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cudaverse 0.4.1

• Reworked the README and tutorials around first-time CUDA users, with clearer Windows and Linux setup, strict CUDA examples, task-oriented workflows, and an evidence-backed performance guide.
• Kept maintainer roadmaps and hardware-validation details out of the public pkgdown site, and added checks that prevent those internal pages and testing machine descriptions from being published again.
• Added the cudaverse package logo and aligned package, website, and organization branding.

cudaverse 0.4.0

• Replaced the base kNN backend’s full per-row stable ordering with bounded C++ stable top-k selection while preserving exact indices, deterministic distance-then-row ties, provenance, and numerical parity.
• Kept torch kNN distance blocks and deterministic stable top-k selection on the selected torch device when the installed torch API supports stable sort; only the final n-by-k indices and distances are transferred to R.
• Bound final 0.4 candidate evidence to two independent, isolated native R sessions with exact source, hardware, injected-error recovery, allocator cleanup, workflow, process-exit, and SHA-256 checks.
• Pinned generated pkgdown Pages commits to Yaoxiang Li’s GitHub-linked identity and made that authorship configuration a release-boundary gate.
• Unified benchmark memory collection with the public cuda_memory_info() contract while retaining native peak reset as an untimed maintainer-only measurement action.
• Added a maintainer native-session contract that installs the exact source in an isolated library, runs two fresh R processes through dense, sparse, PCA/kNN, injected-error recovery, exact allocator cleanup, backend reuse, and clean process exit.
• Added cuda_memory_info() for backend-aware memory observability. Native reports CUDA-driver totals plus cudaverse-owned current and peak bytes; torch reports allocated and reserved allocator bytes, while unsupported counters remain explicit NA values.
• Diffusion maps now retain the device-resident input stage in provenance. Native PCA scores are reused directly by CUDA distance instead of being uploaded again; kernel construction and eigendecomposition remain explicit CPU stages.
• Started the isolated 0.4 development line from the exact review-ready 0.3 candidate while keeping the 0.3 source and evidence unchanged.
• Extended cuda_diagnostics() with a concise health status, human-readable summary, actionable next_steps, and a backend comparison table. Strict CUDA-unavailable conditions now retain the same reason and guidance.
• Added the ordered 0.4 roadmap and enabled development-line CI coverage.
• Made native CUDA reshape allocation-free by separating dense view metadata from shared device-allocation ownership. Nested reshape views remain valid after their sources are released and free the allocation exactly once.
• Kept same-backend CUDA tensor replacement device-resident when the replacement needs a compatible floating dtype cast, with the cast recorded in provenance.
• Made cuda_tensor() cast an existing tensor through its current backend when the requested device is unchanged, avoiding a download/upload round trip.
• Made contiguous native CUDA subsets allocation-free shared views while retaining device gather for non-contiguous selections.
• Added explicit, provenance-recorded distance batching across base, torch, and native backends. Native execution retains input/reference storage and cached reference norms across blocks, bounding peak device memory.
• Added explicit k-means batching with a backward-compatible backend contract. Native Lloyd iterations now keep data, centres, assignments, and updates on the GPU while bounding temporary distance storage by observation batch.
• Kept native PCA prediction scores in shared device storage after returning their compatible R matrix, allowing following distance and kNN stages to reuse the scores without an upload.
• Added device-side finite/constant validation and resident SVD/PCA dispatch for native cudatensor inputs. Float32 and integer inputs cast on the GPU; the full input matrix is no longer downloaded and uploaded for decomposition.
• Kept native sparse-normalization output resident without downloading the margin-sum or normalized-value vectors. The required public COO mirror is updated from its existing host metadata, while device validation returns only one small status flag.
• Made native sparse normalization share immutable CSR/COO index allocations with its source through independent reference counting. Normalized results allocate only new values, remain valid after either release order, and free shared pattern storage exactly once.
• Made cuda_sparse() rematerialize an existing cudasparse object directly from its stable COO mirror. Same-device format changes share storage, while cross-device transfers and zero filtering avoid a temporary Matrix object, summary pass, and redundant coordinate sort.
• Removed Matrix construction from sparse PCA preprocessing and sparse algorithm transfers. Constant-column checks run directly on the COO mirror only when scaling is requested; unscaled PCA skips that scan entirely.

cudaverse 0.3.0.9000

• Added reproducible full-benchmark Markdown generation and validation. The retained assessment is bound to the exact machine-readable report by its SHA-256 and source commit, and incomplete drafts cannot pass the final summary gate.
• Added a machine-readable 0.3 benchmark contract and report runner for synchronized base, torch, and native measurements. The full profile fixes workload sizes, warmup/run counts, transfer boundaries, numerical gates, peak-memory sources, installed size, and provenance without treating an inseparable dense-PCA upload as a measured transfer duration.
• Added an executable public-backend conformance matrix. Every exported function is assigned to a diagnostics, tensor, sparse, algorithm, graph, or embedding contract case, and the shared suite runs the same small workflows on base, torch, and native when CUDA hardware coverage is required.
• Added t() for cudasparse matrices. Native CUDA transposes CSR backing storage on device while preserving stable COO metadata, logical format, dimnames, shared ownership, and same-device provenance; compatibility backends rebuild storage from the already-public COO metadata.
• Added registry-driven resident native CUDA k-means. Observations and centres are uploaded once; distance, stable assignment, accumulation, and Lloyd centre updates remain on device, with compact convergence and final-result transfers. The base and torch compatibility paths are unchanged.
• Added registry-driven, device-native tensor subsetting and replacement for the native CUDA backend, including dtype preservation, dimnames, R recycling, and deterministic last-write handling for duplicate indices.
• Added a backend registry and integrated the lightweight native CUDA implementation into cudaverse without changing the public device API.
• Added native dense casts, reductions, SVD/PCA, exact distance blocks, and deterministic top-k/kNN integration.
• Added shared-ownership native COO/CSR storage, sparse Matrix conversion, sparse matrix-vector/matrix multiplication, row/column reductions, and sparse-preserving normalization.
• Added sparse inputs to cuda_pca() and cuda_knn(); the native path expands them on the GPU and continues through the existing resident dense pipeline.
• Kept PCA -> distance -> top-k intermediate data on the GPU for the native path and retained the cudaverse-stage/1 provenance schema.
• Preserved portable CPU behavior and the optional torch compatibility backend.
• Added capability-gated automatic native selection. Native is preferred only when the native contract, complete tensor/algorithm capability set, driver/cuBLAS/cuSOLVER/PTX runtime, and cached runtime self-test all pass; otherwise torch or the recorded CPU fallback retains compatibility.
• Added native float32 matmul plus device-native element-wise arithmetic, trailing-dimension broadcasting, reshape, and transpose coverage required by the global automatic-selection gate.
• Required SVD and PCA prediction compatibility in that same fail-closed gate, and published the bounded Phase 4 release-candidate assessment with links to the checksum-pinned RTX evidence.

cudaverse 0.1.0

• Establishes the general-purpose cudaverse API.
• Adds dense tensor and sparse matrix functionality.
• Adds numerical algorithms, graph workflows, and embedding workflows.
• Preserves the canonical cuda_provenance() protocol across all modules.
• Keeps SingleCellExperiment support optional and accepts its reduced dimensions at the embedding boundary without making Bioconductor or Seurat required dependencies.
• Fixes CUDA indexing, R column-major reshape semantics, and exact self-distance diagonals for compatibility with R torch 0.17.
• Documents the measured, benchmark-gated roadmap toward a lightweight native CUDA backend while retaining the current portable CPU fallback.

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