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5 changed files with 139 additions and 380 deletions

12
.gitignore vendored
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@ -8,15 +8,3 @@
/h5py-2.3.1.tar.gz /h5py-2.3.1.tar.gz
/h5py-2.4.0.tar.gz /h5py-2.4.0.tar.gz
/h5py-2.5.0.tar.gz /h5py-2.5.0.tar.gz
/h5py-2.6.0.tar.gz
/h5py-2.7.0.tar.gz
/h5py-2.7.1.tar.gz
/h5py-2.8.0.tar.gz
/h5py-2.9.0.tar.gz
/h5py-2.10.0.tar.gz
/h5py-3.0.0.tar.gz
/h5py-3.1.0.tar.gz
/h5py-3.2.1.tar.gz
/h5py-3.4.0.tar.gz
/h5py-3.6.0.tar.gz
/h5py-3.7.0.tar.gz

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@ -1,23 +0,0 @@
diff -up h5py-3.7.0/h5py/h5t.pyx.orig h5py-3.7.0/h5py/h5t.pyx
--- h5py-3.7.0/h5py/h5t.pyx.orig 2022-06-14 16:31:22.964458579 +0000
+++ h5py-3.7.0/h5py/h5t.pyx 2022-06-14 16:31:46.404768118 +0000
@@ -282,18 +282,7 @@ cdef (int, int, int) _correct_float_info
nmant = finfo.nmant
maxexp = finfo.maxexp
minexp = finfo.minexp
- # workaround for numpy's buggy finfo on float128 on ppc64 archs
- if ftype_ == np.longdouble and MACHINE == 'ppc64':
- # values reported by hdf5
- nmant = 116
- maxexp = 1024
- minexp = -1022
- elif ftype_ == np.longdouble and MACHINE == 'ppc64le':
- # values reported by hdf5
- nmant = 52
- maxexp = 1024
- minexp = -1022
- elif nmant == 63 and finfo.nexp == 15:
+ if nmant == 63 and finfo.nexp == 15:
# This is an 80-bit float, correct mantissa size
nmant += 1

46
h5py-system-lzf.patch Normal file
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@ -0,0 +1,46 @@
diff -up h5py-2.4.0/lzf/lzf_filter.c.lzf h5py-2.4.0/lzf/lzf_filter.c
--- h5py-2.4.0/lzf/lzf_filter.c.lzf 2014-12-17 12:05:28.000000000 -0700
+++ h5py-2.4.0/lzf/lzf_filter.c 2015-01-07 11:46:08.880778180 -0700
@@ -26,7 +26,7 @@
#include <stdio.h>
#include <errno.h>
#include "hdf5.h"
-#include "lzf/lzf.h"
+#include "lzf.h"
#include "lzf_filter.h"
/* Our own versions of H5Epush_sim, as it changed in 1.8 */
diff -up h5py-2.4.0/setup_build.py.lzf h5py-2.4.0/setup_build.py
--- h5py-2.4.0/setup_build.py.lzf 2014-12-17 12:05:28.000000000 -0700
+++ h5py-2.4.0/setup_build.py 2015-01-07 11:52:18.209258734 -0700
@@ -30,9 +30,7 @@ MODULES = ['defs','_errors','_objects',
'h5ds', 'h5ac']
-EXTRA_SRC = {'h5z': [ localpath("lzf/lzf_filter.c"),
- localpath("lzf/lzf/lzf_c.c"),
- localpath("lzf/lzf/lzf_d.c")]}
+EXTRA_SRC = {'h5z': [ localpath("lzf/lzf_filter.c")]}
if sys.platform.startswith('win'):
@@ -44,7 +42,7 @@ if sys.platform.startswith('win'):
else:
COMPILER_SETTINGS = {
- 'libraries' : ['hdf5', 'hdf5_hl'],
+ 'libraries' : ['hdf5', 'hdf5_hl', 'lzf'],
'include_dirs' : [localpath('lzf'), '/opt/local/include', '/usr/local/include'],
'library_dirs' : ['/opt/local/lib', '/usr/local/lib'],
'define_macros' : [('H5_USE_16_API', None)] }
@@ -82,10 +80,6 @@ class h5py_build_ext(build_ext):
settings['include_dirs'].insert(0, op.join(config.hdf5, 'include'))
settings['library_dirs'].insert(0, op.join(config.hdf5, 'lib'))
- # TODO: should this only be done on UNIX?
