sherpa: Sherpa 4.8.1

Sherpa 4.8.1

Sherpa 4.8.1 is the standalone counterpart to the 4.8.0 release, which was focused on supporting CIAO 4.8. In particular, this version introduces support for newer versions of the dependencies, along with some feature enhancements, bug fixes and additional, more accurate tests.

The newly supported dependencies:

• matplotlib v1.5
• numpy 1.10 and 1.11 (with and without mkl support)
• xspec v12.9.0i (when building from source)
• astropy v1.1.2
• region library v4.8 (from CIAO 4.8)

Please see the Caveats section for known issues regarding the XSpec support.

Mode details below (infrastructure changes are not shown):

102: fix issues when writing out FITS files using the save_pha and

save_table commands when using the astropy/pyfits backend (bug #46). Fix for when the notice2d_id, notice2d_image, and the ignore version functions are called with an invalid identifier (i.e. an identifier that i snot an integer or string value). The error is now an ArgumentTypeErr with the message "'ids' must be an identifier or list of identifiers". It was a NameError with the message "global name '_argument_type_error' is not defined".

107: Normalize plot labels. There are two main changes for plots of PHA data

sets (and related quantities, such as the source, model, and ARF):

• plots with matplotlib now use the LaTeX support - so that 'cm^2' is now displayed as a superscript; previously they were displayed directly. This does not change the display with the ChIPS backend.

• plots created with plot_source used a different format to other plots when analysis=wavelength, in that LaTeX symbols were used for Angstrom and lambda (in other plots the string 'Angstrom' is used instead). The source plots now match the other plots.

109: fix #103 and #113 in order to support matplotlib v1.5. 116: fix bug #27. The astropy.io.fits/pyfits interface used deprecated

functionality. The code was updated to use the replacement classes/methods when available, falling back to the original code if not. The interfaces that were changed were, when the new symbols are availble, to:

• use astropy.io.fits.BinTableHDU.from_columns rather than astropy.io.fits.new_table

• use astropy.io.fits.Header rather than astropy.io.CardList

137: upgrade CIAO region library to v4.8 138: improve and fix issues in save_all function.

• added a new argument to save_all: if outfile is None then the outfh argument is used to define the output handle (the argument can be any file-like argument, such as a file handle like sys.stdout or the output of open, or a StringIO object)
• setting the clobber argument to save_all now means that the output file (the outfile argument, if not None) is deleted if it already exists; prior to this, the file would be appended to instead
• the source expression is now saved correctly for most cases (e.g. when not using set_full_model); this is bug #97 but also affects non-PHA data sets
• the background model expression was not always written out correctly when using PHA data sets
• quality and grouping arrays of PHA data sets are now stored as 16-byte integers rather than a floating-point value (this has no affect on the results, but matches the OGIP standard)
• fixed up saving the grouping and quality arrays of background PHA data sets (this would only be an issue if the background is being fit, rather than subtracted)
• basic data sets created with the load_arrays function are now written out by save_all as part of the script; this is intended for small datasets and may have problems with precision if used with floating-point arrays
• calls to load_psf are now correctly restored (they may not have been written out correctly if multiple data sets were loaded)
• user models are now written out to disk; this consists of two parts:
• writing out the function that defines the model, which may or may not be possible (if not, a place-holder function is added to the output and a warning displayed).
• the necessary calls to load_user_model and add_user_pars are now included in the output
• the Python code created by save all has undergone several minor changes:
• it now explicitly imports the sherpa.astro.ui module, so that it can be run from the IPython prompt using the %run <filename> command, or directly as python <filename>
• it uses the create_model_component function rather than eval to create model components (this is CXC bug 12146)
• many optional arguments to functions are now given as name=value rather than being a positional argument, to make it clearer what the script is doing.
• calls to load_data have been replaced by more-specific versions - e.g. load_pha and load_image - if appropriate
• there have seen several minor syntactic clean ups to better follow the suggestions from PEP8

When writing out code that defines a user-model, there is no attempt to make sure that modules used by the function are available. These will need to be added, either directly or imported, manually to the output.

151: Ensure AstroPy and Crates behave the same with gzipped files. Change the

behaviour of the AstroPy back end so that it matches that of Crates when given a file name which does not exist, but a compressed version, with the suffix .gz does. The Crates behavior is to read the file. This extends to PHA files whose ancillary files - e.g. those stored in the BACKFILE, ANCRFILE, and RESPFILE keywords - are given as unzipped names, but only the gzipped names exist on disk.

As an example: if pha.fits.gz exists but pha.fits does not, then

load_pha('pha.fits')

will now load the file with either back end. If the response files are set to arf.fits and rmf.fits (via the ANCRFILE and RESPFILE keywords), but only the .gz versions exist, then they will now also be loaded by the AstroPy back end.

153: Make comparison test in calc_chi2datavar_errors less stringent, so to

include the case where sqrt(x)=0.

155: The get_draws function now accepts a user-provided covariance matrix. If

no covariance matrix is provided, the covariance matrix computed by the default implementation is used. Note that covar() must be invoked before invoking get_draws if no covariance matrix is provided, otherwise get_draws will exit with an error.

158: Fix bug that prevented region ascii files to be read in standalone

Sherpa.

165: Remove usage of deprecated numpy API. 185: Fix the problem where if the working directory contained a file called

x or y then the sherpa.astro.ui.image_data() function would fail with the message

DS9Err: Could not display image 187: Fix #92: a more meaningful message is given to the user when

sherpa.astro.io is imported directly and no fits backends are available.

188: Fix #93. The sherpa_test script now tries to install the test

dependencies before running the tests (but not the sherpatest package, which should be installed by the user if necessary, due to its footprint). If this is not possible, and the necessary dependencies (pytest) are not found, then a meaningful message is given to the user with instructions on how to install the dependencies. Also, the dependency on pytest-cov has been removed. Users can enable coverage reports from the command line if necessary.

190: Fix #22 - The datastack package can now be used even if there is no

available plotting backend. In this case, plotting functions will not be available, but the rest of the datastack functionality will.