Addressing reviewer comments.

Author: msoeken

source/pip/benchmarks/bench_qre.py

@@ -5,7 +5,12 @@
 from dataclasses import dataclass, KW_ONLY, field
 from qsharp.qre import linear_function, generic_function
 from qsharp.qre._architecture import _make_instruction
-from qsharp.qre.models import GateBased, SurfaceCode
+from qsharp.qre.models import (
+    GateBased,
+    SurfaceCode,
+    TwoDimensionalYokedSurfaceCode,
+    Litinski19Factory,
+)
 from qsharp.qre._enumeration import _enumerate_instances
 
 
@@ -32,19 +37,13 @@ class LargeDomain:
 
 
 def bench_enumerate_isas():
-    import os
-    import sys
-
-    # Add the tests directory to sys.path to import test_qre
-    # TODO: Remove this once the models in test_qre are moved to a proper module
-    sys.path.append(os.path.join(os.path.dirname(__file__), "../tests/qre/"))
-    from conftest import ExampleLogicalFactory, ExampleFactory  # type: ignore
-
     ctx = GateBased(gate_time=50, measurement_time=100).context()
 
     # Hierarchical factory using from_components
-    query = SurfaceCode.q() * ExampleLogicalFactory.q(
-        source=SurfaceCode.q() * ExampleFactory.q()
+    query = (
+        SurfaceCode.q()
+        * TwoDimensionalYokedSurfaceCode.q(source=SurfaceCode.q())
+        * Litinski19Factory.q()
     )
 
     number = 100

source/pip/qsharp/qre/application/_qir.py

@@ -14,9 +14,10 @@
 
 @dataclass
 class QIRApplication(Application[None]):
-    """Application that produces a resource estimation trace from QIR code.
+    """Application that produces a resource estimation trace from base profile QIR code.
 
-    Accepts QIR input as LLVM IR text or bitcode.
+    Accepts QIR input as LLVM IR text or bitcode.  The QIR input must adhere to
+    the base profile.
 
     Attributes:
         input (str | bytes): QIR input as LLVM IR text (str) or

source/qdk_package/pyproject.toml

@@ -17,13 +17,14 @@ jupyter = ["qsharp-widgets==0.0.0", "qsharp-jupyterlab==0.0.0"]
 azure = ["azure-quantum>=3.8.0"]
 qiskit = ["qiskit>=1.2.2,<3.0.0"]
 cirq = ["cirq-core>=1.6.1,<1.7", "cirq-ionq>=1.6.1,<1.7"]
-qre = ["cirq==1.6.1,<1.7", "pandas>=2.1"]
+qre = ["cirq-core==1.6.1,<1.7", "pandas>=2.1", "ply>=3.11"]
 all = [
   "qsharp-widgets==0.0.0",
   "azure-quantum>=3.8.0",
   "qiskit>=1.2.2,<3.0.0",
   "cirq-core>=1.6.1,<1.7",
   "cirq-ionq>=1.6.1,<1.7",
+  "ply>=3.11",
   "qsharp-jupyterlab==0.0.0",
 ]