- if os.name != 'nt':
- settings['runtime_library_dirs'] = settings['library_dirs']
-
def make_extension(module):
sources = [localpath('h5py', module+'.pyx')] + EXTRA_SRC.get(module, [])
return Extension('h5py.'+module, sources, **settings)

436
h5py.spec
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@ -1,368 +1,116 @@
%global commit a8e82bcd63de14daddbc84c250a36c0ee8c850f6 %global with_python3 1
%global shortcommit %(c=%{commit}; echo ${c:0:7})
%{?filter_provides_in: %filter_provides_in .*/h5py/.*\.so}
%{?filter_setup}
Summary: A Python interface to the HDF5 library Summary: A Python interface to the HDF5 library
Name: h5py Name: h5py
Version: 3.7.0 Version: 2.5.0
Release: 3%{?dist} Release: 1%{?dist}
Group: Applications/Engineering
License: BSD License: BSD
URL: http://www.h5py.org/ URL: http://www.h5py.org/
Source0: https://files.pythonhosted.org/packages/source/h/h5py/h5py-%{version}.tar.gz Source0: https://pypi.python.org/packages/source/h/h5py/h5py-%{version}.tar.gz
# drop the unnecessary workaround for float128 type after # patch to use a system liblzf rather than bundled liblzf
# https://fedoraproject.org/wiki/Changes/PPC64LE_Float128_Transition Patch0: h5py-system-lzf.patch
# in F-36
Patch0: h5py-3.7.0-ppc-float128.patch
BuildRequires: gcc
BuildRequires: hdf5-devel
BuildRequires: liblzf-devel BuildRequires: liblzf-devel
BuildRequires: python%{python3_pkgversion}-Cython >= 0.23 BuildRequires: hdf5-devel >= 1.8.3
BuildRequires: python%{python3_pkgversion}-devel >= 3.2 BuildRequires: python-devel >= 2.6
BuildRequires: python%{python3_pkgversion}-setuptools BuildRequires: python-sphinx
BuildRequires: python%{python3_pkgversion}-cached_property BuildRequires: numpy >= 1.6.1
BuildRequires: python%{python3_pkgversion}-numpy >= 1.7 BuildRequires: Cython
BuildRequires: python%{python3_pkgversion}-pkgconfig %if 0%{?with_python3}
BuildRequires: python%{python3_pkgversion}-pip BuildRequires: python-tools
BuildRequires: python%{python3_pkgversion}-pytest BuildRequires: python3-devel >= 3.2
BuildRequires: python%{python3_pkgversion}-pytest-mpi BuildRequires: python3-sphinx
BuildRequires: python%{python3_pkgversion}-six BuildRequires: python3-numpy >= 1.6.1
BuildRequires: python%{python3_pkgversion}-sphinx BuildRequires: python3-Cython
# MPI builds %endif
BuildRequires: hdf5-openmpi-devel Requires: hdf5 = %{_hdf5_version}
BuildRequires: openmpi-devel Requires: numpy >= 1.6.1
BuildRequires: python%{python3_pkgversion}-mpi4py-openmpi
BuildRequires: hdf5-mpich-devel
BuildRequires: mpich-devel
BuildRequires: python%{python3_pkgversion}-mpi4py-mpich
%global _description\ %description
The h5py package provides both a high- and low-level interface to the\ The h5py package provides both a high- and low-level interface to the
HDF5 library from Python. The low-level interface is intended to be a\ HDF5 library from Python. The low-level interface is intended to be a
complete wrapping of the HDF5 API, while the high-level component\ complete wrapping of the HDF5 API, while the high-level component
supports access to HDF5 files, data sets and groups using established\ supports access to HDF5 files, data sets and groups using established
Python and NumPy concepts.\ Python and NumPy concepts.
