Merge branch 'master' into refactor/pep-518

Author: thangleiter

.readthedocs.yml

@@ -16,7 +16,6 @@ python:
          - doc
          - plotting
          - bloch_sphere_visualization
-         - fancy_progressbar
 
 sphinx:
   builder: html

doc/source/api.rst

@@ -0,0 +1,8 @@
+API
+===
+
+.. autosummary::
+   :toctree: generated
+   :recursive:
+
+   filter_functions

doc/source/conf.py

@@ -38,27 +38,28 @@
     'nbsphinx',
     'sphinx.ext.mathjax',
     'sphinx.ext.todo',
+    'sphinx.ext.autodoc',
     'sphinx.ext.autosummary',
     'numpydoc',
     'sphinx.ext.extlinks',
     'sphinx.ext.viewcode',
     'sphinx.ext.ifconfig',
     'sphinx.ext.napoleon',
     'sphinx.ext.intersphinx',
-    #'sphinxcontrib.apidoc',
+    'sphinxcontrib.apidoc',
     #'IPython.sphinxext.ipython_console_highlighting',
     #'IPython.sphinxext.ipython_directive',
     #'matplotlib.sphinxext.only_directives',
     #'matplotlib.sphinxext.plot_directive',
     #'matplotlib.sphinxext.mathmpl',
-    #'sphinx.ext.autodoc',
     #'sphinx.ext.doctest',
 ]
 
 # Apidoc config
 apidoc_module_dir = '../../filter_functions'
 apidoc_excluded_paths = ['../tests']
 apidoc_separate_modules = True
+apidoc_module_first = True
 
 # Numpydoc settings
 numpydoc_show_inherited_class_members = False

doc/source/filter_functions.rst

@@ -23,7 +23,7 @@ Documentation
    :numbered:
 
    examples/examples
-   filter_functions API Documentation <filter_functions>
+   filter_functions API Documentation <api>
 
 Indices and tables
 ==================

doc/source/index.rst

@@ -6,6 +6,7 @@ channels:
 dependencies:
   - python >= 3.9
   - qutip
+  - pandoc
   - pip
 
 prefix: /home/docs/.conda/envs/filter_functions

environment.yml

@@ -47,7 +47,6 @@
 import numpy as np
 import opt_einsum as oe
 from numpy import linalg as nla
-from numpy.core import ndarray
 from scipy import linalg as sla
 from sparse import COO
 
@@ -56,7 +55,7 @@
 __all__ = ['Basis', 'expand', 'ggm_expand', 'normalize']
 
 
-class Basis(ndarray):
+class Basis(np.ndarray):
     r"""
     Class for operator bases. There are several ways to instantiate a
     Basis object:
@@ -217,22 +216,26 @@ def __eq__(self, other: object) -> bool:
             # Not ndarray
             return np.equal(self, other)
 
-        return np.allclose(self.view(ndarray), other.view(ndarray),
+        return np.allclose(self.view(np.ndarray), other.view(np.ndarray),
                            atol=self._atol, rtol=self._rtol)
 
-    def __contains__(self, item: ndarray) -> bool:
+    def __contains__(self, item: np.ndarray) -> bool:
         """Implement 'in' operator."""
-        return any(np.isclose(item.view(ndarray), self.view(ndarray),
+        return any(np.isclose(item.view(np.ndarray), self.view(np.ndarray),
                               rtol=self._rtol, atol=self._atol).all(axis=(1, 2)))
 
-    def __array_wrap__(self, out_arr, context=None):
+    def __array_wrap__(self, arr, context=None, return_scalar=False):
         """
         Fixes problem that ufuncs return 0-d arrays instead of scalars.
 
