Building from source#
Note
If you are only trying to install SciPy, we recommend using binaries - see Installation for details on that.
Building SciPy from source requires setting up system-level dependencies (compilers, BLAS/LAPACK libraries, etc.) first, and then invoking a build. The build may be done in order to install SciPy for local usage, develop SciPy itself, or build redistributable binary packages. And it may be desired to customize aspects of how the build is done. This guide will cover all these aspects. In addition, it provides background information on how the SciPy build works, and links to up-to-date guides for generic Python build & packaging documentation that is relevant.
System-level dependencies#
SciPy uses compiled code for speed, which means you need compilers and some other system-level (i.e, non-Python / non-PyPI) dependencies to build it on your system.
Note
If you are using Conda, you can skip the steps in this section - with the
exception of installing compilers for Windows or the Apple Developer Tools
for macOS. All other dependencies will be installed automatically by the
mamba env create -f environment.yml
command.
If you want to use the system Python and pip
, you will need:
C, C++, and Fortran compilers (typically
gcc
,g++
, andgfortran
).Python header files (typically a package named
python3-dev
orpython3-devel
)BLAS and LAPACK libraries. OpenBLAS is the SciPy default; other variants include ATLAS and MKL.
pkg-config
for dependency detection.
To install SciPy build requirements, you can do:
sudo apt install -y gcc g++ gfortran libopenblas-dev liblapack-dev pkg-config python3-pip python3-dev
Alternatively, you can do:
sudo apt build-dep scipy
This command installs whatever is needed to build SciPy, with the advantage that new dependencies or updates to required versions are handled by the package managers.
To install SciPy build requirements, you can do:
sudo dnf install gcc-gfortran python3-devel openblas-devel lapack-devel pkgconfig
Alternatively, you can do:
sudo dnf builddep scipy
This command installs whatever is needed to build SciPy, with the advantage that new dependencies or updates to required versions are handled by the package managers.
To install SciPy build requirements, you can do:
sudo yum install gcc-gfortran python3-devel openblas-devel lapack-devel pkgconfig
Alternatively, you can do:
sudo yum-builddep scipy
This command installs whatever is needed to build SciPy, with the advantage that new dependencies or updates to required versions are handled by the package managers.
To install SciPy build requirements, you can do:
sudo pacman -S gcc-fortran openblas pkgconf
Install Apple Developer Tools. An easy way to do this is to open a terminal window, enter the command:
xcode-select --install
and follow the prompts. Apple Developer Tools includes Git, the Clang C/C++ compilers, and other development utilities that may be required.
Do not use the macOS system Python. Instead, install Python with the python.org installer or with a package manager like Homebrew, MacPorts or Fink.
The other system dependencies you need are a Fortran compiler, BLAS and LAPACK libraries, and pkg-config. They’re easiest to install with Homebrew:
brew install gfortran openblas pkg-config
Note
export PKG_CONFIG_PATH="/opt/homebrew/opt/openblas/lib/pkgconfig"
may need to be used in order for the build system to detect OpenBlas.
Note
As of SciPy >=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. This is planned to change in 2023, because macOS 13.3 introduced a major upgrade to Accelerate which resolved all known issues.
A compatible set of C, C++ and Fortran compilers is needed to build SciPy. This is trickier on Windows than on other platforms, because MSVC does not support Fortran, and gfortran and MSVC can’t be used together. You will need one of these sets of compilers:
Mingw-w64 compilers (
gcc
,g++
,gfortran
) - recommended, because it’s easiest to install and is what we use for SciPy’s own CI and binariesMSVC + Intel Fortran (
ifort
)Intel compilers (
icc
,ifort
)
Compared to macOS and Linux, building SciPy on Windows is a little more difficult, due to the need to set up these compilers. It is not possible to just call a one-liner on the command prompt as you would on other platforms.
First, install Microsoft Visual Studio - the 2019 Community Edition or any newer version will work (see the Visual Studio download site). This is needed even if you use the MinGW-w64 or Intel compilers, in order to ensure you have the Windows Universal C Runtime (the other components of Visual Studio are not needed when using Mingw-w64, and can be deselected if desired, to save disk space).
There are several sources of binaries for MinGW-w64. We recommend the RTools versions, which can be installed with Chocolatey (see Chocolatey install instructions here):
choco install rtools -y --no-progress --force --version=4.0.0.20220206
In case of issues, we recommend using the exact same version as used in the SciPy GitHub Actions CI jobs for Windows.
The MSVC installer does not put the compilers on the system path, and
the install location may change. To query the install location, MSVC
comes with a vswhere.exe
command-line utility. And to make the
C/C++ compilers available inside the shell you are using, you need to
run a .bat
file for the correct bitness and architecture (e.g., for
64-bit Intel CPUs, use vcvars64.bat
).
For detailed guidance, see Use the Microsoft C++ toolset from the command line.
Similar to MSVC, the Intel compilers are designed to be used with an
activation script (Intel\oneAPI\setvars.bat
) that you run in the
shell you are using. This makes the compilers available on the path.
For detailed guidance, see
Get Started with the Intel® oneAPI HPC Toolkit for Windows.