\
A strong emphasis on automatic conversion between Python (Numpy)\ A strong emphasis on automatic conversion between Python (Numpy)
data types and data structures and their HDF5 equivalents vastly\ data types and data structures and their HDF5 equivalents vastly
simplifies the process of reading and writing data from Python. simplifies the process of reading and writing data from Python.
%description %_description %if 0%{?with_python3}
%package -n python3-h5py
Summary: A Python 3 interface to the HDF5 library
Group: Applications/Engineering
Requires: python3-numpy >= 1.6.1
%package -n python%{python3_pkgversion}-h5py %description -n python3-h5py
Summary: %{summary} The h5py package provides both a high- and low-level interface to the
Requires: hdf5%{_isa} = %{_hdf5_version} HDF5 library from Python. The low-level interface is intended to be a
Requires: python%{python3_pkgversion}-cached_property complete wrapping of the HDF5 API, while the high-level component
Requires: python%{python3_pkgversion}-numpy >= 1.7 supports access to HDF5 files, data sets and groups using established
Requires: python%{python3_pkgversion}-six Python and NumPy concepts.
%{?python_provide:%python_provide python%{python3_pkgversion}-h5py}
%description -n python%{python3_pkgversion}-h5py %_description
%package -n python%{python3_pkgversion}-h5py-openmpi A strong emphasis on automatic conversion between Python (Numpy)
Summary: A Python interface to the HDF5 library using OpenMPI data types and data structures and their HDF5 equivalents vastly
Requires: hdf5%{_isa} = %{_hdf5_version} simplifies the process of reading and writing data from Python.
Requires: python%{python3_pkgversion}-cached_property This is the Python 3 version of h5py.
Requires: python%{python3_pkgversion}-numpy >= 1.7
Requires: python%{python3_pkgversion}-six
Requires: python3-mpi4py-openmpi
Requires: openmpi
%description -n python%{python3_pkgversion}-h5py-openmpi %_description
%package -n python%{python3_pkgversion}-h5py-mpich
Summary: A Python interface to the HDF5 library using MPICH
Requires: hdf5%{_isa} = %{_hdf5_version}
Requires: python%{python3_pkgversion}-cached_property
Requires: python%{python3_pkgversion}-numpy >= 1.7
Requires: python%{python3_pkgversion}-six
Requires: python3-mpi4py-openmpi
Requires: python3-mpi4py-mpich
Requires: mpich
%description -n python%{python3_pkgversion}-h5py-mpich %_description
%prep
%setup -q -c -n %{name}-%{version}
%patch0
mv %{name}-%{version} serial
cd serial
%{__python3} api_gen.py
cd -
for x in mpich openmpi
do
cp -al serial $x
done
%build
# Upstream requires a specific numpy without this
export H5PY_SETUP_REQUIRES=0
export H5PY_SYSTEM_LZF=1
# serial
export CFLAGS="%{optflags} -fopenmp"
cd serial
%py3_build
cd -
# MPI
export CC=mpicc
export HDF5_MPI="ON"
# openmpi
cd openmpi
%{_openmpi_load}
%py3_build
%{_openmpi_unload}
cd -
# mpich
cd mpich
%{_mpich_load}
%py3_build
%{_mpich_unload}
cd -
%install
# Upstream requires a specific numpy without this
export H5PY_SETUP_REQUIRES=0
export H5PY_SYSTEM_LZF=1
# openmpi
cd openmpi
%py3_install
rm -rf %{buildroot}%{python3_sitearch}/h5py/tests
