From: Leon Anavi <[email protected]> Upgrade to release 3.2.1:
- Added support to use the HDF5 ROS3 driver to access HDF5 files on S3 - Setting the config option default_file_mode to values other than 'r' is deprecated. Pass the desired mode when opening a :class:`~.File` instead. - :exc:`OSError` exceptions raised by h5py should now have a useful .errno attribute, where HDF5 provides this information. Subclasses such as :exc:`FileNotFoundError` should also be raised where appropriate. - Fix reading data with a datatype of variable-length arrays of fixed length strings. - Fix :meth:`.Dataset.read_direct` and :meth:`.Dataset.write_direct` when the source and destination have different shapes. - Fix selecting data using integer indices in :meth:`.Dataset.read_direct` and :meth:`.Dataset.write_direct`. - Fix exception handling in :meth:`.Group.visititems`. - Issue a warning when File(..., swmr=True) is specified with any mode other than 'r', as the SWMR option is ignored in these cases. - Fix NumPy 1.20 deprecation warnings concerning the use of None as shape, and the deprecated aliases np.float, np.int and np.bool. - Fix :attr:`.File.driver` when the read-only S3 driver is available. Add hdf5-native as a dependency to avoid: error: libhdf5.so: cannot open shared object file: No such file or directory Signed-off-by: Leon Anavi <[email protected]> Signed-off-by: Khem Raj <[email protected]> Signed-off-by: Trevor Gamblin <[email protected]> (cherry picked from commit f95812d0bc1bf25778566a44791257e5a113ab63) Signed-off-by: Armin Kuster <[email protected]> --- .../python3-h5py/0001-setup.py-Fix-numpy-version.patch | 8 ++++---- .../0001-setup_build.py-avoid-absolute-path.patch | 4 ++-- .../{python3-h5py_3.1.0.bb => python3-h5py_3.2.1.bb} | 3 ++- 3 files changed, 8 insertions(+), 7 deletions(-) rename meta-python/recipes-devtools/python/{python3-h5py_3.1.0.bb => python3-h5py_3.2.1.bb} (87%) diff --git a/meta-python/recipes-devtools/python/python3-h5py/0001-setup.py-Fix-numpy-version.patch b/meta-python/recipes-devtools/python/python3-h5py/0001-setup.py-Fix-numpy-version.patch index 4881b023c80..9b79cc5395b 100644 --- a/meta-python/recipes-devtools/python/python3-h5py/0001-setup.py-Fix-numpy-version.patch +++ b/meta-python/recipes-devtools/python/python3-h5py/0001-setup.py-Fix-numpy-version.patch @@ -1,4 +1,4 @@ -From e6c0d487fb5e6063305b8b3187896fbfe5720ed2 Mon Sep 17 00:00:00 2001 +From b1d4d171fd13624f3d8bb917f716b62494066501 Mon Sep 17 00:00:00 2001 From: Leon Anavi <[email protected]> Date: Mon, 22 Feb 2021 18:42:43 +0200 Subject: [PATCH] setup.py: Fix numpy version @@ -14,12 +14,12 @@ Signed-off-by: Leon Anavi <[email protected]> 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py -index 7dbe583..6602c97 100755 +index 4b2890c..42ba21b 100755 --- a/setup.py +++ b/setup.py @@ -49,7 +49,7 @@ SETUP_REQUIRES = [ - f"Cython >=0.29; python_version<'3.8'", - f"Cython >=0.29.14; python_version>='3.8'", + "Cython >=0.29.14; python_version=='3.8'", + "Cython >=0.29.15; python_version>='3.9'", ] + [ - f"numpy =={np_min}; python_version{py_condition}" + f"numpy >={np_min}; python_version{py_condition}" diff --git a/meta-python/recipes-devtools/python/python3-h5py/0001-setup_build.py-avoid-absolute-path.patch b/meta-python/recipes-devtools/python/python3-h5py/0001-setup_build.py-avoid-absolute-path.patch index d0c2ece19bb..0b8555734a6 100644 --- a/meta-python/recipes-devtools/python/python3-h5py/0001-setup_build.py-avoid-absolute-path.patch +++ b/meta-python/recipes-devtools/python/python3-h5py/0001-setup_build.py-avoid-absolute-path.patch @@ -1,4 +1,4 @@ -From 1a46082d0889a784037952c4da0cde3822849032 Mon Sep 17 00:00:00 2001 +From 6f8cee826ef9309c174aa97cb6af2ba532ed9dba Mon Sep 17 00:00:00 2001 From: Mingli Yu <[email protected]> Date: Thu, 28 Jan 2021 18:44:10 -0800 Subject: [PATCH] setup_build.py: avoid absolute path @@ -15,7 +15,7 @@ Signed-off-by: Leon Anavi <[email protected]> 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup_build.py b/setup_build.py -index 3c7c7ad..d824bdd 100644 +index 78c6677..64db7f7 100644 --- a/setup_build.py +++ b/setup_build.py @@ -21,7 +21,7 @@ from setup_configure import BuildConfig diff --git a/meta-python/recipes-devtools/python/python3-h5py_3.1.0.bb b/meta-python/recipes-devtools/python/python3-h5py_3.2.1.bb similarity index 87% rename from meta-python/recipes-devtools/python/python3-h5py_3.1.0.bb rename to meta-python/recipes-devtools/python/python3-h5py_3.2.1.bb index 03ae4c9db40..5faa0b8080f 100644 --- a/meta-python/recipes-devtools/python/python3-h5py_3.1.0.bb +++ b/meta-python/recipes-devtools/python/python3-h5py_3.2.1.bb @@ -4,7 +4,7 @@ SECTION = "devel/python" LICENSE = "BSD-3-Clause" LIC_FILES_CHKSUM = "file://LICENSE;md5=113251d71fb0384712c719b567261c5c" -SRC_URI[sha256sum] = "1e2516f190652beedcb8c7acfa1c6fa92d99b42331cbef5e5c7ec2d65b0fc3c2" +SRC_URI[sha256sum] = "89474be911bfcdb34cbf0d98b8ec48b578c27a89fdb1ae4ee7513f1ef8d9249e" SRC_URI_append = " \ file://0001-setup_build.py-avoid-absolute-path.patch \ @@ -19,6 +19,7 @@ DEPENDS = "python3-pkgconfig-native \ python3-cython-native \ python3-numpy-native \ python3-six-native \ + hdf5-native \ python3 \ hdf5 \ " -- 2.17.1
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