diff --git a/Makefile b/Makefile
index 0a7132fd..ca13d66f 100644
--- a/Makefile
+++ b/Makefile
@@ -28,7 +28,7 @@ updatereqs: upgrade-pip  ## Autogenerate requirements.txt
 	$(VENV_BIN)/pip-compile --extra=tests --no-annotate --no-emit-index-url --output-file=requirements.txt --strip-extras pyproject.toml
 
 metadeps: upgrade-pip  ## Install extra dependencies used to develop/build this package
-	$(VENV_BIN)/pip install -U build pip-tools pre-commit wheel pytest
+	$(VENV_BIN)/pip install -U build pip-tools pre-commit wheel pytest hypothesis
 
 # Installation
 # ------------
diff --git a/pyproject.toml b/pyproject.toml
index 04fe7535..30cf393e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -15,7 +15,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "quantum-pecos"
-version = "0.6.0.dev1"
+version = "0.6.0.dev2"
 authors = [
     {name = "The PECOS Developers"},
 ]
@@ -28,7 +28,7 @@ requires-python = ">=3.10"
 license = { file = "LICENSE"}
 keywords = ["quantum", "QEC", "simulation", "PECOS"]
 dependencies = [
-    "phir~=0.3.0",
+    "phir>=0.3.3,<0.4",
     "numpy>=1.15.0,<2.0",
     "scipy>=1.1.0,<2.0",
     "networkx>=2.1.0,<3.0",
@@ -73,7 +73,8 @@ visualization = [
     "plotly~=5.9.0",
 ]
 tests = [
-    "pytest>=5.0.0"
+    "pytest>=5.0.0",
+    "hypothesis"
 ]
 all = [
     "quantum-pecos[simulators]",
diff --git a/python/pecos/__init__.py b/python/pecos/__init__.py
index 4a9a68fd..618b09c0 100644
--- a/python/pecos/__init__.py
+++ b/python/pecos/__init__.py
@@ -29,7 +29,7 @@
 from pecos import circuit_converters, circuits, decoders, engines, error_models, misc, qeccs, simulators, tools
 from pecos.circuits.quantum_circuit import QuantumCircuit
 from pecos.engines import circuit_runners
-from pecos.engines.cvm.binarray import BinArray
+from pecos.engines.cvm.binarray2 import BinArray2 as BinArray
 from pecos.engines.hybrid_engine_old import HybridEngine
 
 __all__ = [
diff --git a/python/pecos/classical_interpreters/phir_classical_interpreter.py b/python/pecos/classical_interpreters/phir_classical_interpreter.py
index 502c265e..14a623fd 100644
--- a/python/pecos/classical_interpreters/phir_classical_interpreter.py
+++ b/python/pecos/classical_interpreters/phir_classical_interpreter.py
@@ -15,11 +15,10 @@
 import warnings
 from typing import TYPE_CHECKING, Any
 
-import numpy as np
 from phir.model import PHIRModel
 
 from pecos.classical_interpreters.classical_interpreter_abc import ClassicalInterpreter
-from pecos.reps.pypmir import PyPMIR
+from pecos.reps.pypmir import PyPMIR, signed_data_types, unsigned_data_types
 from pecos.reps.pypmir import types as pt
 
 if TYPE_CHECKING:
@@ -34,16 +33,7 @@ def version2tuple(v):
     return tuple(map(int, (v.split("."))))
 
 
-data_type_map = {
-    "i8": np.int8,
-    "i16": np.int16,
-    "i32": np.int32,
-    "i64": np.int64,
-    "u8": np.uint8,
-    "u16": np.uint16,
-    "u32": np.uint32,
-    "u64": np.uint64,
-}
+data_type_map = signed_data_types | unsigned_data_types
 
 data_type_map_rev = {v: k for k, v in data_type_map.items()}
 
@@ -276,7 +266,6 @@ def assign_int(self, cvar, val: int):
 
         cid = self.csym2id[cvar]
         dtype = self.cid2dtype[cid]
-        size = self.cvar_meta[cid].size
 
         cval = self.cenv[cid]
         val = dtype(val)
@@ -286,8 +275,11 @@ def assign_int(self, cvar, val: int):
             cval &= ~(1 << i)
             cval |= (val & 1) << i
 
