Feat: Remove all the warnings from tests. Make warnings as errors on …

…CI and locally (#143)

Makefile

@@ -16,3 +16,14 @@ github_actions-default:
 style-fix:
 	black src tests examples benchmarks
 	isort --profile=black src tests examples benchmarks
+
+test:
+	$(PYTHON) -m pytest -W error tests
+
+coverage:
+	$(PYTHON) -m pytest -W error\
+		--cov=src \
+		--cov-fail-under=$(MIN_COVERAGE) tests \
+		--no-cov-on-fail \
+		--cov-report xml \
+		&& echo Code coverage Passed the $(MIN_COVERAGE)% mark!

pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires = ["setuptools", "wheel",  "setuptools_scm>=6.0"]
+requires = ["setuptools<=65.6.3", "wheel",  "setuptools_scm>=6.0"]
 
 # Including this section is same as 'use_scm_version=True' in setup.py
 # See https://github.com/pypa/setuptools_scm for guidance

setup.cfg

@@ -24,8 +24,9 @@ python_requires = >=3.9,!=3.9.7
 install_requires =
     orquestra-quantum==0.12.0
     orquestra-vqa==0.9.0
-    orquestra-qiskit==0.13.0
-    orquestra-cirq==0.11.0
+    orquestra-qiskit==0.14.0
+    orquestra-cirq==0.12.0
+    orquestra-opt==0.10.0
     networkx>=2.8.7
     # Used to define and run Orquestra workflows
     orquestra-sdk[all]>=0.46.0
@@ -34,7 +35,7 @@ install_requires =
     more-itertools~=9.1.0
     pandas==1.5.3
     pyLIQTR==0.3.3
-    openfermion~=1.5.0
+    openfermion[resources]~=1.6.0
     pytest # required by OpenFermion's resource_estimates module
     graph-state-generation==0.2.0
     juliapkg==0.1.10
@@ -44,6 +45,8 @@ install_requires =
     stim==1.10
     optuna==3.3.0
     cvxpy==1.3.2
+    aiohttp~=3.9.0
+    setuptools<=65.6.3
 
 [options.packages.find]
 where = src

src/benchq/compilation/pyliqtr_transpilation.py

@@ -1,6 +1,7 @@
 ################################################################################
 # © Copyright 2022 Zapata Computing Inc.
 ################################################################################
+import warnings
 from typing import Optional, Union
 
 from cirq.circuits import Circuit as CirqCircuit
@@ -56,12 +57,16 @@ def pyliqtr_transpile_to_clifford_t(
         raise ValueError("Please supply gate or circuit precision not both")
 
     cirq_circuit = export_circuit(CirqCircuit, orquestra_circuit)
-    compiled_cirq_circuit = clifford_plus_t_direct_transform(
-        cirq_circuit,
-        precision=gate_precision,
-        circuit_precision=circuit_precision,
-        use_random_decomp=False,
-        num_rotation_gates=n_rotation_gates,
-    )
+    with warnings.catch_warnings():
+        warnings.filterwarnings(
+            "ignore", message=r".* is not a rotation gate, cannot decompose."
+        )
+        compiled_cirq_circuit = clifford_plus_t_direct_transform(
+            cirq_circuit,
+            precision=gate_precision,
+            circuit_precision=circuit_precision,
+            use_random_decomp=False,
+            num_rotation_gates=n_rotation_gates,
+        )
 
     return import_circuit(compiled_cirq_circuit, orquestra_circuit.n_qubits)

src/benchq/data_structures/decoder.py

@@ -118,5 +118,4 @@ def find_next_highest_distance(distances, d):
 
 def invalid_code_distance():
     """Returns the delay for invalid code distance."""
-    warnings.warn("Code distance is too high to be decoded.", RuntimeWarning)
     return np.infty

src/benchq/data_structures/hardware_architecture_models.py

@@ -234,18 +234,15 @@ def num_optical_cross_connect_layers(
         # must be used for connecting to connector switches
         # Each switch has 1000 ports
         # Each group of ELU + neighbor has at most 4 ELUs
-        warnings.warn("This output parameter has yet to be implemented.")
 
-        num_OXC_layers = None
-
-        return num_OXC_layers
+        # Not yet implemented
+        return -1
 
     def num_ELUs_per_optical_cross_connect(
         self, code_distance: int, num_communication_qubits: int
     ):
-        warnings.warn("This output parameter has yet to be implemented.")
-        num_ELUs_per_OXC = None
-        return num_ELUs_per_OXC
+        # Not yet implemented
+        return -1
 
