chore: Tier 2 quick wins — version skew, docs, cleanup, overflow-safe bounds
CI / test (push) Failing after 14s
CI / test (push) Failing after 14s
- Fix version skew: clawhdf5-py (pyproject.toml 1.93.0 -> 2.1.0) and packages/clawhdf5-node (package.json 2.0.0 -> 2.1.0) were both behind the actual crate version. - Correct stale ROADMAP.md claims: the TypeScript bridge already has a complete napi-rs package (not "no package.json"); CI/CD is now wired up via .gitea/workflows/ci.yml. - Fix CLAUDE.md: clawhdf5-gpu uses wgpu with hand-written WGSL compute shaders, not CubeCL. - chunked_read.rs: drop 12 unnecessary chunk_dimensions[..rank].to_vec() allocations — all three callees already accept &[u32]. - btree_v1.rs: add an overflow-safe ensure_len(data, offset, needed) helper (checked_add) and use it at the two plain-arithmetic bounds guards, closing a usize-overflow edge case reachable from a crafted near-usize::MAX B-tree offset. Add a regression test. - Clarify that the integrity hashes in clawhdf5-agent/provenance.rs (FNV-1a) and clawhdf5-format/provenance.rs (SHA-256) are unkeyed and only detect accidental corruption, not tampering — doc-only change. - README.md: document that the mpi-io feature's read/write paths are root-read+broadcast / gather-to-rank-0, not true collective I/O.
This commit is contained in:
Omar Sobh
@@ -386,24 +386,24 @@ pub fn read_chunked_data(
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}
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(4, Some(2)) => {
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// Implicit index — use spatial chunk dims only
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let spatial_chunk_dims: Vec<u32> = chunk_dimensions[..rank].to_vec();
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let spatial_chunk_dims: &[u32] = &chunk_dimensions[..rank];
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generate_implicit_chunks(
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addr,
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&dataspace.dimensions,
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&spatial_chunk_dims,
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spatial_chunk_dims,
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elem_size as u32,
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)
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}
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(4, Some(3)) => {
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// Fixed Array — use spatial chunk dims only
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let spatial_chunk_dims: Vec<u32> = chunk_dimensions[..rank].to_vec();
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let spatial_chunk_dims: &[u32] = &chunk_dimensions[..rank];
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let header =
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FixedArrayHeader::parse(file_data, addr as usize, offset_size, length_size)?;
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read_fixed_array_chunks(
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file_data,
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&header,
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&dataspace.dimensions,
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&spatial_chunk_dims,
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spatial_chunk_dims,
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elem_size as u32,
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offset_size,
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length_size,
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@@ -411,14 +411,14 @@ pub fn read_chunked_data(
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}
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(4, Some(4)) => {
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// Extensible Array — use spatial chunk dims only
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let spatial_chunk_dims: Vec<u32> = chunk_dimensions[..rank].to_vec();
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let spatial_chunk_dims: &[u32] = &chunk_dimensions[..rank];
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let header =
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ExtensibleArrayHeader::parse(file_data, addr as usize, offset_size, length_size)?;
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read_extensible_array_chunks(
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file_data,
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&header,
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&dataspace.dimensions,
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&spatial_chunk_dims,
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spatial_chunk_dims,
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elem_size as u32,
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offset_size,
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length_size,
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@@ -618,30 +618,30 @@ pub fn read_chunked_data_cached(
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}]
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}
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(4, Some(2)) => {
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let spatial_chunk_dims: Vec<u32> = chunk_dimensions[..rank].to_vec();
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let spatial_chunk_dims: &[u32] = &chunk_dimensions[..rank];
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generate_implicit_chunks(
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addr,
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&dataspace.dimensions,
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&spatial_chunk_dims,
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spatial_chunk_dims,
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elem_size as u32,
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)
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}
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(4, Some(3)) => {
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let spatial_chunk_dims: Vec<u32> = chunk_dimensions[..rank].to_vec();
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let spatial_chunk_dims: &[u32] = &chunk_dimensions[..rank];
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let header =
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FixedArrayHeader::parse(file_data, addr as usize, offset_size, length_size)?;
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read_fixed_array_chunks(
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file_data,
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&header,
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&dataspace.dimensions,
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&spatial_chunk_dims,
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spatial_chunk_dims,
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elem_size as u32,
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offset_size,
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length_size,
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)?
