Sherpa

This version fixes many bugs in the Python 3 support. Moreover, it includes a significant
refactoring of the `Fit` and `Stat` classes that made it possible to fix several bugs
related to the recent `wstat` implementation while making these classes more maintainable
and extensible.

Note that this version deprecates the use of `load_table_model` for XSPEC models.
Sherpa/XSPEC users should use the new `load_xstable_model` function instead.

Details

Infrastructure and minor non-functional changes have been omitted.

242 Avoid use of inspect.getargspec in Python3
Finish off the replacement of inspect.getargspec by inspect.signature.

263 List_data_ids() fails on py3 with mixed id types (Fix 262).
Sherpa was sorting the list of dataset IDs in a non-python3 compliant fashion,
which resulted in issues when using strings and integers together as dataset
IDs. This has now been fixed.

267 add wstat tests
Add several regression tests for wstat.

282 Parallel_map not working on py3 with numcores=1 (Fix 277).
The `utils` function `parallel_map` failed on Python 3 when called with `numcores=1`,
i.e. on systems with only one processor/core. This has been fixed.

283 Sample flux and numpy deprecations (Fix 273 and 276).
The `sample_flux` function was not working under Python 3 if the `scales` argument
was provided. This has been fixed. Also, a `DeprecationWarning` was issued by
`numpy` because during the `sample_flux` execution values were extracted from
an array with non-integer indices. This has also been fixed.

284 String representation of data classes under py3 (Fix 275).
Data classes `DataPHA`, `DataARF`, `DataRMF`, `DataIMG`, and `DataIMGInt` in
`sherpa.astro.data` would throw an exception if users tried to print them as
strings, under Python 3. This has been fixed.

287 Rewrite sherpa.stats.Stat.calc_stat and simplify sherpa.fit.Fit (fix 227 248 289 292).
In order to fix several issues related to the WStat support, and in order to
make the code more maintainable, the `sherpa.stats.Stat.calc_stat` and
`sherpa.fit.Fit` classes have gone through a round of refactoring. This fixes
the following issues: 227 Issues using wstat when grouping/filtering data; 248
backscal column not treated properly for WStat; 289 calc_stat does not error out
if background subtracted data is used with Likelihood statistics; 292 stat info
does not include reduced stat/qval for wstat.

295 Fix display of pileup model in Python 3.5 (Fix 294).
Fix display of instances of `sherpa.astro.models.JDPileup` so that, in Python 3.5,
they can be displayed after the model has been evaluated.

304 replace file -> open (Fix 297).
The `save` and `restore` functions used to use the `file` function which is not
compatible with Python 3. This has now been fixed.

305 Fix python 3 issues with some session commands (Fix 303).
The `set_xlog`, `set_ylog`, and `show_bkg_model` functions were not compatible
with Python 3. This has now been fixed (Issue 303).

307 Move XSPEC table support to load_xstable_model and deprecate its support
in load_table_model (Fix 270).
Add the `load_xstable_model` routine to the `sherpa.astro.ui` module, which
supports loading XSPEC additive or multiplicative (atable and mtable) models.
The support for these models is still available via `load_table_model` in this
release, but it is deprecated. The `read_xstable_model` routine has been added
to the `sherpa.astro.xspec` module.

312 Fix over-zealous code clean up in PR 287 affecting sigmarej.
Fits using the sigmarej iterated-fit method were broken if a filter had been
applied to the data before the fit and there are any bins that get ignored at
larger bin values than the filtered-out data. (This fixes a subtle regression
introduced by 287).

313 Allow sequence=None when using gridsearch and Python 3.5 (Fix 309).
Allow the `gridsearch` optimiser to be used with the `sequence` option set
to `None` for Python 3.5.

Caveats

The requirements for Sherpa are to build with Python 2.7 and 3.5. There has been limited testing with Python 3.6, for which we distribute conda binaries. If in doubt, please install Sherpa in 2.7 or 3.5 environments only. Support for Python versions 3.3 and 3.4 is possible but would require community support.

