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Merge sherpa#2176 (Marie-Terrell) - Release 4.17.0
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Release 4.17.0
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@Marie-Terrell
Marie-Terrell authored Oct 9, 2024
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Release Notes

Sherpa 4.17.0
=============

This release of Sherpa includes various enhancements, documentation updates, bug fixes, and infrastructure changes.

* enhancements:
* add calc_model and calc_source functions to return an evaluated model/source array
* added wstat to plot_pvalue for the likelihood ratio test
* changed XSpec interface to use FunctionUtility C++ API instead of XSFortran API
* improved support for PHA data starting at channel 0 and handling of STAT_ERR and SYS_ERR PHA columns which are set to 0
* improved guess for complex models
* improved filtering handling
* several updates to enhance plotting capabilities and layout
* documentation changes:
* added paper citations to front page of Sherpa Read the Docs documentation
* cleaned up various typos and URL references
* added examples such as use of set_x/y_label
* infrastructure and testing:
* improved test coverage
* many updates to CI
* drop support for Python 3.9 and numpy <1.24
* initial/experimental support for Python 3.12
* bug fixes:
* fixed an issue with plotting 1D data with asymmetric errs after filter
* include the default identifier in save_all output if it has been changed

Details
-------

#1757 - Allow the wstat statistic to be used in the likelihood-ratio test
Allow the Likelihood Ratio Test (as used by plot_value) to be run when
using the WStat statistic. Fix #1745.

#1793 - XSPEC move from the xsFortran API to the FunctionUtility API (where possible)
Internal change to the XSPEC interface to use the FunctionUtility C++ API
rather than the XSFortran API. Fix #1225.

#1921 - Clean up of the IO code
Rework the astro data input and output code so that they take advantage of
the new data representation in sherpa.astro.io.types

#1949 - Initial support for Python 3.12
Initial support for building with Python 3.12

#1997 - Add support for XSPEC 12.14.0
Allow building with XSPEC 12.14.0 and include the 50 new models in it.

#2017 - IO: separate pack and set commands
Replace the logic of the packup argument to the set I/O commands

#2033 - utils: add typing rules to random and parallel
Add typing statements to the sherpa.utils.parallel and sherpa.utils.random
modules

#2035 - stats: add typing rules
Add typing rules to sherpa.stats and minor internal clean up to the module.

#2036 - Update sherpa citations
Add Sherpa 4.16.1 to the citation data.

#2045 - Mark code as deprecated in sherpa.utils
Rework sherpa.utils and mark some symbols as deprecated - func_counter,
is_in, and mysgn - along with suggested replacements.

#2046- Post 4.16.1 update to add DOI info
Adds the Sherpa 4.16.1 DOI info to the README.md.

#2048 - CI: update the weekly arch run to add ppc64le and to use a supported python version
Support the weekly test builds using aarch64 and ppc46le architectures.
This support is considered experimental.

#2052 - XSPEC: do not test bvvnei unless 12.14.0i or later is used
Avoid testing the XSbvvnei model if XSPEC <= 12.14.0i is in use, as the
model can cause a crash in this case.

#2054 - Allow a file handle or Path object to be sent to the outfile parameter of fit
The fit call can now be sent a Path object or a file handle, as well as a
string. Fix issue #2063

#2056 - tests: fix fake_pha test failure on crates
Address test failures when using crates after merging #1684 and to address
a numerical tolerance issue on macOS ARM.

#2057 - Improve the guess routine for PHA data
Allow guess to work for composite models, including those with responses,
and improve the guess routine used for the norm parameter of XSPEC additive
models.

#2058 - Address an error introduced in PR 2025
Fix an error made when addressing NumPy 2.0 changes in issue #2025.

#2059 - Copy over typing annotations to the sherpa.ui and sherpa.astro.ui routines
Ensure that annotations are added to the sherpa.ui and sherpa.astro.ui
routines. Fix #2053

#2060 - Simple typing support for sherpa.data
Add some basic typing rules to the sherpa.data module.