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}
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(4, Some(4)) => {
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let spatial_chunk_dims: Vec<u32> = chunk_dimensions[..rank].to_vec();
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let spatial_chunk_dims: &[u32] = &chunk_dimensions[..rank];
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let header = ExtensibleArrayHeader::parse(
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file_data,
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addr as usize,
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@@ -652,7 +652,7 @@ pub fn read_chunked_data_cached(
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file_data,
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&header,
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&dataspace.dimensions,
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&spatial_chunk_dims,
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spatial_chunk_dims,
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elem_size as u32,
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offset_size,
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length_size,
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@@ -974,30 +974,30 @@ pub fn read_chunked_data_sweep(
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}]
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}
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(4, Some(2)) => {
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let spatial_chunk_dims: Vec<u32> = chunk_dimensions[..rank].to_vec();
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let spatial_chunk_dims: &[u32] = &chunk_dimensions[..rank];
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generate_implicit_chunks(
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addr,
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&dataspace.dimensions,
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&spatial_chunk_dims,
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spatial_chunk_dims,
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elem_size as u32,
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)
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}
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(4, Some(3)) => {
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let spatial_chunk_dims: Vec<u32> = chunk_dimensions[..rank].to_vec();
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let spatial_chunk_dims: &[u32] = &chunk_dimensions[..rank];
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let header =
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FixedArrayHeader::parse(file_data, addr as usize, offset_size, length_size)?;
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read_fixed_array_chunks(
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file_data,
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&header,
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&dataspace.dimensions,
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&spatial_chunk_dims,
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spatial_chunk_dims,
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elem_size as u32,
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offset_size,
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length_size,
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)?
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}
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(4, Some(4)) => {
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let spatial_chunk_dims: Vec<u32> = chunk_dimensions[..rank].to_vec();
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let spatial_chunk_dims: &[u32] = &chunk_dimensions[..rank];
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let header = ExtensibleArrayHeader::parse(
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file_data,
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addr as usize,
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@@ -1008,7 +1008,7 @@ pub fn read_chunked_data_sweep(
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file_data,
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&header,
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&dataspace.dimensions,
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&spatial_chunk_dims,
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spatial_chunk_dims,
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elem_size as u32,
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offset_size,
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length_size,
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@@ -1200,30 +1200,30 @@ pub fn read_chunked_data_indexed(
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}]
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}
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(4, Some(2)) => {
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let spatial_chunk_dims: Vec<u32> = chunk_dimensions[..rank].to_vec();
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let spatial_chunk_dims: &[u32] = &chunk_dimensions[..rank];
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generate_implicit_chunks(
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addr,
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&dataspace.dimensions,
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&spatial_chunk_dims,
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spatial_chunk_dims,
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elem_size as u32,
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)
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}
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(4, Some(3)) => {
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let spatial_chunk_dims: Vec<u32> = chunk_dimensions[..rank].to_vec();
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let spatial_chunk_dims: &[u32] = &chunk_dimensions[..rank];
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let header =
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FixedArrayHeader::parse(file_data, addr as usize, offset_size, length_size)?;
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read_fixed_array_chunks(
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file_data,
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&header,
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&dataspace.dimensions,
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&spatial_chunk_dims,
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spatial_chunk_dims,
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elem_size as u32,
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offset_size,
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length_size,
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)?
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}
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(4, Some(4)) => {
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let spatial_chunk_dims: Vec<u32> = chunk_dimensions[..rank].to_vec();
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let spatial_chunk_dims: &[u32] = &chunk_dimensions[..rank];
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let header = ExtensibleArrayHeader::parse(
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file_data,
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addr as usize,
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@@ -1234,7 +1234,7 @@ pub fn read_chunked_data_indexed(
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file_data,
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&header,
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&dataspace.dimensions,
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&spatial_chunk_dims,
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spatial_chunk_dims,
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elem_size as u32,
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offset_size,
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length_size,
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