You cannot select more than 25 topics
Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
250 lines
6.8 KiB
ReStructuredText
250 lines
6.8 KiB
ReStructuredText
Building and installing SciPy
|
|
+++++++++++++++++++++++++++++
|
|
|
|
See https://www.scipy.org/install.html
|
|
|
|
.. Contents::
|
|
|
|
|
|
INTRODUCTION
|
|
============
|
|
|
|
It is *strongly* recommended that you use either a complete scientific Python
|
|
distribution or binary packages on your platform if they are available, in
|
|
particular on Windows and Mac OS X. You should not attempt to build SciPy if
|
|
you are not familiar with compiling software from sources.
|
|
|
|
Recommended distributions are:
|
|
|
|
- Enthought Canopy (https://www.enthought.com/products/canopy/)
|
|
- Anaconda (https://www.anaconda.com)
|
|
- Python(x,y) (https://python-xy.github.io/)
|
|
- WinPython (https://winpython.github.io/)
|
|
|
|
The rest of this install documentation summarizes how to build Scipy. Note
|
|
that more extensive (and possibly more up-to-date) build instructions are
|
|
maintained at https://scipy.github.io/devdocs/building/
|
|
|
|
|
|
PREREQUISITES
|
|
=============
|
|
|
|
SciPy requires the following software installed for your platform:
|
|
|
|
1) Python__ 2.7 or >= 3.4
|
|
|
|
__ https://www.python.org
|
|
|
|
2) NumPy__ >= 1.8.2
|
|
|
|
__ https://www.numpy.org/
|
|
|
|
3) For building from source: setuptools__
|
|
|
|
__ https://github.com/pypa/setuptools
|
|
|
|
4) If you want to build the documentation: Sphinx__ >= 1.2.1
|
|
|
|
__ http://www.sphinx-doc.org/
|
|
|
|
5) If you want to build SciPy master or other unreleased version from source
|
|
(Cython-generated C sources are included in official releases):
|
|
Cython__ >= 0.23.4
|
|
|
|
__ http://cython.org/
|
|
|
|
Windows
|
|
-------
|
|
|
|
Compilers
|
|
~~~~~~~~~
|
|
|
|
There are two ways to build Scipy on Windows:
|
|
|
|
1. Use Intel MKL, and Intel compilers or ifort + MSVC. This is what Anaconda
|
|
and Enthought Canopy use.
|
|
2. Use MSVC + gfortran with OpenBLAS. This is how the SciPy Windows wheels are
|
|
built.
|
|
|
|
Mac OS X
|
|
--------
|
|
|
|
It is recommended to use gcc or clang, both work fine. Gcc is available for
|
|
free when installing Xcode, the developer toolsuite on Mac OS X. You also
|
|
need a fortran compiler, which is not included with Xcode: you should use a
|
|
recent gfortran from an OS X package manager (like Homebrew).
|
|
|
|
Please do NOT use gfortran from `hpc.sourceforge.net <http://hpc.sourceforge.net>`_,
|
|
it is known to generate buggy scipy binaries.
|
|
|
|
You should also use a BLAS/LAPACK library from an OS X package manager.
|
|
ATLAS, OpenBLAS, and MKL all work.
|
|
|
|
As of Scipy version 1.2.0, we do not support compiling against the system
|
|
Accelerate library for BLAS and LAPACK. It does not support a sufficiently
|
|
recent LAPACK interface.
|
|
|
|
Linux
|
|
-----
|
|
|
|
Most common distributions include all the dependencies. You will need to
|
|
install a BLAS/LAPACK (all of ATLAS, OpenBLAS, MKL work fine) including
|
|
development headers, as well as development headers for Python itself. Those
|
|
are typically packaged as python-dev
|
|
|
|
|
|
INSTALLING SCIPY
|
|
================
|
|
|
|
For the latest information, see the web site:
|
|
|
|
https://www.scipy.org
|
|
|
|
|
|
Development version from Git
|
|
----------------------------
|
|
Use the command::
|
|
|
|
git clone https://github.com/scipy/scipy.git
|
|
|
|
cd scipy
|
|
git clean -xdf
|
|
python setup.py install --user
|
|
|
|
Documentation
|
|
-------------
|
|
Type::
|
|
|
|
cd scipy/doc
|
|
make html
|
|
|
|
From tarballs
|
|
-------------
|
|
Unpack ``SciPy-<version>.tar.gz``, change to the ``SciPy-<version>/``
|
|
directory, and run::
|
|
|
|
pip install . -v --user
|
|
|
|
This may take several minutes to half an hour depending on the speed of your
|
|
computer.
