Unable to install h5py 3.4

To assist reproducing bugs, please include the following:

• Operating System (e.g. Windows 10, MacOS 10.11, Ubuntu 16.04.2 LTS, CentOS 7) Ubuntu 20.04 LTS
• Python version (e.g. 2.7, 3.5) 3.8
• Where Python was acquired (e.g. system Python on MacOS or Linux, Anaconda on Windows) system python
• h5py version (e.g. 2.6) 3.4
• HDF5 version (e.g. 1.8.17) 1.12.0
• The full traceback/stack trace shown (if it appears) I am getting this error when I type python3.8 setup.py install

running install
running bdist_egg
running egg_info
writing h5py.egg-info/PKG-INFO
writing dependency_links to h5py.egg-info/dependency_links.txt
writing requirements to h5py.egg-info/requires.txt
writing top-level names to h5py.egg-info/top_level.txt
reading manifest file 'h5py.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'AUTHORS'
no previously-included directories found matching 'docs/_build'
no previously-included directories found matching 'docs_api/_build'
warning: no previously-included files matching '.DS_Store' found under directory '*'
warning: no previously-included files found matching 'ci'
warning: no previously-included files found matching 'other'
warning: no previously-included files found matching '.github'
warning: no previously-included files matching '*' found under directory 'ci'
warning: no previously-included files matching '*' found under directory 'other'
warning: no previously-included files matching '*' found under directory '.github'
warning: no previously-included files found matching '*.yml'
warning: no previously-included files found matching '*.yaml'
warning: no previously-included files matching '__pycache__' found under directory '*'
warning: no previously-included files matching '*.py[co]' found under directory '*'
warning: no previously-included files found matching '.coveragerc'
warning: no previously-included files found matching '.coverage_dir'
warning: no previously-included files matching '*' found under directory '.coverage_dir'
warning: no previously-included files found matching '.mailmap'
warning: no previously-included files found matching 'github_deploy_key_h5py_h5py.enc'
warning: no previously-included files found matching 'rever.xsh'
no previously-included directories found matching 'news'
writing manifest file 'h5py.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
running build_ext
Loading library to get build settings and version: libhdf5.so
********************************************************************************
                       Summary of the h5py configuration

HDF5 include dirs: []
HDF5 library dirs: []
     HDF5 Version: (1, 12, 0)
      MPI Enabled: False
 ROS3 VFD Enabled: False
 Rebuild Required: True

