jtiosue / qubovert

The one-stop package for formulating, simulating, and solving problems in boolean and spin form

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qubovert's Issues

`.normalize()` fails for an empty QUBO

In [38]: qv.QUBO({}).normalize()
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-38-18b132978996> in <module>
----> 1 qv.QUBO({}).normalize()

~.../python3.8/site-packages/qubovert/utils/_dict_arithmetic.py in normalize(self, value)
    781 
    782         """
--> 783         mult = value / max(abs(v) for v in self.values())
    784         for k in self:
    785             self[k] *= mult

ValueError: max() arg is an empty sequence

@jtiosue I'm happy to make a pull request so that this case would simply return the empty QUBO (or PCBO or whatever) back unchanged.

two simulated annealer give different solution

Hello Joseph,

I got different solutions from qubovert.sim.anneal_qubo() and neal.SimulatedAnnealingSampler().sample_qubo().

Here is my code if you would like to run it on your side:
simulated_annealer.zip
Please let me know if you have some explanations, or there is something wrong in my code.

Also I am confused of SimulatedAnnealingSampler().sample_qubo(dwave_qubo, num_runs=10)
I looked into cource code of neal: I did not find any statement about num_runs. Could you please clarify it with me?

Thank you,
Yuxin

TypeError: loop of ufunc does not support argument 0 of type Float which has no callable log10 method

Error obtained in the line:
res = qv.sim.anneal_qubo(Q, num_anneals=1000)

parameter Q that is being passed is:

