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sherpa/sherpa: Sherpa 4.12.2

Doug Burke; Omar Laurino; wmclaugh; dtnguyen2; Hans Moritz Günther; Marie-Terrell; Aneta Siemiginowska; Jamie Budynkiewicz; Tom Aldcroft; Christoph Deil; Brigitta Sipőcz; Johannes Buchner; Iva Laginja; Katrin Leinweber; nplee; Todd

Sherpa 4.12.2

This release of Sherpa serves as the baseline release of Sherpa for CIAO 4.13. It contains numerous enhancements and fixes including items which are stand alone sherpa specific. Notable highlights include:

  • plotting improvements
    • improved support for matplotlib (linestyle changes in matplotlib 3.3, support of alpha channels)
    • overplot support for plotfit plt_bkgfit
    • updates to histograms, residual plots
  • data I/O and data handling
    • several bug fixes to handling of the PHA, ARF, RMF files
  • modeling
    • support for regrid models in the binary expressions
    • improvements and bug fixes to background treatment in spectral models
    • improvements in the flux calculations and resampling
    • added the Voigt model
  • documentation changes
    • improvements to Sherpa display in IPython/Jupyter notebooks
    • updates to the content of the docstrings for generation of ahelp files
Details

Testing and infrastructure fixes are not shown.