It has been reported during testing that some versions of the matplotlib conda package do not install properly because of a pyqt v5 dependency. If you encounter this issue, please pin down pyqt to version 4, e.g. `conda install matplotlib pyqt=4`.

The `sherpatest` package is not distributed as a conda package anymore. This will probably be true for the foreseeable future. The `sherpatest` package contains data and functional tests that relies on external datasets, so it allows users and developers to run the entire regression tests suite. If you want to install `sherpatest`, please use pip and github:


$ pip install https://github.com/sherpa/sherpa-test-data/archive/4.9.0.tar.gz


If you decide to run the full regression tests suite you should also have matplotlib installed. If matplotlib is not installed a test will run and fail rather than being skipped. This issue will be fixed in the next release.


ciao4.9
This is a CIAO release.
Binaries will be provided with the next standalone release.
Release notes are collected for all changes since CIAO 4.8, which may be included from multiple standalone releases.

Release Notes

Sherpa 4.9 now runs under both Python 2.7 and Python 3.5. The test infrastructure
has been modified including simplification of the smoke test. Several bug fixes and
enhancements are also included. Specific details are identified below.

14361: Sherpa and Chips wrapper need to replace execfile for python 3 compatibility
This fix modifies the sherpa and chips wrapper scripts to replace the
'execfile' command with an 'exec' command sequence that allows the
wrapper script to be utilized by python 2.7 or python 3.5. Without the
change, the option to specify a command script at the sherpa or chips
command prompt (ie. 'chips /pool1/runme.py') will not work on python 3.5
since the execfile does not exist in python 3.5.

107: Normalize plot labels.
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.

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 been 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.

153: Minor bug with calc_chi2datavar_errors (Fix 148).
Make comparison test in `calc_chi2datavar_errors` less stringent, so to
include the case where `sqrt(x)=0`.

155: Add argument to get_draws for supplying a covariance matrix.
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.

165: Remove usage of deprecated numpy API.

185: Protect XPA command to avoid shell confusion.
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: Issue a more meaningful message when
`sherpa.astro.io` is imported directly and no fits backends are available. (Fix 92).

190: Datastack can be used if no plotter available.
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. (Fix 22).

195 Generalize calc_stat API + example of how to have several datasets with
different fit statistics. Attempts to generalize the `calc_stat` API and
enable simultaneous fits with different statistics for different data sets.

209: Fix docstrings for `group_snr()` and `group_adapt_snr()`.
Updates to the docstrings for clarity.

210: New Smoke Test
The smoke test has been greatly simplified: rather than running all the unit and regression tests that do not require test data, the smoke test now simply ensures that the basic installation works, i.e. that basic commands can be run and that dependencies can be reached.

211: Cleanup of documentation and code in `sherpa.astro.utils`.
The `calc_kcorr` function is now exported by sherpa.astro.utils. Minor
changes to the documentation in `sherpa.astro.utils` were also made to conform
to Sphinx standards.

221 Add model documentation (Fix 217).
Integrate existing model documentation (from external sources and the CIAO
ahelp documentation system) into the model classes.

229: Code is both Python 2.7 and 3.5 compliant. (Fix 76).

242: Avoid use of `inspect.argspec` in Python 3
This change replaces the deprecated 'inspect.argspec' call with 'inspect.signature'.

252: Fix `plot_photon_flux` function. (Fix 241).
A bug where plotting photon flux was fixed by adding a missing argument to the `sample_photon_flux` call.

253 Make sure background is taken into account in calc_stat_info (Fix 147).
`calc_stat_info` call failed when `wstat` was selected, as the background
was not taken into account. This issue has now been fixed.

254 Fix the documentation for set_rmf (Fix 236).
The documentation for `set_rmf` incorrectly referred to ARF rather than RMF.

256 Fix docstring in set_quality (Fix 205).
The docstring in `set_quality` now correctly indicates the quality flags.
The previous documentation didn't describe the values of such flags properly.

