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Update embedded compression libraries and filters: bitshuffle v0.5.2, c-blosc2 v2.17.0#334

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t20100 merged 5 commits intosilx-kit:mainfrom
t20100:update-embedded
Mar 17, 2025
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Update embedded compression libraries and filters: bitshuffle v0.5.2, c-blosc2 v2.17.0#334
t20100 merged 5 commits intosilx-kit:mainfrom
t20100:update-embedded

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@t20100 t20100 commented Mar 14, 2025

This MR updates embedded filters/compression libraries:

t20100 added 4 commits March 14, 2025 16:59
52aec3b Merge pull request silx-kit#160 from kiyo-masui/fixwheels
2d0487a Fix python 3.13 rc version.
2fafffe Fix python 3.13 rc version.
3417948 Fix python 3.13 rc version.
4e37682 Merge pull request silx-kit#141 from DimitriPapadopoulos/pedantic
dbe3938 Merge pull request silx-kit#143 from DimitriPapadopoulos/F841
c8f0ef3 Merge pull request silx-kit#151 from DimitriPapadopoulos/ISC
1f02840 Merge pull request silx-kit#159 from DimitriPapadopoulos/lz4
a3e7314 Merge pull request silx-kit#157 from kiyo-masui/fixwheels
a871211 fix(install_hdf5): handle patch version in tar download
b0e32ea fix(wheels): hdf5 does not have a 1.14.4 distribution
7ed1152 build: update minimum supported numpy and build with numpy 2.0 compatibility
2becd62 fix(wheels): require valid minimum supported python for cibuildwheel
1066614 test and build on all supported version of python.
a3d3d15 Avoid unnecessary line continuations
6b72fb2 Declare a function with a prototype
628033a You indent this code with spaces, so discard the tab
91e7403 Discard trailing spaces and empty lines
82e79b7 Macros starting with if should be enclosed by a do - while loop to avoid possible if/else logic defects
7a8e9a0 Update lz4 to 1.10.0
9e9c955 Apply ruff/flake8-implicit-str-concat rule ISC001
e34056f Local variable `c` is assigned to but never used
f219f50 Merge pull request silx-kit#152 from mattjala/master
b2aec12 Support numpy 2.0.0
333b459 Merge pull request silx-kit#145 from DimitriPapadopoulos/http
68d84c6 Merge pull request silx-kit#155 from ljgray/fix-compiler-issues
b80f735 fix(lzf_filter.c): fix H5Z_class_t definition for newer hdf5 api
5d2bbe0 feat(ci): bump HDF5 version in wheels
1bab815 feat(ci): bump python versions in main workflow
af9ab04 fix(ci-main): update apt-get/brew before install
6fee24b http:// → https://

git-subtree-dir: src/bitshuffle
git-subtree-split: 52aec3b80d05606c090956aecfe868489d96b95c
55a10323 Getting ready for release 2.17.0
b8f69772 Fixed issue #633 Handle leak in parallel (nThread > 1) zstd decompression
bafa95d1 Fix macOS build with zstd-1.5.7
4c5e7a26 Update zstd to 1.5.7
34db770e Fix for recent fuzzer issue
ac116b4b Make deprecation warning compatible with MSVC
ceba6ad2 Add BLOSC2_MAXTYPESIZE and fix deprecation warning
0a0099bf Support repeated values larger than 8-bit, also for n-dim arrays
cf8d63c2 Some fixes and new b2nd_copy_buffer2 API func
26d05bff Support repeated values larger than 8-bit
14c3af1c Post 2.16.0 release actions done
5fc02a00 Getting ready for release 2.16.0
b74a7491 Add 12-byte sse2 unshuffle
5588bb63 12-byte unshuffle for avx512
d92b88e5 More fixes for Blosc/python-blosc2#359
d7c0a066 Use qemu-system-aarch64 for qemu package in recent ubuntu systems
6e812eef Use _fseeki64/_ftelli64 on win
1405a45f Use _lseek64 on win
d65eeb71 Go back to params that provide better cratios in general
07a76d18 Relax the condition for C contiguity for finding a fast path
867ddb31 Update README_FORMAT.rst
2c4e182a Remove the Python-Blosc link in menu
24883ac1 More consistency in docs
43135d71 Redirected the format docs
04fde65f Fix typo
f64f3140 Be consistent with case for names
068c57dc Ok, scale does not work for github
eba8adb5 Scale diagram down
20cfd0d6 Diagram for the CFrame
0560b614 More accurate description to Blosc2 format
5c36318f Add a new section on recommended extensions for blosc2 files
35b82e6d Get rid of dangling blosc2_tell_cb and blosc2_seek_cb callbacks
584a7895 Better description of the Blosc2 format as a whole
b2f1e9e9 Post 2.15.2 release actions done
f1278b90 Getting ready for release 2.15.2
5e0e856e Restrict flag to GCC/clang. Fixes #640.
9a573833 Fix public include directories for blosc2 targets:
458d26fc Fix compiler warning
99e8c427 add back csize param
1c18c469 fix warnings and missing return type
2e2c9718 update comments
15ac6280 fix segv in blosc2_schunk_free if blosc2_init() was not called as well as adding additional test cases
52e7e4e5 fix removing const from _src rather than _dest
58ab7f5e fix ub in shuffle and unshuffle by marking _dst non-const
f8723dc5 Support wasm32 by disabling ZLIB WITH_OPTIM
af8b50a9 Avoid rip-relative addressing for OSX x86_64
b179abf1 Remove the (obsolete now) contrib directory
50db9571 Protect getauxval call in C-Blos2
3f2dc4b9 Post 2.15.1 release actions done

git-subtree-dir: src/c-blosc2
git-subtree-split: 55a103239b24f8b4e07dafa5a289ad62bfade524
@t20100 t20100 added this to the Next release milestone Mar 14, 2025
@t20100 t20100 self-assigned this Mar 14, 2025
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t20100 commented Mar 14, 2025

h5z-sperr adds an extra cd_values:

   * Get the user-specified parameters. It has mandatory and optional fields.
   * -- One integer (mandatory): compression mode, quality, rank swap
   * -- One integer (optional) : missing value mode
   * -- One/two integers (optional): a float or double specifying the missing value
   *    (not implemented)
...

   * `missing_val_mode` meaning:
   * 0: no missing value
   * 1: any NAN is a missing value
   * 2: any value where abs(value) >= 1e35 is a missing value.
   * 3: use a single 32-bit float as the missing value. (not implemented)
   * 4: use a single 64-bit double as the missing value. (not implemented)

@t20100 t20100 changed the title Update embedded compression libraries and filters: bitshuffle v0.5.2, c-blosc2 v2.17.0, h5z-sperr v0.2.1 Update embedded compression libraries and filters: bitshuffle v0.5.2, c-blosc2 v2.17.0 Mar 17, 2025
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t20100 commented Mar 17, 2025

Removed h5z-sperr update from this PR, to be done in a separate one.

@t20100 t20100 requested review from kif and payno March 17, 2025 10:35
@t20100 t20100 merged commit 4eaa8f2 into silx-kit:main Mar 17, 2025
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@t20100 t20100 deleted the update-embedded branch March 17, 2025 12:40
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Bitshuffle 0.5.2 released

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