 
 DETAILED_ION_TRAP_ARCHITECTURE_MODEL = DetailedIonTrapModel()

src/benchq/problem_ingestion/molecule_instance_generation.py

@@ -2,6 +2,7 @@
 # © Copyright 2022 Zapata Computing Inc.
 ################################################################################
 import os
+import warnings
 from copy import deepcopy
 from dataclasses import asdict, dataclass
 from typing import Iterable, List, Optional, Tuple
@@ -11,11 +12,25 @@
 import urllib3  # type: ignore
 from mlflow import MlflowClient  # type: ignore
 from openfermion import MolecularData
-from openfermion.resource_estimates.molecule import (
-    avas_active_space,
-    localize,
-    stability,
-)
+
+with warnings.catch_warnings():
+    warnings.filterwarnings(
+        "ignore",
+        message="\n\n"
+        "  `numpy.distutils` is deprecated since NumPy 1.23.0, as a result\n",
+    )
+
+    # we need to disable pyscf GC as it throws around bunch of warnings
+    import pyscf
+
+    pyscf.gto.mole.DISABLE_GC = True
+
+    from openfermion.resource_estimates.molecule import (
+        avas_active_space,
+        localize,
+        stability,
+    )
+
 from openfermionpyscf import PyscfMolecularData
 from openfermionpyscf._run_pyscf import compute_integrals
 from orquestra import sdk
@@ -43,11 +58,19 @@ def truncate_with_avas(
     mean_field_object = stability(mean_field_object)
 
     # localize before automatically selecting active space with AVAS
-    mean_field_object = localize(
-        mean_field_object, loc_type="pm"
-    )  # default is loc_type ='pm' (Pipek-Mezey)
 
-    return avas_active_space(mean_field_object, ao_list=ao_list, minao=minao)
+    with warnings.catch_warnings():
+        warnings.filterwarnings(
+            "ignore", message="The 'sym_pos' keyword is deprecated and should be"
+        )
+        mean_field_object = localize(
+            mean_field_object, loc_type="pm"
+        )  # default is loc_type ='pm' (Pipek-Mezey)
+        active_space = avas_active_space(
+            mean_field_object, ao_list=ao_list, minao=minao
+        )
+
+    return active_space
 
 
 def _create_mlflow_setup(
@@ -210,7 +233,12 @@ def _run_pyscf(scf_info: SCFInfo) -> Tuple[gto.Mole, scf.hf.SCF]:
             if "callback" in scf_info.scf_options:
                 # we want to log to mlflow, AND we've defined the
                 # callback in scf_options
-                mean_field_object.run(**scf_info.scf_options)
+                with warnings.catch_warnings():
+                    warnings.filterwarnings(
+                        "ignore",
+                        message="The 'sym_pos' keyword is deprecated and should be",
+                    )
+                    mean_field_object.run(**scf_info.scf_options)
             else:
                 # we want to log to mlflow, BUT haven't defined the
                 # callback in scf_options
@@ -231,7 +259,12 @@ def _run_pyscf(scf_info: SCFInfo) -> Tuple[gto.Mole, scf.hf.SCF]:
                     client.log_param(run_id, key, val)
                 temp_options = deepcopy(scf_info.scf_options)
                 temp_options["callback"] = create_mlflow_scf_callback(client, run_id)
-                mean_field_object.run(**temp_options)
+                with warnings.catch_warnings():
+                    warnings.filterwarnings(
+                        "ignore",
+                        message="The 'sym_pos' keyword is deprecated and should be",
+                    )
+                    mean_field_object.run(**temp_options)
         else:
             # we want to log to mlflow, but haven't defined scf_options
             if not isinstance(scf_info.orq_workspace_id, str):
@@ -250,14 +283,29 @@ def _run_pyscf(scf_info: SCFInfo) -> Tuple[gto.Mole, scf.hf.SCF]:
             for key, val in flat_active_dict.items():
                 client.log_param(run_id, key, val)
             temp_options = {"callback": create_mlflow_scf_callback(client, run_id)}
-            mean_field_object.run(**temp_options)
+            with warnings.catch_warnings():
+                warnings.filterwarnings(
+                    "ignore",
+                    message="The 'sym_pos' keyword is deprecated and should be",
+                )
+                mean_field_object.run(**temp_options)
     else:
         if scf_info.scf_options is not None:
             # we don't want to run on mlflow, but we've specified scf_options
-            mean_field_object.run(**scf_info.scf_options)
+            with warnings.catch_warnings():
+                warnings.filterwarnings(
+                    "ignore",
+                    message="The 'sym_pos' keyword is deprecated and should be",
+                )
+                mean_field_object.run(**scf_info.scf_options)
         else:
             # we don't want to run on mlflow, and haven't specified scf_options
-            mean_field_object.run()
+            with warnings.catch_warnings():
+                warnings.filterwarnings(
+                    "ignore",
+                    message="The 'sym_pos' keyword is deprecated and should be",
+                )
+                mean_field_object.run()
 
     if not mean_field_object.converged:
         raise SCFConvergenceError()

src/benchq/resource_estimation/graph/extrapolation_estimator.py

@@ -167,7 +167,11 @@ def _logarithmic_objective(params):
     y_mean = np.mean(y)
     total_sum_of_squares = np.sum((y - y_mean) ** 2)
     residual_sum_of_squares = np.sum((y - (a_opt * np.log(x) + b_opt)) ** 2)
-    r_squared = 1 - (residual_sum_of_squares / total_sum_of_squares)
+
+    if total_sum_of_squares == 0:
+        r_squared = 1
+    else:
+        r_squared = 1 - (residual_sum_of_squares / total_sum_of_squares)
 
     return extrapolated_point, r_squared
 
@@ -190,7 +194,11 @@ def _linear_objective(params):
     y_mean = np.mean(y)
     total_sum_of_squares = np.sum((y - y_mean) ** 2)
     residual_sum_of_squares = np.sum((y - (a_opt * x + b_opt)) ** 2)
-    r_squared = 1 - (residual_sum_of_squares / total_sum_of_squares)
+
+    if total_sum_of_squares == 0:
+        r_squared = 1
+    else:
+        r_squared = 1 - (residual_sum_of_squares / total_sum_of_squares)
 
     return extrapolated_point, r_squared
 

src/benchq/resource_estimation/openfermion_re.py

@@ -2,10 +2,21 @@
 # © Copyright 2023 Zapata Computing Inc.
 ################################################################################
 