257 Fix docstring for levmar tolerance (Fix 257).
The documentation string for the Levenberg-Marquardt optimization function now
correctly states that the parameter default values are equal to the single
precision epsilon, rather than the square root of the double precision epsilon.

263 List_data_ids() fails on py3 with mixed id types (Fix 262).
Sherpa was sorting the list of dataset IDs in a non-python3 compliant fashion,
which resulted in issues when using strings and integers together as dataset
IDs. This has now been fixed.

267 add wstat tests
Add several regression tests for wstat.

282 Parallel_map not working on py3 with numcores=1 (Fix 277).
The `utils` function `parallel_map` failed on Python 3 when called with `numcores=1`,
i.e. on systems with only one processor/core. This has been fixed.

283 Sample flux and numpy deprecations (Fix 273 and 276).
The `sample_flux` function was not working under Python 3 if the `scales` argument
was provided. This has been fixed. Also, a `DeprecationWarning` was issued by
`numpy` because during the `sample_flux` execution values were extracted from
an array with non-integer indices. This has also been fixed.

284 String representation of data classes under py3 (Fix 275).
Data classes `DataPHA`, `DataARF`, `DataRMF`, `DataIMG`, and `DataIMGInt` in
`sherpa.astro.data` would throw an exception if users tried to print them as
strings, under Python 3. This has been fixed.

287 Rewrite sherpa.stats.Stat.calc_stat and simplify sherpa.fit.Fit (fix 227 248 289 292).
In order to fix several issues related to the WStat support, and in order to
make the code more maintainable, the `sherpa.stats.Stat.calc_stat` and
`sherpa.fit.Fit` classes have gone through a round of refactoring. This fixes
the following issues: 227 Issues using wstat when grouping/filtering data; 248
backscal column not treated properly for WStat; 289 calc_stat does not error out
if background subtracted data is used with Likelihood statistics; 292 stat info
does not include reduced stat/qval for wstat.

295 Fix display of pileup model in Python 3.5 (Fix 294).
Fix display of instances of `sherpa.astro.models.JDPileup` so that, in Python 3.5,
they can be displayed after the model has been evaluated.

304 replace file -> open (Fix 297).
The `save` and `restore` functions used to use the `file` function which is not
compatible with Python 3. This has now been fixed.

305 Fix python 3 issues with some session commands (Fix 303).
The `set_xlog`, `set_ylog`, and `show_bkg_model` functions were not compatible
with Python 3. This has now been fixed (Issue 303).

307 Move XSPEC table support to load_xstable_model and deprecate its support
in load_table_model (Fix 270).
Add the `load_xstable_model` routine to the `sherpa.astro.ui` module, which
supports loading XSPEC additive or multiplicative (atable and mtable) models.
The support for these models is still available via `load_table_model` in this
release, but it is deprecated. The `read_xstable_model` routine has been added
to the `sherpa.astro.xspec` module.

312 Fix over-zealous code clean up in PR 287 affecting sigmarej.
Fits using the sigmarej iterated-fit method were broken if a filter had been
applied to the data before the fit and there are any bins that get ignored at
larger bin values than the filtered-out data. (This fixes a subtle regression
introduced by 287).

313 Allow sequence=None when using gridsearch and Python 3.5 (Fix 309).
Allow the `gridsearch` optimiser to be used with the `sequence` option set
to `None` for Python 3.5.

Caveats

319: `image_getregion` returns byte string on Py3.

SH-2: The new `test_save_restore` test in the CIAO regression tests suite is failing on all platforms. We are investigating the reasons of the failure. The failure is triggered when the test is not run in isolation, and only when certain other tests are run before it. Also, this only applies to CIAO and not to standalone Sherpa.

SH-3: Some tests are skipped during the CIAO regression tests.

SH-4: Several OS X regression tests are failing.

Note: The SH-2/3/4 caveats are issues with the tests themselves, not with the code, and only appear when running the full CIAO regression tests suite. User will not be affected by the above issues unless they run the full CIAO regression tests suite.