********************************************************************************
Executing cythonize()
Traceback (most recent call last):
  File "setup.py", line 156, in <module>
    setup(
  File "/usr/lib/python3/dist-packages/setuptools/__init__.py", line 144, in setup
    return distutils.core.setup(**attrs)
  File "/usr/lib/python3.8/distutils/core.py", line 148, in setup
    dist.run_commands()
  File "/usr/lib/python3.8/distutils/dist.py", line 966, in run_commands
    self.run_command(cmd)
  File "/usr/lib/python3.8/distutils/dist.py", line 985, in run_command
    cmd_obj.run()
  File "/usr/lib/python3/dist-packages/setuptools/command/install.py", line 67, in run
    self.do_egg_install()
  File "/usr/lib/python3/dist-packages/setuptools/command/install.py", line 109, in do_egg_install
    self.run_command('bdist_egg')
  File "/usr/lib/python3.8/distutils/cmd.py", line 313, in run_command
    self.distribution.run_command(command)
  File "/usr/lib/python3.8/distutils/dist.py", line 985, in run_command
    cmd_obj.run()
  File "/usr/lib/python3/dist-packages/setuptools/command/bdist_egg.py", line 172, in run
    cmd = self.call_command('install_lib', warn_dir=0)
  File "/usr/lib/python3/dist-packages/setuptools/command/bdist_egg.py", line 158, in call_command
    self.run_command(cmdname)
  File "/usr/lib/python3.8/distutils/cmd.py", line 313, in run_command
    self.distribution.run_command(command)
  File "/usr/lib/python3.8/distutils/dist.py", line 985, in run_command
    cmd_obj.run()
  File "/usr/lib/python3/dist-packages/setuptools/command/install_lib.py", line 23, in run
    self.build()
  File "/usr/lib/python3.8/distutils/command/install_lib.py", line 109, in build
    self.run_command('build_ext')
  File "/usr/lib/python3.8/distutils/cmd.py", line 313, in run_command
    self.distribution.run_command(command)
  File "/usr/lib/python3.8/distutils/dist.py", line 985, in run_command
    cmd_obj.run()
  File "/home/winash12/libPython/h5py-3.4.0/setup_build.py", line 170, in run
    self.extensions = cythonize(self._make_extensions(config),
  File "/usr/local/lib/python3.8/dist-packages/Cython-0.29.24-py3.8-linux-x86_64.egg/Cython/Build/Dependencies.py", line 963, in cythonize
    ctx = c_options.create_context()
  File "/usr/local/lib/python3.8/dist-packages/Cython-0.29.24-py3.8-linux-x86_64.egg/Cython/Compiler/Main.py", line 596, in create_context
    return Context(self.include_path, self.compiler_directives,
  File "/usr/local/lib/python3.8/dist-packages/Cython-0.29.24-py3.8-linux-x86_64.egg/Cython/Compiler/Main.py", line 80, in __init__
    from . import Builtin, CythonScope
  File "/usr/local/lib/python3.8/dist-packages/Cython-0.29.24-py3.8-linux-x86_64.egg/Cython/Compiler/CythonScope.py", line 5, in <module>
    from .UtilityCode import CythonUtilityCode
  File "/usr/local/lib/python3.8/dist-packages/Cython-0.29.24-py3.8-linux-x86_64.egg/Cython/Compiler/UtilityCode.py", line 3, in <module>
    from .TreeFragment import parse_from_strings, StringParseContext
  File "/usr/local/lib/python3.8/dist-packages/Cython-0.29.24-py3.8-linux-x86_64.egg/Cython/Compiler/TreeFragment.py", line 17, in <module>
    from .Visitor import VisitorTransform
  File "Cython/Compiler/Visitor.py", line 16, in init Cython.Compiler.Visitor
  File "/usr/local/lib/python3.8/dist-packages/Cython-0.29.24-py3.8-linux-x86_64.egg/Cython/Compiler/Nodes.py", line 31, in <module>
    from .Pythran import has_np_pythran, pythran_type, is_pythran_buffer
  File "/usr/local/lib/python3.8/dist-packages/Cython-0.29.24-py3.8-linux-x86_64.egg/Cython/Compiler/Pythran.py", line 10, in <module>
    import pythran
  File "/usr/local/lib/python3.8/dist-packages/pythran-0.9.12.post1-py3.8.egg/pythran/__init__.py", line 41, in <module>
    from pythran.toolchain import (generate_cxx, compile_cxxfile, compile_cxxcode,
  File "/usr/local/lib/python3.8/dist-packages/pythran-0.9.12.post1-py3.8.egg/pythran/toolchain.py", line 6, in <module>
    from pythran.backend import Cxx, Python
  File "/usr/local/lib/python3.8/dist-packages/pythran-0.9.12.post1-py3.8.egg/pythran/backend.py", line 7, in <module>
    from pythran.analyses import LocalNodeDeclarations, GlobalDeclarations, Scope
  File "/usr/local/lib/python3.8/dist-packages/pythran-0.9.12.post1-py3.8.egg/pythran/analyses/__init__.py", line 12, in <module>
    from .aliases import Aliases, StrictAliases
  File "/usr/local/lib/python3.8/dist-packages/pythran-0.9.12.post1-py3.8.egg/pythran/analyses/aliases.py", line 6, in <module>
    from pythran.syntax import PythranSyntaxError
  File "/usr/local/lib/python3.8/dist-packages/pythran-0.9.12.post1-py3.8.egg/pythran/syntax.py", line 7, in <module>
    from pythran.tables import MODULES
  File "/usr/local/lib/python3.8/dist-packages/pythran-0.9.12.post1-py3.8.egg/pythran/tables.py", line 4580, in <module>
    save_arguments((), MODULES)
  File "/usr/local/lib/python3.8/dist-packages/pythran-0.9.12.post1-py3.8.egg/pythran/tables.py", line 4547, in save_arguments
    save_arguments(module_name + (elem,), signature)
  File "/usr/local/lib/python3.8/dist-packages/pythran-0.9.12.post1-py3.8.egg/pythran/tables.py", line 4547, in save_arguments
    save_arguments(module_name + (elem,), signature)
  File "/usr/local/lib/python3.8/dist-packages/pythran-0.9.12.post1-py3.8.egg/pythran/tables.py", line 4551, in save_arguments
    themodule = __import__(".".join(module_name))
  File "/usr/local/lib/python3.8/dist-packages/scipy-1.7.1-py3.8-linux-x86_64.egg/scipy/special/__init__.py", line 643, in <module>
    from . import _ufuncs
  File "_ufuncs.pyx", line 1, in init scipy.special._ufuncs
ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 88 from C header, got 80 from PyObject

[winash12]

@tacaswell That is great ! I just did a pip3 install --no-binary=h5py h5py and it compiled and installed just fine. No more sudo setup.py for me ! Finally can close this issue for good.

[tacaswell]

Have not had an issue with sudo in 7 years of Ubuntu.

This is a similar statement to “I have ridden by bike with out a helmet for years without issues”. You should be thankful you got lucky!

There has been enough trouble with sudo + python installation that some distributions have patched pip to fail with sudo and there is an active PEP (https://discuss.python.org/t/graceful-cooperation-between-external-and-python-package-managers-pep-668/10302 / https://github.com/python/peps/blob/013d50de0e07aa9e7fecc8dc3cd55b115c12ddf4/pep-0668.rst) on how to make sure that pip and system package managers play nice!

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If you run python setup.py you do indeed get a .eggs directory with cython and numpy due to our use of setup_requires in setup.py: https://github.com/h5py/h5py/blob/a7c3f0c1b5faf01ec3f53af4947eeae971c7fbea/setup.py#L46-L54 and https://github.com/h5py/h5py/blob/a7c3f0c1b5faf01ec3f53af4947eeae971c7fbea/setup.py#L178-L180

If you use pip install . rather that python setup.py install you can avoid creating the eggs.

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That said, if you want to use system python without a virtual env, please use the h5py packaged my your system packager (in your case managed via apt).