stabilizer-qec 1.6.0

The Python package and the Rust crate both at 1.6.0, "know your circuit": where each fault of
an error model comes from and how few faults defeat a circuit, both as Stim reports them, and
the exact circuit distance by integer programming; Stim's result formats, samplers and command
line; Stim's text timeline and time-slice diagrams; and a paper for the Journal of Open Source
Software. The first release archived on Zenodo.

Added

• The text timeline (diagram("timeline-text"), and the command line's) is now Stim's,
  character for character: Stim's moments, labels and boxes, loops between | columns headed
  /REP n with records, detectors and coordinates in terms of iter, detectors drawn at their
  qubit's coordinates. Checked on hand-made circuits pinning each rule, Stim's generated
  memories and 200 random circuits using every gate.
• diagram("timeslice-svg") and diagram("detslice-with-ops-svg"), and tick as a range
  (with rows) for these and detslice-svg: a panel per tick, each the qubits at their
  coordinates with that tick's operations and/or the detector slice after them (Rust:
  DiagramKind::TimeSliceSvg, DetectorSliceWithOpsSvg, DetectorSlicesSvg).
• Circuit.explain_detector_error_model_errors(*, dem_filter=None, reduce_to_one_representative_error=False) (Rust: Circuit::explain_errors): where each
  fault of a circuit's error model comes from: the instruction (numbered as Stim numbers
  them, adjacent identical instructions joined), its targets, the Pauli product or the
  measurement it flips, the TICKs before it and the loop passes around it. The results
  (ExplainedError, CircuitErrorLocation and their parts, Stim's names) print as Stim's
  character for character, each part on its own as well (Rust: Display for
  TargetWithCoords and CircuitErrorLocation, and CircuitErrorLocation::instruction_text),
  for every location and for the representative Stim picks, on
  Stim's generated memories and on 1,000 random circuits using every gate, noise channel and
  tag.
• shortest_graphlike_error on circuits and on detector error models (Rust:
  Circuit::shortest_graphlike_error, DetectorErrorModel::shortest_graphlike_error): the
  graph-like circuit distance, the fewest faults of at most two detectors that together flip
  an observable and no detector, found as Stim finds it (decomposed faults left out unless
  ignore_ungraphlike_errors=False). Its length equals Stim's on Stim's generated surface,
  repetition and colour codes up to d = 15. On a model it takes Stim's time at d = 11 (3.5 ms)
  and 2.5 times it at d = 15; tools/bench.py holds it to Stim's.
• search_for_undetectable_logical_errors on circuits and models: Stim's breadth-first
  search through hyperedges, with its three limits, giving the same number of faults as
  Stim's on its colour codes, surface codes, the Steane code and the [[72, 12, 6]] code.
• DetectorErrorModel.distance(): the exact distance of a model by integer programming (scipy's
  HiGHS), hyperedges included, proven optimal or refused; method="graphlike" or "search"
  for the two searches. It finds that Stim's generated XYZ colour-code memory has circuit
  distance 2 at d = 3 and 3 at d = 5 (two or three correlated two-qubit faults; Stim's own
  search agrees given room), and that the generic CssCode schedule loses the colour code's
  distance likewise, while the surface codes and the Hamming hypergraph product keep theirs.
  tools/distances.py measures every memory the package builds.
• write_shot_data_file and read_shot_data_file, Stim's functions with Stim's arguments, in
  all six of its result formats (01, b8, r8, ptb64, hits, dets): files byte for
  byte as Stim writes them, and Stim's read back to the same shots.
• The command line, stabilizer-qec (or python -m stabilizer_qec), after Stim's: gen,
  sample, detect, m2d, analyze_errors, explain_errors, diagram, convert,
  sample_dem and help, with Stim's flags and formats, and decode after PyMatching's
  predict (any of the package's decoders). Tested end to end against the stim command: the
  same bytes from gen (its header and qubit layout included), analyze_errors, m2d,
  convert, explain_errors, and from sample and detect on deterministic circuits.
• Circuit.reference_sample(): the noiseless run's measurement record, as Stim's.
• Circuit.compile_sampler(*, skip_reference_sample=False, seed=None): raw measurement
  records, as Stim's measurement sampler: a noiseless reference run with each shot's flips,
  equal to Stim's on deterministic circuits and to its rates otherwise.
• DetectorErrorModel.compile_sampler(seed=...) (Rust: DetectorErrorModel::sampler): shots
  drawn from a model's faults directly, as Stim's CompiledDemSampler, with the faults that
  fired (return_errors) and recorded faults replayed (recorded_errors_to_replay); rates
  and pairwise correlations agree with Stim's sampler, and a seed's shots do not depend on the
  number of threads.
• detector_error_model(..., ignore_decomposition_failures=True) (Rust:
  DemOptions::ignore_decomposition_failures), Stim's option: a fault that cannot be split
  into graph-like pieces is kept whole. The text equals Stim's on its colour codes.
• Documentation: the guide's "Knowing a circuit" and "The command line"; tutorial 01's "How
  far from failing"; the README's and the report's "Circuit distance", every memory the package
  builds measured three ways (tools/distances.py, data/distances.json), where the
  integer program's best solution is kept as an upper bound when it does not finish. It finds
  the 2-round [[90, 8, 10]] memory has circuit distance at most 9 (checked: 9 faults, no
  detector, five logical qubits flipped).
• A paper for the Journal of Open Source Software (paper/, built by the Paper workflow) and
  its submission checklist (docs/joss.md); CONTRIBUTING.md says where to ask for help.

Changed

• An explicit zero argument on M, MX, MR, MRX and MPAD (M(0) 0) is kept and
  written back, as Stim keeps it.