-        # mask off bits give the size of the register
-        cval &= (1 << size) - 1
+        if type(cval) not in signed_data_types.values():
+            # mask off bits given the size of the register
+            # (only valid for unsigned data types)
+            size = self.cvar_meta[cid].size
+            cval &= (1 << size) - 1
         self.cenv[cid] = cval
 
     def handle_cops(self, op):
diff --git a/python/pecos/engines/cvm/binarray2.py b/python/pecos/engines/cvm/binarray2.py
index 4a66120b..31364524 100644
--- a/python/pecos/engines/cvm/binarray2.py
+++ b/python/pecos/engines/cvm/binarray2.py
@@ -13,9 +13,13 @@
 
 import numpy as np
 
+from pecos.reps.pypmir import unsigned_data_types
+
 
 class BinArray2:
-    def __init__(self, size, value=0, dtype=np.int32) -> None:
+    """As opposed to the original unsigned 32-bit BinArray, this class defaults to signed 64-bit type."""
+
+    def __init__(self, size, value=0, dtype=np.int64) -> None:
         self.size = size
         self.value = None
         self.dtype = dtype
@@ -33,6 +37,8 @@ def __init__(self, size, value=0, dtype=np.int32) -> None:
     def set(self, value):
         if isinstance(value, self.dtype):
             self.value = value
+        elif isinstance(value, BinArray2):
+            self.value = value.value
         else:
             if isinstance(value, str):
                 value = int(value, 2)
@@ -41,7 +47,8 @@ def set(self, value):
 
     def new_val(self, value):
         b = BinArray2(self.size, value, self.dtype)
-        b.clamp(self.size)
+        if self.dtype in unsigned_data_types.values():
+            b.clamp(self.size)
         return b
 
     def num_bits(self):
diff --git a/python/pecos/engines/cvm/classical.py b/python/pecos/engines/cvm/classical.py
index f7443e8d..f810eac8 100644
--- a/python/pecos/engines/cvm/classical.py
+++ b/python/pecos/engines/cvm/classical.py
@@ -11,7 +11,7 @@
 
 from __future__ import annotations
 
-from pecos.engines.cvm.binarray import BinArray
+from pecos.engines.cvm.binarray2 import BinArray2 as BinArray
 
 
 def set_output(state, circuit, output_spec, output):
diff --git a/python/pecos/engines/cvm/wasm.py b/python/pecos/engines/cvm/wasm.py
index 4ab5bda0..5383bdf5 100644
--- a/python/pecos/engines/cvm/wasm.py
+++ b/python/pecos/engines/cvm/wasm.py
@@ -12,7 +12,7 @@
 import pickle
 from pathlib import Path
 
-from pecos.engines.cvm.binarray import BinArray
+from pecos.engines.cvm.binarray2 import BinArray2 as BinArray
 from pecos.engines.cvm.sim_func import sim_exec
 from pecos.engines.cvm.wasm_vms.pywasm import read_pywasm
 from pecos.engines.cvm.wasm_vms.pywasm3 import read_pywasm3
diff --git a/python/pecos/engines/hybrid_engine_old.py b/python/pecos/engines/hybrid_engine_old.py
index f322c9a3..4754c609 100644
--- a/python/pecos/engines/hybrid_engine_old.py
+++ b/python/pecos/engines/hybrid_engine_old.py
@@ -15,7 +15,8 @@
 
 import numpy as np
 
-from pecos.engines.cvm.classical import BinArray, eval_condition, eval_cop, set_output
+from pecos.engines.cvm.binarray2 import BinArray2 as BinArray
+from pecos.engines.cvm.classical import eval_condition, eval_cop, set_output
 from pecos.engines.cvm.wasm import eval_cfunc, get_ccop
 from pecos.error_models.fake_error_model import FakeErrorModel
 from pecos.errors import NotSupportedGateError
diff --git a/python/pecos/reps/pypmir/__init__.py b/python/pecos/reps/pypmir/__init__.py
index 76527bee..0800c3b8 100644
--- a/python/pecos/reps/pypmir/__init__.py
+++ b/python/pecos/reps/pypmir/__init__.py
@@ -9,4 +9,4 @@
 # "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the
 # specific language governing permissions and limitations under the License.
 