Note
Compilers should be on the system path (i.e., the PATH
environment
variable should contain the directory in which the compiler executables
can be found) in order to be found, with the exception of MSVC which
will be found automatically if and only if there are no other compilers
on the PATH
. You can use any shell (e.g., Powershell, cmd
or
Git Bash) to invoke a build. To check that this is the case, try
invoking a Fortran compiler in the shell you use (e.g., gfortran
--version
or ifort --version
).
Warning
When using a conda environment it is possible that the environment
creation will not work due to an outdated Fortran compiler. If that
happens, remove the compilers
entry from environment.yml
and
try again. The Fortran compiler should be installed as described in
this section.
Building SciPy from source#
If you want to only install SciPy from source once and not do any development
work, then the recommended way to build and install is to use pip
.
Otherwise, conda is recommended.
Note
If you don’t have a conda installation yet, we recommend using Mambaforge; any conda flavor will work though.
Building from source to use SciPy#
If you are using a conda environment, pip
is still the tool you use to
invoke a from-source build of SciPy. It is important to always use the
--no-build-isolation
flag to the pip install
command, to avoid
building against a numpy
wheel from PyPI. In order for that to work you
must first install the remaining build dependencies into the conda
environment:
# Either install all SciPy dev dependencies into a fresh conda environment
mamba env create -f environment.yml
# Or, install only the required build dependencies
mamba install python numpy cython pythran pybind11 compilers openblas meson-python pkg-config
# To build the latest stable release:
pip install scipy --no-build-isolation --no-binary scipy
# To build a development version, you need a local clone of the SciPy git repository:
git clone https://github.com/scipy/scipy.git
cd scipy
git submodule update --init
pip install . --no-build-isolation
# To build the latest stable release:
pip install scipy --no-binary scipy
# To build a development version, you need a local clone of the SciPy git repository:
git clone https://github.com/scipy/scipy.git
cd scipy
git submodule update --init
pip install .
Building from source for SciPy development#
If you want to build from source in order to work on SciPy itself, first clone the SciPy repository:
git clone https://github.com/scipy/scipy.git
cd scipy
git submodule update --init
Then you want to do the following:
Create a dedicated development environment (virtual environment or conda environment),
Install all needed dependencies (build, and also test, doc and optional dependencies),
Build SciPy with our
dev.py
developer interface.
Step (3) is always the same, steps (1) and (2) are different between conda and virtual environments:
To create a scipy-dev
development environment with every required and
optional dependency installed, run:
mamba env create -f environment.yml
mamba activate scipy-dev
Note
There are many tools to manage virtual environments, like venv
,
virtualenv
/virtualenvwrapper
, pyenv
/pyenv-virtualenv
,
Poetry, PDM, Hatch, and more. Here we use the basic venv
tool that
is part of the Python stdlib. You can use any other tool; all we need is
an activated Python environment.
Create and activate a virtual environment in a new directory named venv
(
note that the exact activation command may be different based on your OS and shell
- see “How venvs work”
in the venv
docs).
python -m venv venv
source venv/bin/activate
python -m venv venv
source venv/bin/activate
python -m venv venv
.\venv\Scripts\activate
Then install the Python-level dependencies (see pyproject.toml
) from
PyPI with:
# All dependencies
python -m pip install -r requirements/all.txt
# Alternatively, you can install just the dependencies for certain
# development tasks:
# Build and dev dependencies (for `python dev.py {build, lint, mypy}`)
python -m pip install -r requirements/build.txt -r requirements/dev.txt
# Doc dependencies (for `python dev.py {doc, refguide-check}`)
python -m pip install -r requirements/doc.txt
# Test dependencies (for `python dev.py {test, bench, refguide-check}`)
python -m pip install -r requirements/test.txt
To build SciPy in an activated development environment, run:
python dev.py build
This will install SciPy inside the repository (by default in a
build-install
directory). You can then run tests (python dev.py test
),
drop into IPython (python dev.py ipython
), or take other development steps
like build the html documentation or running benchmarks. The dev.py
interface is self-documenting, so please see python dev.py --help
and
python dev.py <subcommand> --help
for detailed guidance.
IDE support & editable installs
While the dev.py
interface is our recommended way of working on SciPy,
it has one limitation: because of the custom install location, SciPy
installed using dev.py
will not be recognized automatically within an
IDE (e.g., for running a script via a “run” button, or setting breakpoints
visually). This will work better with an in-place build (or “editable
install”).
Editable installs are supported. It is important to understand that you
may use either an editable install or dev.py in a given repository clone,
but not both. If you use editable installs, you have to use pytest
and other development tools directly instead of using dev.py
.
To use an editable install, ensure you start from a clean repository (run
git clean -xdf
if you’ve built with dev.py
before) and have all
dependencies set up correctly as described higher up on this page. Then
do:
# Note: the --no-build-isolation is important! meson-python will
# auto-rebuild each time SciPy is imported by the Python interpreter.
pip install -e . --no-build-isolation
# To run the tests for, e.g., the `scipy.linalg` module:
pytest scipy/linalg
When making changes to SciPy code, including to compiled code, there is no
need to manually rebuild or reinstall. When you run git clean -xdf
,
which removes the built extension modules, remember to also uninstall SciPy
with pip uninstall scipy
.
See the meson-python documentation on editable installs for more details on how things work under the hood.