0.4.2 patch release (#234)

* adding sympy as an explicit requirement (#233)

* Add warning for JAX versions on import of Dynamics (#232)

* Add probability normalization to DynamicsBackend sampling routine (#239)

* Add warning if digital carrier exceeds Nyquist frequency in pulse -> signal conversion (#242)

* Fix bug with carrier_freq being a JAX tracer if envelope is constant in Signal (#247)

* Remove subsystem_labels option from DynamicsBackend (#248)

* Rename subsystem_dims Dict to subsystem_dims_dict (#250)

* Fix ClassicalRegister counting in DynamicsBackend (#252)

* temporary fix for docs (#253)

* Drop support for backendV2 in from_backend (#249)

* incrementing version number

* cleaning up reno files

---------

Co-authored-by: Kento Ueda <38037695+to24toro@users.noreply.github.com>

docs/conf.py

@@ -21,7 +21,7 @@
 # The short X.Y version
 version = ''
 # The full version, including alpha/beta/rc tags
-release = '0.4.1'
+release = '0.4.2'
 
 extensions = [
     'sphinx.ext.napoleon',
@@ -82,3 +82,7 @@
 nbsphinx_execute = 'always'
 nbsphinx_widgets_path = ''
 exclude_patterns = ['_build', '**.ipynb_checkpoints']
+
+# this is tied to the temporary restriction to JAX versions <=0.4.6. See issue #190
+import os
+os.environ["JAX_JIT_PJIT_API_MERGE"] = "0"

