sherpa/sherpa: Sherpa 4.9.0

Sherpa 4.9.0

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.