{(0, 0): -6,
(0, 54): 12,
(0, 57): 12,
(0, 60): 12,
(1, 1): -6,
(1, 55): 12,
(1, 58): 12,
(1, 61): 12,
(2, 2): -6,
(2, 56): 12,
(2, 59): 12,
(2, 62): 12,
(3, 3): -73,
(3, 4): 48,
(3, 5): 12,
(3, 6): 24,
(3, 7): 12,
(3, 8): 24,
(3, 27): 12,
(3, 45): 12,
(3, 46): 24,
(3, 47): 48,
(3, 54): -24,
(4, 4): -122,
(4, 5): 24,
(4, 6): 48,
(4, 7): 24,
(4, 8): 48,
(4, 27): 24,
(4, 45): 24,
(4, 46): 48,
(4, 47): 96,
(4, 54): -48,
(5, 5): -73,
(5, 6): 48,
(5, 7): 12,
(5, 8): 24,
(5, 28): 12,
(5, 45): 12,
(5, 46): 24,
(5, 47): 48,
(5, 55): -24,
(6, 6): -122,
(6, 7): 24,
(6, 8): 48,
(6, 28): 24,
(6, 45): 24,
(6, 46): 48,
(6, 47): 96,
(6, 55): -48,
(7, 7): -73,
(7, 8): 48,
(7, 29): 12,
(7, 45): 12,
(7, 46): 24,
(7, 47): 48,
(7, 56): -24,
(8, 8): -122,
(8, 29): 24,
(8, 45): 24,
(8, 46): 48,
(8, 47): 96,
(8, 56): -48,
(9, 9): -73,
(9, 10): 48,
(9, 11): 96,
(9, 12): 12,
(9, 13): 24,
(9, 14): 48,
(9, 15): 12,
(9, 16): 24,
(9, 17): 48,
(9, 30): 12,
(9, 31): 24,
(9, 48): 12,
(9, 49): 24,
(9, 50): 48,
(9, 57): -48,
(10, 10): -122,
(10, 11): 192,
(10, 12): 24,
(10, 13): 48,
(10, 14): 96,
(10, 15): 24,
(10, 16): 48,
(10, 17): 96,
(10, 30): 24,
(10, 31): 48,
(10, 48): 24,
(10, 49): 48,
(10, 50): 96,
(10, 57): -96,
(11, 11): -148,
(11, 12): 48,
(11, 13): 96,
(11, 14): 192,
(11, 15): 48,
(11, 16): 96,
(11, 17): 192,
(11, 30): 48,
(11, 31): 96,
(11, 48): 48,
(11, 49): 96,
(11, 50): 192,
(11, 57): -192,
(12, 12): -73,
(12, 13): 48,
(12, 14): 96,
(12, 15): 12,
(12, 16): 24,
(12, 17): 48,
(12, 32): 12,
(12, 33): 24,
(12, 48): 12,
(12, 49): 24,
(12, 50): 48,
(12, 58): -48,
(13, 13): -122,
(13, 14): 192,
(13, 15): 24,
(13, 16): 48,
(13, 17): 96,
(13, 32): 24,
(13, 33): 48,
(13, 48): 24,
(13, 49): 48,
(13, 50): 96,
(13, 58): -96,
(14, 14): -148,
(14, 15): 48,
(14, 16): 96,
(14, 17): 192,
(14, 32): 48,
(14, 33): 96,
(14, 48): 48,
(14, 49): 96,
(14, 50): 192,
(14, 58): -192,
(15, 15): -73,
(15, 16): 48,
(15, 17): 96,
(15, 34): 12,
(15, 35): 24,
(15, 48): 12,
(15, 49): 24,
(15, 50): 48,
(15, 59): -48,
(16, 16): -122,
(16, 17): 192,
(16, 34): 24,
(16, 35): 48,
(16, 48): 24,
(16, 49): 48,
(16, 50): 96,
(16, 59): -96,
(17, 17): -148,
(17, 34): 48,
(17, 35): 96,
(17, 48): 48,
(17, 49): 96,
(17, 50): 192,
(17, 59): -192,
(18, 18): -73,
(18, 19): 48,
(18, 20): 96,
(18, 21): 12,
(18, 22): 24,
(18, 23): 48,
(18, 24): 12,
(18, 25): 24,
(18, 26): 48,
(18, 36): 12,
(18, 37): 24,
(18, 38): 48,
(18, 51): 12,
(18, 52): 24,
(18, 53): 48,
(18, 60): -60,
(19, 19): -122,
(19, 20): 192,
(19, 21): 24,
(19, 22): 48,
(19, 23): 96,
(19, 24): 24,
(19, 25): 48,
(19, 26): 96,
(19, 36): 24,
(19, 37): 48,
(19, 38): 96,
(19, 51): 24,
(19, 52): 48,
(19, 53): 96,
(19, 60): -120,
(20, 20): -148,
(20, 21): 48,
(20, 22): 96,
(20, 23): 192,
(20, 24): 48,
(20, 25): 96,
(20, 26): 192,
(20, 36): 48,
(20, 37): 96,
(20, 38): 192,
(20, 51): 48,
(20, 52): 96,
(20, 53): 192,
(20, 60): -240,
(21, 21): -73,
(21, 22): 48,
(21, 23): 96,
(21, 24): 12,
(21, 25): 24,
(21, 26): 48,
(21, 39): 12,
(21, 40): 24,
(21, 41): 48,
(21, 51): 12,
(21, 52): 24,
(21, 53): 48,
(21, 61): -60,
(22, 22): -122,
(22, 23): 192,
(22, 24): 24,
(22, 25): 48,
(22, 26): 96,
(22, 39): 24,
(22, 40): 48,
(22, 41): 96,
(22, 51): 24,
(22, 52): 48,
(22, 53): 96,
(22, 61): -120,
(23, 23): -148,
(23, 24): 48,
(23, 25): 96,
(23, 26): 192,
(23, 39): 48,
(23, 40): 96,
(23, 41): 192,
(23, 51): 48,
(23, 52): 96,
(23, 53): 192,
(23, 61): -240,
(24, 24): -73,
(24, 25): 48,
(24, 26): 96,
(24, 42): 12,
(24, 43): 24,
(24, 44): 48,
(24, 51): 12,
(24, 52): 24,
(24, 53): 48,
(24, 62): -60,
(25, 25): -122,
(25, 26): 192,
(25, 42): 24,
(25, 43): 48,
(25, 44): 96,
(25, 51): 24,
(25, 52): 48,
(25, 53): 96,
(25, 62): -120,
(26, 26): -148,
(26, 42): 48,
(26, 43): 96,
(26, 44): 192,
(26, 51): 48,
(26, 52): 96,
(26, 53): 192,
(26, 62): -240,
(27, 27): 6,
(27, 54): -24,
(28, 28): 6,
(28, 55): -24,
(29, 29): 6,
(29, 56): -24,
(30, 30): 6,
(30, 31): 24,
(30, 57): -48,
(31, 31): 24,
(31, 57): -96,
(32, 32): 6,
(32, 33): 24,
(32, 58): -48,
(33, 33): 24,
(33, 58): -96,
(34, 34): 6,
(34, 35): 24,
(34, 59): -48,
(35, 35): 24,
(35, 59): -96,
(36, 36): 6,
(36, 37): 24,
(36, 38): 48,
(36, 60): -60,
(37, 37): 24,
(37, 38): 96,
(37, 60): -120,
(38, 38): 96,
(38, 60): -240,
(39, 39): 6,
(39, 40): 24,
(39, 41): 48,
(39, 61): -60,
(40, 40): 24,
(40, 41): 96,
(40, 61): -120,
(41, 41): 96,
(41, 61): -240,
(42, 42): 6,
(42, 43): 24,
(42, 44): 48,
(42, 62): -60,
(43, 43): 24,
(43, 44): 96,
(43, 62): -120,
(44, 44): 96,
(44, 62): -240,
(45, 45): -78,
(45, 46): 24,
(45, 47): 48,
(46, 46): -144,
(46, 47): 96,
(47, 47): -240,
(48, 48): -78,
(48, 49): 24,
(48, 50): 48,
(49, 49): -144,
(49, 50): 96,
(50, 50): -240,
(51, 51): -78,
(51, 52): 24,
(51, 53): 48,
(52, 52): -144,
(52, 53): 96,
(53, 53): -240,
(54, 54): 18,
(54, 57): 12,
(54, 60): 12,
(55, 55): 18,
(55, 58): 12,
(55, 61): 12,
(56, 56): 18,
(56, 59): 12,
(56, 62): 12,
(57, 57): 90,
(57, 60): 12,
(58, 58): 90,
(58, 61): 12,
(59, 59): 90,
(59, 62): 12,
(60, 60): 144,
(61, 61): 144,
(62, 62): 144}