docs/release_notes.rst

@@ -1 +1,152 @@
-.. release-notes:: Release Notes
+=============
+Release Notes
+=============
+
+.. _Release Notes_0.4.1-12:
+
+0.4.1-12
+========
+
+.. _Release Notes_0.4.1-12_Prelude:
+
+Prelude
+-------
+
+.. releasenotes/notes/patch-0.4.2-6a7c7bf380e54187.yaml @ None
+
+Qiskit Dynamics 0.4.2 is an incremental release with minor bug fixes and additional warnings to help guide users through issues.
+
+
+.. _Release Notes_0.4.1-12_Upgrade Notes:
+
+Upgrade Notes
+-------------
+
+.. releasenotes/notes/subsystem_labels-removal-9fcc71c310eff220.yaml @ b'cf256192ce1c0ef7c2f4c696d9be64234b48b68f'
+
+- The ``subsystem_labels`` option has been removed from the :class:`.DynamicsBackend`. This
+  removal impacts some technical aspects of the backend returned by
+  :meth:`.DynamicsBackend.from_backend` when the ``subsystem_list`` argument is used. Using the
+  ``subsystem_list`` argument with :meth:`.DynamicsBackend.from_backend` restricts the internally
+  constructed model to the qubits in ``subsystem_list``. When doing so previously, the option
+  ``subsystem_labels`` would be set to ``subsystem_labels``, and ``subsystem_dims`` would record
+  only the dimensions for the systems in ``subsystem_labels``. To account for the fact that
+  ``subsystem_labels`` no longer exists, :meth:`.DynamicsBackend.from_backend` now constructs
+  ``subsystem_dims`` to list a dimension for all of the qubits in the original backend, however
+  now the dimensions of the removed systems are given as 1 (i.e. they are treated as trivial
+  quantum systems with a single state). This change is made only for technical bookkeping
+  purposes, and has no impact on the core simulation behaviour.
+
+
+.. _Release Notes_0.4.1-12_Bug Fixes:
+
+Bug Fixes
+---------
+
+.. releasenotes/notes/carrier-freq-0-19ad4362c874944f.yaml @ None
+
+- In the case that ``envelope`` is a constant, the :meth:`.Signal.__init__` method has been
+  updated to not attempt to evaluate ``carrier_freq == 0.0`` if ``carrier_freq`` is a JAX tracer.
+  In this case, it is not possible to determine if the :class:`.Signal` instance is constant. This
+  resolves an error that was being raised during JAX tracing if ``carrier_freq`` is abstract.
+
+.. releasenotes/notes/classical-registers-9bb117398a4d21d5.yaml @ None
+
+- Fixes bug in :meth:`.DynamicsBackend.run` that caused miscounting of the number of classical
+  registers in a :class:`~qiskit.circuit.QuantumCircuit` (issue #251).
+
+.. releasenotes/notes/normalize-probabilities-d729245bb3fe5f10.yaml @ b'6ede10a2bc8c61e8640db9085d4d1d9423341550'
+
+- ``DynamicsBackend.options.normalize_states`` now also controls whether or not the probability
+  distribution over outcomes is normalized before sampling outcomes. 
+
+
+.. _Release Notes_0.4.1-12_Other Notes:
+
+Other Notes
+-----------
+
+.. releasenotes/notes/patch-0.4.2-6a7c7bf380e54187.yaml @ None
+
+- For users that have JAX installed, a warning has been added upon import of Qiskit Dynamics to
+  notify the user of issues with certain versions: JAX versions newer than ``0.4.6`` break the
+  ``perturbation`` module, and to use ``perturbation`` module with versions ``0.4.4``, ``0.4.5``,
+  or ``0.4.6``, it is necessary to set ``os.environ['JAX_JIT_PJIT_API_MERGE'] = '0'`` before
+  importing JAX or Dynamics.
+
+.. releasenotes/notes/patch-0.4.2-6a7c7bf380e54187.yaml @ None
+
+- A warning has been added to :class:`.InstructionToSignals` class when converting pulse schedules
+  to signals to notify the user if the usage of ``SetFrequency`` or ``ShiftFrequency`` commands 
+  result in a digital carrier frequency larger than the Nyquist frequency of the envelope sample
+  size ``dt``.
+
+
+.. _Release Notes_0.4.1:
+
+0.4.1
+=====
+
+.. _Release Notes_0.4.1_Prelude:
+
+Prelude
+-------
+
+.. releasenotes/notes/0.4/patch-0.4.1-d339aa8669341341.yaml @ b'd6e280259d120d31723e0220a91cbd7dd8099298'
+
+Qiskit Dynamics 0.4.1 is an incremental release with minor bug fixes, documentation updates, and usability features.
+
+.. _Release Notes_0.4.1_New Features:
+
+New Features
+------------
+
+.. releasenotes/notes/measurement_property_bug_fix-12461088823a943c.yaml @ b'807edf92d7f5d6f34715fff9d21614d77cd096d3'
+
+- The :meth:`DynamicsBackend.from_backend` method has been updated to automatically populate the 
+  ``control_channel_map`` option based on the supplied backend if the user does not supply one.
+
+
+.. _Release Notes_0.4.1_Known Issues:
+
+Known Issues
+------------
+
+.. releasenotes/notes/0.4/diffrax-bound-0bd80c01b7f4b48f.yaml @ b'd6e280259d120d31723e0220a91cbd7dd8099298'
+
+- Due to a bug in JAX, Dynamics can only be used with jax<=0.4.6. As they depend on newer versions
+  of JAX, Dynamics is also now only compatible with diffrax<=0.3.1 and equinox<=0.10.3.
+
+
+.. _Release Notes_0.4.1_Bug Fixes:
+
+Bug Fixes
+---------
+
+.. releasenotes/notes/0.4/multiset-order-bug-fix-1f1603ee1e230cba.yaml @ b'd6e280259d120d31723e0220a91cbd7dd8099298'
+
+- Fixes a bug in the perturbation module with internal sorting of ``Multiset`` instances, which
+  caused incorrect computation of perturbation theory terms when ``>10`` perturbations are
+  present.
+
+.. releasenotes/notes/measurement_property_bug_fix-12461088823a943c.yaml @ b'807edf92d7f5d6f34715fff9d21614d77cd096d3'
+
+- A bug in :meth:`DynamicsBackend.__init__` causing existing measurement instructions for a
+  user-supplied :class:`Target` to be overwritten has been fixed.
+
+
+.. _Release Notes_0.4.1_Other Notes:
+
+Other Notes
+-----------
+
+.. releasenotes/notes/0.4/move-repo-c0b48ba3b0ced8db.yaml @ b'd6e280259d120d31723e0220a91cbd7dd8099298'
+
+- The repository has been moved from 
+  [github.com/Qiskit/qiskit-dynamics](https://github.com/Qiskit/qiskit-dynamics) to 
+  [github.com/Qiskit-Extensions/qiskit-dynamics](https://github.com/Qiskit-Extensions/qiskit-dynamics), 
+  and the documentation has been moved from
+  [qiskit.org/documentation/dynamics](https://qiskit.org/documentation/dynamics) to 
+  [qiskit.org/ecosystem/dynamics](https://qiskit.org/ecosystem/dynamics/).
+
+

