Joss revisions main

[theo-barfoot]

Summary

This PR addresses the JOSS review follow-up items tracked in:

• Fix CUDA torch to CuPy sparse conversion (use DLPack) #73
• CuPy solver kwarg compatibility (tol vs rtol/atol) across CuPy versions #74
• Improve optional dependency handling and install documentation #75
• Paper: add repo/docs links, code examples, and benchmark summary #76
• Fix typos in paper and docs and run spell check pass #77
• Fix invalid DOI and strengthen bibliography references #78

What changed

• updated the JOSS paper to add the requested GitHub and ReadTheDocs links in the body
• added compact usage examples to the paper and shortened the benchmark summary to match reviewer expectations
• reduced repetition in the paper to keep the manuscript concise
• fixed bibliography formatting for the Laporte reference and cleaned up reference/link handling
• fixed the installation docs to use the correct optional extra name: torchsparsegradutils[all]

Reviewer feedback addressed

• paper now includes explicit repository and RTD links
• paper now includes short usage examples
• paper now includes a brief benchmark summary with hardware caveat
• typo / wording cleanup completed
• bibliography/reference formatting improved

Validation

• reviewed the rendered paper source changes locally
• targeted CuPy/JAX regression tests were re-run locally during the JOSS fix pass:
  • test_cupy_bindings.py::test_t2c_and_c2t_coo
  • test_cupy_sparse_solve.py::test_cupy_cg_kwargs
  • test_quickstart_guide.py::test_cupy_backend
  • test_quickstart_guide.py::test_jax_backend

Notes

This PR focuses on source changes relevant to the JOSS review response.
Generated artifacts such as the rendered PDF/JATS are not included.