Any help here is appreciated.

Missing attribute after using multiprocessing Queue

When using multiprocessing's Queue class to share PCBO instances between processes, the attribute _degree is missing after extraction. A minimal example:

import multiprocessing as mp
from qubovert import PCBO

def produce(queue):
    pcbo = PCBO({(0,1): -5})
    queue.put(pcbo)

def consume(queue):
    pcbo = queue.get() # AttributeError occurs here
    print(pcbo)

if __name__ == '__main__':
    queue = mp.Queue()

    process1 = mp.Process(target=produce, args=(queue,))
    process2 = mp.Process(target=consume, args=(queue,))

    process1.start()
    process2.start()

    process1.join()
    process2.join()

Executing this produces the following error:

Process Process-2:
Traceback (most recent call last):
  File "/usr/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/usr/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "test.py", line 9, in consume
    pcbo = queue.get()
  File "/usr/lib/python3.8/multiprocessing/queues.py", line 116, in get
    return _ForkingPickler.loads(res)
  File "/home/muecke/.local/lib/python3.8/site-packages/qubovert/utils/_bo_parentclass.py", line 219, in __setitem__
    super().__setitem__(key, value)
  File "/home/muecke/.local/lib/python3.8/site-packages/qubovert/utils/_pubomatrix.py", line 384, in __setitem__
    self._degree = max(self._degree, len(k))
AttributeError: 'PCBO' object has no attribute '_degree'

OS: Linux (Manjaro, kernel 5.7.9-1-MANJARO)
Python version 3.8.3, qubovert version 1.2.3

Thanks in advance!

