Add pydcostyle + pylint in ruff rules

docs/articles.bib

@@ -35,6 +35,19 @@ @article{Bandyopadhyay_2014_Conclusive
    year={2014},
    month={Feb}}
 
+@article{Bandyopadhyay_2015_Limitations,
+   title={Limitations on Separable Measurements by Convex Optimization},
+   volume={61},
+   ISSN={1557-9654},
+   url={http://dx.doi.org/10.1109/TIT.2015.2417755},
+   DOI={10.1109/tit.2015.2417755},
+   number={6},
+   journal={IEEE Transactions on Information Theory},
+   publisher={Institute of Electrical and Electronics Engineers (IEEE)},
+   author={Bandyopadhyay, Somshubhro and Cosentino, Alessandro and Johnston, Nathaniel and Russo, Vincent and Watrous, John and Yu, Nengkun},
+   year={2015},
+   month=jun, pages={3593-3604} }
+
 @article{Bennett_1999_QuantumNonlocality,
    title={Quantum nonlocality without entanglement},
    volume={59},
@@ -92,6 +105,14 @@ @article{Cabello_2002_NParticle
   url = {https://link.aps.org/doi/10.1103/Cabello_2002_NParticle}
 }
 
+@misc{Chen_2003_Matrix,
+      title={A matrix realignment method for recognizing entanglement}, 
+      author={Kai Chen and Ling-An Wu},
+      year={2003},
+      eprint={quant-ph/0205017},
+      archivePrefix={arXiv},
+      primaryClass={quant-ph}
+}
 
 @article{Chen_2014_Symmetric,
    title={Symmetric extension of two-qubit states},
@@ -652,6 +673,18 @@ @article{Sych_2009_AComplete
 }
 
 #Last name begins with T
+@article{Terhal_2001_Hiding,
+   title={Hiding Bits in Bell States},
+   volume={86},
+   ISSN={1079-7114},
+   url={http://dx.doi.org/10.1103/PhysRevLett.86.5807},
+   DOI={10.1103/physrevlett.86.5807},
+   number={25},
+   journal={Physical Review Letters},
+   publisher={American Physical Society (APS)},
+   author={Terhal, Barbara M. and DiVincenzo, David P. and Leung, Debbie W.},
+   year={2001},
+   month=jun, pages={5807-5810} }
 
 #Last name begins with U
 
@@ -929,7 +962,7 @@ @misc{WikiMUB
 
 @misc{WikiNorm,
   author  = "Wikipedia",
-  title   = "Outer product",
+  title   = "Normal Matrix",
   howpublished = {https://en.wikipedia.org/wiki/Normal_matrix}
 
 }
@@ -944,7 +977,7 @@ @misc{WikiOrthog
 
 @misc{WikiOuterProd,
   author  = "Wikipedia",
-  title   = "Normal matrix",
+  title   = "Outer Product",
   howpublished = {https://en.wikipedia.org/wiki/Outer_product}
 
 }

pyproject.toml

@@ -58,7 +58,7 @@ line-length = 120
 target-version = "py311"
 
 [tool.ruff.lint]
-select = ["I", "E", "W"]
+select = ["I", "E", "W", "D", "PL"]
 # ruff configuration
 # E, W -- pycodestyle
 # D -- pydocstyle
@@ -68,7 +68,7 @@ select = ["I", "E", "W"]
 # Rules considered over other incompatible ones
 exclude = ["docs/conf.py", "setup.py"]
 
-ignore = ["D407", "D203", "D213", "D416", "PLR0912", "PLR0911", "PLR0915"]
+ignore = ["D407", "D203", "D213", "D416", "PLR0912", "PLR0911", "PLR0915", "PLR2004"]
 # Rules Ignored
 
 # D407 - Ignored because ==== under a section heading is considered as a missing underline.
@@ -84,6 +84,7 @@ ignore = ["D407", "D203", "D213", "D416", "PLR0912", "PLR0911", "PLR0915"]
 # PLR0912 -- Checks for functions or methods with too many branches. The default number is 12. 
 # PLR0911 -- Checks for functions or methods with too many return statements. The default number is 6.
 # PLR0915 -- Checks for functions or methods with too many statements. The default number is 50. 
+# PLR2004 -- Checks if an equality or an inequality is compared to a variable or a num (prefers variable pre)
 
 [tool.ruff.lint.per-file-ignores]
 "__init__.py" = ["I001"]

toqito/channel_metrics/channel_fidelity.py

@@ -6,8 +6,7 @@
 
 
 def channel_fidelity(choi_1: np.ndarray, choi_2: np.ndarray) -> float:
-    r"""
-    Compute the channel fidelity between two quantum channels :cite:`Katariya_2021_Geometric`.
+    r"""Compute the channel fidelity between two quantum channels :cite:`Katariya_2021_Geometric`.
 