#2061 - Avoid warning messages from AstroPy about unclosed files
Initial cleanup of the astro IO code in preparation for future changes.
This fixes an issue when using the AstroPy IO backend (pyfits) which could
cause Python to report an unclosed file on exit

#2065 - CI: enforce NumPy does not use version 2.0 for the builds
Ensure the CI builds use numpy<2

#2068 - CM-887: Updating macos gitlab runner images to version 12 and update the MacOS SDK to version 11.0
This ups the actions macOS Intel version to 12, and updates the macOS SDK
to version 11.0, which is consistent with CIAO.

#2069 - Allow the tests to pass with NumPy 2.0
Allow the tests to pass when using NumPy 2.0, as long as pytest-doctestplus
is not installed.

#2070 - Migrate to cxc xspec conda test channel
Use the cxc xspec test channel for Sherpa test workflows.

#2072 - Use the correct case for the symbol name in the parameter warning message
Change how the warning message for deprecated parameter names for models
is displayed

#2078 - Include the default identifier in save_all output if it has been changed
Record the default identifier in save_all output if the user has changed
it. Fix #2077

#2079 - minor cleanup of sherpa.optmethods
Internal clean up of the sherpa.optmethods code.

#2081 - minor plot cleanup
Clean up some plot code to make better use of modern Python idioms.

#2086 - data: allow axis labels to be changed
Allow the independent and dependent axis labels to be changed. Addresses
#2083

#2089 - minor cleanup of sherpa.optmethods
Internal change to handling of the optional output file option when calling
fit. There is no functional change.

#2091 - Asymmetric filter plot
Allow 1D data with asymmetric errors to be plotted after a filter. Fixes
#2090.

#2092 - Add a name field to the IO backends
Add a name field to the I/O backends. This is mainly useful for testing
and debugging.

#2094 - Improve messages about invalid file types (PHA)
Tweak the warning messages when files can not be read to better indicate
the type of file being loaded (for PHA related files).

#2102 - Change the URL for XPA
Change the URL used for XPA. Fix #2100.

#2103 - Ensure crates file reads are read-only
Ensure that we read in table data as read-only when using the crates I/O
backend.

#2105 - docs: typo fixes and remove some references.
Fix a typo in a docstring and change how two references are included in
the text.

#2107 - XSPEC: add show_xsabund command
Add the show_xsabund command to the sherpa.astro.ui module and
get_xsabundances to sherpa.astro.xspec.

#2108 - Asymmetric settings
Allow the statistic and optimizer to be changed when re-sampling data with
asymmetric errors. Fixes #2093.

#2109 - Add a set_xsabundances call for XSPEC users
Add a set_xsabundances call to make it easier to change one or more
elemental abundances for the XSPEC models and ensure that both the get
and set calls are available from the sherpa.astro.ui module.

#2111 - IO: ensure NUMELT/GRP are written out as integers for RMF header
Ensure the NUMELT and NUMGRP keywords for RMF files are written out as
integers.

#2112 - Minor typing cleanup
Clean up some of the recently-added typing rules.

#2115 - doc: add examples of using set_xlabel/ylabel
Add documentation showing the new set_xlabel/ylabel functionality from
#2086

#2118 - Improve support for PHA data starting at channel 0
Improve the handling of PHA files that start at channel 0. PHA data that
are read in from such a file no longer renumber the CHANNEL column to start
at 0 rather than 1, which will mean that notice and ignore filter ranges
that are given in channel units will need to be reduced by 1.

#2120 - Improve handling of STAT/SYS_ERR PHA columns
Improve handling of STAT_ERR and SYS_ERR PHA columns which are set to 0.

#2121 - UI: add calc_model/source commands
Add calc_model and calc_source routines to return the model expression
evaluated per bin.

#2123 - Data cleanups
Internal clean up of some of the data code.

#2125 - Allow per plot kwargs for plot_xxx_components calls
Allow per-plot keyword arguments for plot_model_components and
plot_source_components.

#2126 - Allow plot and contour to change the plot layout and have per-plot settings.
Expand the plot and contour commands to allow per-plot options to be given,
matching the plot_model_components/plot_source_components commands.

#2129 - Fix plot overplot
Improve the behaviour of plot() and contour() when called with
overplot=True or overcontour=True respectively. Fix #2128.

#2130 - data: fixup numpy import
Fix up several typing annotations from a recent refactoring.

#2133 - UI: add format and delim arguments to get_filter.
Allow the get_filter call to override the format and delim arguments. Fix
#1277

#2135 - Tests: tweak tolerances for macOS ARM #2135
Updated macOS ARM test tolerances

#2137 - Fix doctests in `sherpa.plot.__init__`
Changed documentation to match backends as objects instead of modules

#2138 - UI: add documentation for table to show_xsabund
The show_xsabund command now includes a description of the abundance table.

#2139 - Update helpdesk URL
Changed helpdesk link - fixes issue #1931

#2140 - Updated docs for asymmetric errors
Expanded documentation for load_ascii_with_errors to clarify assumptions for elo and ehi settings.

#2141 - Update LaTeX labels and docs for bokeh
Correctly render LaTeX labels in bokeh

#2144 - Fix xspec missing doc
Add get_xsabund_doc to the list of functions in the documentation. There
is no functional change.

#2147 - Improve corner-case handling of filtering and empty data handling
A clean-up pass for the data classes, in particular DataPHA, to normalize
the filtering and handling of an empty object

#2151 - updating Sherpa citations
Added a citation to the most recent sherpa paper

#2152 - DATA: clean up DataPHA.get_x
Internal clean up of the DataPHA.get_x method.

#2153 - updated the front page of Sherpa RTD with references
Added references to three sherpa papers in the sherpa docs

#2154 - Update README
Added additional text regarding acknowledging/citing sherpa

#2155 - Drop support for Python 3.9 and add 3.12
Drop support for Python 3.9 and numpy < 1.24 and note Python 3.12
experimental support.

#2157 - Improve test coverage of ignore_bad
Add more corner-case of quality channel handling for PHA data. There is no
functional change here.

#2160 - Fixup test failures from #2118
Fix up a test case when writing out the range of a FITS column.

#2161 - UI: note when a 1D filter command has failed
Provide more information for the UI user if a filter command has failed.

#2162 - TEST: ignore fork deprecation warnings
Ignore the deprecation warnings about the use of the fork method for
multiprocessing.

#2177 - Read the Docs build failures with newer sphinx versions and sphinx_rtd_theme deprecation warning
Specify sphinx < 8 for the read the doc environment and remove the call
to get_html_theme_path no longer needed.


Sherpa 4.16.1
=============

Expand Down Expand Up @@ -56,7 +338,7 @@ Details
Updates from running codespell on source distribution

#1945 - Better error checks for table loads
Insure that table models are sent numeric columns, to catch cases like #1943.
Ensure that table models are sent numeric columns, to catch cases like #1943.

#1946 - versioneer: update to version 0.29
Update the vendored copy of versioneer from 0.28 to 0.29.
Expand Down Expand Up @@ -288,7 +570,7 @@ from NumPy

#1791 - Tests: ensure repeatable test of get_draws
Ensure tests of get_draws use a fixed seed to make the results
reproducible. There is no functional changes in this commit.
reproducible. There are no functional changes in this commit.

#1794 - docs: note requirement on ar for building Sherpa
Add ar to the list of requirements for building Sherpa. Fix #1792
Expand Down Expand Up @@ -376,7 +658,7 @@ model
files). Fix #1699, #1695, and #203.

#1839 - ui: add get_plot_prefs/get_contour_prefs calls
Add the get_plot_prefs and get_contour_prefs call to simplify access to
Add the get_plot_prefs and get_contour_prefs calls to simplify access to
the plot and contour preferences.

#1840 - Fix #1828 - histogram plot issue
Expand Down Expand Up @@ -720,7 +1002,7 @@ This release of Sherpa includes various enhancements, documentation updates, bu
* arrays sent to Data objects are now converted to ndarrays
* the independent axis is now made read-only
* the size of a data object is now fixed.
* Filter setting with notice/ignore are reported to the screen for the users of the UI layer.
* Filter settings with notice/ignore are reported to the screen for the users of the UI layer.
* Increased test coverage for plotting
* documentation changes:
* updated readthedocs to use pip and pytest instead of setup.py
Expand Down Expand Up @@ -857,7 +1139,7 @@ Details
#1579 - Add back --python removed in #1566
reinserts --python flag that was accidentally removed in #1566

#1580 -add a versionchanged note for the fake_pha command
#1580 -add a version changed note for the fake_pha command
Update the documentation to note the change to fake_pha in #1567

#1585 - Tests: work around matplotlib 3.6.0 warning
Expand Down

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