Merge pull request #126 from Qiskit/master

fetch from origin

.pylintdict

@@ -92,6 +92,7 @@ composable
 conda
 conf
 config
+contravariance
 conv
 coord
 coords
@@ -384,6 +385,7 @@ msq
 multiclass
 multinomial
 multiprocess
+mypy
 nakanishi
 namelist
 nan
@@ -689,6 +691,7 @@ wavefunctions
 weightedpaulioperator
 wf
 whitespace
+whitespaces
 wigner
 wikipedia
 workq

.travis.yml

@@ -14,7 +14,7 @@ notifications:
   email:
     if: fork = false AND type = cron
     recipients:
-      - manoel@us.ibm.com
+      - manoel.marques@ibm.com
     on_success: never
     on_failure: always
 
@@ -122,24 +122,39 @@ jobs:
   include:
     - stage: Checks and Tests
       <<: *stage_dependencies
-      name: "Pip, spell, style, lint, copyright and docs checks"
+      name: "Pip, spell, style, lint, copyright and docs checks Python 3.7"
       if: tag IS blank
       install:
         # install spell check libraries
         - sudo apt-get -y install python3-enchant
         - sudo apt-get -y install hunspell-en-us
         - pip install pyenchant
         - pip install cplex
-        - pip install "cvxpy>1.0.0,<1.1.0"
+        - pip install "cvxpy>1.0.0"
         - pip install https://github.com/rpmuller/pyquante2/archive/master.zip --progress-bar off
       script:
         - pip check
         - make spell
         - make style
         - make lint
+        # Lint with latest pylint also
+        - pip install -U pylint
+        - make lint
         - make copyright
         - make html SPHINXOPTS=-W
         - make doctest
+    - name: "Lint check Python 3.8"
+      <<: *stage_dependencies
+      if: tag IS blank
+      python: 3.8
+      install:
+        - pip install "cvxpy>1.0.0"
+        - pip install https://github.com/rpmuller/pyquante2/archive/master.zip --progress-bar off
+      script:
+        - make lint
+        # Lint with latest pylint also
+        - pip install -U pylint
+        - make lint
     - name: "Mypy check"
       <<: *stage_dependencies
       if: tag IS blank
@@ -159,7 +174,7 @@ jobs:
             - aqua137.dep
       before_script:
         - pip install cplex
-        - pip install "cvxpy>1.0.0,<1.1.0"
+        - pip install "cvxpy>1.0.0"
         - export PYTHON="coverage3 run --source qiskit/aqua,qiskit/chemistry,qiskit/finance,qiskit/ml,qiskit/optimization --omit */gauopen/* --parallel-mode"
       script:
         - stestr --test-path test/aqua run --blacklist-file selection.txt 2> >(tee /dev/stderr out.txt > /dev/null)
@@ -175,7 +190,7 @@ jobs:
           paths: aqua138.dep
       python: 3.8
       before_script:
-        - pip install "cvxpy>1.0.0,<1.1.0"
+        - pip install "cvxpy>1.0.0"
       script:
         - stestr --test-path test/aqua run --blacklist-file selection.txt 2> >(tee /dev/stderr out.txt > /dev/null)
         - python tools/extract_deprecation.py -file out.txt -output aqua138.dep
@@ -190,7 +205,7 @@ jobs:
             - aqua237.dep
       before_script:
         - pip install cplex
-        - pip install "cvxpy>1.0.0,<1.1.0"
+        - pip install "cvxpy>1.0.0"
         - export PYTHON="coverage3 run --source qiskit/aqua,qiskit/chemistry,qiskit/finance,qiskit/ml,qiskit/optimization --omit */gauopen/* --parallel-mode"
       script:
         - stestr --test-path test/aqua run --whitelist-file selection.txt 2> >(tee /dev/stderr out.txt > /dev/null)
@@ -206,7 +221,7 @@ jobs:
           paths: aqua238.dep
       python: 3.8
       before_script:
-        - pip install "cvxpy>1.0.0,<1.1.0"
+        - pip install "cvxpy>1.0.0"
       script:
         - stestr --test-path test/aqua run --whitelist-file selection.txt 2> >(tee /dev/stderr out.txt > /dev/null)
         - python tools/extract_deprecation.py -file out.txt -output aqua238.dep
@@ -228,7 +243,7 @@ jobs:
         - sudo apt-get -y install libgfortran5
         # Installing pyquante2 master branch...
         - pip install https://github.com/rpmuller/pyquante2/archive/master.zip --progress-bar off
-        - pip install cplex
+        - pip install cplex pyscf
       before_script:
         - export PYTHON="coverage3 run --source qiskit/aqua,qiskit/chemistry,qiskit/finance,qiskit/ml,qiskit/optimization --omit */gauopen/* --parallel-mode"
       script:
@@ -251,6 +266,7 @@ jobs:
         - sudo apt-get -y install libgfortran5
         # Installing pyquante2 master branch...
         - pip install https://github.com/rpmuller/pyquante2/archive/master.zip --progress-bar off
+        - pip install pyscf
       script:
         - stestr --test-path test/chemistry run 2> >(tee /dev/stderr out.txt > /dev/null)
         - python tools/extract_deprecation.py -file out.txt -output chemistry38.dep