Suspected bug in subgraph()

I think I've found a bug in subgraph(). Here's a minimal reproducer:

from qubovert.utils import subgraph
import numpy as np

G = {(2,): 1, (2, 3): -1}
connections={3: 1}
qubo = subgraph(G, [2], connections)
print(qubo)

The output I get is:

{(2,): 1.0}

Whereas the output I expect is:

{}

I suspect the issue is at the end of subgraph(), where we have:

        if value:
            D[key] = value

which I think should be changed to something like this:

        if value:
            D[key] = value
        else:
            try:
                del D[key]
            except KeyError:
                pass

To deal with the situation in which substituting the values from connections causes value to be zero. I've assumed here that it is possible that key is not in D, since I see that just above there is D.get(key, 0) which was designed to work in that scenario. But if that's impossible then we could get rid of the try/except.

qubovert doesn't install with python 3.10 on macOS 13.2.1

$ python3.10 -m venv qubovert-venv
$ source qubovert-venv/bin/activate
(qubovert-venv)$ python3.10 -c "import platform; print(platform.mac_ver())"
('13.2.1', ('', '', ''), 'x86_64')
(qubovert-venv)$ python3.10 -m pip install qubovert

Here is the generated output:

Collecting qubovert Using cached qubovert-1.2.5.tar.gz (97 kB) Preparing metadata (setup.py) ... done Collecting numpy Using cached numpy-1.24.2-cp310-cp310-macosx_10_9_x86_64.whl (19.8 MB) Installing collected packages: numpy, qubovert WARNING: The scripts f2py, f2py3 and f2py3.10 are installed in '/Library/Frameworks/Python.framework/Versions/3.10/bin' which is not on PATH. Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location. DEPRECATION: qubovert is being installed using the legacy 'setup.py install' method, because it does not have a 'pyproject.toml' and the 'wheel' package is not installed. pip 23.1 will enforce this behaviour change. A possible replacement is to enable the '--use-pep517' option. Discussion can be found at https://github.com/pypa/pip/issues/8559 Running setup.py install for qubovert ... error error: subprocess-exited-with-error

