determines if instance is "alice" or "bob" node.
         working (bool): shows if protocol is currently working on a key.
@@ -107,7 +107,7 @@ def __init__(self, owner: "QKDNode", name: str, lightsource: str, qsdetector: st
         """Constructor for BB84 class.
 
         Args:
-            own (QKDNode): node hosting protocol instance.
+            owner (QKDNode): node hosting protocol instance.
             name (str): name of protocol instance.
             lightsource (str): name of lightsource for QKD
             qsdetector (str): name of QSDetector for QKD

From 936be452eabb0065c241a9afed7c7e18a9c69ff6 Mon Sep 17 00:00:00 2001
From: Caitao Zhan <caitaozhan@gmail.com>
Date: Tue, 24 Sep 2024 16:10:15 -0500
Subject: [PATCH 5/9] [minor] update README, comments, and logging

---
 README.md                     | 19 ++++++++++++++++++-
 docs/requirements.txt         |  1 +
 sequence/components/memory.py |  2 +-
 sequence/utils/log.py         |  3 ++-
 4 files changed, 22 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index de133628..987f804c 100644
--- a/README.md
+++ b/README.md
@@ -5,7 +5,24 @@
   </picture>
 </p>
 
-<h3><p align="center">Quantum Networking in SeQUeNCe: Scalable, Customizable, Easy Debugging</p></h3>
+<h3><p align="center">Quantum Networking in SeQUeNCe: Customizable, Scalable, Easy Debugging</p></h3>
+
+
+
+<p align="center">
+    <a href="sequence-rtd-tutorial.readthedocs.io/">
+        <img alt="Documentation" src="https://img.shields.io/readthedocs/sequence-rtd-tutorial">
+    </a>
+   <a href="https://pypi.org/project/sequence/">
+        <img alt="Pypi" src="https://img.shields.io/pypi/v/sequence">
+    </a>
+   </a>
+       <a href="https://qutip.org/">
+        <img alt="Pypi" src="https://img.shields.io/badge/integration%20-Qutip-blue">
+    </a>
+    </a>
+
+</p>
 
 <br>
 
diff --git a/docs/requirements.txt b/docs/requirements.txt
index 9e07c5cd..ebdac0a3 100644
--- a/docs/requirements.txt
+++ b/docs/requirements.txt
@@ -1,2 +1,3 @@
 recommonmark
 sphinx-rtd-theme
+numpy
diff --git a/sequence/components/memory.py b/sequence/components/memory.py
index 35dd1b56..50d0a40f 100644
--- a/sequence/components/memory.py
+++ b/sequence/components/memory.py
@@ -119,7 +119,7 @@ class Memory(Entity):
         fidelity (float): (current) fidelity of memory.
         frequency (float): maximum frequency at which memory can be excited.
         efficiency (float): probability of emitting a photon when excited.
-        coherence_time (float): average usable lifetime of memory (in seconds).
+        coherence_time (float): average usable lifetime of memory (in seconds). Negative value means infinite coherence time.
         wavelength (float): wavelength (in nm) of emitted photons.
         qstate_key (int): key for associated quantum state in timeline's quantum manager.
         memory_array (MemoryArray): memory array aggregating current memory.
diff --git a/sequence/utils/log.py b/sequence/utils/log.py
index 30259163..04ef5e4f 100644
--- a/sequence/utils/log.py
+++ b/sequence/utils/log.py
@@ -67,7 +67,8 @@ def track_module(module_name: str):
     """Sets a given module to be tracked by logger."""
 
     global _log_modules
-    _log_modules.append(module_name)
+    if module_name not in _log_modules:
+        _log_modules.append(module_name)
 
 
 def remove_module(module_name: str):

From fe8c80ed2a00c4bcc410fdabbe2b8dd9c1397c56 Mon Sep 17 00:00:00 2001
From: Caitao Zhan <caitaozhan@gmail.com>
Date: Wed, 25 Sep 2024 14:50:23 -0500
Subject: [PATCH 6/9] [minor] update documentations