-from pecos.reps.pypmir.pypmir import PyPMIR
+from pecos.reps.pypmir.pypmir import PyPMIR, signed_data_types, unsigned_data_types
diff --git a/python/pecos/reps/pypmir/pypmir.py b/python/pecos/reps/pypmir/pypmir.py
index 1f83d3ca..80c87be9 100644
--- a/python/pecos/reps/pypmir/pypmir.py
+++ b/python/pecos/reps/pypmir/pypmir.py
@@ -15,6 +15,8 @@
 from math import pi
 from typing import TYPE_CHECKING, Callable, TypeVar
 
+import numpy as np
+
 from pecos.reps.pypmir import block_types as blk
 from pecos.reps.pypmir import data_types as d
 from pecos.reps.pypmir import op_types as op
@@ -25,6 +27,20 @@
 
 TypeOp = TypeVar("TypeOp", bound=op.Op)
 
+signed_data_types = {
+    "i8": np.int8,
+    "i16": np.int16,
+    "i32": np.int32,
+    "i64": np.int64,
+}
+
+unsigned_data_types = {
+    "u8": np.uint8,
+    "u16": np.uint16,
+    "u32": np.uint32,
+    "u64": np.uint64,
+}
+
 
 class PyPMIR:
     """Pythonic PECOS Middle-level IR. Used to convert PHIR into an object and optimize the data structure for
@@ -229,10 +245,14 @@ def from_phir(cls, phir: dict, name_resolver=None) -> PyPMIR:
                 name = o["data"]
 