|
|
|
|
|
|
TESTING
|
|
=======
|
|
|
|
To test SciPy after installation (highly recommended), execute in Python
|
|
|
|
>>> import scipy
|
|
>>> scipy.test()
|
|
|
|
To run the full test suite use
|
|
|
|
>>> scipy.test('full')
|
|
|
|
If you are upgrading from an older SciPy release, please test your code for any
|
|
deprecation warnings before and after upgrading to avoid surprises:
|
|
|
|
$ python -Wd -c my_code_that_shouldnt_break.py
|
|
|
|
Please note that you must have version 1.0 or later of the Pytest test
|
|
framework installed in order to run the tests. More information about Pytest is
|
|
available on the website__.
|
|
|
|
__ https://pytest.org/
|
|
|
|
COMPILER NOTES
|
|
==============
|
|
|
|
You can specify which Fortran compiler to use by using the following
|
|
install command::
|
|
|
|
python setup.py config_fc --fcompiler=<Vendor> install
|
|
|
|
To see a valid list of <Vendor> names, run::
|
|
|
|
python setup.py config_fc --help-fcompiler
|
|
|
|
IMPORTANT: It is highly recommended that all libraries that scipy uses (e.g.
|
|
BLAS and ATLAS libraries) are built with the same Fortran compiler. In most
|
|
cases, if you mix compilers, you will not be able to import Scipy at best, have
|
|
crashes and random results at worst.
|
|
|
|
UNINSTALLING
|
|
============
|
|
|
|
When installing with ``python setup.py install`` or a variation on that, you do
|
|
not get proper uninstall behavior for an older already installed Scipy version.
|
|
In many cases that's not a problem, but if it turns out to be an issue, you
|
|
need to manually uninstall it first (remove from e.g. in
|
|
``/usr/lib/python3.4/site-packages/scipy`` or
|
|
``$HOME/lib/python3.4/site-packages/scipy``).
|
|
|
|
Alternatively, you can use ``pip install . --user`` instead of ``python
|
|
setup.py install --user`` in order to get reliable uninstall behavior.
|
|
The downside is that ``pip`` doesn't show you a build log and doesn't support
|
|
incremental rebuilds (it copies the whole source tree to a tempdir).
|
|
|
|
TROUBLESHOOTING
|
|
===============
|
|
|
|
If you experience problems when building/installing/testing SciPy, you
|
|
can ask help from scipy-user@python.org or scipy-dev@python.org mailing
|
|
lists. Please include the following information in your message:
|
|
|
|
NOTE: You can generate some of the following information (items 1-5,7)
|
|
in one command::
|
|
|
|
python -c 'from numpy.f2py.diagnose import run; run()'
|
|
|
|
1) Platform information::
|
|
|
|
python -c 'import os, sys; print(os.name, sys.platform)'
|
|
uname -a
|
|
OS, its distribution name and version information
|
|
etc.
|
|
|
|
2) Information about C,C++,Fortran compilers/linkers as reported by
|
|
the compilers when requesting their version information, e.g.,
|
|
the output of
|
|
::
|
|
|
|
gcc -v
|
|
g77 --version
|
|
|
|
3) Python version::
|
|
|
|
python -c 'import sys; print(sys.version)'
|
|
|
|
4) NumPy version::
|
|
|
|
python -c 'import numpy; print(numpy.__version__)'
|
|
|
|
5) ATLAS version, the locations of atlas and lapack libraries, building
|
|
information if any. If you have ATLAS version 3.3.6 or newer, then
|
|
give the output of the last command in
|
|
::
|
|
|
|
cd scipy/Lib/linalg
|
|
python setup_atlas_version.py build_ext --inplace --force
|
|
python -c 'import atlas_version'
|
|
|
|
7) The output of the following commands
|
|
::
|
|
|
|
python INSTALLDIR/numpy/distutils/system_info.py
|
|
|
|
where INSTALLDIR is, for example, /usr/lib/python3.4/site-packages/.
|
|
|
|
8) Feel free to add any other relevant information.
|
|
For example, the full output (both stdout and stderr) of the SciPy
|
|
installation command can be very helpful. Since this output can be
|
|
rather large, ask before sending it into the mailing list (or
|
|
better yet, to one of the developers, if asked).
|
|
|
|
9) In case of failing to import extension modules, the output of
|
|
::
|
|
|
|
ldd /path/to/ext_module.so
|
|
|
|
can be useful.
|