---
 docs/source/index.rst                                  | 10 +++++-----
 docs/source/references/application/request_app.rst     |  5 +++++
 docs/source/references/application/top.rst             |  1 +
 docs/source/references/misc/constants.rst              |  5 +++++
 docs/source/references/misc/top.rst                    |  1 +
 docs/source/references/misc/utils/config_generator.rst |  5 +++++
 docs/source/references/misc/utils/top.rst              |  3 ++-
 7 files changed, 24 insertions(+), 6 deletions(-)
 create mode 100644 docs/source/references/application/request_app.rst
 create mode 100644 docs/source/references/misc/constants.rst
 create mode 100644 docs/source/references/misc/utils/config_generator.rst

diff --git a/docs/source/index.rst b/docs/source/index.rst
index 66325334..ddbcc0e5 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -24,15 +24,15 @@ Welcome to the SeQUeNCe documentation page
     :maxdepth: 1
     :caption: Module References:
 
-    references/kernel/top
+    references/application/top
     references/components/top
     references/entanglement_management/top
-    references/resource_management/top
+    references/kernel/top
+    references/misc/top
     references/network_management/top
-    references/application/top
-    references/topology/top
     references/qkd/top
-    references/misc/top
+    references/resource_management/top
+    references/topology/top
 
 .. toctree::
     :maxdepth: 1
diff --git a/docs/source/references/application/request_app.rst b/docs/source/references/application/request_app.rst
new file mode 100644
index 00000000..1f365826
--- /dev/null
+++ b/docs/source/references/application/request_app.rst
@@ -0,0 +1,5 @@
+Request Request
+==============
+
+.. automodule:: sequence.app.request_app
+    :members:
diff --git a/docs/source/references/application/top.rst b/docs/source/references/application/top.rst
index e87cb3fc..774fa955 100644
--- a/docs/source/references/application/top.rst
+++ b/docs/source/references/application/top.rst
@@ -6,4 +6,5 @@ The Application module contains code to utilize and test quantum network resourc
 .. toctree::
     :maxdepth: 2
 
+    request_app
     random_request
diff --git a/docs/source/references/misc/constants.rst b/docs/source/references/misc/constants.rst
new file mode 100644
index 00000000..b8642acc
--- /dev/null
+++ b/docs/source/references/misc/constants.rst
@@ -0,0 +1,5 @@
+Constants
+========
+
+.. automodule:: sequence.constants
+    :members:
diff --git a/docs/source/references/misc/top.rst b/docs/source/references/misc/top.rst
index eb9bc529..c9cb12e9 100644
--- a/docs/source/references/misc/top.rst
+++ b/docs/source/references/misc/top.rst
@@ -6,6 +6,7 @@ Miscellaneous SeQUeNCe modules.
 .. toctree::
     :maxdepth: 2
 
+    constants
     message
     protocol
     utils/top
diff --git a/docs/source/references/misc/utils/config_generator.rst b/docs/source/references/misc/utils/config_generator.rst
new file mode 100644
index 00000000..8493ef56
--- /dev/null
+++ b/docs/source/references/misc/utils/config_generator.rst
@@ -0,0 +1,5 @@
+Config Generator
+========
+
+.. automodule:: sequence.utils.config_generator
+    :members:
diff --git a/docs/source/references/misc/utils/top.rst b/docs/source/references/misc/utils/top.rst
index 4715a946..c0fc90f7 100644
--- a/docs/source/references/misc/utils/top.rst
+++ b/docs/source/references/misc/utils/top.rst
@@ -6,5 +6,6 @@ Utilities for SeQUeNCe.
 .. toctree::
     :maxdepth: 2
 
+    config_generator
     encoding
-    log
+    log
\ No newline at end of file

From de1a87e9f9fbd63043211a0999bed56da1569d0b Mon Sep 17 00:00:00 2001
From: Alex-Kolar <alexkolar@comcast.net>
Date: Thu, 26 Sep 2024 16:16:01 -0500
Subject: [PATCH 7/9] Cosmetic updates to README (add spaces and remove
 redundant $)

---
 README.md | 21 +++++++++------------
 1 file changed, 9 insertions(+), 12 deletions(-)

diff --git a/README.md b/README.md
index 987f804c..294eb6c1 100644
--- a/README.md
+++ b/README.md
@@ -7,21 +7,18 @@
 
 <h3><p align="center">Quantum Networking in SeQUeNCe: Customizable, Scalable, Easy Debugging</p></h3>
 
-
-
 <p align="center">
     <a href="sequence-rtd-tutorial.readthedocs.io/">
         <img alt="Documentation" src="https://img.shields.io/readthedocs/sequence-rtd-tutorial">
     </a>
-   <a href="https://pypi.org/project/sequence/">
+    &nbsp;
+    <a href="https://pypi.org/project/sequence/">
         <img alt="Pypi" src="https://img.shields.io/pypi/v/sequence">
     </a>
-   </a>
-       <a href="https://qutip.org/">
+    &nbsp;
+    <a href="https://qutip.org/">
         <img alt="Pypi" src="https://img.shields.io/badge/integration%20-Qutip-blue">
     </a>
-    </a>
-
 </p>
 
