guix_mirror_bot pushed a commit to branch master
in repository guix.
commit d3e00eb4d8e8ceb124fa3b48317d1fb61e0d8843
Author: Sharlatan Hellseher <[email protected]>
AuthorDate: Fri Oct 3 15:02:28 2025 +0100
gnu: bitshuffle: Update to 0.5.2, fix build with gcc-14.
* gnu/packages/python-compression.scm (bitshuffle): Update to 0.5.2. Use
G-Expressions, enable tests, fix build.
[build-system]: Switch to pyproejct-build-system.
[arguments] <tests?>: Enable, the most tests are working now.
<test-flags>: Skip one test.
<phases>: Remove 'fix-neon-detection as resolved upstream,
'dont-build-native the build script is changed and no longer compatible
with the phase; add 'pre-build providing new set of build time
environment variables..
[inputs]: Remove labels.
[native-inputs]: Add python-pytest and python-setuptools; remove labels.
(bitshuffle-for-snappy)[arguments]: Don't inherit from bitshuffle, use
G-Expressions.
Change-Id: I3467658c877e50a35a40594990ad8fc5b953eb3c
---
gnu/packages/python-compression.scm | 78 +++++++++++++++++++------------------
1 file changed, 41 insertions(+), 37 deletions(-)
diff --git a/gnu/packages/python-compression.scm
b/gnu/packages/python-compression.scm
index 66691cac7c..c5c59946ae 100644
--- a/gnu/packages/python-compression.scm
+++ b/gnu/packages/python-compression.scm
@@ -739,44 +739,49 @@ directly from the command line.")
(define-public bitshuffle
(package
(name "bitshuffle")
- (version "0.3.5")
+ (version "0.5.2")
(source (origin
(method url-fetch)
(uri (pypi-uri "bitshuffle" version))
(sha256
(base32
- "1823x61kyax4dc2hjmc1xraskxi1193y8lvxd03vqv029jrj8cjy"))
+ "139xz3m2m8sal8riicvmb9i0sq4085s2hc6c148bwhmzpnvky3nw"))
(modules '((guix build utils)))
(snippet
'(begin
+ ;; TODO Remove bundled libraries: lz4, lzf, and zstd.
;; Remove generated Cython files.
(delete-file "bitshuffle/h5.c")
- (delete-file "bitshuffle/ext.c")
- #t))))
- (build-system python-build-system)
+ (delete-file "bitshuffle/ext.c")))))
+ (build-system pyproject-build-system)
(arguments
- `(#:tests? #f ; fail: https://github.com/h5py/h5py/issues/769
- #:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'fix-neon-detection
- ;; Neon is only for aarch64 ATM
- ;; see: https://github.com/kiyo-masui/bitshuffle/pull/73
- (lambda _
- (substitute* "src/bitshuffle_core.c"
- (("#define USEARMNEON")
- "#ifdef __aarch64__\n#define USEARMNEON\n#endif"))
- #t))
- (add-after 'unpack 'dont-build-native
- (lambda _
- (substitute* "setup.py"
- (("'-march=native', ") ""))
- #t)))))
- (inputs
- `(("numpy" ,python-numpy)
- ("h5py" ,python-h5py)
- ("hdf5" ,hdf5)))
+ (list
+ #:test-flags
+ ;; FileNotFoundError: [Errno 2] Unable to synchronously open file
+ ;; (unable to open file: name =
+ ;; '/tmp/<...>/tests/data/regression_0.1.3.h5', errno = 2, error message
+ ;; = 'No such file or directory', flags = 0, o_flags = 0)
+ #~(list "--deselect=tests/test_regression.py::TestAll::test_regression")
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-before 'build 'pre-build
+ ;; TODO: Check how to build on other architectures.
+ ;; Taken form .github/workflows/wheels.yml.
+ (lambda _
+ #$@(if (target-x86-64?)
+ '((setenv "BITSHUFFLE_ARCH" "haswell")
+ (setenv "CIBW_SKIP" "pp* *musllinux* cp311-macosx*")
+ (setenv "CIBW_ARCHS" "x86_64"))
+ '())
+ (setenv "HDF5_DIR" #$(this-package-input "hdf5")))))))
(native-inputs
- `(("cython" ,python-cython)))
+ (list python-cython
+ python-pytest
+ python-setuptools))
+ (inputs
+ (list python-numpy
+ python-h5py
+ hdf5))
(home-page "https://github.com/kiyo-masui/bitshuffle";)
(synopsis "Filter for improving compression of typed binary data")
(description "Bitshuffle is an algorithm that rearranges typed, binary data
@@ -789,15 +794,15 @@ algorithm within the Numpy framework.")
(name "bitshuffle-for-snappy")
(build-system gnu-build-system)
(arguments
- (substitute-keyword-arguments (package-arguments bitshuffle)
- ((#:tests? _ #f) #f)
- ((#:phases phases)
- `(modify-phases %standard-phases
- (replace 'configure
- (lambda* (#:key outputs #:allow-other-keys)
- (with-output-to-file "Makefile"
- (lambda _
- (format #t "\
+ (list
+ #:tests? #f
+ #:phases
+ #~(modify-phases %standard-phases
+ (replace 'configure
+ (lambda _
+ (with-output-to-file "Makefile"
+ (lambda _
+ (format #t "\
libbitshuffle.so: src/bitshuffle.o src/bitshuffle_core.o src/iochain.o
lz4/lz4.o
\tgcc -O3 -ffast-math -std=c99 -o $@ -shared -fPIC $^
@@ -816,8 +821,7 @@ install: libbitshuffle.so
\tinstall -m644 src/bitshuffle_core.h $(INCLUDEDIR)
\tinstall -m644 src/iochain.h $(INCLUDEDIR)
\tinstall -m644 lz4/lz4.h $(INCLUDEDIR)
-" (assoc-ref outputs "out"))))
- #t))))))
+" #$output))))))))
(inputs '())
(native-inputs '())))