qiskit_dynamics/VERSION.txt

@@ -1 +1 @@
-0.4.1
+0.4.2

qiskit_dynamics/backend/backend_string_parser/hamiltonian_string_parser.py

@@ -163,12 +163,12 @@ def parse_backend_hamiltonian_dict(
     # force keys in hamiltonian['qub'] to be ints
     qub_dict = {int(key): val for key, val in hamiltonian_dict["qub"].items()}
 
-    subsystem_dims = {int(qubit): qub_dict[int(qubit)] for qubit in subsystem_list}
+    subsystem_dims_dict = {int(qubit): qub_dict[int(qubit)] for qubit in subsystem_list}
 
     # Parse the Hamiltonian
     system = _regex_parser(
         operator_str=hamiltonian_dict["h_str"],
-        subsystem_dims=subsystem_dims,
+        subsystem_dims_dict=subsystem_dims_dict,
         subsystem_list=subsystem_list,
     )
 
@@ -227,7 +227,12 @@ def parse_backend_hamiltonian_dict(
             *sorted(zip(reduced_channels, hamiltonian_operators))
         )
 
-    return static_hamiltonian, list(hamiltonian_operators), list(reduced_channels), subsystem_dims
+    return (
+        static_hamiltonian,
+        list(hamiltonian_operators),
+        list(reduced_channels),
+        subsystem_dims_dict,
+    )
 
 
 def _hamiltonian_pre_parse_exceptions(hamiltonian_dict: dict):

qiskit_dynamics/backend/backend_string_parser/operator_from_string.py

@@ -26,14 +26,14 @@
 
 
 def _operator_from_string(
-    op_label: str, subsystem_label: int, subsystem_dims: Dict[int, int]
+    op_label: str, subsystem_label: int, subsystem_dims_dict: Dict[int, int]
 ) -> np.ndarray:
     r"""Generates a dense operator acting on a single subsystem, tensoring
     identities for remaining subsystems.
 
     The single system operator is specified via a string in ``op_label``,
     the list of subsystems and their corresponding dimensions are specified in the
-    dictionary ``subsystem_dims``, with system label being the keys specified as ``int``s,
+    dictionary ``subsystem_dims_dict``, with system label being the keys specified as ``int``s,
     and system dimensions the values also specified as ``int``s, and ``subsystem_label``
     indicates which subsystem the operator specified by ``op_label`` acts on.
 
@@ -61,7 +61,7 @@ def _operator_from_string(
     Args:
         op_label: The string labelling the single system operator.
         subsystem_label: Index of the subsystem to apply the operator.
-        subsystem_dims: Dictionary of subsystem labels and dimensions.
+        subsystem_dims_dict: Dictionary of subsystem labels and dimensions.
 
     Returns:
         np.ndarray corresponding to the specified operator.
@@ -75,12 +75,12 @@ def _operator_from_string(
     if op_func is None:
         raise QiskitError(f"String {op_label} does not correspond to a known operator.")
 