mkdir -p %{buildroot}%{python3_sitearch}/openmpi
mv %{buildroot}%{python3_sitearch}/%{name}/ \
%{buildroot}%{python3_sitearch}/%{name}*.egg-info \
%{buildroot}%{python3_sitearch}/openmpi
cd -
# mpich
cd mpich
%py3_install
rm -rf %{buildroot}%{python3_sitearch}/h5py/tests
mkdir -p %{buildroot}%{python3_sitearch}/mpich
mv %{buildroot}%{python3_sitearch}/%{name}/ \
%{buildroot}%{python3_sitearch}/%{name}*.egg-info \
%{buildroot}%{python3_sitearch}/mpich
cd -
# serial part must be last (not to overwrite files)
cd serial
%py3_install
rm -rf %{buildroot}%{python3_sitearch}/h5py/tests
cd -
%check
# Upstream requires a specific numpy without this
export H5PY_SETUP_REQUIRES=0
export H5PY_SYSTEM_LZF=1
# i686 test failure
# https://github.com/h5py/h5py/issues/1337
# s390x test failure
# https://github.com/h5py/h5py/issues/1739
%ifarch %ix86
fail=0
%else
fail=1
%endif %endif
export PYTHONPATH=$(echo serial/build/lib*) %prep
%{__python3} -m pytest --pyargs h5py -rxXs ${PYTHONPATH} || exit $fail %setup -q
# use system libzlf and remove private copy
%patch0 -p1 -b .lzf
rm -rf lzf/lzf
%{__python} api_gen.py
%if 0%{?with_python3}
rm -rf %{py3dir}
cp -a . %{py3dir}
%endif
# openmpi %build
export PYTHONPATH=$(echo openmpi/build/lib*) export CFLAGS="%{optflags} -fopenmp"
%{_openmpi_load} %{__python} setup.py build
mpirun %{__python3} -m pytest --pyargs h5py -rxXs --with-mpi ${PYTHONPATH} || exit $fail
%{_openmpi_unload}
# mpich %if 0%{?with_python3}
export PYTHONPATH=$(echo mpich/build/lib*) pushd %{py3dir}
%{_mpich_load} %{__python3} setup.py build
mpirun %{__python3} -m pytest --pyargs h5py -rxXs --with-mpi ${PYTHONPATH} || exit $fail popd
%{_mpich_unload} %endif
%install
%{__python} setup.py install -O1 --skip-build --root %{buildroot}
chmod 0755 %{buildroot}%{python_sitearch}/%{name}/*.so
%files -n python%{python3_pkgversion}-h5py %if 0%{?with_python3}
%license serial/licenses/*.txt pushd %{py3dir}
#doc serial/ANN.rst serial/README.rst serial/examples %{__python3} setup.py install -O1 --skip-build --root %{buildroot}
%doc serial/README.rst serial/examples chmod 0755 %{buildroot}%{python3_sitearch}/%{name}/*.so
%endif
%check
%{__python} setup.py test || :
%if 0%{?with_python3}
pushd %{py3dir}
%{__python3} setup.py test || :
popd
%endif
%files
%doc licenses/*.txt ANN.rst README.rst examples
%{python_sitearch}/%{name}/
%{python_sitearch}/%{name}-%{version}-*.egg-info
%if 0%{?with_python3}
%files -n python3-h5py
%doc licenses/*.txt ANN.rst README.rst
%{python3_sitearch}/%{name}/ %{python3_sitearch}/%{name}/
%{python3_sitearch}/%{name}-%{version}-*.egg-info %{python3_sitearch}/%{name}-%{version}-*.egg-info
%endif
%files -n python%{python3_pkgversion}-h5py-openmpi
%license openmpi/licenses/*.txt
%doc openmpi/README.rst
%{python3_sitearch}/openmpi/%{name}/
%{python3_sitearch}/openmpi/%{name}-%{version}-*.egg-info
%files -n python%{python3_pkgversion}-h5py-mpich
%license mpich/licenses/*.txt
%doc mpich/README.rst
%{python3_sitearch}/mpich/%{name}/
%{python3_sitearch}/mpich/%{name}-%{version}-*.egg-info
%changelog %changelog
* Thu Jul 21 2022 Fedora Release Engineering <releng@fedoraproject.org> - 3.7.0-3
- Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild
* Mon Jun 13 2022 Python Maint <python-maint@redhat.com> - 3.7.0-2
- Rebuilt for Python 3.11
* Tue May 24 2022 Terje Rosten <terje.rosten@ntnu.no> - 3.7.0-1
- Update to 3.7.0
* Sun Jan 23 2022 Terje Rosten <terje.rosten@ntnu.no> - 3.6.0-1
- Update to 3.6.0
* Thu Jan 20 2022 Fedora Release Engineering <releng@fedoraproject.org> - 3.4.0-4
- Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild
* Sun Nov 21 2021 Orion Poplawski <orion@nwra.com> - 3.4.0-3
- Rebuild for hdf5 1.12.1
* Sun Oct 03 2021 Terje Rosten <terje.rosten@ntnu.no> - 3.4.0-2
- Revert an upstream commit that caused crash in PySCF (rhbz#2009628)
* Sat Sep 18 2021 Terje Rosten <terje.rosten@ntnu.no> - 3.4.0-1
- Update to 3.4.0
* Tue Aug 10 2021 Orion Poplawski <orion@nwra.com> - 3.2.1-4
- Rebuild for hdf5 1.10.7
* Thu Jul 22 2021 Fedora Release Engineering <releng@fedoraproject.org> - 3.2.1-3
- Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild
* Fri Jun 04 2021 Python Maint <python-maint@redhat.com> - 3.2.1-2
- Rebuilt for Python 3.10
* Tue Mar 09 2021 Orion Poplawski <orion@nwra.com> - 3.2.1-1
- Update to 3.2.1
* Tue Jan 26 2021 Fedora Release Engineering <releng@fedoraproject.org> - 3.1.0-2
- Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild
* Sat Nov 07 2020 Terje Rosten <terje.rosten@ntnu.no> - 3.1.0-1
- Update to 3.1.0
* Fri Oct 30 2020 Orion Poplawski <orion@nwra.com> - 3.0.0-1
- Update to 3.0.0
* Mon Jul 27 2020 Terje Rosten <terje.rosten@ntnu.no> - 2.10.0-4
- Add openmpi and mpich subpackages
* Thu Jun 25 2020 Orion Poplawski <orion@cora.nwra.com> - 2.10.0-3
- Rebuild for hdf5 1.10.6
* Tue May 26 2020 Miro Hrončok <mhroncok@redhat.com> - 2.10.0-2
- Rebuilt for Python 3.9
* Sun May 17 2020 Terje Rosten <terje.rosten@ntnu.no> - 2.10.0-1
- Add commits from 2.10.x branch
* Wed Jan 29 2020 Fedora Release Engineering <releng@fedoraproject.org> - 2.9.0-8
- Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild
* Thu Oct 03 2019 Miro Hrončok <mhroncok@redhat.com> - 2.9.0-7
- Rebuilt for Python 3.8.0rc1 (#1748018)
* Mon Aug 19 2019 Miro Hrončok <mhroncok@redhat.com> - 2.9.0-6
- Rebuilt for Python 3.8
* Thu Jul 25 2019 Fedora Release Engineering <releng@fedoraproject.org> - 2.9.0-5
- Rebuilt for https://fedoraproject.org/wiki/Fedora_31_Mass_Rebuild
* Sat Mar 16 2019 Orion Poplawski <orion@nwra.com> - 2.9.0-4
- Rebuild for hdf5 1.10.5
* Fri Feb 01 2019 Fedora Release Engineering <releng@fedoraproject.org> - 2.9.0-3
- Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild
* Mon Jan 14 2019 Miro Hrončok <mhroncok@redhat.com> - 2.9.0-2
- Subpackage python2-h5py has been removed
See https://fedoraproject.org/wiki/Changes/Mass_Python_2_Package_Removal
* Mon Jan 7 2019 Orion Poplawski <orion@nwra.com> - 2.9.0-1
- Update to 2.9.0
- Drop python2 for Fedora 30+ (bug #1663834)
* Fri Jul 13 2018 Fedora Release Engineering <releng@fedoraproject.org> - 2.8.0-3
- Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild
* Tue Jun 19 2018 Miro Hrončok <mhroncok@redhat.com> - 2.8.0-2
- Rebuilt for Python 3.7
* Tue Jun 05 2018 Terje Rosten <terje.rosten@ntnu.no> - 2.8.0-1