× Running setup.py install for qubovert did not run successfully.
│ exit code: 1
╰─> [235 lines of output]
running install
/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
warnings.warn(
running build
running build_py
creating build
creating build/lib.macosx-10.9-universal2-cpython-310
creating build/lib.macosx-10.9-universal2-cpython-310/qubovert
copying qubovert/_pcso.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert
copying qubovert/_pcbo.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert
copying qubovert/_version.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert
copying qubovert/init.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert
copying qubovert/_qubo.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert
copying qubovert/_quso.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert
copying qubovert/_pubo.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert
copying qubovert/main.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert
copying qubovert/_puso.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert
creating build/lib.macosx-10.9-universal2-cpython-310/qubovert/problems
copying qubovert/problems/init.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/problems
copying qubovert/problems/_problem_parentclass.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/problems
copying qubovert/problems/main.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/problems
creating build/lib.macosx-10.9-universal2-cpython-310/qubovert/utils
copying qubovert/utils/_normalize.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/utils
copying qubovert/utils/_qubomatrix.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/utils
copying qubovert/utils/_pusomatrix.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/utils
copying qubovert/utils/_ordering_key.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/utils
copying qubovert/utils/_info.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/utils
copying qubovert/utils/_approximate_extrema.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/utils
copying qubovert/utils/_conversions.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/utils
copying qubovert/utils/init.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/utils
copying qubovert/utils/_warn.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/utils
copying qubovert/utils/_qusomatrix.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/utils
copying qubovert/utils/_pubomatrix.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/utils
copying qubovert/utils/_solve_bruteforce.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/utils
copying qubovert/utils/_binary_helpers.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/utils
copying qubovert/utils/_values.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/utils
copying qubovert/utils/_subgraph.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/utils
copying qubovert/utils/main.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/utils
copying qubovert/utils/_dict_arithmetic.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/utils
copying qubovert/utils/_bo_parentclass.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/utils
creating build/lib.macosx-10.9-universal2-cpython-310/qubovert/sat
copying qubovert/sat/init.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/sat
copying qubovert/sat/_satisfiability.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/sat
copying qubovert/sat/main.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/sat
creating build/lib.macosx-10.9-universal2-cpython-310/qubovert/sim
copying qubovert/sim/_anneal_temperature_range.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/sim
copying qubovert/sim/_anneal.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/sim
copying qubovert/sim/init.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/sim
copying qubovert/sim/_anneal_results.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/sim
copying qubovert/sim/main.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/sim
creating build/lib.macosx-10.9-universal2-cpython-310/qubovert/problems/np
copying qubovert/problems/np/init.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/problems/np
copying qubovert/problems/np/main.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/problems/np
creating build/lib.macosx-10.9-universal2-cpython-310/qubovert/problems/benchmarking
copying qubovert/problems/benchmarking/init.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/problems/benchmarking
copying qubovert/problems/benchmarking/_alternating_sectors_chain.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/problems/benchmarking
copying qubovert/problems/benchmarking/main.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/problems/benchmarking
creating build/lib.macosx-10.9-universal2-cpython-310/qubovert/problems/np/cycles
copying qubovert/problems/np/cycles/init.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/problems/np/cycles
copying qubovert/problems/np/cycles/main.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/problems/np/cycles
creating build/lib.macosx-10.9-universal2-cpython-310/qubovert/problems/np/tree
copying qubovert/problems/np/tree/init.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/problems/np/tree
copying qubovert/problems/np/tree/main.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/problems/np/tree
creating build/lib.macosx-10.9-universal2-cpython-310/qubovert/problems/np/bilp
copying qubovert/problems/np/bilp/init.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/problems/np/bilp
copying qubovert/problems/np/bilp/main.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/problems/np/bilp
copying qubovert/problems/np/bilp/_bilp.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/problems/np/bilp
creating build/lib.macosx-10.9-universal2-cpython-310/qubovert/problems/np/coloring
copying qubovert/problems/np/coloring/_job_sequencing.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/problems/np/coloring
copying qubovert/problems/np/coloring/init.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/problems/np/coloring
copying qubovert/problems/np/coloring/main.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/problems/np/coloring
creating build/lib.macosx-10.9-universal2-cpython-310/qubovert/problems/np/partitioning
copying qubovert/problems/np/partitioning/_graph_partitioning.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/problems/np/partitioning
copying qubovert/problems/np/partitioning/init.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/problems/np/partitioning
copying qubovert/problems/np/partitioning/_number_partitioning.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/problems/np/partitioning
copying qubovert/problems/np/partitioning/main.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/problems/np/partitioning
creating build/lib.macosx-10.9-universal2-cpython-310/qubovert/problems/np/covering
copying qubovert/problems/np/covering/_set_cover.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/problems/np/covering
copying qubovert/problems/np/covering/_vertex_cover.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/problems/np/covering
copying qubovert/problems/np/covering/init.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/problems/np/covering
copying qubovert/problems/np/covering/main.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/problems/np/covering
creating build/lib.macosx-10.9-universal2-cpython-310/qubovert/problems/np/packing
copying qubovert/problems/np/packing/init.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/problems/np/packing
copying qubovert/problems/np/packing/main.py -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/problems/np/packing
running egg_info
writing qubovert.egg-info/PKG-INFO
writing dependency_links to qubovert.egg-info/dependency_links.txt
writing requirements to qubovert.egg-info/requires.txt
writing top-level names to qubovert.egg-info/top_level.txt
reading manifest file 'qubovert.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
adding license file 'LICENSE'
writing manifest file 'qubovert.egg-info/SOURCES.txt'
/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'qubovert.sim.src' as data is deprecated, please list it in packages.
!!

      ############################
      # Package would be ignored #
      ############################
      Python recognizes 'qubovert.sim.src' as an importable package,
      but it is not listed in the `packages` configuration of setuptools.
  
      'qubovert.sim.src' has been automatically added to the distribution only
      because it may contain data files, but this behavior is likely to change
      in future versions of setuptools (and therefore is considered deprecated).
  
      Please make sure that 'qubovert.sim.src' is included as a package by using
      the `packages` configuration field or the proper discovery methods
      (for example by using `find_namespace_packages(...)`/`find_namespace:`
      instead of `find_packages(...)`/`find:`).
  
      You can read more about "package discovery" and "data files" on setuptools
      documentation page.
  