-    dim = subsystem_dims[subsystem_label]
+    dim = subsystem_dims_dict[subsystem_label]
     out = qi.Operator(op_func(dim), input_dims=[dim], output_dims=[dim])
 
     # sort subsystem labels and dimensions according to subsystem label
     sorted_subsystem_keys, sorted_subsystem_dims = zip(
-        *sorted(zip(subsystem_dims.keys(), subsystem_dims.values()))
+        *sorted(zip(subsystem_dims_dict.keys(), subsystem_dims_dict.values()))
     )
 
     # get subsystem location in ordered list

qiskit_dynamics/backend/backend_string_parser/regex_parser.py

@@ -29,20 +29,20 @@
 
 
 def _regex_parser(
-    operator_str: List[str], subsystem_dims: Dict[int, int], subsystem_list: List[int]
+    operator_str: List[str], subsystem_dims_dict: Dict[int, int], subsystem_list: List[int]
 ) -> List[Tuple[np.array, str]]:
     """Function wrapper for regex parsing object.
 
     Args:
         operator_str: List of strings in accepted format as described in
                       string_model_parser.parse_hamiltonian_dict.
-        subsystem_dims: Dictionary mapping subsystem labels to dimensions.
+        subsystem_dims_dict: Dictionary mapping subsystem labels to dimensions.
         subsystem_list: List of subsystems on which the operators are to be constructed.
     Returns:
         List of tuples containing pairs operators and their string coefficients.
     """
 
-    return _HamiltonianParser(h_str=operator_str, subsystem_dims=subsystem_dims).parse(
+    return _HamiltonianParser(h_str=operator_str, subsystem_dims_dict=subsystem_dims_dict).parse(
         subsystem_list
     )
 
@@ -66,15 +66,17 @@ class _HamiltonianParser:
         BrkR=re.compile(r"\)"),
     )
 
-    def __init__(self, h_str, subsystem_dims):
+    def __init__(self, h_str, subsystem_dims_dict):
         """Create new quantum operator generator
 
         Parameters:
             h_str (list): list of Hamiltonian string
-            subsystem_dims (dict): dimension of subsystems
+            subsystem_dims_dict (dict): dimension of subsystems
         """
         self.h_str = h_str
-        self.subsystem_dims = {int(label): int(dim) for label, dim in subsystem_dims.items()}
+        self.subsystem_dims_dict = {
+            int(label): int(dim) for label, dim in subsystem_dims_dict.items()
+        }
         self.str2qopr = {}
 
     def parse(self, qubit_list=None):
@@ -194,15 +196,15 @@ def _tokenizer(self, op_str, qubit_list=None):
                             if qubit_list is not None and idx not in qubit_list:
                                 return 0, None
                             name = p.group("opr")
-                            opr = _operator_from_string(name, idx, self.subsystem_dims)
+                            opr = _operator_from_string(name, idx, self.subsystem_dims_dict)
                             self.str2qopr[p.group()] = opr
                     elif key == "PrjOpr":
                         _key = key
                         _name = p.group()
                         if p.group() not in self.str2qopr:
                             idx = int(p.group("idx"))
                             name = "P"
-                            opr = _operator_from_string(name, idx, self.subsystem_dims)
+                            opr = _operator_from_string(name, idx, self.subsystem_dims_dict)
                             self.str2qopr[p.group()] = opr
                     elif key in ["Func", "Ext"]:
                         _name = p.group("name")

qiskit_dynamics/backend/backend_utils.py

@@ -146,21 +146,31 @@ def _get_memory_slot_probabilities(
 
 
 def _sample_probability_dict(
-    probability_dict: Dict, shots: int, seed: Optional[int] = None
+    probability_dict: Dict,
+    shots: int,
+    normalize_probabilities: bool = True,
+    seed: Optional[int] = None,
 ) -> List[str]:
     """Sample outcomes based on probability dictionary.
 
     Args:
         probability_dict: Dictionary representing probability distribution, with keys being
             outcomes, values being probabilities.
         shots: Number of shots.
+        normalize_probabilities: Whether or not to normalize the probabilities to sum to 1 before
+            sampling.
         seed: Seed to use in rng construction.
 
     Return:
         List: of entries of probability_dict, sampled according to the probabilities.
     """
     rng = np.random.default_rng(seed=seed)
     alphabet, probs = zip(*probability_dict.items())
+
+    if normalize_probabilities:
+        probs = np.array(probs)
+        probs = probs / probs.sum()
+
     return rng.choice(alphabet, size=shots, replace=True, p=probs)