         https://github.com/numpy/numpy/issues/5819#issue-72454838
         """
-        if out_arr.ndim:
-            return ndarray.__array_wrap__(self, out_arr, context)
+        try:
+            return super().__array_wrap__(arr, context, return_scalar=True)
+        except TypeError:
+            if arr.ndim:
+                # Numpy < 2
+                return np.ndarray.__array_wrap__(self, arr, context)
 
     def _print_checks(self) -> None:
         """Print checks for debug purposes."""
@@ -265,7 +268,7 @@ def isorthonorm(self) -> bool:
                 actual = U.conj() @ U.T
                 target = np.identity(dim)
                 atol = self._eps*(self.d**2)**3
-                self._isorthonorm = np.allclose(actual.view(ndarray), target,
+                self._isorthonorm = np.allclose(actual.view(np.ndarray), target,
                                                 atol=atol, rtol=self._rtol)
 
         return self._isorthonorm
@@ -278,13 +281,16 @@ def istraceless(self) -> bool:
         if self._istraceless is None:
             trace = np.einsum('...jj', self)
             trace = util.remove_float_errors(trace, self.d**2)
-            nonzero = trace.nonzero()
+            nonzero = np.atleast_1d(trace).nonzero()
             if nonzero[0].size == 0:
                 self._istraceless = True
             elif nonzero[0].size == 1:
                 # Single element has nonzero trace, check if (proportional to)
                 # identity
-                elem = self[nonzero][0].view(ndarray) if self.ndim == 3 else self.view(ndarray)
+                if self.ndim == 3:
+                    elem = self[nonzero][0].view(np.ndarray)
+                else:
+                    elem = self.view(np.ndarray)
                 offdiag_nonzero = elem[~np.eye(self.d, dtype=bool)].nonzero()
                 diag_equal = np.diag(elem) == elem[0, 0]
                 if diag_equal.all() and not offdiag_nonzero[0].any():
@@ -597,7 +603,7 @@ def _full_from_partial(elems: Sequence, traceless: bool, labels: Sequence[str])
             # sort Identity label to the front, default to first if not found
             # (should not happen since traceless checks that it is present)
             id_idx = next((i for i, elem in enumerate(elems)
-                           if np.allclose(Id.view(ndarray), elem.view(ndarray),
+                           if np.allclose(Id.view(np.ndarray), elem.view(np.ndarray),
                                           rtol=elems._rtol, atol=elems._atol)), 0)
             labels.insert(0, labels.pop(id_idx))
 
@@ -606,7 +612,7 @@ def _full_from_partial(elems: Sequence, traceless: bool, labels: Sequence[str])
     return basis, labels
 
 
-def _norm(b: Sequence) -> ndarray:
+def _norm(b: Sequence) -> np.ndarray:
     """Frobenius norm with two singleton dimensions inserted at the end."""
     b = np.asanyarray(b)
     norm = nla.norm(b, axis=(-1, -2))
@@ -633,8 +639,8 @@ def normalize(b: Basis) -> Basis:
     return (b/_norm(b)).squeeze().view(Basis)
 
 
-def expand(M: Union[ndarray, Basis], basis: Union[ndarray, Basis],
-           normalized: bool = True, hermitian: bool = False, tidyup: bool = False) -> ndarray:
+def expand(M: Union[np.ndarray, Basis], basis: Union[np.ndarray, Basis],
+           normalized: bool = True, hermitian: bool = False, tidyup: bool = False) -> np.ndarray:
     r"""
     Expand the array *M* in the basis given by *basis*.
 
@@ -684,8 +690,8 @@ def cast(arr):
     return util.remove_float_errors(coefficients) if tidyup else coefficients
 
 
-def ggm_expand(M: Union[ndarray, Basis], traceless: bool = False,
-               hermitian: bool = False) -> ndarray:
+def ggm_expand(M: Union[np.ndarray, Basis], traceless: bool = False,
+               hermitian: bool = False) -> np.ndarray:
     r"""
     Expand the matrix *M* in a Generalized Gell-Mann basis [Bert08]_.
     This function makes use of the explicit construction prescription of
@@ -767,7 +773,7 @@ def cast(arr):
     return coeffs.squeeze() if square else coeffs
 
 
-def equivalent_pauli_basis_elements(idx: Union[Sequence[int], int], N: int) -> ndarray:
+def equivalent_pauli_basis_elements(idx: Union[Sequence[int], int], N: int) -> np.ndarray:
     """
     Get the indices of the equivalent (up to identities tensored to it)
     basis elements of Pauli bases of qubits at position idx in the total
@@ -780,7 +786,7 @@ def equivalent_pauli_basis_elements(idx: Union[Sequence[int], int], N: int) -> n
     return elem_idx
 
