fix various lints, and remove deprecated numpy constants

pyproject.toml

@@ -98,7 +98,7 @@ indent-width = 4
 target-version = "py39"
 
 [tool.ruff.lint]
-select = ["D", "E4", "E7", "E9", "F", "I", "B", "S", "UP", "W"]
+select = ["D", "E4", "E7", "E9", "F", "I", "B", "S", "UP", "W", "NPY201"]
 ignore = [
   "D105",  # Allow missing documentation in dunder method.
   "D203",  # This conflicts with D211.

pyquil/latex/_ipython.py

@@ -79,4 +79,4 @@ def display(circuit: Program, settings: Optional[DiagramSettings] = None, **imag
                 msg += " Transcript:\n\n" + result.stderr.decode("utf-8")
             raise RuntimeError(msg)
 
-        return Image(filename=png, **image_options)
+        return Image(filename=png, **image_options)  # type: ignore

pyquil/paulis.py

@@ -936,7 +936,7 @@ def combined_exp_wrap(param: float) -> Program:
 
 def exponentiate_pauli_sum(
     pauli_sum: Union[PauliSum, PauliTerm],
-) -> NDArray[np.complex_]:
+) -> NDArray[np.complex128]:
     r"""Exponentiate a sequence of PauliTerms, which may or may not commute.
 
     The Pauliterms must have fixed (non-parametric) coefficients. The coefficients are interpreted in cycles rather than
@@ -995,7 +995,7 @@ def exponentiate_pauli_sum(
         matrices.append(matrix)
     generated_unitary = expm(-1j * np.pi * sum(matrices))
     phase = np.exp(-1j * np.angle(generated_unitary[0, 0]))
-    return np.asarray(phase * generated_unitary, dtype=np.complex_)
+    return np.asarray(phase * generated_unitary, dtype=np.complex128)
 
 
 def _exponentiate_general_case(pauli_term: PauliTerm, param: float) -> Program:

pyquil/pyqvm.py

@@ -64,7 +64,7 @@
 
 log = logging.getLogger(__name__)
 
-QUIL_TO_NUMPY_DTYPE = {"INT": np.int_, "REAL": np.float_, "BIT": np.int8, "OCTET": np.uint8}
+QUIL_TO_NUMPY_DTYPE = {"INT": np.int32, "REAL": np.float64, "BIT": np.int8, "OCTET": np.uint8}
 
 
 class AbstractQuantumSimulator(ABC):
@@ -387,7 +387,7 @@ def transition(self) -> bool:
             target = instruction.target
             old = self.ram[target.name][target.offset]
             if isinstance(instruction, ClassicalNeg):
-                if not isinstance(old, (int, float, np.int_, np.float_)):
+                if not isinstance(old, (int, float, np.int32, np.float64)):
                     raise ValueError(f"NEG requires a data type of REAL or INTEGER; not {type(old)}")
                 self.ram[target.name][target.offset] *= -1
             elif isinstance(instruction, ClassicalNot):

pyquil/quilbase.py

@@ -2825,8 +2825,9 @@ def instructions(self) -> list[AbstractInstruction]:
     def instructions(self, instructions: list[AbstractInstruction]) -> None:
         self.instrs = instructions
 
-    @property
+    @property  # type: ignore[override]
     def name(self) -> str:
+        """Get the name of the calibration."""
         return super().identifier.name
 
     @name.setter

pyquil/quiltcalibrations.py

@@ -58,7 +58,8 @@ def _convert_to_calibration_match(
         target_values = (
             [] if not instruction.target else [MemoryReference._from_rs_memory_reference(instruction.target)]
         )
-        parameter_qubits = [] if not calibration.qubit() else [calibration.qubit()]
+        calibration_qubit = calibration.qubit()
+        parameter_qubits = [] + [calibration_qubit] if calibration_qubit else []
         parameter_values = [MemoryReference._from_parameter_str(calibration.identifier.parameter)]
         py_calibration = DefMeasureCalibration._from_rs_measure_calibration_definition(calibration)
     else:

test/unit/test_noise.py

@@ -256,9 +256,9 @@ def test_readout_compensation():
     for ap in aps:
         ap.flat[ap.flat < 0] = 0.0
         ap /= ap.sum()
-        assert np.alltrue(ap >= 0)
+        assert (ap >= 0).all()
 
-    assert np.alltrue(p >= 0)
+    assert (p >= 0).all()
 
     p_corrupted = corrupt_bitstring_probs(p, aps)
     p_restored = correct_bitstring_probs(p_corrupted, aps)

test/unit/test_quilatom.py

@@ -76,5 +76,5 @@ def test_qubit_placeholder():
 
 def test_arithmetic_with_numpy():
     x = Parameter("x")
-    expression = np.float_(1.0) + x
-    assert expression == Add(np.float_(1.0), x)
+    expression = np.float64(1.0) + x
+    assert expression == Add(np.float64(1.0), x)