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gnu: python-tables: Update to 3.10.2.

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* gnu/packages/python-xyz.scm (python-tables): Update to 3.10.2.
[build-system]: Switch to pyproject-build-system.
[phases]{set-LD_LIBRARY_PATH}: Replace by {pre-build} with setting up
environment variables for each library path which is available in
setup.py.  Regenerate C code with Cython before build.
{pre-check}: New phase.
{check}: Rework test invocation to run just bare minimal test suite, add
a notes popping up during tests invocation describing it.
[native-inputs]: Add python-pytest, python-setuptools-next, and
python-sphinx.
[inputs]: Remove hdf5-1.10, and zlib; add bzip2, and hdf5.

Fixes: guix/guix#2342.
Change-Id: Ia1d00979123e459640d74a0dfd7fd52b25f8b9b7
This commit is contained in:
Sharlatan Hellseher 2025-09-06 17:12:15 +01:00
parent f4ca04a820
commit ad1941a08f
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1 changed files with 37 additions and 12 deletions
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gnu/packages/python-xyz.scm
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@ -17809,18 +17809,20 @@ tasks, sockets, files, locks, and queues.")
(define-public python-tables
(package
(name "python-tables")
(version "3.10.1")
(version "3.10.2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "tables" version))
(sha256
(base32
"1kr6y4qivqy462gva4bqym3x4alhxijfqjplxax3gh5r6k3pm82a"))
"0469jrkmp0qv8cmlqkizm3b8imyc97mk9pfn66ldpyl6f4m82i15"))
(snippet '(begin
(use-modules (guix build utils))
;; TODO: Unbundle.
;; (delete-file-recursively "hdf5-blosc")
(delete-file-recursively "c-blosc")))))
(build-system python-build-system)
(build-system pyproject-build-system)
(arguments
(list
#:phases
@ -17839,25 +17841,48 @@ tasks, sockets, files, locks, and queues.")
"\""
(search-input-file inputs "/lib/libblosc2.so")
"\",\n" m)))))
(add-before 'build 'set-LD_LIBRARY_PATH
(add-before 'build 'pre-build
(lambda _
;; The setup.py build system makes use of ctypes.CDLL, which
;; uses dlopen, which looks up library names from standard
;; locations or LD_LIBRARY_PATH.
(setenv "LD_LIBRARY_PATH" (getenv "LIBRARY_PATH"))))
(invoke "make" "distclean") ;Regenerate C code with Cython
(setenv "BLOSC2_DIR" #$(this-package-input "cblosc2"))
(setenv "BLOSC_DIR" #$(this-package-input "c-blosc"))
(setenv "BZIP2_DIR" #$(this-package-input "bzip2"))
(setenv "HDF5_DIR" #$(this-package-input "hdf5"))
(setenv "LZO_DIR" #$(this-package-input "lzo"))))
(add-before 'check 'pre-check
(lambda _
(setenv "HOME" "/tmp")))
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(invoke "python" "setup.py" "check")))))))
(with-directory-excursion "/tmp"
;; Performing only a light (yet comprehensive) subset of the
;; test suite. If you want a more complete test, try
;; passing the --heavy flag to this script (or set the
;; 'heavy' parameter in case you are using tables.test()
;; call). The whole suite will take more than 4 hours to
;; complete on a relatively modern CPU and around 512 MB of
;; main memory.
(invoke "python" "-m" "tables.tests.test_all"))))))))
(native-inputs
(list pkg-config
python-cython
python-pytest
python-setuptools-next
python-sphinx))
(inputs
(list bzip2
c-blosc
c-blosc2
hdf5
lzo))
(propagated-inputs
(list python-blosc2
python-numpy
python-numexpr
python-numpy
python-packaging
python-py-cpuinfo
python-typing-extensions))
(native-inputs (list pkg-config python-cython))
(inputs (list c-blosc c-blosc2 hdf5-1.10 bzip2 lzo zlib))
(home-page "https://www.pytables.org/")
(synopsis "Hierarchical datasets for Python")
(description "PyTables is a package for managing hierarchical datasets and