351 - fix handling of AREASCAL column in PHA files (fix #350)
Adds support for handling the AREASCAL value (either scalar of vector) for PHA 
data sets. This array is used in XMM RGS data to handle missing chips.
385 - Properly handle Swift RMF when using Astropy backend
Fixes an issue where some low lever xpa calls were returning byte strings rather 
than strings in Python 3. This had particular impact on the image_getregion 
function.
483 - An initial release of simultaneous fit on multicores (slower for most…
Distributes the evaluations of the multiple independent data sets using the 
multi-cores built-in the user's workstation. The current default setting for this 
PR is to evaluate the multiple independent data sets sequentially since the 
overhead for distributing the workload across multi-cores is high if the evaluation 
of the data sets is not time consuming.
631 - Add HTML representations of common classes for IPython display (fix #345)
An initial version of HTML display support for Sherpa objects for users of 
IPython/Jupyter notebooks. 
634 - Added invitation for native software citation
Adds a citation method to the sherpa module and updates CITATION to refer to this 
new functionality
693 - Address matplotlib linestyle removal in Matplotlib version 3.3
Matplotlib version 3.3 now requires you to split out the drawstyle and linestyle 
arguments. This set of PRs changes the code so that the two arguments are now set: 
linestyle defaults to solid and drawstyle to default for plots and step-mid for 
histograms. This appears to replicate the old version, and should be backwards 
compatible (drawstyle is supported in Matplotlib 2.2.5 and 1.5.3)
709 - Residual-style plots ignore the ylog setting (fi#586)
Residual, ratio, and delchi plots always use a linear scale for the y axis, no 
matter what the ylog setting is.
740 - resample_data: when the error range on a bin includes -1 and no-longer restrict
   sampling to +/-1 sigma
Fixes resample_data/ReSampleData so that it correctly handles bins where the range 
of data values (i.e. low to high limit) includes the value -1.
741 - Fix issue 638, guess needs to update fwhm/sigma bounds
Adds support for guessing the fwhm or sigma parameters of the Gauss2D, 
NormGauss2D, and SigmaGauss2D models
750 - Add xspec convolution api
Adds support for XSPEC convolution-style models - this link is valid for XSPEC 
12.10.1 documentation
765 - Add docs for setting up all dependencies of the source build with conda
Adds documentation on how to use conda to install source build dependencies
766 - No error for no-ops in ungroup and friends
Removes DataErrs when ungrouping a dataset that is not grouped or unsubtracting 
a dataset that was not subtracted
770 - Replace EmissionVoigt/AbsorptionVoigt models by Voigt model (fix #597)
Replaces the EmissionVoigt and AbsorptionVoigt models with a single model, 
Voigt1D. The EmissionVoigt and AbsorptionVoigt models will error out when an 
instance is created, pointing users to Voigt1D (as the parameter definitions 
have changed).
772 - Add XSPEC 12.11.0 support (HEAsoft 6.27)
Adds support for XSPEC 12.11.0 (released March 31 2020)
782 - Add a pyproject.toml file
Adds a pyproject.toml file to the top level (PEP 518) to document build 
requirements
789 - fix issue #788, fit using moncar with verbose=1 and/or numcores!=1
Fixes NameError in moncar when verbose setting >0
791 - Fix ignore/notice error-ing out when all bins have been set bad #790
Allow notice and ignore to be called on a dataset which has no "good" bins 
after ignore_bad has been called
793 - Accept masked arrays for Data XXX creation
Allows use the mask of numpy arrays when initializing DataXXX
798 - enable regrid for the BinaryOpModel class
Adds the regrid method to the BinaryOpModel. 
803 - Updates to sampling of energy and photon fluxes: bug fixes and calculate
   unabsorbed components
Fixes and improvements to the energy_flux and photon_flux set of commands: 
sample_energy_flux, sample_photon_flux, plot_energy_flux, plot_photon_flux, 
get_energy_flux_hist, and get_photon_flux_hist
811 - Remove all future imports
Removes __future__ imports that were in place when sherpa supported python 2
812 - Add unsubtract and ungroup to datastack
Adds  corresponding unsubtract and ungroup methods to match subtract and group
815 - fix typo in rst docs
Fixes a typo in the rst docs
821 - Add hyperlink to similarly named SHERPA package
Documentation update to include a link to thethe similarly named package "SHERPA" 
for hyperparameter tuning of machine learning models
842 - Fix scaling of staterror when reading PHA file with rate instead of counts
Fixes scaling of STAT_ERR when reading a PHA spectra with a RATES column instead of 
COUNTS
845 - xspec table models: add out-of-bound check to avoid segfault
Adds explicit out of bounds checks to avoid segv when calling an Xspec table model
851 - Updates to the Read-The-Docs build environment
Update the Read-The-Docs configuration to the latest version (2), and switch to a 
cleaner build (using conda) for the documentation. The minimum Sphinx requirement is 
now 1.8 (updated from 1.3).
856 - Support setting the id value in load_pha with pha2 files (fix #666)
Updates load_pha to set the data ids of PHA2 datasets  to: id to id + nfiles - 1 
(when id is an integer), or "{}1".format(id) to "{}{}".format(id, nfiles) when id 
is a string.
858 - Minor documentation improvements to ReadTheDocs
Adds minor updates to the convolution, regrid, and model evaluation sections of 
the ReadTheDocs documentation
859 - Clean up of the XSPEC interface code
Internal changes to the XSPEC interface code, which reduces the amount of similar 
(sometimes identical) code. There is no change to the behavior of the XSPEC models.
865 - Minor documentation fixes
Several documentation fixes: XSPEC parameter names, avoiding confusion over links on 
references (Sphinx pages), and adding some basic documentation to the 
sherpa.astro.background module
866 - Add parameter-clipping strategy to routines that generate samples (fix #846)
The addition of the clip parameter lets users control how parameter values are 
clipped before use in sample_energy_flux, sample_photon_flux, plot_energy_flux, 
plot_photon_flux, get_energy_flux_hist, and get_photon_flux_hist.
868 - Add delete_pileup_model (fix #441), list_pileup_model_ids, list_psf_ids functions,
   fix list_models (fix #749)
Add the delete_pileup_model() function to allow a pileup model to be removed from 
