Installation

Quick overview

For those users who have already read this page, and need a quick refresher (or prefer to act first, and read documentation later), the following commands can be used to install Sherpa, depending on your environment and set up.

conda install -c sherpa sherpa
pip install sherpa
python setup.py install

Requirements

Sherpa has the following requirements:

  • Python 3.5, 3.6, or 3.7 (there has been limited testing with Python 3.8)

  • NumPy (the exact lower limit has not been determined, but it is likely to be 1.7.0 or later)

  • Linux or OS-X (patches to add Windows support are welcome)

Sherpa can take advantage of the following Python packages if installed:

  • Astropy: for reading and writing files in FITS format. The minimum required version of astropy is version 1.3, although only versions 2 and higher are used in testing (version 3.2 is known to cause problems, but version 3.2.1 is okay).

  • matplotlib: for visualisation of one-dimensional data or models, one- or two- dimensional error analysis, and the results of Monte-Carlo Markov Chain runs. There are no known incompatabilities with matplotlib, but there has only been limited testing. Please report any problems you find.

The Sherpa build can be configured to create the sherpa.astro.xspec module, which provides the models and utility functions from the XSPEC. The supported versions of XSPEC are 12.11.1, 12.11.0, 12.10.1 (patch level a or later), 12.10.0, 12.9.1, and 12.9.0.

Interactive display and manipulation of two-dimensional images is available if the DS9 image viewer and the XPA commands are installed. It is expected that any recent version of DS9 can be used.

Releases and version numbers

The Sherpa release policy has a major release at the start of the year, corresponding to the code that is released in the previous December as part of the CIAO release, followed by several smaller releases throughout the year.

Information on the Sherpa releases is available from the Zenodo page for Sherpa, using the Digital Object Identifier (DOI) 10.5281/zenodo.593753.

What version of Sherpa is installed?

The version number and git commit id of Sherpa can be retrieved from the sherpa._version module using the following command:

% python -c 'import sherpa._version; print(sherpa._version.get_versions())'
{'version': '4.10.0', 'full': 'c7732043124b08d5e949b9a95c2eb6833e009421'}

Citing Sherpa

Information on citing Sherpa can be found from the CITATION document in the Sherpa repository, or from the Sherpa Zenodo page.

Installing a pre-compiled version of Sherpa

Additional useful Python packages include astropy, matplotlib, and ipython-notebook.

Using the Anaconda python distribution

The Chandra X-ray Center provides releases of Sherpa that can be installed using Anaconda from the sherpa channel. First check to see what the latest available version is by using:

conda install -c sherpa sherpa --dry-run

and then, if there is a version available and there are no significant upgrades to the dependencies, Sherpa can be installed using:

conda install -c sherpa sherpa

It is strongly suggested that Sherpa is installed into a named conda environment (i.e. not the default environment).

Using pip

Sherpa is also available from PyPI at https://pypi.python.org/pypi/sherpa and can be installed with the command:

pip install sherpa

The NumPy package must already have been installed for this to work.

Building from source

Prerequisites

The prerequisites for building from source are:

  • Python versions: 3.5, 3.6, 3.7

  • Python packages: setuptools, numpy

  • System: gcc, g++, make, flex, bison (the aim is to support recent versions of these tools; please report problems to the Sherpa issue tracker).

It is highly recommended that matplotlib and astropy be installed before building Sherpa, to avoid skipping a number of tests in the test suite.

The full Sherpa test suite requires pytest and pytest-xvfb. These packages should be installed automatically for you by the test suite if they do not already exist.

Note

As of the Sherpa 4.10.1 release, a Fortran compiler is no-longer required to build Sherpa.

Obtaining the source package

The source code can be obtained as a release package from Zenodo - e.g. the Sherpa 4.10.0 release - or from the Sherpa repository on GitHub, either a release version, such as the 4.10.0 tag, or the master branch (which is not guaranteed to be stable).

For example:

git clone git://github.com/sherpa/sherpa.git
cd sherpa
git checkout 4.10.0

will use the 4.10.0 tag (although we strongly suggest using a newer release now!).

Configuring the build

The Sherpa build is controlled by the setup.cfg file in the root of the Sherpa source tree. These configuration options include:

FFTW

Sherpa ships with the fftw library source code and builds it by default. To use a different version, change the fftw options in the sherpa_config section of the setup.cfg file. The options to change are:

fftw=local
fftw-include_dirs=/usr/local/include
fftw-lib-dirs=/use/local/lib
fftw-libraries=fftw3

The fftw option must be set to local and then the remaining options changed to match the location of the local installation.

XSPEC

Note

The version number of XSPEC must be specified using the xspec_version configuration option, as described below. This is a change from previous releases of Sherpa, but is required in order to support changes made in XSPEC 12.10.0.