  
  !!
  
    check.warn(importable)
  copying qubovert/sim/_canneal.c -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/sim
  creating build/lib.macosx-10.9-universal2-cpython-310/qubovert/sim/src
  copying qubovert/sim/src/anneal_puso.c -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/sim/src
  copying qubovert/sim/src/anneal_puso.h -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/sim/src
  copying qubovert/sim/src/anneal_quso.c -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/sim/src
  copying qubovert/sim/src/anneal_quso.h -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/sim/src
  copying qubovert/sim/src/pcg_basic.c -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/sim/src
  copying qubovert/sim/src/pcg_basic.h -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/sim/src
  copying qubovert/sim/src/random.c -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/sim/src
  copying qubovert/sim/src/random.h -> build/lib.macosx-10.9-universal2-cpython-310/qubovert/sim/src
  running build_ext
  building 'qubovert.sim._canneal' extension
  creating build/temp.macosx-10.9-universal2-cpython-310
  creating build/temp.macosx-10.9-universal2-cpython-310/qubovert
  creating build/temp.macosx-10.9-universal2-cpython-310/qubovert/sim
  creating build/temp.macosx-10.9-universal2-cpython-310/qubovert/sim/src
  clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g -I./qubovert/sim/src/ -I/Library/Frameworks/Python.framework/Versions/3.10/include/python3.10 -c ./qubovert/sim/_canneal.c -o build/temp.macosx-10.9-universal2-cpython-310/./qubovert/sim/_canneal.o
  In file included from ./qubovert/sim/_canneal.c:1:
  In file included from /Library/Frameworks/Python.framework/Versions/3.10/include/python3.10/Python.h:11:
  In file included from /Library/Developer/CommandLineTools/usr/lib/clang/11.0.3/include/limits.h:21:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/limits.h:63:
  /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:807:2: error: Unsupported architecture
  #error Unsupported architecture
   ^
  In file included from ./qubovert/sim/_canneal.c:1:
  In file included from /Library/Frameworks/Python.framework/Versions/3.10/include/python3.10/Python.h:11:
  In file included from /Library/Developer/CommandLineTools/usr/lib/clang/11.0.3/include/limits.h:21:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/limits.h:64:
  /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/machine/limits.h:8:2: error: architecture not supported
  #error architecture not supported
   ^
  In file included from ./qubovert/sim/_canneal.c:1:
  In file included from /Library/Frameworks/Python.framework/Versions/3.10/include/python3.10/Python.h:25:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:64:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/_stdio.h:71:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/_types.h:27:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/_types.h:33:
  /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/machine/_types.h:34:2: error: architecture not supported
  #error architecture not supported
   ^
  In file included from ./qubovert/sim/_canneal.c:1:
  In file included from /Library/Frameworks/Python.framework/Versions/3.10/include/python3.10/Python.h:25:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:64:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/_stdio.h:71:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/_types.h:27:
  /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/_types.h:55:9: error: unknown type name '__int64_t'
  typedef __int64_t       __darwin_blkcnt_t;      /* total blocks */
          ^
  /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/_types.h:56:9: error: unknown type name '__int32_t'; did you mean '__int128_t'?
  typedef __int32_t       __darwin_blksize_t;     /* preferred block size */
          ^
  note: '__int128_t' declared here
  /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/_types.h:57:9: error: unknown type name '__int32_t'; did you mean '__int128_t'?
  typedef __int32_t       __darwin_dev_t;         /* dev_t */
          ^
  note: '__int128_t' declared here
  /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/_types.h:60:9: error: unknown type name '__uint32_t'; did you mean '__uint128_t'?
  typedef __uint32_t      __darwin_gid_t;         /* [???] process and group IDs */
          ^
  note: '__uint128_t' declared here
  /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/_types.h:61:9: error: unknown type name '__uint32_t'; did you mean '__uint128_t'?
  typedef __uint32_t      __darwin_id_t;          /* [XSI] pid_t, uid_t, or gid_t*/
          ^
  note: '__uint128_t' declared here
  /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/_types.h:62:9: error: unknown type name '__uint64_t'
  typedef __uint64_t      __darwin_ino64_t;       /* [???] Used for 64 bit inodes */
          ^
  /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/_types.h:68:9: error: unknown type name '__darwin_natural_t'
  typedef __darwin_natural_t __darwin_mach_port_name_t; /* Used by mach */
          ^
  /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/_types.h:70:9: error: unknown type name '__uint16_t'; did you mean '__uint128_t'?
  typedef __uint16_t      __darwin_mode_t;        /* [???] Some file attributes */
          ^
  note: '__uint128_t' declared here
  /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/_types.h:71:9: error: unknown type name '__int64_t'
  typedef __int64_t       __darwin_off_t;         /* [???] Used for file sizes */
          ^
  /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/_types.h:72:9: error: unknown type name '__int32_t'; did you mean '__int128_t'?
  typedef __int32_t       __darwin_pid_t;         /* [???] process and group IDs */
          ^
  note: '__int128_t' declared here
  /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/_types.h:73:9: error: unknown type name '__uint32_t'; did you mean '__uint128_t'?
  typedef __uint32_t      __darwin_sigset_t;      /* [???] signal set */
          ^
  note: '__uint128_t' declared here
  /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/_types.h:74:9: error: unknown type name '__int32_t'; did you mean '__int128_t'?
  typedef __int32_t       __darwin_suseconds_t;   /* [???] microseconds */
          ^
  note: '__int128_t' declared here
  /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/_types.h:75:9: error: unknown type name '__uint32_t'; did you mean '__uint128_t'?
  typedef __uint32_t      __darwin_uid_t;         /* [???] user IDs */
          ^
  note: '__uint128_t' declared here
  /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/_types.h:76:9: error: unknown type name '__uint32_t'; did you mean '__uint128_t'?
  typedef __uint32_t      __darwin_useconds_t;    /* [???] microseconds */
          ^
  note: '__uint128_t' declared here
  In file included from ./qubovert/sim/_canneal.c:1:
  In file included from /Library/Frameworks/Python.framework/Versions/3.10/include/python3.10/Python.h:25:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:64:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/_stdio.h:71:
  /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/_types.h:43:9: error: unknown type name '__uint32_t'; did you mean '__uint128_t'?
  typedef __uint32_t      __darwin_wctype_t;
          ^
  note: '__uint128_t' declared here
  In file included from ./qubovert/sim/_canneal.c:1:
  In file included from /Library/Frameworks/Python.framework/Versions/3.10/include/python3.10/Python.h:25:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:64:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/_stdio.h:75:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/_types/_va_list.h:31:
  /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/machine/types.h:37:2: error: architecture not supported
  #error architecture not supported
   ^
  fatal error: too many errors emitted, stopping now [-ferror-limit=]
  20 errors generated.
  error: command '/usr/bin/clang' failed with exit code 1
  [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
error: legacy-install-failure