a fit (issue #441), and list_psf_ids() and list_pileup_model_ids() routines to list 
those datasets with an associated PSF or pileup model. The list_models() routine 
no-longer returns an iterator but a list when given an option (issue #749).
871 - Add MacOS LDFLAGS warning to devdocs
Copies the warning about setting PYTHON_LDFLAGS from the install page to the 
developer docs
884 - Move logic from ui layer to DataPHA class: background responses (fix #879, #880)
Moves the logic for adding a background response, if one doesn't exist, from the UI 
layer to the DataPHA class to clear up several edge cases
888 - Support vector backscales and bugfix for background modeling
Supports fitting backgrounds to PHA datasets which have a variable BACKSCAL array 
(rather than a scalar), which can come from combining spectra (e.g. the CIAO contrib 
script combine_spectra) or from the data extraction process. In doing so a number of 
routines related to the scaling of background-to-source aperture data have seen 
adjustments to behavior and some enhanced functionality (such as 
sherpa.astro.ui.get_bkg_scale and the sherpa.astro.data.DataPHA.get_background_scale 
method).
897 - Add support for XSPEC 12.11.1
Allows Sherpa to be built against XSPEC 12.11.1. There are no new or changed models 
in this release compared to XSPEC 12.11.0.
899 - Update likelihood descriptions
Updates likelihood description in several doc-strings and clarifies descriptions 
of statistics.
900 - Ensure that 1D and 2D models are not combined in an expression.
Checks that models have the correct dimensionality when combining them, so 
expressions like gauss2d.src + const1d.bgnd will now raise a ModelErr.
906 - Improve and add support for histogram plots
Updates to the display of histogram-style plots, in particular for 1D integrated 
datasets and some model display for PHA data. The histograms now cover the full 
length of each bin (previously they only showed half the bin for the first and 
last bins), and gaps in the histogram (where the high edge of a bin is less than 
the lower edge of the next bin) are now correctly displayed.
907 - FEATURE: support alpha transparency for matplotlib plots
Supports the 'alpha' preference setting for most plots and contours generated 
by Matplotlib
909 - Refactor: remove _get_model/source methods
Removes the _get_source and _get_model methods as they are the same as 
get_source and get_model
910 - Docs: fix several minor issues
Documentation clean up - the load_template_interpolator function was named 
incorrectly in the example, and the examples for 
get_source_component_plot/get_model_component_plot were missing the trailing 
_plot for the function names
911 - Docstring: changes for ahelp
Formatting changes to the docstrings for several routines that are useful for 
SDS in generating ahelp files
918 - fix an issue with PHA filtering that affects plot_model
Fixes an issue when applying filters to generate the plot_model and 
plot_model_component plots for PHA datasets
919 - enable regrid for the BinaryOpModel class (rebased #798)
Enables composite models (created by a binary operation between two models) to 
be regridded. The composite model is evaluated at the new grid, and it is only 
the combined model expression that is rebinned to the data grid.
922 - channel settings with grouped PHA data and model plotting
Fixes a bug when filtering a grouped PHA dataset using analysis=channel. The 
selected bin ranges did not always match the versions you would have received 
when doing the same operation with energy or wavelength analysis (the first or 
last bin may have been different).
924 - Updated to ignore the .vscode directory
updates system .gitignore to skip over vscode directories
929 - Support overplot option in plot_fit_xxx (issue #700)
The overplot argument can now be used with the plot_fit_xxx and plot_bkg_fit_xxx 
routines (e.g. plot_fit_ratio).
931 - Update Data1DInt / DataPHA data plots to use the histogram plot style
Switch the plot_data/plot_bkg plots to draw the data as histograms for Data1DInt 
and DataPHA plots.  This will change the behavior of code that accesses the plot 
data - e.g. get_data_plot() or the dataplot element of get_fit_plot() - since for 
DataPHA and Data1DInt datasets the data will no-longer have an x attribute but 
xlo and xhi. To reduce the need for code changes for existing scripts - as many 
people use get_model_plot and get_data_plot to get the data - the histogram 
plots will return (xlo+xhi)/2 when asked for the x attribute.
939 - Docs: note XSPEC convolution models are new in 4.12.2
Documentation only change noting  that the support for XSPEC convolution models 
is new to 4.12.2.
940 - Minor documentation improvements
Fixed several minor issues in the existing documentation
944 - Improve handling of the default id with PHA background datasets (fix issue #943)
The sherpa.astro.ui.set_default_id call no-longer sets the default identifier for 
background ids, which are now kept as the value 1. This avoids several issues when 
using set_default_id with the background components of PHA datasets
950 - Documentation fixes
Minor documentation updates and adding ReSampleData to the RTD documentation
953 - docstring fixes
Cleans up typos in documentation
957 - Docs: include the example notebook in the RTD pages
Adds the example notebook (SherpaQuickStart.ipynb) to the Sphinx documentation 
under the "Notebooks" heading
961 - Update notebook support for Data1DInt/PHA data
Improves the display of Data1DInt and DataPHA objects when displayed directly 
by Jupyter notebook and add a new notebook showing off the notebook support
963 -Docs: note plot_fit_xxx overplot change and add info on notebook support
Adds documentation updates including notes on overplot support in plot_fit_xxx 
and plot_bkg_fit_xxx functions and RTD notes on adding notebooks 
964 - Docs: avoid invalid escape sequence warning
Very-minor tweak to the Chi2 docstring
968 - Fix 2d image filtering (fix #965)
Fix problems with ignore2d and notice2d when multiple regions are used.
969 - Support Python 3.8 for MacOSX
Add a new multiprocessing_start_method option to sherpa.rc and 
sherpa-standalone.rc and init code to set start multiprocessing method 
to fork by default.
971 - Docs: fix sphinx warnings
Fix documentation in sherpa.sim.sample on the ReadTheDocs site.
984 - Address set_xlog/ylog problems with DataPHA/Data1DInt classes (#981)
Fix the set_xlog/ylog routines for PHA and 1D integrated datasets.
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