     Let :math:`\Phi : \text{L}(\mathcal{Y}) \rightarrow \text{L}(\mathcal{X})` and
     :math:`\Psi: \text{L}(\mathcal{Y}) \rightarrow \text{L}(\mathcal{X})` be quantum channels. Then

toqito/channel_metrics/completely_bounded_trace_norm.py

@@ -8,8 +8,7 @@
 
 
 def completely_bounded_trace_norm(phi: np.ndarray) -> float:
-    r"""
-    Find the completely bounded trace norm of a quantum channel.
+    r"""Find the completely bounded trace norm of a quantum channel.
 
     Also known as the completely bounded diamond norm of a quantum
     channel (Section 3.3.2 of :cite:`Watrous_2018_TQI`). The algorithm in p.11 of :cite:`Watrous_2012_Simpler` with

toqito/channel_metrics/diamond_norm.py

@@ -4,8 +4,7 @@
 
 
 def diamond_norm(choi_1: np.ndarray, choi_2: np.ndarray) -> float:
-    r"""
-    Return the diamond norm distance between two quantum channels.
+    r"""Return the diamond norm distance between two quantum channels.
 
     The calculation uses the simplified semidefinite program of Watrous in
     :cite:`Watrous_2009_Semidefinite`.

toqito/channel_metrics/tests/test_completely_bounded_spectral_norm.py

@@ -10,6 +10,7 @@
 
 
 def test_dual_is_cb_trace_norm():
+    """Test CB Spectral norm of a dephasing channel is the same as the CB Trace norm of a dephasing channel."""
     phi = dephasing(2)
     np.testing.assert_equal(
         completely_bounded_spectral_norm(phi), completely_bounded_trace_norm(dual_channel(phi))

toqito/channel_metrics/tests/test_completely_bounded_trace_norm.py

@@ -20,8 +20,10 @@ def test_cb_trace_norm_CP():
 
 
 def test_cb_trace_norm_unitaries_channel():
-    """The diamond norm of phi = id- U id U* is the diameter of the smallest circle that contains the
-    eigenvalues of U."""
+    """Test the CB trace norm of phi.
+
+    The diamond norm of phi = id- U id U* is the diameter of the smallest circle that contains the eigenvalues of U.
+    """
     U = 1 / np.sqrt(2) * np.array([[1, 1], [-1, 1]])  # Hadamard gate
     phi = kraus_to_choi([[np.eye(2), np.eye(2)], [U, -U]])
     lam, _ = np.linalg.eig(U)

toqito/channel_ops/choi_to_kraus.py

@@ -11,8 +11,7 @@
 def choi_to_kraus(
     choi_mat: np.ndarray, tol: float = 1e-9, dim: int | list[int] | np.ndarray = None
 ) -> list[np.ndarray] | list[list[np.ndarray]]:
-    r"""
-    Compute a list of Kraus operators from the Choi matrix from :cite:`Rigetti_2022_Forest`.
+    r"""Compute a list of Kraus operators from the Choi matrix from :cite:`Rigetti_2022_Forest`.
 
     Note that unlike the Choi or natural representation of operators, the Kraus representation is
     *not* unique.

toqito/channel_ops/tests/test_apply_channel.py

@@ -8,8 +8,7 @@
 
 
 def test_apply_channel_choi():
-    """
-    The swap operator is the Choi matrix of the transpose map.
+    """The swap operator is the Choi matrix of the transpose map.
 
     The following test is a (non-ideal, but illustrative) way of computing
     the transpose of a matrix.
@@ -25,8 +24,7 @@ def test_apply_channel_choi():
 
 
 def test_apply_channel_choi_non_square():
-    """
-    The swap operator is the Choi matrix of the transpose map.
+    """The swap operator is the Choi matrix of the transpose map.
 