This version of Sherpa is the first one to run under both Python 2.7
and Python 3.5. The python 3 conversion is considered a beta designed
to maintain backwards compatibility with python 2.7. As such, we
expect to have some iterations before the Python 3.5 support stabilizes.

The smoke test has been greatly simplified: rather that running all of
the unit and regression tests that do not require test data, the smoke
test now simply ensures that the basic installation works, i.e. that
basic commands can be run and that dependencies can be reached. This
allows the use of more advanced tools for actual unit and regression
tests without having to ship such tools to users.

Several bugs were fixed, some enhancements implemented, and some
deprecated calls to external API replaced. In particular:
- more documentation was migrated and is not part of the code base
as _docstrings_.
- the `calc_stat` API has been generalized to make statistic
functions more extensible.
- `calc_stat_info` now properly takes background into account when
`wstat` is selected.

Details

Infrastructure and minor non-functional changes have been omitted.

209: Fix docstrings for `group_snr()` and `group_adapt_snr()`. Docstrings
used to say "Combine the data so that each bin has a signal-to-noise
ratio of at least minimum" but the end of the groups are marked only
if the SNR exceeds the given SNR.

210: The smoke test has been greatly simplified and it now simply ensures
that the basic installation works, i.e. that basic commands can be run
and that dependencies can be reached. Previously, the smoke test would
run all unit tests. Units and regression tests can now take advantage of
`py.test` and `mock` packages (the latter is part of the standard
library in Python3).

211: Cleanup of documentation and code in `sherpa.astro.utils`. The
`calc_kcorr` function is now exported by sherpa.astro.utils. Minor
changes to the documentation in `sherpa.astro.utils` to conform to
Sphinx standards.

221: Integrate existing model documentation (from external sources and
the CIAO ahelp documentation system) into the model classes.

229: Code is both Python 2.7 and 3.5 compliant. This included updating
the CIAO dependencies: region, group, and stack libraries, which were
ported to Python 3 as well.

242: Avoid use of `inspect.argspec`, which was deprecated in Python3.

252: `plot_photon_flux` function was calling an internal function with
the wrong number of arguments and thus raising an error. This has been
fixed.

253: `calc_stat_info` call failed when `wstat` was selected, as the
background was not taken into account. This issue has now been fixed.

256: Fix docstring in `set_quality`, which were listing the wrong values
of the quality flag.

257: Fix docstring for `levmar` tolerance, which was listing the wrong
function defaults.

Caveats/Known Issues

The following are known issues with the standalone 4.8.2 release

**`show_all` does not work on Python3 with PHA**. E.g., the following
code throws an exception:

python
from sherpa.astro.ui.utils import Session
from sherpa.astro.data import DataPHA
session = Session()
session.load_arrays(1, [1, 2, 3], [1, 2, 3], DataPHA)
session.show_all()


**the `parallel_map` function throws an exception on Python 3** when
only one core is available on the system running Sherpa. This impacts
a number of functions taking advantage of tasks parallelization on
multi-core systems. This functions include `calc_flux`, `sample_flux`,
a number of functions for plotting parameter projections, and the
`grid_search` optimization algorithm.

**string representation of some (but not all) dataset classes is broken
on Python 3**. For instance, the following code will result in an exception:

python
from sherpa.astro.ui import *
load_pha('3c273.pi')
print(get_data())


**`sample_flux` does not work on Python 3 when called with the `scales`
argument**, e.g.:

python
from sherpa.astro import ui

ui.load_pha('sherpa-test-data/sherpatest/3c273.pi')
ui.set_model('polynom1d.p1')
ui.fit()
ui.covar()
scal = ui.get_covar_results().parmaxes
ui.sample_flux(p1, 0.5, 1, num=5, correlated=False, scales=scal)

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 available, 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`

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 been 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.