× Encountered error while trying to install package.
╰─> qubovert

note: This is an issue with the package mentioned above, not pip.
hint: See above for output from the failure.


PUBO to QUBO: The ancillary parameter

If I try to transform a PUBO
x(0) x(1) x(2)

to QUBO, it will give me
6 x(3) + 2 x(0) x(1) - 4 x(0) x(3) - 4 x(1) x(3) + x(2) x(3)

QUESTION 1 = BUT should not the QUBO formula instead be:
-( 6 x(3) + 2 x(0) x(1) - 4 x(0) x(3) - 4 x(1) x(3) ) + x(2) x(3)
and obviously x(3) = x(0) x(1)

QUESTION 2 =
In this case I am assuming that the ancillary*** x(3) was based on
x(3) = x(0) x(1)

the new cost function is this
x(2) x(3)

and the constraint to make QUBO work is
6 x(3) + 2 x(0) x(1) - 4 x(0) x(3) - 4 x(1) x(3)

Is there a way to get the ancillary*** formula?

Dealing with "force fields"

I'm working on a PUBO encoding for polymer lattice models and I need a way to include interactions between nearest-neighbour monomers. The Hamiltonian to be minimised takes the form

$$ H_{targer} = \sum_E \sum_{i=1}^D \sum_{j=1}^D (1-e^E) q_i^{E-} q_j^{E+} \epsilon_{ij} $$