 
-def remap_pauli_basis_elements(order: Sequence[int], N: int) -> ndarray:
+def remap_pauli_basis_elements(order: Sequence[int], N: int) -> np.ndarray:
     """
     For a N-qubit Pauli basis, transpose the order of the subsystems and
     return the indices that permute the old basis to the new.

filter_functions/basis.py

@@ -237,6 +237,17 @@ class PulseSequence:
     Due to the heavy use of NumPy's :func:`~numpy.einsum` function,
     results have a floating point error of ~1e-13.
     """
+    __array_interface__ = {
+        'shape': (),
+        'typestr': '|O',
+        'version': 3
+    }
+    """Describes to NumPy how to convert this object into an array.
+
+    Since :class:`PulseSequence` is iterable (through
+    :meth:`__getitem__`), NumPy would otherwise try to create an
+    ndarray of single-segment :class:`PulseSequence` s.
+    """
 
     def __init__(self, *args, **kwargs) -> None:
         """Initialize a PulseSequence instance."""

filter_functions/pulse_sequence.py

@@ -26,8 +26,7 @@
 :func:`abs2`
     Absolute value squared
 :func:`get_indices_from_identifiers`
-    The the indices of a subset of identifiers within a list of
-    identifiers.
+    The indices of a subset of identifiers within a list of identifiers.
 :func:`tensor`
     Fast, flexible tensor product of an arbitrary number of inputs using
     :func:`~numpy.einsum`
@@ -70,6 +69,7 @@
 import functools
 import inspect
 import operator
+import os
 import string
 from itertools import zip_longest
 from typing import Callable, Iterable, List, Optional, Sequence, Tuple, Union
@@ -79,17 +79,25 @@
 
 from .types import Operator, State
 
-try:
-    import ipynbname
-    _NOTEBOOK_NAME = ipynbname.name()
-except (ImportError, IndexError, FileNotFoundError):
-    _NOTEBOOK_NAME = ''
 
-if _NOTEBOOK_NAME:
-    from tqdm.notebook import tqdm as _tqdm
+def _in_notebook_kernel():
+    # https://github.com/jupyterlab/jupyterlab/issues/16282
+    return 'JPY_SESSION_NAME' in os.environ and os.environ['JPY_SESSION_NAME'].endswith('.ipynb')
+
+
+def _in_jupyter_kernel():
+    # https://discourse.jupyter.org/t/how-to-know-from-python-script-if-we-are-in-jupyterlab/23993
+    return 'JPY_PARENT_PID' in os.environ
+
+
+if not _in_notebook_kernel():
+    if _in_jupyter_kernel():
+        # (10/24) Autonotebook gets confused in jupyter consoles
+        from tqdm.std import tqdm
+    else:
+        from tqdm.autonotebook import tqdm
 else:
-    # Either not running notebook or not able to determine
-    from tqdm import tqdm as _tqdm
+    from tqdm.notebook import tqdm
 
 __all__ = ['paulis', 'abs2', 'all_array_equal', 'dot_HS', 'get_sample_frequencies',
            'hash_array_along_axis', 'mdot', 'oper_equiv', 'progressbar', 'remove_float_errors',
@@ -1067,7 +1075,7 @@ def progressbar(iterable: Iterable, *args, **kwargs):
         for i in progressbar(range(10)):
             do_something()
     """
-    return _tqdm(iterable, *args, **kwargs)
+    return tqdm(iterable, *args, **kwargs)
 
 
 def progressbar_range(*args, show_progressbar: bool = True, **kwargs):

filter_functions/util.py

@@ -39,19 +39,17 @@ bloch_sphere_visualization = [
     "filter_functions[plotting]",
     "qutip",
 ]
-fancy_progressbar = [
-    "ipynbname",
-    "jupyter"
-]
 doc = [
     "jupyter",
     "nbsphinx",
     "numpydoc",
     "sphinx",
     "sphinx_rtd_theme",
+    "sphinxcontrib-apidoc",
     "ipympl",
     "qutip-qip",
-    "qutip-qtrl"
+    "qutip-qtrl",
+    "numpy<2"
 ]
 tests = [
     "pytest >= 4.6",
@@ -61,7 +59,6 @@ tests = [
 all = [
     "filter_functions[plotting]",
     "filter_functions[bloch_sphere_visualization]",
-    "filter_functions[fancy_progressbar]",
     "filter_functions[doc]",
     "filter_functions[tests]",
 ]