Caveats

The following are known issues with the standalone 4.8.1 release

**XSpec support**: Several issues have been encountered with the optional source building with XSpec models on OSX platforms (Linux support appears unaffected). The issues include a name clash between the libcfitsio library and the astropy.io.fits Python extensions that results in XSpec failing to load fits files possibly resulting in a crash.

**SAO DS9 issue on Ubuntu 14.04**: the ds9 binaries shipped with Ubuntu and installed through apt-get install do not seem to work as expected. Binaries downloaded directly from the SAO ds9 page seem to work instead. (Note: this issue was listed in the 4.8.0 release as well).

**Wrong save_data header keywords**: when using astropy as a FITS backend to save PHA data with save_data some header keywords are incorrectly set by Sherpa. In particular, range information for certain columns may be inaccurate (see issue 203 for details).

This version of Sherpa introduces 'wstat' statistics which is an extension
of 'cstat' with Poisson background data. It also provides the ability to include
background data with the 'user statistics'.

Many changes were aimed at improving the Xspec extension by making it more
robust, intuitive, and by fixing several bugs. Sherpa 4.8.0 supports Xspec 12.9.0d
and was also tested against versions 12.8.2e, 12.8.2l, and 12.8.2q.

Most of the codebase was reviewed and cleaned up, in particular to remove the
use of deprecated functionality and to comply with Python's PEP8 standard.
More tests were added to the test suite, and
a new testing infrastructure was put in place in order to simplify writing and
running tests, and to measure the test suite code coverage.

More details below (infrastructure changes are not shown):

32: Fix segfault from CRATES update in 4.8b1. Since v4.8b1 CRATES returns
variable length arrays by default, rather than the zero-padded fixed length
ones it used to return. Sherpa manipulated the arrays so to remove the
zero-padding and obtaining variable length arrays. The change in the CRATES
API resulted in Sherpa segfaulting when trying to manipulate the data coming
from CRATES. In the patch, we use a new API offered by CRATES to get the
old-style fixed-length arrays instead of the new default ones. In the future,
we may want to update the Sherpa code to deal with the new arrays directly.

44: `save_quality` now correctly outputs 'QUALITY' as the column name,
instead of 'GROUPS'.

48: Fix up several issues seen in plot labels - titles and Y-axis labels -
for commands such as `sherpa.ui.plot_data`, `sherpa.ui.plot_fit_resid`, and
`sherpa.ui.plot_chisqr`.

59: Fix bug 38 (grouping twice gives an IndexError exception). An un-handled
corner case in one of the Sherpa internal methods (`utils.create_expr`) was
triggering an `IndexError` when two `group_counts` operations were performed
back to back. The fix handles the case so that applying `group_counts` twice
does not result in an Exception.

77: Replace `==` and `!=` comparisons to `None` with `is` and `is not`.

78: OutOfBoundErr exceptions in some sherpa.utils
functions are properly caught. There were several places where screen output
used either `print` or `sys.stderr.write`.

81: Ensure that XSPEC models which fail - for instance, because a data file
it needs is missing - return 0's for all bins, rather than random values. This
should make it more obvious that something has gone wrong (for instance if the
XSPEC chatter level is low enough not to show any error messages, as is the
case for the default setting used by Sherpa, namely 0).

82: The XSpec "spectrum number" value is now set to 1 rather than 0, as this
value is 1-based in Xspec.

83: Removed S-Lang scripts, files, and references in the code.

84: Clarified error messages in Xspec extension. Also, changed the class of
the exception from `RuntimeError` to more appropriate exception types, in
particular `LookupError`, `ValueError`, `KeyError`. This is a
backwards-incompatible change, in that code that caught the `RuntimeError`
will not catch the new error.

87: Some methods in `sherpa/fit.py` assigned mutable objects to default
arguments. This has now been fixed. More instances of this issue have been
identified (Bug 95) and will removed in the future.

90: Added background data to the UserStat class.

94: Implement wstat statistic as described at the following url:
https://heasarc.gsfc.nasa.gov/xanadu/xspec/manual/XSappendixStatistics.html

96: Remove the unused myoptfct module.