README.md

@@ -73,7 +73,7 @@ these on a quantum backend, whether a real device or simulator.
 * **IBM CPLEX** may be [installed](https://qiskit.org/documentation/apidoc/qiskit.aqua.algorithms.minimum_eigen_solvers.cplex.html)
   to allow use of the `ClassicalCPLEX` classical solver algorithm. `pip install cplex` may be used
   as an alternative.
-* **PyTorch**, may be installed either using command `pip install qiskit-aqua[torch]` to install the
+* **PyTorch**, may be installed either using command `pip install torch` to install the
   package or refer to PyTorch [getting started](https://pytorch.org/get-started/locally/). PyTorch
   being installed will enable the neural networks `PyTorchDiscriminator` component to be used with
   the QGAN algorithm.
@@ -161,10 +161,6 @@ Several, as listed below, are supported, and while logic to interface these prog
 the chemistry module via the above pip installation, the dependent programs/libraries themselves need
 to be installed separately.
 
-Note: As `PySCF` can be installed via pip the installation of Qiskit (Aqua) will install PySCF
-where it's supported (MacOS and Linux x86). For other platforms see the PySCF information as to
-whether this might be possible manually.
-
 1. [Gaussian 16™](https://qiskit.org/documentation/apidoc/qiskit.chemistry.drivers.gaussiand.html), a commercial chemistry program
 2. [PSI4](https://qiskit.org/documentation/apidoc/qiskit.chemistry.drivers.psi4d.html), a chemistry program that exposes a Python interface allowing for accessing internal objects
 3. [PySCF](https://qiskit.org/documentation/apidoc/qiskit.chemistry.drivers.pyscfd.html), an open-source Python chemistry program

qiskit/aqua/algorithms/algorithm_result.py

@@ -45,7 +45,7 @@ def pop(self, key: object, default: Optional[object] = None) -> object:
     def popitem(self) -> Tuple[object, object]:
         raise TypeError("'popitem' invalid for this object.")
 
-    def update(self, *args, **kwargs) -> None:
+    def update(self, *args, **kwargs) -> None:  # pylint: disable=arguments-differ,signature-differs
         raise TypeError("'update' invalid for this object.")
 
     def combine(self, result: 'AlgorithmResult') -> None:

qiskit/aqua/algorithms/amplitude_amplifiers/grover.py

@@ -246,9 +246,15 @@ def construct_circuit(self, measurement=False):
         Returns:
             QuantumCircuit: the QuantumCircuit object for the constructed circuit
         """
-        if self._qc_amplitude_amplification is None:
-            self._qc_amplitude_amplification = \
-                QuantumCircuit() + self.qc_amplitude_amplification_iteration
+        if self._incremental:
+            if self._qc_amplitude_amplification is None:
+                self._qc_amplitude_amplification = \
+                    QuantumCircuit() + self.qc_amplitude_amplification_iteration
+        else:
+            self._qc_amplitude_amplification = QuantumCircuit()
+            for _ in range(self._num_iterations):
+                self._qc_amplitude_amplification += self.qc_amplitude_amplification_iteration
+
         qc = QuantumCircuit(self._oracle.variable_register, self._oracle.output_register)
         qc.u3(pi, 0, pi, self._oracle.output_register)  # x
         qc.u2(0, pi, self._oracle.output_register)  # h
@@ -291,8 +297,6 @@ def _try_target_num_iterations():
 
         else:
             self._qc_amplitude_amplification = QuantumCircuit()
-            for _ in range(self._num_iterations):
-                self._qc_amplitude_amplification += self.qc_amplitude_amplification_iteration
             assignment, oracle_evaluation = self._run_with_existing_iterations()
 
         self._ret['result'] = assignment

qiskit/aqua/algorithms/classifiers/qsvm/_qsvm_binary.py

@@ -147,7 +147,7 @@ def run(self):
 