     The following test is a (non-ideal, but illustrative) way of computing
     the transpose of a non square matrix.
@@ -42,8 +40,7 @@ def test_apply_channel_choi_non_square():
 
 
 def test_apply_channel_kraus():
-    """
-    Apply Kraus map.
+    """Apply Kraus map.
 
     The following test computes PHI(X) where X = [[1, 2], [3, 4]] and
     where PHI is the superoperator defined by:
@@ -67,9 +64,7 @@ def test_apply_channel_kraus():
 
 @pytest.mark.parametrize("nested", [1, 2, 3])
 def test_apply_channel_cpt_kraus(nested):
-    """
-    Apply Kraus map of single qubit depolarizing channel.
-    """
+    """Apply Kraus map of single qubit depolarizing channel."""
     test_input_mat = np.array([[1, 0], [0, 0]])
 
     expected_res = np.array([[0.5, 0], [0, 0.5]])

toqito/channel_ops/tests/test_choi_to_kraus.py

@@ -7,7 +7,6 @@
 
 def test_choi_to_kraus():
     """Choi matrix of the swap operator."""
-
     choi_mat = np.array([[1, 0, 0, 0], [0, 0, 1, 0], [0, 1, 0, 0], [0, 0, 0, 1]])
     kraus_ops = [
         [
@@ -58,7 +57,6 @@ def test_choi_to_kraus_cpt():
 
 def test_choi_to_kraus_non_square():
     """Choi matrix of the swap operator for non square input/output."""
-
     choi_mat = swap_operator([2, 3])
     kraus_ops = [
         [

toqito/channel_ops/tests/test_dual_channel.py

@@ -100,14 +100,17 @@ def test_dual_channel_not_matrix():
 
 
 def test_dual_channel_unspecified_dims():
-    """If the size of the Choi matrix is not a perfect square,
-    the dimensions of the input and output spaces must be specified."""
+    """Test output of function when the dimensions must be specified.
+
+    If the size of the Choi matrix is not a perfect square, the dimensions of the input and output spaces must be
+    specified.
+    """
     with np.testing.assert_raises(ValueError):
         j = np.arange(36).reshape(6, 6)
         dual_channel(j)
 
 
 def test_dual_channel_invalid_input():
-    """Invalid input"""
+    """Test error is raised for an invalid input."""
     with np.testing.assert_raises(ValueError):
         dual_channel([0])

toqito/channel_ops/tests/test_partial_channel.py

@@ -8,10 +8,7 @@
 
 
 def test_partial_channel_depolarizing_first_system():
-    """
-    Perform the partial map using the depolarizing channel as the Choi
-    matrix on first system.
-    """
+    """Perform the partial map using the depolarizing channel as the Choi matrix on first system."""
     rho = np.array(
         [
             [
@@ -56,10 +53,7 @@ def test_partial_channel_depolarizing_first_system():
 
 
 def test_partial_channel_depolarizing_second_system():
-    """
-    Perform the partial map using the depolarizing channel as the Choi
-    matrix on second system.
-    """
+    """Perform the partial map using the depolarizing channel as the Choi matrix on second system."""
     rho = np.array(
         [
             [
@@ -104,9 +98,9 @@ def test_partial_channel_depolarizing_second_system():
 
 
 def test_partial_channel_dim_list():
-    """
-    Perform the partial map using the depolarizing channel as the Choi
-    matrix on first system when the dimension is specified as list.
+    """Perform the partial map.
+
+    Test uses the depolarizing channel as the Choi matrix on first system when the dimension is specified as list.
     """
     rho = np.array([[1, 2, 3, 4], [5, 6, 7, 8], [9, 10, 11, 12], [13, 14, 15, 16]])
     res = partial_channel(rho, depolarizing(2), 2, [2, 2])
@@ -126,10 +120,7 @@ def test_partial_channel_dim_list():
 
 @pytest.mark.parametrize("nested", [1, 2, 3])
 def test_partial_channel_cpt_kraus(nested):
-    """
-    Perform the partial map using the Kraus representation of
-    the depolarizing channel.
-    """
+    """Perform the partial map using the Kraus representation of the depolarizing channel."""
     rho = np.array([[1, 2, 3, 4], [5, 6, 7, 8], [9, 10, 11, 12], [13, 14, 15, 16]])
     kraus = [0.5 * pauli(ind) for ind in range(4)]
     if nested == 2:

toqito/channel_props/is_trace_preserving.py

@@ -14,8 +14,7 @@ def is_trace_preserving(
     sys: int | list[int] = 2,
     dim: list[int] | np.ndarray = None,
 ) -> bool:
-    r"""
-    Determine whether the given channel is trace-preserving.
+    r"""Determine whether the given channel is trace-preserving.
 