99: Correct the documentation for the `set_exposure` function.

100 Fix bug 97, whereby the save_all function would not create the necessary
`set_source()` line. This does not fix all cases, but it does the simple PHA
case such as


load_pha('src.pi')
set_source(xsphabs.gal * powlaw1d.pl)
save_all('test.out).


It also ensures that files created by `save_all`
can be run using IPython's %run directive, by explicitly importing the
`sherpa.astro.ui` module.

101: Fix handling of non-contiguous bins in Xspec - i.e. when a model is
called with both xlo and xhi arguments but the bins do not fully cover the
energy, or wavelenth, range. This fixes 62 (for XSPEC 12.8.2; switching to
XSPEC 12.9.0 should also fix it) and 56. It also fixes an (un-reported)
problem with handling of non-contiguous grids when using a table model, where
a crash was likely. When an XSPEC model is called with both low and high
values for the grid - i.e. with two arguments - then the two arrays are
checked to have the same length, and a ValueError is raised if this condition
does not hold. This is a breaking change, but the results are not guaranteed
to be correct if the two arrays are not the same length. The experimental
interface for XSPEC convolution models has changed, so that the function call
takes pars, fluxes, xlo, with optional xhi whereas before it was pars, xlo,
xhi, fluxes. This is a breaking change, but this is in the low-level API that
is not documented to users, and adds useful functionality (the ability to have
xhi be optional). The cpflux convolution model has been added. Note that these
models do not have Python classes associated with them as they are still an
experimental interface. The test suite has been updated to test the new and
changed functionality in this PR. The choice of models is made so as to avoid
known problematic models (with a version check where relevant). It is
believed that the changes in this PR fixes 42, although this is hard to prove
conclusively given the erratic nature of the bug.

110: Update the sherpa.astro.datastack module documentation to include information from the
CIAO ahelp documentation and to match the style used by the sherpa.astro.ui module.

111: Update the documentation to include more information about the pyBLoCXS code.

Caveats

These caveats are being fixed for the 4.8.1 release.

Incompatibility with matplotlib 1.5: Sherpa 4.8.0 is not compatible with matplotlib 1.5. Unfortunately, this version is currently the default package installed by conda. Users should install sherpa with matplotlib=1.4 numpy=1.9.

Test requirements are not installed automatically: sherpa_test does not work out of the box. Users should issue "pip install pytest-cov" in order for sherpa_test to run.

SAO DS9 issue on Ubuntu 14.04: the ds9 binaries shipped with Ubuntu and installed through apt-get install do not seem to work as expected. Binaries downloaded directly from the SAO ds9 page seem to work instead.

Release Notes

This standalone release is based on CIAO Sherpa v4.7.

Release notes for this baseline version can be found at the following link:
http://cxc.harvard.edu/ciao/releasenotes/ciao_4.7_release.html#Sherpa

Additionally, the present release includes some changes listed below:
- Standalone Sherpa and CIAO sherpa now look for different configuration files in the $HOME directory. For standalone this is `$HOME/.sherpa-standalone.rc`. If this file is not present, Sherpa falls back to the internal configuration file. This file has defaults better suited for the standalone mode: `pyfits` and `pylab` are set as backends, and the stack trace is not silenced. Users can still override the configuration file location by exporting the `SHERPARC` environment variable, as supported by previous versions of Sherpa and CIAO.
- All source files now have copyright and licensing information. A summary is included upfront in the repository main directory.
- Orphan code that was not actually used has been removed.
- Fixed code triggering deprecation warnings from Numpy 1.9.
- Fixed code triggering compiler warnings.
- Added documentation (README, ipython notebook).
- The version string (`sherpa.__version__`) depends on the git commit/tag, unlike in CIAO where it is fixed to 40701.
- Some classes from the template module were not exposed by `__all__`, and template models were not imported in the sherpa session. Now they are.

Known issues
- the datastack module is not imported if no plotting packages are available. Installing `matplotlib` in the same environment as Sherpa fixes the issue.