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256 lines
6.9 KiB
ReStructuredText
Building and installing SciPy
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+++++++++++++++++++++++++++++
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See https://www.scipy.org/install.html
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.. Contents::
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INTRODUCTION
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============
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It is *strongly* recommended that you use either a complete scientific Python
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distribution or binary packages on your platform if they are available, in
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particular on Windows and Mac OS X. You should not attempt to build SciPy if
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you are not familiar with compiling software from sources.
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Recommended distributions are:
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- Enthought Canopy (https://www.enthought.com/products/canopy/)
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- Anaconda (https://www.anaconda.com)
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- Python(x,y) (https://python-xy.github.io/)
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- WinPython (https://winpython.github.io/)
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The rest of this install documentation summarizes how to build Scipy. Note
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that more extensive (and possibly more up-to-date) build instructions are
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maintained at https://scipy.github.io/devdocs/building/
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PREREQUISITES
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=============
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SciPy requires the following software installed for your platform:
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1) Python__ >= 3.7
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__ https://www.python.org
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2) NumPy__ >= 1.16.5
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__ https://www.numpy.org/
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If building from source, SciPy also requires:
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3) setuptools__
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__ https://github.com/pypa/setuptools
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4) pybind11__ >= 2.4.3
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__ https://github.com/pybind/pybind11
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5) If you want to build the documentation: Sphinx__ >= 1.2.1
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__ http://www.sphinx-doc.org/
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6) If you want to build SciPy master or other unreleased version from source
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(Cython-generated C sources are included in official releases):
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Cython__ >= 0.29.18
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__ http://cython.org/
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Windows
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-------
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Compilers
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~~~~~~~~~
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There are two ways to build SciPy on Windows:
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1. Use Intel MKL, and Intel compilers or ifort + MSVC. This is what Anaconda
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and Enthought Canopy use.
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2. Use MSVC + GFortran with OpenBLAS. This is how the SciPy Windows wheels are
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built.
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Mac OS X
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--------
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It is recommended to use GCC or Clang, both work fine. Gcc is available for
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free when installing Xcode, the developer toolsuite on Mac OS X. You also
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need a Fortran compiler, which is not included with Xcode: you should use a
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recent GFortran from an OS X package manager (like Homebrew).
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Please do NOT use GFortran from `hpc.sourceforge.net <http://hpc.sourceforge.net>`_,
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it is known to generate buggy SciPy binaries.
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You should also use a BLAS/LAPACK library from an OS X package manager.
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ATLAS, OpenBLAS, and MKL all work.
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As of SciPy version 1.2.0, we do not support compiling against the system
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Accelerate library for BLAS and LAPACK. It does not support a sufficiently
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recent LAPACK interface.
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Linux
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-----
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Most common distributions include all the dependencies. You will need to
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install a BLAS/LAPACK (all of ATLAS, OpenBLAS, MKL work fine) including
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development headers, as well as development headers for Python itself. Those
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are typically packaged as python-dev.
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INSTALLING SCIPY
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================
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For the latest information, see the website:
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https://www.scipy.org
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Development version from Git
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----------------------------
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Use the command::
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git clone https://github.com/scipy/scipy.git
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cd scipy
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git clean -xdf
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python setup.py install --user
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Documentation
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-------------
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Type::
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cd scipy/doc
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make html
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From tarballs
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-------------
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Unpack ``SciPy-<version>.tar.gz``, change to the ``SciPy-<version>/``
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directory, and run::
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pip install . -v --user
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This may take several minutes to half an hour depending on the speed of your
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computer.
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TESTING
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=======
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To test SciPy after installation (highly recommended), execute in Python::
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>>> import scipy
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>>> scipy.test()
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To run the full test suite use::
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>>> scipy.test('full')
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If you are upgrading from an older SciPy release, please test your code for any
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deprecation warnings before and after upgrading to avoid surprises:
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$ python -Wd -c my_code_that_shouldnt_break.py
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Please note that you must have version 1.0 or later of the Pytest test
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framework installed in order to run the tests. More information about Pytest is
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available on the website__.
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__ https://pytest.org/
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COMPILER NOTES
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==============
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You can specify which Fortran compiler to use by using the following
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install command::
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python setup.py config_fc --fcompiler=<Vendor> install
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To see a valid list of <Vendor> names, run::
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python setup.py config_fc --help-fcompiler
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IMPORTANT: It is highly recommended that all libraries that SciPy uses (e.g.
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BLAS and ATLAS libraries) are built with the same Fortran compiler. In most
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cases, if you mix compilers, you will not be able to import SciPy at best, and will have
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crashes and random results at worst.
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UNINSTALLING
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============
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When installing with ``python setup.py install`` or a variation on that, you do
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not get proper uninstall behavior for an older already installed SciPy version.
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In many cases that's not a problem, but if it turns out to be an issue, you
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need to manually uninstall it first (remove from e.g. in
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``/usr/lib/python3.4/site-packages/scipy`` or
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``$HOME/lib/python3.4/site-packages/scipy``).
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Alternatively, you can use ``pip install . --user`` instead of ``python
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setup.py install --user`` in order to get reliable uninstall behavior.
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The downside is that ``pip`` doesn't show you a build log and doesn't support
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incremental rebuilds (it copies the whole source tree to a tempdir).
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TROUBLESHOOTING
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===============
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If you experience problems when building/installing/testing SciPy, you
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can ask help from scipy-user@python.org or scipy-dev@python.org mailing
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lists. Please include the following information in your message:
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NOTE: You can generate some of the following information (items 1-5,7)
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in one command::
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python -c 'from numpy.f2py.diagnose import run; run()'
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1) Platform information::
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python -c 'import os, sys; print(os.name, sys.platform)'
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uname -a
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OS, its distribution name and version information
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etc.
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2) Information about C, C++, Fortran compilers/linkers as reported by
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the compilers when requesting their version information, e.g.,
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the output of
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::
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gcc -v
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g77 --version
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3) Python version::
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python -c 'import sys; print(sys.version)'
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4) NumPy version::
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python -c 'import numpy; print(numpy.__version__)'
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5) ATLAS version, the locations of atlas and lapack libraries, building
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information if any. If you have ATLAS version 3.3.6 or newer, then
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give the output of the last command in
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::
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cd scipy/Lib/linalg
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python setup_atlas_version.py build_ext --inplace --force
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python -c 'import atlas_version'
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7) The output of the following commands
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::
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python INSTALLDIR/numpy/distutils/system_info.py
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where INSTALLDIR is, for example, /usr/lib/python3.4/site-packages/.
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8) Feel free to add any other relevant information.
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For example, the full output (both stdout and stderr) of the SciPy
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installation command can be very helpful. Since this output can be
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rather large, ask before sending it into the mailing list (or
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better yet, to one of the developers, if asked).
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9) In case of failing to import extension modules, the output of
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::
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ldd /path/to/ext_module.so
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can be useful.
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