     A map :math:`\Phi \in \text{T} \left(\mathcal{X}, \mathcal{Y} \right)` is
     *trace-preserving* if it holds that

toqito/channel_props/is_unital.py

@@ -12,8 +12,7 @@ def is_unital(
     atol: float = 1e-08,
     dim: int | list[int] | np.ndarray = None,
 ) -> bool:
-    r"""
-    Determine whether the given channel is unital.
+    r"""Determine whether the given channel is unital.
 
     A map :math:`\Phi \in \text{T} \left(\mathcal{X}, \mathcal{Y} \right)` is *unital* if it holds that:
 

toqito/channel_props/tests/test_choi_rank.py

@@ -6,7 +6,7 @@
 
 
 def test_choi_rank_list_kraus():
-    """Verify that a list of Kraus operators gives correct Choi rank"""
+    """Verify that a list of Kraus operators gives correct Choi rank."""
     kraus_1 = np.array([[1, 0], [0, 0]])
     kraus_2 = np.array([[1, 0], [0, 0]]).conj().T
     kraus_3 = np.array([[0, 1], [0, 0]])
@@ -32,8 +32,10 @@ def test_choi_rank_choi_matrix():
 
 
 def test_choi_bad_input():
-    """Verify that a bad input (such as a string which still passes
-    with `numpy.linalg.matrix_rank`) raises an error"""
+    """Verify that a bad input raises an error.
+
+    The bad input is a string which still passes with `numpy.linalg.matrix_rank`.
+    """
     with pytest.raises(ValueError, match="Not a valid"):
         bad_input = "string"
         choi_rank(bad_input)

toqito/channels/choi.py

@@ -5,8 +5,7 @@
 
 
 def choi(a_var: int = 1, b_var: int = 1, c_var: int = 0) -> np.ndarray:
-    r"""
-    Produce the Choi channel or one of its generalizations :cite:`Choi_1992_Generalized`.
+    r"""Produce the Choi channel or one of its generalizations :cite:`Choi_1992_Generalized`.
 
     The *Choi channel* is a positive map on 3-by-3 matrices that is capable of detecting some
     entanglement that the transpose map is not.

toqito/channels/partial_trace.py

@@ -14,8 +14,7 @@ def partial_trace(
     sys: int | list[int] = None,
     dim: int | list[int] = None,
 ) -> np.ndarray | Expression:
-    r"""
-    Compute the partial trace of a matrix :cite:`WikiPartialTr`.
+    r"""Compute the partial trace of a matrix :cite:`WikiPartialTr`.
 
     The *partial trace* is defined as
 

toqito/channels/realignment.py

@@ -8,8 +8,7 @@
 
 
 def realignment(input_mat: np.ndarray, dim: int | list[int] = None) -> np.ndarray:
-    r"""
-    Compute the realignment of a bipartite operator :cite:`Lupo_2008_Bipartite`.
+    r"""Compute the realignment of a bipartite operator :cite:`Lupo_2008_Bipartite`.
 
     Gives the realignment of the matrix :code:`input_mat`, where it is assumed that the number
     of rows and columns of :code:`input_mat` are both perfect squares and both subsystems have

toqito/channels/reduction.py

@@ -6,8 +6,7 @@
 
 
 def reduction(dim: int, k: int = 1) -> np.ndarray:
-    r"""
-    Produce the reduction map or reduction channel :cite:`WikiReductionCrit`.
+    r"""Produce the reduction map or reduction channel :cite:`WikiReductionCrit`.
 
     If :code:`k = 1`, this returns the Choi matrix of the reduction map which is a positive map
     on :code:`dim`-by-:code:`dim` matrices. For a different value of :code:`k`, this yields the

toqito/channels/tests/test_choi.py

@@ -27,8 +27,7 @@ def test_choi_standard():
 
 
 def test_choi_reduction():
-    """
-    The reduction map is the map R defined by: R(X) = Tr(X)I - X.
+    """The reduction map is the map R defined by: R(X) = Tr(X)I - X.
 
     The reduction map is the Choi map that arises when a = 0, b = c = 1.
     """