                 if name == "cvar_define":
+                    data_type = o["data_type"]
+                    size = int(data_type[1:])
+                    if "size" in o:
+                        size = o["size"]
                     data = d.CVarDefine(
-                        data_type=o["data_type"],
+                        data_type=data_type,
                         variable=o["variable"],
-                        size=o["size"],
+                        size=size,
                         cvar_id=len(p.cvar_meta),
                         metadata=o.get("metadata"),
                     )
diff --git a/requirements.txt b/requirements.txt
index 6b4b606f..d0d27e16 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,9 +5,11 @@
 #    pip-compile --extra=tests --no-annotate --no-emit-index-url --output-file=requirements.txt --strip-extras pyproject.toml
 #
 annotated-types==0.6.0
+attrs==23.2.0
 contourpy==1.2.0
 cycler==0.12.1
 fonttools==4.50.0
+hypothesis==6.100.1
 iniconfig==2.0.0
 kiwisolver==1.4.5
 markdown-it-py==3.0.0
@@ -16,7 +18,7 @@ mdurl==0.1.2
 networkx==2.8.8
 numpy==1.26.4
 packaging==24.0
-phir==0.3.2
+phir==0.3.3
 pillow==10.2.0
 pluggy==1.4.0
 pydantic==2.6.4
@@ -28,4 +30,5 @@ python-dateutil==2.9.0.post0
 rich==13.7.1
 scipy==1.12.0
 six==1.16.0
+sortedcontainers==2.4.0
 typing-extensions==4.10.0
diff --git a/tests/integration/test_phir_64_bit.py b/tests/integration/test_phir_64_bit.py
new file mode 100644
index 00000000..66ea4929
--- /dev/null
+++ b/tests/integration/test_phir_64_bit.py
@@ -0,0 +1,35 @@
+from pecos.engines.hybrid_engine import HybridEngine
+
+
+def bin2int(result: list[str]) -> int:
+    return int(result[0], base=2)
+
+
+def test_setting_cvar():
+    phir = {
+        "format": "PHIR/JSON",
+        "version": "0.1.0",
+        "ops": [
+            {"data": "cvar_define", "data_type": "i32", "variable": "var_i32"},
+            {"data": "cvar_define", "data_type": "u32", "variable": "var_u32", "size": 32},
+            {"data": "cvar_define", "data_type": "i64", "variable": "var_i64"},
+            {"data": "cvar_define", "data_type": "u64", "variable": "var_u64", "size": 64},
+            {"data": "cvar_define", "data_type": "i32", "variable": "var_i32neg"},
+            {"data": "cvar_define", "data_type": "i64", "variable": "var_i64neg"},
+            {"cop": "=", "returns": ["var_i32"], "args": [2**31 - 1]},
+            {"cop": "=", "returns": ["var_u32"], "args": [2**32 - 1]},
+            {"cop": "=", "returns": ["var_i64"], "args": [2**63 - 1]},
+            {"cop": "=", "returns": ["var_u64"], "args": [2**64 - 1]},
+            {"cop": "=", "returns": ["var_i32neg"], "args": [-(2**31)]},
+            {"cop": "=", "returns": ["var_i64neg"], "args": [-(2**63)]},
+        ],
+    }
+
+    results = HybridEngine(qsim="stabilizer").run(program=phir, shots=5)
+
+    assert bin2int(results["var_i32"]) == 2**31 - 1
+    assert bin2int(results["var_u32"]) == 2**32 - 1
+    assert bin2int(results["var_i64"]) == 2**63 - 1
+    assert bin2int(results["var_u64"]) == 2**64 - 1
+    assert bin2int(results["var_i32neg"]) == -(2**31)
+    assert bin2int(results["var_i64neg"]) == -(2**63)
diff --git a/tests/unit/test_binarray.py b/tests/unit/test_binarray.py
new file mode 100644
index 00000000..d6f013d2
--- /dev/null
+++ b/tests/unit/test_binarray.py
@@ -0,0 +1,104 @@
+from typing import Final
+
+import numpy as np
+from hypothesis import assume, given
+from hypothesis import strategies as st
+from pecos.engines.cvm.binarray2 import BinArray2 as BinArray
+
+DEFAULT_SIZE: Final = 63
+MIN: Final = -(2**DEFAULT_SIZE)
+MAX: Final = 2**DEFAULT_SIZE - 1
+int_range = st.integers(min_value=MIN, max_value=MAX)
+
+
+@given(st.text(alphabet=["0", "1"], min_size=1))
+def test_init(x):
+    ba = BinArray(x)
+    assert ba == f"0b{x}"
+
+
+def test_set_bit():
+    ba = BinArray("0000")
+    ba[2] = 1
+    assert ba == 0b0100
+
+
+def test_get_bit():
+    ba = BinArray("1010")
+    assert ba[2] == 0
+    assert ba[3] == 1
+
+
+def test_to_int():
+    ba = BinArray("1010")
+    assert int(ba) == 10
+
+
+@given(int_range, int_range)
+def test_addition(x, y):
+    assume(MIN <= x + y <= MAX)
+    ba1 = BinArray(DEFAULT_SIZE, x)
+    ba2 = BinArray(DEFAULT_SIZE, y)
+    result = ba1 + ba2
+    assert int(result) == x + y
+
+
+def test_subtraction():
+    ba1 = BinArray("1101")  # 13
+    ba2 = BinArray("1010")  # 10
+    result = ba1 - ba2
+    assert int(result) == 3
+
+
+@given(int_range, int_range)
+def test_multiplication(x, y):
+    assume(MIN <= x * y <= MAX)
+    ba1 = BinArray(DEFAULT_SIZE, x)
+    ba2 = BinArray(DEFAULT_SIZE, y)
+    result = ba1 * ba2
+    assert int(result) == x * y
+
+
+def test_comparison():
+    ba1 = BinArray("1010")  # 10
+    ba2 = BinArray("1010")  # 10
+    ba3 = BinArray("1101")  # 13
+    assert ba1 == ba2
+    assert ba1 != ba3
+    assert ba1 != ba3
+    assert ba1 < ba3
+    assert ba3 > ba1
+
+
+def test_bitwise_and():
+    ba1 = BinArray("1010")  # 10
+    ba2 = BinArray("1101")  # 13
+    result = ba1 & ba2
+    assert result == 0b1000
+
+
+def test_bitwise_or():
+    ba1 = BinArray("1010")  # 10
+    ba2 = BinArray("1101")  # 13
+    result = ba1 | ba2
+    assert result == 0b1111
+
+
+def test_bitwise_xor():
+    ba1 = BinArray("1010")  # 10
+    ba2 = BinArray("1101")  # 13
+    result = ba1 ^ ba2
+    assert result == 0b0111
+
+
+def test_unsigned_bitwise_not():
+    ba = BinArray("1010", dtype=np.uint64)  # 10
+    result = ~ba
+    assert result == 0b0101
+
+
+@given(int_range)
+def test_signed_bitwise_not(x):
+    ba = BinArray(DEFAULT_SIZE, x)
+    result = ~ba
+    assert int(result) == -x - 1  # (two's complement)