     def load_model(self, file_path):
         """ load model """
-        model_npz = np.load(file_path, allow_pickle=True)
+        model_npz = np.load(file_path, allow_pickle=True)  # pylint: disable=unexpected-keyword-arg
         model = {'alphas': model_npz['alphas'],
                  'bias': model_npz['bias'],
                  'support_vectors': model_npz['support_vectors'],

qiskit/aqua/algorithms/classifiers/qsvm/_qsvm_multiclass.py

@@ -72,7 +72,7 @@ def run(self):
 
     def load_model(self, file_path):
         """ load model """
-        model_npz = np.load(file_path, allow_pickle=True)
+        model_npz = np.load(file_path, allow_pickle=True)  # pylint: disable=unexpected-keyword-arg
         for i in range(len(self.multiclass_classifier.estimators)):
             self.multiclass_classifier.estimators.ret['svm']['alphas'] = \
                 model_npz['alphas_{}'.format(i)]

qiskit/aqua/algorithms/classifiers/sklearn_svm/_sklearn_svm_binary.py

@@ -154,7 +154,7 @@ def run(self):
 
     def load_model(self, file_path):
         """ load model """
-        model_npz = np.load(file_path, allow_pickle=True)
+        model_npz = np.load(file_path, allow_pickle=True)  # pylint: disable=unexpected-keyword-arg
         model = {'alphas': model_npz['alphas'],
                  'bias': model_npz['bias'],
                  'support_vectors': model_npz['support_vectors'],

qiskit/aqua/algorithms/classifiers/sklearn_svm/_sklearn_svm_multiclass.py

@@ -71,7 +71,7 @@ def run(self):
 
     def load_model(self, file_path):
         """ load model """
-        model_npz = np.load(file_path, allow_pickle=True)
+        model_npz = np.load(file_path, allow_pickle=True)  # pylint: disable=unexpected-keyword-arg
         for i in range(len(self.multiclass_classifier.estimators)):
             self.multiclass_classifier.estimators.ret['svm']['alphas'] = \
                 model_npz['alphas_{}'.format(i)]

qiskit/aqua/algorithms/classifiers/vqc.py

@@ -589,7 +589,7 @@ def class_to_label(self):
 
     def load_model(self, file_path):
         """ load model """
-        model_npz = np.load(file_path, allow_pickle=True)
+        model_npz = np.load(file_path, allow_pickle=True)  # pylint: disable=unexpected-keyword-arg
         self._ret['opt_params'] = model_npz['opt_params']
 
     def save_model(self, file_path):

qiskit/aqua/algorithms/distribution_learners/qgan.py

@@ -270,6 +270,9 @@ def _store_params(self, e, d_loss, g_loss, rel_entr):
     def train(self):
         """
         Train the qGAN
+
+        Raises:
+            AquaError: Batch size bigger than the number of items in the truncated data set
         """
         if self._snapshot_dir is not None:
             with open(os.path.join(self._snapshot_dir, 'output.csv'), mode='w') as csv_file:
@@ -278,6 +281,11 @@ def train(self):
                 writer = csv.DictWriter(csv_file, fieldnames=fieldnames)
                 writer.writeheader()
 
+        if len(self._data) < self._batch_size:
+            raise AquaError(
+                'The batch size needs to be less than the '
+                'truncated data size of {}'.format(len(self._data)))
+
         for e in range(self._num_epochs):
             aqua_globals.random.shuffle(self._data)
             index = 0

qiskit/aqua/algorithms/factorizers/shor.py

@@ -59,7 +59,7 @@ def __init__(self,
         """
         Args:
             N: The integer to be factored, has a min. value of 3.
-            a: A random integer that satisfies a < N and gcd(a, N) = 1, has a min. value of 2.
+            a: Any integer that satisfies 1 < a < N and gcd(a, N) = 1.
             quantum_instance: Quantum Instance or Backend
 
          Raises:

qiskit/aqua/algorithms/minimum_eigen_solvers/vqe.py

@@ -150,6 +150,7 @@ def __init__(self,
         self._max_evals_grouped = max_evals_grouped
         self._circuit_sampler = None  # type: Optional[CircuitSampler]
         self._expectation = expectation
+        self._user_valid_expectation = self._expectation is not None
         self._include_custom = include_custom
         self._expect_op = None
         self._operator = None
@@ -184,26 +185,29 @@ def operator(self, operator: Union[OperatorBase, LegacyBaseOperator]) -> None:
         self._operator = operator
         self._expect_op = None
         self._check_operator_varform()
-        if self._expectation is None:
+        # Expectation was not passed by user, try to create one
+        if not self._user_valid_expectation:
             self._try_set_expectation_value_from_factory()
 