- Update to 2.8.0
* Thu Mar 01 2018 Iryna Shcherbina <ishcherb@redhat.com> - 2.7.1-4
- Update Python 2 dependency declarations to new packaging standards
(See https://fedoraproject.org/wiki/FinalizingFedoraSwitchtoPython3)
- Minor clean up
* Tue Feb 13 2018 Christian Dersch <lupinix@mailbox.org> - 2.7.1-3
- Added patch h5py-Dont-reorder-compound-types (required for new numpy>=1.14)
* Wed Feb 07 2018 Fedora Release Engineering <releng@fedoraproject.org> - 2.7.1-2
- Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild
* Mon Sep 04 2017 Terje Rosten <terje.rosten@ntnu.no> - 2.7.1-1
- Update to 2.7.1
* Wed Aug 02 2017 Fedora Release Engineering <releng@fedoraproject.org> - 2.7.0-4
- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild
* Wed Jul 26 2017 Fedora Release Engineering <releng@fedoraproject.org> - 2.7.0-3
- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild
* Fri Jul 07 2017 Igor Gnatenko <ignatenko@redhat.com> - 2.7.0-2
- Rebuild due to bug in RPM (RHBZ #1468476)
* Mon Mar 20 2017 Orion Poplawski <orion@cora.nwra.com> - 2.7.0-1
- Update to 2.7.0
* Fri Feb 10 2017 Fedora Release Engineering <releng@fedoraproject.org> - 2.6.0-7
- Rebuilt for https://fedoraproject.org/wiki/Fedora_26_Mass_Rebuild
* Mon Dec 19 2016 Miro Hrončok <mhroncok@redhat.com> - 2.6.0-6
- Rebuild for Python 3.6
* Tue Dec 06 2016 Orion Poplawski <orion@cora.nwra.com> - 2.6.0-5
- Rebuild for hdf5 1.8.18
* Tue Dec 06 2016 Orion Poplawski <orion@cora.nwra.com> - 2.6.0-4
- Rebuild for hdf5 1.8.18
* Tue Jul 19 2016 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 2.6.0-3
- https://fedoraproject.org/wiki/Changes/Automatic_Provides_for_Python_RPM_Packages
* Wed Jun 29 2016 Orion Poplawski <orion@cora.nwra.com> - 2.6.0-2
- Rebuild for hdf5 1.8.17
* Sun Apr 10 2016 Orion Poplawski <orion@cora.nwra.com> - 2.6.0-1
- Update to 2.6.0
- Modernize spec and ship python2-h5py package
* Wed Mar 23 2016 Orion Poplawski <orion@cora.nwra.com> - 2.5.0-8
- Tests run okay now
* Wed Feb 03 2016 Fedora Release Engineering <releng@fedoraproject.org> - 2.5.0-7
- Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild
* Thu Jan 21 2016 Orion Poplawski <orion@cora.nwra.com> - 2.5.0-6
- Rebuild for hdf5 1.8.16
* Tue Nov 10 2015 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 2.5.0-5
- Rebuilt for https://fedoraproject.org/wiki/Changes/python3.5
* Wed Jun 17 2015 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 2.5.0-4
- Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild
* Mon May 18 2015 Terje Rosten <terje.rosten@ntnu.no> - 2.5.0-3
- Add six and pkgconfig dep (thanks Orion!)
* Sun May 17 2015 Orion Poplawski <orion@cora.nwra.com> - 2.5.0-2
- Rebuild for hdf5 1.8.15
* Mon Apr 13 2015 Orion Poplawski <orion@cora.nwra.com> - 2.5.0-1 * Mon Apr 13 2015 Orion Poplawski <orion@cora.nwra.com> - 2.5.0-1
- Update to 2.5.0 - Update to 2.5.0

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@ -1 +1 @@
SHA512 (h5py-3.7.0.tar.gz) = c10a9a623c88dbc965238cb2057b8924492c762c29610cfdb24f26f878a7322e414d3e5c90d750c2f5cfe1b4949f884bc17f09a126b01a4721ad6e14761174a2 6e4301b5ad5da0d51b0a1e5ac19e3b74 h5py-2.5.0.tar.gz