 <br>
@@ -75,7 +72,7 @@ publisher = {IOP Publishing},
 ## Running the GUI
 Once SeQUeNCe has been installed as described above, simply run the `gui.py` script found in the root of the project directory
 ```
-$ python gui.py
+python gui.py
 ```
 
 ## Usage Examples
@@ -87,12 +84,12 @@ Code for the experiments performed in our paper can be found in the file `starli
 ### Jupyter Notebook Examples
 The example folder contains several scripts that can be run with jupyter notebook for easy editing and visualization. These files require that the notebook package be installed (Anaconda recommended):
 ```
-$ pip install notebook
-$ pip install ipywidgets
+pip install notebook
+pip install ipywidgets
 ```
 To run each file, simply run
 ```
-$ jupyter notebook <filename>
+jupyter notebook <filename>
 ```
 These examples include:
 * `BB84_eg.ipynb`, which uses the BB84 protocol to distribute secure keys between two quantum nodes
@@ -106,7 +103,7 @@ The example directory contains an example json file `starlight.json` to specify
 
 To view a network, simply run the script and specify the relative location of your json file:
 ```
-$ python utils/draw_topo.py example/starlight.json
+python utils/draw_topo.py example/starlight.json
 ```
 This script also supports a flag `-m` to visualize BSM nodes created by default on quantum links between routers.
 

From 842324aeeac9e78badbe3658c11de3e903ff85dc Mon Sep 17 00:00:00 2001
From: Caitao Zhan <caitaozhan@gmail.com>
Date: Thu, 26 Sep 2024 16:37:10 -0500
Subject: [PATCH 8/9] [minor] fix README issue

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 294eb6c1..aba279c9 100644
--- a/README.md
+++ b/README.md
@@ -8,7 +8,7 @@
 <h3><p align="center">Quantum Networking in SeQUeNCe: Customizable, Scalable, Easy Debugging</p></h3>
 
 <p align="center">
-    <a href="sequence-rtd-tutorial.readthedocs.io/">
+    <a href="https://sequence-rtd-tutorial.readthedocs.io/">
         <img alt="Documentation" src="https://img.shields.io/readthedocs/sequence-rtd-tutorial">
     </a>
     &nbsp;

From 3badc4c5c31e89eaf80439e296cd6608093bb54b Mon Sep 17 00:00:00 2001
From: Caitao Zhan <caitaozhan@gmail.com>
Date: Thu, 26 Sep 2024 17:21:54 -0500
Subject: [PATCH 9/9] [minor] update badges in README

---
 README.md | 20 +++++++-------------
 1 file changed, 7 insertions(+), 13 deletions(-)

diff --git a/README.md b/README.md
index aba279c9..c3833735 100644
--- a/README.md
+++ b/README.md
@@ -7,19 +7,13 @@
 
 <h3><p align="center">Quantum Networking in SeQUeNCe: Customizable, Scalable, Easy Debugging</p></h3>
 
-<p align="center">
-    <a href="https://sequence-rtd-tutorial.readthedocs.io/">
-        <img alt="Documentation" src="https://img.shields.io/readthedocs/sequence-rtd-tutorial">
-    </a>
-    &nbsp;
-    <a href="https://pypi.org/project/sequence/">
-        <img alt="Pypi" src="https://img.shields.io/pypi/v/sequence">
-    </a>
-    &nbsp;
-    <a href="https://qutip.org/">
-        <img alt="Pypi" src="https://img.shields.io/badge/integration%20-Qutip-blue">
-    </a>
-</p>
+
+[![Documentation](https://img.shields.io/readthedocs/sequence-rtd-tutorial)](https://sequence-rtd-tutorial.readthedocs.io/)
+[![PyPi](https://img.shields.io/pypi/v/sequence)](https://pypi.org/project/sequence/)
+[![Qutip](https://img.shields.io/badge/integration%20-Qutip-blue)](https://qutip.org/)
+[![Paper](https://img.shields.io/badge/10.1088%2F2058-9565%2Fac22f6?label=DOI)](https://iopscience.iop.org/article/10.1088/2058-9565/ac22f6)
+
+
 
 <br>