Merge branch 'master' into feature/small_improvements

.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/index.rst

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

environment.yml

@@ -1,12 +1,12 @@
 name: filter_functions
 
 channels:
-  - defaults
   - conda-forge
 
 dependencies:
   - python >= 3.9
   - qutip
+  - pandoc
   - pip
 
 prefix: /home/docs/.conda/envs/filter_functions

filter_functions/basis.py

@@ -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:
@@ -211,22 +210,26 @@ 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."""
@@ -595,7 +598,7 @@ 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))
 
@@ -604,7 +607,7 @@ 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))
@@ -631,8 +634,8 @@ 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*.
 
@@ -682,7 +685,7 @@ def cast(arr):
     return util.remove_float_errors(coefficients) if tidyup else coefficients
 
 
-def ggm_expand(M: Union[ndarray, Basis], traceless: bool = False,
+def ggm_expand(M: Union[np.ndarray, Basis], traceless: bool = False,
                hermitian: bool = False, tidyup: bool = False) -> ndarray:
     r"""
     Expand the matrix *M* in a Generalized Gell-Mann basis [Bert08]_.
@@ -771,7 +774,7 @@ def cast(arr):
     return 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
@@ -784,7 +787,7 @@ 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/util.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):

setup.py

@@ -18,9 +18,8 @@ def extract_version(version_file):
 
 extras_require = {'plotting': ['matplotlib'],
                   'bloch_sphere_visualization': ['qutip', 'matplotlib'],
-                  'fancy_progressbar': ['ipynbname', 'jupyter'],
                   'doc': ['jupyter', 'nbsphinx', 'numpydoc', 'sphinx', 'sphinx_rtd_theme',
-                          'ipympl', 'qutip-qip', 'qutip-qtrl'],
+                          'sphinxcontrib-apidoc', 'ipympl', 'qutip-qip', 'qutip-qtrl', 'numpy<2'],
                   'tests': ['pytest>=4.6', 'pytest-cov', 'codecov']}
 
 extras_require['all'] = list({dep for deps in extras_require.values() for dep in deps})

tests/test_basis.py

@@ -24,6 +24,7 @@
 from copy import copy
 from itertools import product
 
+import filter_functions as ff
 import numpy as np
 import pytest
 from opt_einsum import contract
@@ -153,9 +154,21 @@ def test_basis_properties(self):
 
             base._print_checks()
 
-        basis = util.paulis[1].view(ff.Basis)
-        self.assertTrue(basis.isorthonorm)
-        self.assertArrayEqual(basis.T, basis.view(np.ndarray).T)
+        # single element always considered orthonormal
+        orthonorm = rng.normal(size=(d, d))
+        self.assertTrue(orthonorm.view(ff.Basis).isorthonorm)
+
+        herm = testutil.rand_herm(d).squeeze()
+        self.assertTrue(herm.view(ff.Basis).isherm)
+
+        herm[0, 1] += 1
+        self.assertFalse(herm.view(ff.Basis).isherm)
+
+        traceless = testutil.rand_herm_traceless(d).squeeze()
+        self.assertTrue(traceless.view(ff.Basis).istraceless)
+
+        traceless[0, 0] += 1
+        self.assertFalse(traceless.view(ff.Basis).istraceless)
 
     def test_transpose(self):
         arr = rng.normal(size=(2, 3, 3))

tests/test_extras.py

@@ -31,21 +31,11 @@
 
 from . import matplotlib
 
-all_extras = ['fancy_progressbar', 'plotting', 'bloch_sphere_visualization']
+all_extras = ['plotting', 'bloch_sphere_visualization']
 
 
 class MissingExtrasTest(testutil.TestCase):
 
-    @pytest.mark.skipif(
-        'fancy_progressbar' in os.environ.get('INSTALL_EXTRAS', all_extras),
-        reason='Skipping tests for missing fancy progressbar extra in build with ipynbname')
-    def test_fancy_progressbar_not_available(self):
-        from tqdm import tqdm
-
-        from filter_functions import util
-        self.assertEqual(util._NOTEBOOK_NAME, '')
-        self.assertIs(tqdm, util._tqdm)
-
     @pytest.mark.skipif(
         any(extra in os.environ.get('INSTALL_EXTRAS', all_extras)
             for extra in ['plotting', 'bloch_sphere_visualization']),