Sherpa can be built to use the Astronomy models provided by XSPEC versions 12.11.1, 12.11.0, 12.10.1 (patch level a or later), 12.10.0, 12.9.1, and 12.9.0. To enable XSPEC support, several changes must be made to the xspec_config section of the setup.cfg file. The available options (with default values) are:

with-xspec = False
xspec_version = 12.9.0
xspec_lib_dirs = None
xspec_include_dirs = None
xspec_libraries = XSFunctions XSModel XSUtil XS
cfitsio_lib_dirs = None
cfitsio_libraries = cfitsio
ccfits_lib_dirs = None
ccfits_libraries = CCfits
wcslib_lib_dirs = None
wcslib_libraries = wcs
gfortran_lib_dirs = None
gfortran_libraries = gfortran

To build the sherpa.astro.xspec module, the with-xspec option must be set to True and the xspec_version option set to the correct version string (the XSPEC patch level must not be included), and then the remaining options depend on the version of XSPEC and whether the XSPEC model library or the full XSPEC system has been installed.

In the examples below, the $HEADAS value must be replaced by the actual path to the HEADAS installation, and the versions of the libraries - such as CCfits_2.5 - may need to be changed to match the contents of the XSPEC installation.

  1. If the full XSPEC 12.11.1 system has been built then use:

    with-xspec = True
    xspec_version = 12.11.1
    xspec_lib_dirs = $HEADAS/lib
    xspec_include_dirs = $HEADAS/include
    xspec_libraries = XSFunctions XSUtil XS hdsp_6.28
    ccfits_libraries = CCfits_2.5
    wcslib_libraries = wcs-5.19.1
    

    where the version numbers were taken from version 6.28 of HEASOFT and may need updating with a newer release.

  2. If the full XSPEC 12.11.0 system has been built then use:

    with-xspec = True
    xspec_version = 12.11.0
    xspec_lib_dirs = $HEADAS/lib
    xspec_include_dirs = $HEADAS/include
    xspec_libraries = XSFunctions XSUtil XS hdsp_6.27
    ccfits_libraries = CCfits_2.5
    wcslib_libraries = wcs-5.19.1
    

    where the version numbers were taken from version 6.27 of HEASOFT and may need updating with a newer release.

  3. If the full XSPEC 12.10.1 system has been built then use:

    with-xspec = True
    xspec_version = 12.10.1
    xspec_lib_dirs = $HEADAS/lib
    xspec_include_dirs = $HEADAS/include
    xspec_libraries = XSFunctions XSUtil XS hdsp_6.26
    ccfits_libraries = CCfits_2.5
    wcslib_libraries = wcs-5.19.1
    

    where the version numbers were taken from version 6.26.1 of HEASOFT and may need updating with a newer release.

  4. If the full XSPEC 12.10.0 system has been built then use:

    with-xspec = True
    xspec_version = 12.10.0
    xspec_lib_dirs = $HEADAS/lib
    xspec_include_dirs = $HEADAS/include
    xspec_libraries = XSFunctions XSModel XSUtil XS hdsp_3.0
    ccfits_libraries = CCfits_2.5
    wcslib_libraries = wcs-5.16
    
  5. If the full XSPEC 12.9.x system has been built then use:

    with-xspec = True
    xspec_version = 12.9.1
    xspec_lib_dirs = $HEADAS/lib
    xspec_include_dirs = $HEADAS/include
    xspec_libraries = XSFunctions XSModel XSUtil XS
    ccfits_libraries = CCfits_2.5
    wcslib_libraries = wcs-5.16
    

    changing 12.9.1 to 12.9.0 as appropriate.

  6. If the model-only build of XSPEC has been installed, then the configuration is similar, but the library names may not need version numbers and locations, depending on how the cfitsio, CCfits, and wcs libraries were installed.

    Note that XSPEC 12.10.0 introduces a new --enable-xs-models-only flag when building HEASOFT which simplifies the installation of these extra libraries, but can cause problems for the Sherpa build.

A common problem is to set one or both of the xspec_lib_dirs and xspec_lib_include options to the value of $HEADAS instead of $HEADAS/lib and $HEADAS/include (after expanding out the environment variable). Doing so will cause the build to fail with errors about being unable to find various XSPEC libraries such as XSFunctions and XSModel.

The gfortran options should be adjusted if there are problems using the XSPEC module.

In order for the XSPEC module to be used from Python, the HEADAS environment variable must be set before the sherpa.astro.xspec module is imported.

The Sherpa test suite includes an extensive set of tests of this module, but a quick check of an installed version can be made with the following command:

% python -c 'from sherpa.astro import xspec; print(xspec.get_xsversion())'
12.11.1

Warning

The --enable-xs-models-only flag with XSPEC 12.10.0 is known to cause problems for Sherpa. It is strongly recommended that either that the full XSPEC distribution is built, or that the XSPEC installation from CIAO 4.11 is used.

