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Test julia-format action on 1152 #1154

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Test julia-format action on 1152 #1154

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504ce58
Guard malloc in compression filters
mkitti May 27, 2024
b709574
Update filters/H5Zblosc/src/H5Zblosc.jl
mkitti May 30, 2024
f38f28a
Switch to julia-format action
mkitti May 30, 2024
ef7886d
Merge branch 'mkitti-format-action' into mkitti-test-julia-format-on-…
mkitti May 30, 2024
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32 changes: 0 additions & 32 deletions .github/workflows/Format-check.yml
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13 changes: 13 additions & 0 deletions .github/workflows/Format.yml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,13 @@
name: Format suggestions
on:
pull_request:
# this argument is not required if you don't use the `suggestion-label` input
types: [ opened, reopened, synchronize, labeled, unlabeled ]
jobs:
code-style:
runs-on: ubuntu-latest
steps:
- uses: julia-actions/julia-format@v3
with:
version: '1' # Set `version` to '1.0.54' if you need to use JuliaFormatter.jl v1.0.54 (default: '1')
suggestion-label: 'format-suggest' # leave this unset or empty to show suggestions for all PRs
1 change: 1 addition & 0 deletions filters/H5Zbitshuffle/src/H5Zbitshuffle.jl
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Expand Up @@ -196,6 +196,7 @@ function H5Z_filter_bitshuffle(
end

size = nbytes_uncomp ÷ elem_size
buf_size_out <= 0 && error("bitshuffle_h5plugin: Non-positive buf_size_out for malloc: $buf_size_out")
out_buf = Libc.malloc(buf_size_out)
if out_buf == C_NULL
error(
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2 changes: 2 additions & 0 deletions filters/H5Zblosc/src/H5Zblosc.jl
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Expand Up @@ -96,6 +96,7 @@ function blosc_filter(
# the result is larger, we simply return 0. The filter is flagged
# as optional, so HDF5 marks the chunk as uncompressed and proceeds.
outbuf_size = unsafe_load(buf_size)
outbuf_size <= 0 && return Csize_t(0)
outbuf = Libc.malloc(outbuf_size)
outbuf == C_NULL && return Csize_t(0)

Expand All @@ -121,6 +122,7 @@ function blosc_filter(
# See https://github.com/JuliaLang/julia/issues/43402
# Resolved in https://github.com/JuliaLang/julia/pull/43408
outbuf_size, cbytes, blocksize = Blosc.cbuffer_sizes(in)
outbuf_size <= 0 && return Csize_t(0)
outbuf = Libc.malloc(outbuf_size)
outbuf == C_NULL && return Csize_t(0)
status = Blosc.blosc_decompress(in, outbuf, outbuf_size)
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2 changes: 2 additions & 0 deletions filters/H5Zbzip2/src/H5Zbzip2.jl
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Expand Up @@ -40,6 +40,7 @@ function H5Z_filter_bzip2(
# Decompress

outbuflen = nbytes * 3 + 1
outbuflen <= 0 && error("H5Zbzip2: Non-positive outbuflen for malloc: $outbuflen.")
outbuf = Libc.malloc(outbuflen)
if outbuf == C_NULL
error("H5Zbzip2: memory allocation failed for bzip2 decompression.")
Expand Down Expand Up @@ -106,6 +107,7 @@ function H5Z_filter_bzip2(

# Prepare the output buffer
outbuflen = nbytes + nbytes ÷ 100 + 600 # worse case (bzip2 docs)
outbuflen <= 0 && error("H5Zbzip2: Non-positive outbuflen for malloc: $outbuflen.")
outbuf = Libc.malloc(outbuflen)
@debug "Allocated" outbuflen outbuf
if outbuf == C_NULL
Expand Down
6 changes: 5 additions & 1 deletion filters/H5Zlz4/src/H5Zlz4.jl
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Expand Up @@ -66,7 +66,9 @@ function H5Z_filter_lz4(
# malloc a byte buffer of origSize
# outBuf = Vector{UInt8}(undef, origSize)
@debug "OrigSize" origSize
origSize <= 0 && error("H5Zlz4: Non-positive origSize for malloc: $origSize")
outBuf = Libc.malloc(origSize)
outBuf == C_NULL && error("H5Zlz4: Could not allocate memory via malloc")
# Julia should throw an error if it cannot allocate this
roBuf = Ptr{UInt8}(outBuf)
decompSize = 0
Expand Down Expand Up @@ -126,7 +128,9 @@ function H5Z_filter_lz4(
nBlocks = (nbytes - 1) ÷ blockSize + 1
maxDestSize =
nBlocks * CodecLz4.LZ4_compressBound(blockSize) + 4 + 8 + nBlocks * 4
maxDestSize <= 0 && error("H5Zlz4: Non-positive maxDestSize for malloc: $maxDestSize")
outBuf = Libc.malloc(maxDestSize)
outBuf == C_NULL && error("H5Zlz4: Could not allocate memory via malloc")

rpos = Ptr{UInt8}(unsafe_load(buf))
roBuf = Ptr{UInt8}(outBuf)
Expand Down Expand Up @@ -189,7 +193,7 @@ function H5Z_filter_lz4(
catch err
# "In the case of failure, the return value is 0 (zero) and all pointer arguments are left unchanged."
ret_value = Csize_t(0)
@error "H5Zlz4.jl Non-Fatal ERROR: " err
@async @error "H5Zlz4.jl Non-Fatal ERROR: " err
display(stacktrace(catch_backtrace()))
finally
if outBuf != C_NULL
Expand Down
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