fixing conflicts

.gitignore

@@ -134,6 +134,7 @@ dmypy.json
 
 # tmp files
 tmp/
+tmp.npy
 
 # Mac
 .DS_Store

.pre-commit-config.yaml

@@ -13,7 +13,7 @@ repos:
     hooks:
       - id: black
   - repo: https://github.com/pycqa/isort
-    rev: 5.12.0
+    rev: 5.13.1
     hooks:
       - id: isort
         args: ["--profile", "black"]

doc/source/api-reference/qibo.rst

@@ -203,6 +203,23 @@ Iterative Quantum Amplitude Estimation (IQAE)
     :member-order: bysource
 
 
+Double Bracket Iteration algorithm for Diagonalization
+""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+The Double Bracket Flow (DBF) has been presented `here <https://arxiv.org/abs/2206.11772>`_
+as a novel strategy for preparing eigenstates of a quantum system. We implement in
+Qibo a discretized version of the algorithm, which executes sequential Double
+Bracket Iterations.
+
+.. autoclass:: qibo.models.dbi.double_bracket.DoubleBracketGeneratorType
+    :members:
+    :member-order: bysource
+
+.. autoclass:: qibo.models.dbi.double_bracket.DoubleBracketIteration
+    :members:
+    :member-order: bysource
+
+
 .. _timeevolution:
 
 Time evolution
@@ -548,6 +565,13 @@ Controlled-NOT (CNOT)
     :members:
     :member-order: bysource
 
+Controlled-Y (CY)
+"""""""""""""""""""""
+
+.. autoclass:: qibo.gates.CY
+    :members:
+    :member-order: bysource
+
 Controlled-phase (CZ)
 """""""""""""""""""""
 
@@ -1500,6 +1524,12 @@ Expressibility of parameterized quantum circuits
 .. autofunction:: qibo.quantum_info.expressibility
 
 
+Frame Potential
+"""""""""""""""
+
+.. autofunction:: qibo.quantum_info.frame_potential
+
+
 Random Ensembles
 ^^^^^^^^^^^^^^^^
 

doc/source/code-examples/advancedexamples.rst

@@ -2011,10 +2011,9 @@ Multiple transpilation steps can be implemented using the :class:`qibo.transpile
     from qibo import gates
     from qibo.models import Circuit
     from qibo.transpiler.pipeline import Passes, assert_transpiling
-    from qibo.transpiler.abstract import NativeType
     from qibo.transpiler.optimizer import Preprocessing
     from qibo.transpiler.router import ShortestPaths
-    from qibo.transpiler.unroller import NativeGates
+    from qibo.transpiler.unroller import Unroller, NativeGates
     from qibo.transpiler.placer import Random
 
     # Define connectivity as nx.Graph
@@ -2040,10 +2039,10 @@ Multiple transpilation steps can be implemented using the :class:`qibo.transpile
     # Routing step
     custom_passes.append(ShortestPaths(connectivity=star_connectivity()))
     # Gate decomposition step
-    custom_passes.append(NativeGates(two_qubit_natives=NativeType.iSWAP))
+    custom_passes.append(Unroller(native_gates=NativeGates.default()))
 
     # Define the general pipeline
-    custom_pipeline = Passes(custom_passes, connectivity=star_connectivity(), native_gates=NativeType.iSWAP)
+    custom_pipeline = Passes(custom_passes, connectivity=star_connectivity(), native_gates=NativeGates.default())
 
     # Call the transpiler pipeline on the circuit
     transpiled_circ, final_layout = custom_pipeline(circuit)
@@ -2057,10 +2056,10 @@ Multiple transpilation steps can be implemented using the :class:`qibo.transpile
         connectivity=star_connectivity(),
         initial_layout=initial_layout,
         final_layout=final_layout,
-        native_gates=NativeType.iSWAP
+        native_gates=NativeGates.default()
     )
 
 In this case circuits will first be transpiled to respect the 5-qubit star connectivity, with qubit 2 as the middle qubit. This will potentially add some SWAP gates.
-Then all gates will be converted to native. The :class:`qibo.transpiler.unroller.NativeGates` transpiler used in this example assumes Z, RZ, GPI2 or U3 as
+Then all gates will be converted to native. The :class:`qibo.transpiler.unroller.Unroller` transpiler used in this example assumes Z, RZ, GPI2 or U3 as
 the single-qubit native gates, and supports CZ and iSWAP as two-qubit natives. In this case we restricted the two-qubit gate set to CZ only.
 The final_layout contains the final logical-physical qubit mapping.

doc/source/code-examples/applications-by-algorithm.rst

@@ -68,3 +68,12 @@ Clustering
     :maxdepth: 1
 
     tutorials/qclustering/README.md
+
+
+Diagonalization Algorithms
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. toctree::
+    :maxdepth: 1
+
+    tutorials/dbi/dbi.ipynb

doc/source/code-examples/applications-by-topic.rst

@@ -61,6 +61,7 @@ Quantum Physics
     tutorials/bell-variational/README.md
     tutorials/falqon/README.md
     tutorials/grover/README.md
+    tutorials/dbi/dbi.ipynb
 
 Quantum Machine Learning
 ^^^^^^^^^^^^^^^^^^^^^^^^

doc/source/code-examples/applications.rst

@@ -6,6 +6,171 @@ Applications
 In this section we present some examples of quantum circuits applied to specific
 problems.
 