Other options

The remaining options in the setup.cfg file allow Sherpa to be built in specific environments, such as when it is built as part of the CIAO analysis system. Please see the comments in the setup.cfg file for more information on these options.

Installing all dependencies with conda

See Install from source in conda for details on how to set up all dependencies for the Sherpa build with conda.

Building and Installing

It is highly recommended that some form of virtual environment, such as a conda environment or that provided by Virtualenv, be used when building and installing Sherpa.

Warning

When building Sherpa on macOS within a conda environment, the following environment variable must be set otherwise importing Sherpa will crash Python:

export PYTHON_LDFLAGS=' '

That is, the variable is set to a space, not the empty string.

A standard installation

From the root of the Sherpa source tree, Sherpa can be built by saying:

python setup.py build

and installed with one of:

python setup.py install
python setup.py install --user

A development build

The develop option should be used when developing Sherpa (such as adding new functionality or fixing a bug):

python setup.py develop

Tests can then be run with the test option:

python setup.py test

The test command is a wrapper that calls pytest under the hood, and includes the develop command.

You can pass additional arguments to pytest with the -a or --pytest-args arguments. As examples, the following two commands run all the tests in test_data.py and then a single named test in this file:

python setup.py test -a sherpa/tests/test_data.py
python setup.py test -a sherpa/tests/test_data.py::test_data_eval_model

The full set of options, including those added by the Sherpa test suite - which are listed at the end of the custom options section - can be found with:

python setup.py test -a "--pyargs sherpa --help"

and to pass an argument to the Sherpa test suite (there are currently two options, namely --test-data and --runslow):

python setup.py test -a "--pyargs sherpa --runslow"

Note

If you run both install and develop or test in the same Python environment you end up with two competing installations of Sherpa which result in unexpected behavior. If this happens, simply run pip uninstall sherpa as many times as necessary, until you get an error message that no more Sherpa installations are available. At this point you can re-install Sherpa.

The same issue may occur if you install a Sherpa binary release and then try to build Sherpa from source in the same environment.

The Sherpa test data suite can be installed to reduce the number of tests that are skipped with the following (this is only for those builds which used git to access the source code):

git submodule init
git submodule update

When both the DS9 image viewer and XPA toolset are installed, the test suite will include tests that check that DS9 can be used from Sherpa. This causes several copies of the DS9 viewer to be created, which can be distracting, as it can cause loss of mouse focus (depending on how X-windows is set up). This can be avoided by installing the X virtual-frame buffer (Xvfb).

Note

Although the standard Python setuptools approach is used to build Sherpa, there may be issues when using some of the other build targets, such as build_ext. Please report these to the Sherpa issues page.

Building the documentation

Building the documentation requires the Sherpa source code and several additional packages:

  • Sphinx, version 1.8 or later

  • The sphinx_rtd_theme

  • NumPy and sphinx-astropy (the latter can be installed with pip).

  • Graphviz (for the inheritance diagrams)

With these installed, the documentation can be built with the build_sphinx target:

python setup.py build_sphinx

This can be done without building Sherpa (either an installation or development version), since Mock objects are used to represent compiled and optional components.

The documentation should be placed in build/sphinx/html/index.html, although this may depend on what version of Sphinx is used.

It is also possible to build the documentation from within the docs/ directory:

cd docs
make html

This places the documentation in _build/html/index.html.

Testing the Sherpa installation

A very-brief “smoke” test can be run from the command-line with the sherpa_smoke executable:

sherpa_smoke
WARNING: failed to import sherpa.astro.xspec; XSPEC models will not be available
----------------------------------------------------------------------
Ran 7 tests in 0.456s

OK (skipped=5)

or from the Python prompt:

>>> import sherpa
>>> sherpa.smoke()
WARNING: failed to import sherpa.astro.xspec; XSPEC models will not be available
----------------------------------------------------------------------
Ran 7 tests in 0.447s

OK (skipped=5)

This provides basic validation that Sherpa has been installed correctly, but does not run many functional tests. The screen output will include additional warning messages if the astropy or matplotlib packages are not installed, or Sherpa was built without support for the XSPEC model library.

The Sherpa installation also includes the sherpa_test command-line tool which will run through the Sherpa test suite (the number of tests depends on what optional packages are available and how Sherpa was configured when built):

sherpa_test

The sherpa Anaconda channel contains the sherpatest package, which provides a number of data files in ASCII and FITS formats. This is only useful when developing Sherpa, since the package is large. It will automatically be picked up by the sherpa_test script once it is installed.

Testing the documentation with Travis

There is a documentation build included as part of the Travis-CI test suite, but it is not set up to do much validation. That is, you need to do something quite severe to break this build. Please see issue 491 for more information.