Where $e^E=1$ if the E-th edge is active, in which case I don't count the interaction (because the monomers are bounded). $q_i^{E-}, q_j^{E+}$ indicate which monomers sit at the sides of the edge. $D$ is the number of monomer species. $\epsilon_{ij}$ is the interaction coefficient between a monomer of type i and type j.
In the HP model, $\epsilon = \begin{pmatrix} -1&0 \ 0&0 \end{pmatrix}$.
Now, I'm trying to translate this formula into code, but I'm having trouble accounting for the interaction coefficients.
I came up with the following
H_t = sum(sum(sum((1-e[E])*qi[pm[E][0]+i]*qi[pm[E][1]+j]*epsilon[D*i+j] for j in range(D)) for i in range(D)) for E in range(edges))

The problem is that by using this, the $\epsilon_{ij}$ coefficients become part of my state and I don't want that.
Thanks for the help

During the calculation, a variable is missing

>>> import qubovert as qv
>>> x = qv.PUBO({('a[0][0][0]', 'q_w_L[1][0][0]'): 4.0, ('a[0][0][0]', 'q_w_L[0][0][0]'): 2.0, ('a[0][0][0]',): -2.0, ('q_w_L[1][0][0]',): -2.0, ('q_w_L[0][0][0]',): -1.0, (): 1.0})
>>> x * x
{('q_w_L[0][0][0]', 'q_w_L[1][0][0]'): 4.0, ('q_w_L[0][0][0]',): -1.0, (): 1.0}

why is 'a[0][0][0]' missing?

Pairs

I have my cost function:

C: qubovert.PUBO = x[0] * x[1] * x[2]

I am testing Qubovert to force pair 0, 2 rather than the default it does, which is 0, 1

so I call it as following:

Q: qubovert.utils._qubomatrix.QUBOMatrix = C.to_qubo(pairs=((0, 2),))

However, I still get the following answer:

6 x(3) + 2 x(0) x(1) - 4 x(0) x(3) - 4 x(1) x(3) + x(2) x(3)

I was expecting last part to be x(1) x(3).

Am I doing something wrong? Full code follows:

import qubovert
from qubovert import boolean_var
from sympy import Symbol

x = [boolean_var("x%d" % i) for i in range(5)]
C: qubovert.PUBO = x[0] * x[1] * x[2]
lam = Symbol("lam", real=True, positive=True)
Q: qubovert.utils._qubomatrix.QUBOMatrix = C.to_qubo(pairs=((0, 2),))

print("num PUBO variables", C.num_binary_variables)
print("num QUBO variables", Q.num_binary_variables)
print(Q.pretty_str())

Suspected bug: cannot pickle and unpickle

Pickling and then unpickling a PUSO currently fails even for a trivial PUSO, see below. This severely limits the ability to use qubovert since one cannot save and load problems...

Minimal example:

import pickle
pickle.loads(pickle.dumps(PUSO({('a',):1})))

which gives an AttributeError that is tracked back to the degree property:

    380 k = self.__class__.squash_key(key)
    381 if value:
--> 382     self._degree = max(self._degree, len(k))
    383     for i in filter(lambda x: x not in self._variables, k):
    384         self._variables.add(i)

AttributeError: 'PUSO' object has no attribute '_degree'

Process 3SAT problems in CNF form

Hello

Is there any interface where a 3SAT problem in a DIMACS CNF file format can be read from a file and automatically be parsed in PCBO().add_constraint ?

for example, can a CNF formula (x0 or x1 or ~x2)(x1 or x2 or x3) be represented as [0,1,-2][1,2,3] ?

Extending DictArithmetic to include vector non_zero_min??

Hiya,

I have a constrained binary optimization which involved site selection based on a distance matrix.

• my space is
  • X = vector of binary decision variables
  • site in solution?
• and my objective is of the form
  • model = sum(non_zero_min(dist_matrix @ X[i] , axis=1) )
  • sum of travel to each nearest site in solution
• with constraint
  • model.add_constraint_eq _zero(sum(x.values()) - num_selected_sites ,lam=10)
  • limited number of sites

The space is very large so Gurobi and other exact solvers fail on the hardware we have available. So, heuristics are the only way forward.

I could extend the DictArithmetic class to include "non_zero_min" but would this work. Or, is there and easier way forward that I'm not seeing.

thanks

I cannot import qubo_solver from any_module

I am using the conda IDE, using Jupyter an testing the simple example for the Set Cover and it doesn't work.