-    def _try_set_expectation_value_from_factory(self):
-        if self.operator and self.quantum_instance:
-            self.expectation = ExpectationFactory.build(operator=self.operator,
-                                                        backend=self.quantum_instance,
-                                                        include_custom=self._include_custom)
+    def _try_set_expectation_value_from_factory(self) -> None:
+        if self.operator is not None and self.quantum_instance is not None:
+            self._set_expectation(ExpectationFactory.build(operator=self.operator,
+                                                           backend=self.quantum_instance,
+                                                           include_custom=self._include_custom))
+
+    def _set_expectation(self, exp: ExpectationBase) -> None:
+        self._expectation = exp
+        self._user_valid_expectation = False
+        self._expect_op = None
 
     @QuantumAlgorithm.quantum_instance.setter
     def quantum_instance(self, quantum_instance: Union[QuantumInstance, BaseBackend]) -> None:
         """ set quantum_instance """
         super(VQE, self.__class__).quantum_instance.__set__(self, quantum_instance)
 
-        if self._circuit_sampler is None:
-            self._circuit_sampler = CircuitSampler(self._quantum_instance)
-        else:
-            self._circuit_sampler.quantum_instance = self._quantum_instance
-
-        if self._expectation is None:
+        self._circuit_sampler = CircuitSampler(self._quantum_instance)
+        # Expectation was not passed by user, try to create one
+        if not self._user_valid_expectation:
             self._try_set_expectation_value_from_factory()
 
     @property
@@ -214,8 +218,8 @@ def expectation(self) -> ExpectationBase:
 
     @expectation.setter
     def expectation(self, exp: ExpectationBase) -> None:
-        self._expectation = exp
-        self._expect_op = None
+        self._set_expectation(exp)
+        self._user_valid_expectation = self._expectation is not None
 
     @property
     def aux_operators(self) -> Optional[List[Optional[OperatorBase]]]:
@@ -299,9 +303,9 @@ def print_settings(self):
         ret += "===============================================================\n"
         return ret
 
-    def construct_circuit(self,
-                          parameter: Union[List[float], List[Parameter], np.ndarray]
-                          ) -> OperatorBase:
+    def construct_expectation(self,
+                              parameter: Union[List[float], List[Parameter], np.ndarray]
+                              ) -> OperatorBase:
         r"""
         Generate the ansatz circuit and expectation value measurement, and return their
         runnable composition.
@@ -328,14 +332,47 @@ def construct_circuit(self,
         else:
             wave_function = self.var_form.construct_circuit(parameter)
 
-        # If ExpectationValue was never created, create one now.
-        if not self.expectation:
+        # Expectation was never created, try to create one
+        if self._expectation is None:
             self._try_set_expectation_value_from_factory()
 
+        # If setting the expectation failed, raise an Error:
+        if self._expectation is None:
+            raise AquaError('No expectation set and could not automatically set one, please '
+                            'try explicitly setting an expectation or specify a backend so it '
+                            'can be chosen automatically.')
+
         observable_meas = self.expectation.convert(StateFn(self.operator, is_measurement=True))
         ansatz_circuit_op = CircuitStateFn(wave_function)
         return observable_meas.compose(ansatz_circuit_op).reduce()
 
+    def construct_circuit(self,
+                          parameter: Union[List[float], List[Parameter], np.ndarray]
+                          ) -> List[QuantumCircuit]:
+        """Return the circuits used to compute the expectation value.
+
+        Args:
+            parameter: Parameters for the ansatz circuit.
+
+        Returns:
+            A list of the circuits used to compute the expectation value.
+        """
+        expect_op = self.construct_expectation(parameter).to_circuit_op()
+
+        circuits = []
+
+        # recursively extract circuits
+        def extract_circuits(op):
+            if isinstance(op, CircuitStateFn):
+                circuits.append(op.primitive)
+            elif isinstance(op, ListOp):
+                for op_i in op.oplist:
+                    extract_circuits(op_i)
+
+        extract_circuits(expect_op)
+
+        return circuits
+
     def supports_aux_operators(self) -> bool:
         return True
 
@@ -436,7 +473,7 @@ def _energy_evaluation(self, parameters: Union[List[float], np.ndarray]
             RuntimeError: If the variational form has no parameters.
         """
         if not self._expect_op:
-            self._expect_op = self.construct_circuit(self._var_form_params)
+            self._expect_op = self.construct_expectation(self._var_form_params)
 
         num_parameters = self.var_form.num_parameters
         if self._var_form.num_parameters == 0: