Software Open Access
Doug Burke; Omar Laurino; dtnguyen2; wmclaugh; Jamie Budynkiewicz; Tom Aldcroft; Aneta Siemiginowska; Christoph Deil; Marie-Terrell; Brigitta Sipőcz; Hans Moritz Günther; Todd; Katrin Leinweber
This release of Sherpa is based on the CIAO 4.12 release and includes additional bug fixes and improvements.
This version of Sherpa has been tested with Python 3.5, 3.6, and 3.7.
This release also provides support for XSPEC 12.10.1 (patch 'a' or later) in addition to versions 12.10.0 (included in CIAO) and version 12.9.1.Details
Documentation and infrastructure fixes are not shown.388 - Address indexing DeprecationWarning/IndexError from NumPy for PHA data with filter + ignore_bad (fix #361) 602 - Reduce integration tol
606 - stop using numpy.typeNA which is now deprecated
Changed integration routine tolerance from double epsilon to float epsilon since opt routines hove tolerance of ~ 1.0e-7
608 - update ciao default plotter to matplotlib
A numpy deprecation warning was fixed by removing the usage of typeNA, which was not documented and will be removed in a future release of numpy. The print_fields function has been changed to include a default mapping using the current typeNA implementation.
616 - enable run-time-option to test cache (default=True)
The default Sherpa plotting package has been changed to matplotlib for CIAO users as well (it had been the default for standalone users for several years). The update will be applied to new users when the `sherpa` command is run. Users of previous versions would need to edit/regenerate the file.
622 - Do not create warnings about error bars in plots if no error bars are to be shown (fix #621)
Capability to allow the user to turn off caching at runtime for testing purpose.
626 - add plot_fit_ratio and plot_bkg_fit_ratio functions
Remove the The displayed errorbars have been supplied with the data or calculated using chi2xspecvar... warnings that appear for data, residual/ratio, and fit plots when the user has explicitly turned off the display of errorbars (by setting the yerrorbars plot-preference setting to False).
640 - fix 'tuple index out of range' error in the fit.est_errors method
Add the plot_fit_ratio function to the sherpa.ui layer (to match plot_fit_resid and plot_fit_delchi) and plot_bkg_fit_ratio to the sherpa.astro.ui layer. Added tests for a number of plot types.
647 - fix numpy hist warnings
Sherpa's Confidence class is confused if a parameter is frozen then thawed after a fit resulting with an exception of the form: IndexError: tuple index out of range. The error does not show up if conf is called from the ui level
658 - Handle files with MJD_OBS or MJD-OBS keywords (datastack module)
When plotting a PDF Sherpa now calls numpy.histogram with density=True | False rather than normed=True|False. There is no change visible to the user other than a warning that will not be issued anymore. normed=True was broken for non uniform bins, but our code always produces uniform bins, so we should never hit the problematic case.
665 - Remove python 2.7 support (fix #498)
The sherpa.astro.datastack module has been updated to deal with files that use the MJD-OBS keyword instead of MJD_OBS. This is only used by the show_stack routine, which prints out several keywords from each file in the stack.
667 - improve matplotlib plot_fit plots (order of data and model)
Remove support for Python 2.7 from Sherpa. The metadata used by pip now requires python 3.5 or higher (but not version 4),
674 - Add link/unlink parameter tests
Changes to Zorder of plot objects drawn by matplotlib to be more readible
677 - XSPEC: build against 12.10.1m by removing support for models
This PR adds three tests for sherpa's un/link commands.
680 - Remove the unused parameter in sherpa.astro.optical.LogEmission model (fix #219)
Remove support for XSrelline, XSrelline_lp, and XSrelline_lp_ext models. These were added in 12.10.1 but removed in 12.10.1m. It does not seem worth supporting just those versions where they were available.
682 - jointplot now respects the ratio argument (top plot is larger) with matplotlib backend
Remove the unused parameter in the sherpa.astro.optical.LogEmission model. The LogEmission model only has four parameters (fwhm, pos, flux and skew) consistent within the calc method. The hidden parameter limit and it doc were removed.
683 - Remove chips from the documentation
The matplotlib back end now makes the main (top) plot taller than the secondary (bottom) plot when using the sherpa.ui.plot_fit_resid and sherpa.ui.plot_fit_delchi routines (this also holds for the sherpa.astro.ui variants).
684 - Add default config options
Remove mention of ChIPS from the documentation (both on read the docs and in the sherpa.astro.ui and sherpa.ui modules), replacing with matplotlib where appropriate.
685 - raise ModelErr when model using Data1DInt have overlapping bins
Whenever an option is read from the configuration file (~/.sherpa.rc) provide a default option in case the configuration file is missing (or is missing this option).
688 - Improve documentation and testing for get_source_plot when sent lo/hi arguments
Adds a check to regrid make sure the integrated bins do not overlap. The PR is a fix for issue #569
691 - add warning when chips is selected but cannot be imported (rebase of #648)
Improve the documentation for the sherpa.astro.ui.get_source_plot routine, describing how touse the result when the lo or hi arguments are sent.
692 - Allow users to override plot preferences when creating a plot
Sherpa now warns the user if Chips is selected as a backend but it is not available in the installation
698 - Add warnings in documentation about masked arrays
Change to allow kwargs to be specified to change plot preferences at creation time
701 - a fix for /data/lenin2/Test/CIAO4.11/SherpaRegressionBeta1/45
Updates docstring to indicate that sherpa doesn't support numpy masked arrays
704 - change calc_ftest from delta dof to dof (similar to XSPEC) - fix for #641
Enables the testers to turn on (or off) caching at runtime to test #444
705 - modelCacher1d needs to have a couple of deep instead of shallow copy()
Update to make sherpa's calc_ftest provide same results as XSPEC's ftest (fix to #641)
710 - Add warning about masked array to sherpa.astro.ui.load_arrays
Update to make deep copy of cached function values (fix to #673)
712 Minor typo in docs
Updates docstring to contain warning consistent with #698
716 Fix for plot_cdf: plot() got an unexpected keyword argument 'clearwindpw'
Corrects a typo "is is" in the documentation.
721 Docs: update installation notes for conda environment
Recent changes broke plot_cdf()due to a typo 'clearwindpw'. This update corrects the typo.
725 convert a list to np.array to avoid warning messages
Add a warning about the need to set PYTHON_LDFLAGS to ' ' on macOS when building within an anaconda environment. This is a documentation-only change.
728 a fix cause using load_multi_arfs causes caching error
Fixes issue #723 (a lot of warnings while running 'resample_data()' in CIAO4.12 Sherpa)
Fixes issue #717 (unable to fit if script uses load_multi_arfs/rmfs)