Fix cpp source flags in new API

[waltsims]

Fixes #697.

Greptile Summary

This PR fixes a bug in CppSimulation._write_hdf5 where p_source_flag, ux_source_flag, uy_source_flag, and uz_source_flag were written as plain booleans (0 or 1) instead of the number of time steps the C++ binary actually expects. Without the fix, the C++ solver would always see a count of 1 regardless of the source signal length, causing incorrect simulations for any source with more than one time step.

• Root cause fixed: Replaces int(has_p) / int(has_ux) etc. with np.asarray(source.*).shape[-1], correctly encoding the time-step count.
• Safer indexing: The new shape[-1] idiom works for both 1-D (Nt,) and 2-D (n_elements, Nt) source arrays, avoiding the TypeError that len(source.p[0]) would raise on a 1-D input.
• Clarity: An inline comment is added explaining the non-obvious semantics of the *_source_flag fields, which will help future contributors.
• No new tests are introduced, but the change is straightforward and the fix is clearly correct given the C++ binary's documented contract.

Confidence Score: 5/5

Safe to merge — the fix is a targeted correctness patch with no regressions introduced.

The single changed file contains a clearly correct bug fix: source flags now carry the actual time-step count the C++ binary requires. The safer shape[-1] indexing resolves the previously flagged 1-D array edge case. No new code paths, no API changes, and no test regressions are present.

No files require special attention.

Important Files Changed

Filename	Overview
kwave/solvers/cpp_simulation.py	Fixes source flags to encode the number of time steps instead of a boolean; uses safe shape[-1] indexing and adds an explanatory comment.

Sequence Diagram

sequenceDiagram
    participant Caller
    participant CppSimulation
    participant HDF5 as HDF5 Input File
    participant Binary as C++ k-Wave Binary

    Caller->>CppSimulation: run(source, ...)
    CppSimulation->>CppSimulation: _write_hdf5()
    Note over CppSimulation: Compute p_source_flag = source.p.shape[-1]<br/>(was: int(has_p) always 1)
    CppSimulation->>HDF5: write p_source_flag = Nt_source
    CppSimulation->>HDF5: write ux/uy/uz_source_flag = Nt_source
    CppSimulation->>HDF5: write p_source_input[n_elements, Nt_source]
    Binary->>HDF5: read p_source_flag → knows Nt_source time steps
    Binary->>Binary: simulate for Nt steps using Nt_source-length signal

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_{Reviews (2): Last reviewed commit: "Merge branch 'master' into fix-cpp-sourc..." | Re-trigger Greptile}

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 74.40%. Comparing base (2ea27db) to head (aab1fea).
⚠️ Report is 1 commits behind head on master.

Additional details and impacted files

@@           Coverage Diff           @@
##           master     #698   +/-   ##
=======================================
  Coverage   74.40%   74.40%           
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  Files          56       56           
  Lines        8026     8026           
  Branches     1570     1570           
=======================================
  Hits         5972     5972           
  Misses       1437     1437           
  Partials      617      617           

Flag	Coverage Δ
3.10	74.40% <ø> (ø)
3.11	74.40% <ø> (ø)
3.12	74.40% <ø> (ø)
3.13	74.40% <ø> (ø)
macos-latest	74.38% <ø> (ø)
ubuntu-latest	74.38% <ø> (ø)
windows-latest	74.39% <ø> (ø)

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[waltsims]

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