+import warnings
 from typing import Tuple
 
 import numpy as np
-from openfermion.resource_estimates import df, sf
+
+with warnings.catch_warnings():
+    warnings.filterwarnings(
+        "ignore",
+        message="\n\n"
+        "  `numpy.distutils` is deprecated "
+        "since NumPy 1.23.0, as a result\n",
+    )
+    # openfermion throws deprecation warning thru pyscf and numpy
+    # Could be fixed by using old setuptools, but there would be dependency conflict
+    from openfermion.resource_estimates import df, sf
 
 from benchq.data_structures import (
     BASIC_SC_ARCHITECTURE_MODEL,

tests/benchq/data_structures/test_hardware_architecture_models.py

@@ -137,8 +137,8 @@ def test_hardware_resource_estimates(
                 num_communication_qubits_per_elu=qubits,
                 num_memory_qubits_per_elu=code_distance,
                 num_computational_qubits_per_elu=num_computational_qubits_per_elu,
-                num_optical_cross_connect_layers=None,
-                num_ELUs_per_optical_cross_connect=None,
+                num_optical_cross_connect_layers=-1,
+                num_ELUs_per_optical_cross_connect=-1,
                 total_num_ions=n_logical_qubits
                 * (num_computational_qubits_per_elu + code_distance + qubits),
                 total_num_communication_qubits=n_logical_qubits * qubits,

tests/benchq/problem_embeddings/test_qsp.py

@@ -2,6 +2,7 @@
 # © Copyright 2023 Zapata Computing Inc.
 ################################################################################
 """Unit tests for benchq.problem_embeddings._qsp."""
+import warnings
 from collections import Counter
 from typing import Mapping
 
@@ -56,14 +57,16 @@ def test_example_circuit(use_random_angles: bool):
         np.random.seed(42)
 
         # When
-        circuit = _qsp.get_qsp_circuit(
-            operator=operator,
-            required_precision=required_precision,
-            dt=dt,
-            tmax=tmax,
-            sclf=sclf,
-            use_random_angles=use_random_angles,
-        )
+        with warnings.catch_warnings():
+            warnings.filterwarnings("ignore", category=RuntimeWarning)
+            circuit = _qsp.get_qsp_circuit(
+                operator=operator,
+                required_precision=required_precision,
+                dt=dt,
+                tmax=tmax,
+                sclf=sclf,
+                use_random_angles=use_random_angles,
+            )
 
         # Then
         # We expect this many gates being applied in the circuit

tests/benchq/resource_estimation/test_decoder_resource_estimator.py

@@ -35,15 +35,15 @@ def test_decoder_model_produces_none_and_throws_warning_for_distance_too_high(
     distance, expected_warning_message, decoder_data
 ):
     decoder_model = DecoderModel.from_csv(file_path(decoder_data + ".csv"))
-    with warnings.catch_warnings(record=True) as w:
+    with pytest.warns(RuntimeWarning) as record:
         assert (
             get_decoder_info(BASIC_SC_ARCHITECTURE_MODEL, decoder_model, distance, 2, 3)
             is None
         )
 
-        assert len(w) == 1
-        assert issubclass(w[0].category, RuntimeWarning)
-        assert expected_warning_message in str(w[0].message)
+    assert len(record) == 1
+    assert issubclass(record[0].category, RuntimeWarning)
+    assert expected_warning_message in str(record[0].message)
 
 
 def test_if_decoder_equations_have_changed():

tests/benchq/resource_estimation/test_openfermion_re.py

@@ -1,7 +1,24 @@
+import warnings
+
 import numpy
 import numpy as np
 import pytest
-from openfermion.resource_estimates.molecule import pyscf_to_cas
+
+with warnings.catch_warnings():
+    warnings.filterwarnings(
+        "ignore",
+        message="\n\n"
+        "  `numpy.distutils` is deprecated since NumPy 1.23.0, as a result\n",
+    )
+    # openfermion throws deprecation warning thru pyscf and numpy
+    # Could be fixed by using old setuptools, but there would be dependency conflict
+
+    # We also need to disable GC for pyscf. It causes resources warnings
+    import pyscf
+
+    pyscf.gto.mole.DISABLE_GC = True
+
+    from openfermion.resource_estimates.molecule import pyscf_to_cas
 
 from benchq.data_structures import BasicArchitectureModel
 from benchq.problem_ingestion.molecule_instance_generation import (