+Applications by topic
+---------------------
+
+Complexity theory
+^^^^^^^^^^^^^^^^^
+
+.. toctree::
+    :maxdepth: 1
+
+    tutorials/grover3sat/README.md
+    tutorials/adiabatic3sat/README.md
+
+
+Condensed Matter Physics
+^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. toctree::
+    :maxdepth: 1
+
+    tutorials/aavqe/README.md
+
+
+Cryptography
+^^^^^^^^^^^^
+
+.. toctree::
+    :maxdepth: 1
+
+    tutorials/hash-grover/README.md
+
+
+Finance
+^^^^^^^
+
+.. toctree::
+    :maxdepth: 1
+
+    tutorials/unary/README.md
+
+
+High-Energy Physics
+^^^^^^^^^^^^^^^^^^^
+
+.. toctree::
+    :maxdepth: 1
+
+    tutorials/qPDF/qPDF.ipynb
+    tutorials/anomaly_detection/README.md
+
+
+Quantum Physics
+^^^^^^^^^^^^^^^
+
+.. toctree::
+    :maxdepth: 1
+
+    tutorials/qsvd/README.md
+    tutorials/3_tangle/README.md
+    tutorials/adiabatic/README.md
+    tutorials/shor/README.md
+    tutorials/bell-variational/README.md
+    tutorials/falqon/README.md
+    tutorials/grover/README.md
+    tutorials/dbi/dbi.ipynb
+
+
+Quantum Machine Learning
+^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. toctree::
+    :maxdepth: 1
+
+    tutorials/variational_classifier/README.md
+    tutorials/reuploading_classifier/README.md
+    tutorials/vqregressor/README.md
+    tutorials/autoencoder/README.md
+    tutorials/EF_QAE/README.md
+    tutorials/qfiae/qfiae_demo.ipynb
+    tutorials/qcnn_classifier/qcnn_demo.ipynb
+    tutorials/qclustering/README.md
+    tutorials/adiabatic_qml/adiabatic-qml.ipynb
+
+Combinatorics
+^^^^^^^^^^^^^
+
+.. toctree::
+    :maxdepth: 1
+
+    tutorials/qap/README.md
+    tutorials/mvc/README.md
+
+
+Applications by algorithm
+-------------------------
+
+Variational Quantum Circuits
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. toctree::
+    :maxdepth: 1
+
+    tutorials/aavqe/README.md
+    tutorials/variational_classifier/README.md
+    tutorials/reuploading_classifier/README.md
+    tutorials/vqregressor/README.md
+    tutorials/autoencoder/README.md
+    tutorials/qsvd/README.md
+    tutorials/3_tangle/README.md
+    tutorials/EF_QAE/README.md
+    tutorials/unary/README.md
+    tutorials/bell-variational/README.md
+    tutorials/qPDF/qPDF.ipynb
+    tutorials/anomaly_detection/README.md
+    tutorials/qcnn_classifier/qcnn_demo.ipynb
+    tutorials/adiabatic_qml/adiabatic-qml.ipynb
+
+Grover's Algorithm
+^^^^^^^^^^^^^^^^^^
+
+.. toctree::
+    :maxdepth: 1
+
+    tutorials/grover3sat/README.md
+    tutorials/hash-grover/README.md
+    tutorials/grover/README.md
+    tutorials/qfiae/qfiae_demo.ipynb
+
+
+Shor's Factorization Algorithms
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. toctree::
+    :maxdepth: 1
+
+    tutorials/shor/README.md
+
+
+Adiabatic Evolution
+^^^^^^^^^^^^^^^^^^^
+
+.. toctree::
+    :maxdepth: 1
+
+    tutorials/adiabatic/README.md
+    tutorials/adiabatic3sat/README.md
+
+
+Diagonalization
+^^^^^^^^^^^^^^^
+
+.. toctree::
+    :maxdepth: 1
+
+    tutorials/dbi/dbi.ipynb
+
+FALQON
+^^^^^^
+
+.. toctree::
+    :maxdepth: 1
+
+    tutorials/falqon/README.md
+
+Clustering
+^^^^^^^^^^
 
 .. toctree::
     :maxdepth: 2

doc/source/code-examples/tutorials/dbi/dbi.ipynb

@@ -0,0 +1 @@
+../../../../../examples/dbi/dbi.ipynb

doc/source/getting-started/backends.rst

@@ -50,6 +50,12 @@ be controlled using the ``QIBO_LOG_LEVEL`` environment variable. This can be set
 to 3 to hide info messages or 4 to hide both info and warning messages. The
 default value is 1 allowing all messages to appear.
 
+.. note::
+  The `qibojit` backend implements in-place updates. This
+  implies that the initial state is modified at runtime without performing any copies to save memory.
+  For algorithms that require access to the initial state after its modification, such as quantum machine learning applications,
+  it is suggested to perform a copy of the state explicitly if really needed by the algorithm.
+
 
 .. _hardware-backends: