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sherpa/sherpa: Sherpa 4.14.0

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 4.14.0

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

  • enhancements:
    • filtering and grouping area for binned (1D) spectral data has been improved with changes to the default behavior and many bug fixes resulting in changes to the statistics, degrees-of-freedom and energy flux in comparison to the previous version for the same data with the same filter.
    • updates to allow users to change the hard limits of XSPEC model parameters
    • the sample_flux routine now returns correct information for the clip column
  • documentation changes:
    • improved PHA simulation documentation
    • improved Filtering and grouping of PHA data documentation
    • added sherpa.image module documentation
    • added section on running tests to developer docs
  • Infrastructure Changes:
    • updates to support Apple ARM
    • update to support Xspec version 12.12
    • update fftw from version 3.3.8 to 3.3.9
    • clean up of compiler and sphinx warnings
    • changes to support gcc 9.3.0 in conda defaults
    • updates to support python 3.9 including readline 8.1 upgrade, numpy minimum 1.19 (numpy 1.18 minimum for python 3.7/8)
    • test infrastructure clean up and updates
  • bug fixes:
    • updates to fix several 'unable to parse region string: None' errors
    • fix issue where save_all() of a loaded image with no region filter would fail on reload
    • fixed issue with plot_model() being called before notice or ignore could lead to filters not getting applied
    • fix to error out instead of crash when grouping data using an unsupported method
Details 1031 - Update fwhm calculation
Update the estimation of FWHM for 1D profiles, and hence the guess method for 
Gauss1D and related routines. The 2D models use the same routine so see these 
changes.
1073 - Allow fake_pha to be called with an identifier of None
The fake_pha command now treats id=None as the default id. This addresses #1064.
1106 - The sample_flux routine now returns the correct information for the clip column
The sample_flux routine now returns correct information for the clip column
(that is, it matches the clipping done by this routine). There may be changes to 
the reported error ranges because of this change.
1107 - Add some grating related keywords for _reprhtml for ARF, RMF, PHA
Add keywords to the default output in the _repr_html_ for some X-ray classes.
1113 - XSPEC: support etable table models
Allow XSPEC ETABLE table model files to be read by load_xstable_model by 
setting the etable parameter.
1118 - Improve test cases for source plots with PHA data
Add additional test cases for source plots with PHA data to check out 
rarely-used combinations.
1127 - PHA filtering changes
Improve some corner cases for filtering PHA data, including fixing #921 (channel
bounds are integers, not half-integers).
1131 - Test: fix a test failure when XSPEC installed but no fits backend
Avoid running a test we know to fail for an uncommon combination of options.
1134 - This is a doc-string only update for load_multi_XXX
The previous example implied that a spectrum may contain both positive and 
negative orders in the same spectrum. That can happen only after coadding - 
and in that case one would co-add the arfs as well.
1135 - Added docstring and removed unused no-op class
Remove sherpa.astro.models.MultiResponseSumModel which did nothing and seems 
to be unused (except in a test that explicitly skip this class).
1136 - Replace error message "too few columns" with a more generic word
Change the wording of an error message. Potentially breaking if someone tests 
for the wording of the error message in their code, but certainly more correct.
1137 - Correct docstring for fake_pha
The old docstring claims that the background is just scaled and not simulated, 
but there is definitely a call to poisson_noise for the background in the code.
1138 - Address NumPy 1.20 bool/int/float deprecation warnings
NumPy 1.20 notes that numpy.bool, numpy.int, and numpy.float will be removed 
and users should just use bool, int, and float instead, so these symbols have 
been changed. This is a follow on to #1092
1140 - Fix some remaining master/main renames
clean up references to master with main
1143 - add basic test and documentation for Integrate1D
Add basic testing of the integrate1d model class and improve its documentation.
1144 - A minor cleanup of estmethods
A minor cleanup of the sherpa.estmethods code.
1147 - Tests: support use of data directory being local, not absolute
Allow a test to pass when given a relative path for the test data directory.
1154 - Update docs on RTD builds
Update docs on how the docs are build in CI
1155 - Remove Meta class for fits hdu headers
Remove Meta class for header information that is used only rudimentary and 
acts almost, but not quite, like a dict
1163 - XMM/RGS triggers a notice/ignore bug because channels are in reverse-energy order in RMF
Recent work on the ignore / notice logic in #1127 implicitly assumes that the 
energy grid in PHA/ARF/RMF files is in increasing order, which does not hold 
true for XMM/RGS data
1164 - Fix plots with wavelength general:visualization type:bug
For some data files, plots with a reversed grid (i.e. plots in wavelength) were 
drawn with disjoint lines since #906.
1165 - Add a section on running the tests to the developer docs
Add a section on running the tests to the developer docs
1168 - Logging tweaks
Include the sherpa.utils.logging module in the documentation and update a test 
to use the caplog feature of pytest (the code had been written to work with 
python 2.7 version of unittest).
1170 - Update Python and particularly number versions in documentation
Updates to doc pages that list dangerously old numpy versions
1171- Improve the grouping/filtering tests
Add a number of tests for corner cases of filtering and grouping of PHA data.
1172 - Improve data pha docs
Improve the documentation of the filtering and grouping of PHA data.
1173 - Improve DataPha documentation
Minor improvements to the documentation of the DataPHA class.
1175 - Store UI contour plots in a dictionary, not directly
Change the internal storage handling of contour objects
1177 - minor rework of image handling for ui layer
Change the internal storage handling of image objects and improved testing
1178 - Define physical constant hc in fewer places
hc (as in "Planck constant * speed of light") is a physical constant that does 
not depend on the DataPHA and thus it should not be defined as a class attribute.
1180 - Minor improvements to model/parameter documentation
Minor fixes and improvements to the documentation (both docstrings and RTD) 
for the model- and parameter-related code.
1182 - Simulations with multiple responses
Enable simulations with multiple ARF/RMF present (e.g. LETG/HRC).
1183 - Check parameter link behavior
Minor tweaks to the parameter tests.
1184 - Better pha model component plotting (fix #1020)
The use of plot_model_component and get_model_component will now automatically 
add the response for PHA data sets, if there is one. Model expressions which 
contain a response will not be changed. Fixes #1020.
1187 - Conda GCC 9.3.0 update issue
update to support environment changes due to conda defaults updates for 
gcc 9.3.0
1192 - Remove Python 3.6 and add Python 3.9
updates to switch python support to python 3.7-3.9
1194 - datastack: Improve show_stack and add _reprhtml for stack
Improve datastack display (via show_stack and in the notebook) for datastacks.
1198 - XSPEC test cleanup
Very minor improvement to the XSPEC test suite.
1199 - Move the regrid code out into a separate method
Very minor code reorganization for the regrid code.
1203 - Update GitLab Conda recipe to numpy 1.19
updates gitlab conda recipe to python 1.19+ and adds run time pin
1204 - region lib updates for CIAO 4.14
updates to fold in changes to CIAO region lib for CIAO 4.14. Specifically, 
fixes for SM-89: bug in pie shape (extent/inside logic), SL-243: region - 
deprecate obsoleted Warning.
1205 - Remove the SherpaTestCase class
Remove the SherpaTestCase class from sherpa.utils.testing and switch the tests 
that used it to use pytest functionality where appropriate.
1208 - Fix get_xerr for Data1DInt when all data is filtered
The get_xerr method of Data1DInt would fail if all bins had been ignored and 
it now returns the empty list.
1215 - Restrict the values used in PHA notice/filter calls
Ensure that the low and high limits for notice and ignore calls for DataPHA 
objects are sensible (hi >= lo and that for energy or wavelength filters they 
are >= 0). When filtering DataPHA objects in channel units the lo and hi 
arguments must be integers otherwise an error is raised.
1216 - filter improvements for DataPHA and Data1DInt
Energy and wavelength filters (with notice and ignore) for PHA data are now 
treated as lo <= x < hi in all cases, and channel filters are lo <= x <= hi 
(where the channel values must be integers). For Data1DInt cases the notice 
and ignore filters are treated as lo <= x < hi. This changes address a number 
of corner cases.
This can result in slightly different fit results because the data used in the 
fit can be changed and hence changing the number of degrees of freedom (by one 
or two depending on whether the first and last bins have been removed).
1218 - Update fftw from version 3.3.8 to 3.3.9
This change updates the version of the fftw module in sherpa's external 
dependencies (extern) directory to utilize version 3.3.9 (www.fftw.org) instead 
of the previous version 3.3.8
1219 - Fix filter expressions
Filter expressions for Data1DInt and DataPHA cases now report the start and end 
value of each set of grouped data rather than use the end points. For PHA data 
sets users now see the same ranges displayed whether the data is grouped or not. 
The actual filter remains the same even if the filter expressions has changed 
slightly.
1223 - XSPEC 12.12.0 support
Support the new additive and multiplicative models in XSPEC 12.12.0 - XSgrbjet, 
XSwdem, XSvwdem, XSvvwdem are additive and XSzxipab is multiplicative - and 
note the additional abundance tables that are available when running with XSPEC 
12.12.0 (lpgp and lpgs).
1227 - Support AstroPy 4.3 for tests
The AstroPy FITS reader is less tolerant of invalid FITS files in AstroPy 4.3 
which trips one of our tests. The test has been updated with a FITS file that 
doesn't trigger the error case. There is no functional change in this commit.
1228 - Fix three parameter names for XSPEC models
Fix three XSPEC models which had some internal confusion over parameter names: 
XSzkerrbb should have uses fcol but had instead used hd, and XSzashift and 
XSzmshift used Redshift instead of Velocity. The old names have been kept as 
aliases.
1230 - Update submodule to pick up submodule README
Updates submodule to pick up the submodule README
1231 - Remove init.py from tests directory
Clean up of a test directory. There is no functional change in this commit.
1236 - Remove compiler warnings
Avoid compiler warnings from clang, fixing #1232 and several other warnings.
1241 - to get sherpa to run Apple M1 (arm)
Initial support of sherpa for ARM build 
1244 - Fix "unable to parse region string: None" errors (issue #1214)
In certain circumstances (such as plot_pvalue with an explicit 2D PSF 
convolution operator read from a file) the code would fail with the error 
unable to parse region string: None (issue #1214). This PR fixes this problem 
and several minor related issues.
1246 - Image region filters are now specified correctly (Fix #1245)
Update the image filter code so that the region description matches what the 
filter actually is: rather than use & to combine regions we now use | as it 
is a logical or rather than logical and. This is mainly going to affect users 
who: have used the output of get_filter() as input to calc_data_sum2d, have 
very-complex spatial filters, or are restoring Sherpa sessions created by save 
or save_all.
1247 - Allow save_all to work well with images with no filters (Fix #437)
Fix a problem with the output of the save_all command if an image had been 
loaded but no region filter applied (fix #437): the output file would contain 
a notice2d_id call with a filter of "" which would fail if you tried to load 
the file back in. It now no-longer creates this line.
1248 - Docs: note that set_stat can be sent a stats object
Update the documentation for set_stat to note you can send in a stats object
1250 - Stop odd interaction between plot_model and PHA filters (Fix #1024)
plot_model(), if done before calling notice or ignore, could lead to strange 
filters (e.g. filter not getting applied). This has been fixed. Fixes #1024
1253 - More numpy 1.20 warning fixes
Avoid warnings from NumPy 1.20 about using the deprecated np.int symbol.
1254 - FIX: #1235 change XSPEC chatter to 10 from 0
Change the default X-Spec chatter level from 0 to 10. This may result in screen 
output the first time an XSPEC model is evaluated (e.g. from a plot_model or 
fit call). There have been a number of cases where APEC models appeared to be 
creating no output because of missing data files (due to old ~/.xspec/Xspec.init 
settings) which would have been more obvious with this change. To get back to 
the previous behavior users can call set_xschatter(0).
1259 - XSPEC parameter changes - you can change the hard limits of most XSPEC parameters
XSPEC model parameters now use the same limits for soft and hard (the hard 
limit from the model.dat file). This is handled by the XSBaseParameter class 
which is used for XSPEC table models. The XSParameter class, which extends this 
and is used by most other parameters, allows the user to change the hard limits 
of the model. This follows XSPEC, and allows using some models which are 
documented as supporting a value outside the normal parameter range (normally 
by setting the value to a negative value). Note that this is potentially 
dangerous (it could crash the program) so should be used carefully. It is 
strongly suggested that any parameter set to a value outside of the original 
limits is also frozen.
1260 - Add a module to parse XSPEC model.dat and helper scripts #1260
Add support for parsing XSPEC model.dat files (useful for updating the XSPEC 
module or if you want to use XSPEC local models).
1261 - update to match recent XSPEC model.dat settings
Update the XSPEC models to match the latest model.dat file (from HEASOFT 6.29 / 
XSPEC 12.12.0). This primarily changes the hard limits of the models, but there 
are some changes to the default parameter values as well, as well as some unit 
changes, including adding and removing units.
1264 - Fix crash from grouping data using an unsupported method
It was possible to cause Sherpa to crash by passing an invalid function as the 
groupfunc argument to apply_filter and apply_group. The code now errors out 
instead. There are improvements to the documentation (docstring and RTD) for 
PHA filtering and grouping.
1268 - Doc: switch default sphinx role
Multiply the number of working references on readthedocs, while at the same 
time reduce verbosity in the docstrings.
1270 - Cleanup setup
Update the Python supported status in the package metadata (drop 3.5, add 3.8) 
and bump the minimum version to 3.6.
1273 - crates backend strip preceding/trailing whitespace when determining ascii file colnames (Fix #1262)
This change modifies the crates backend ascii file handling to resolve issue 
#1262 where a test added in PR #1253 causes the tests to fail. This change may 
potential result in behavior changes for crates use on ascii data files (see 
caveat section for details).
1276 - Fix Inconsistent behavior in save_arrays when optional parameter ascii = True/False (Fixes issue #1251)
Updates the data I/O so that write_arrays behaves consistently whether writing 
ascii or fits files via the pyfits backend.
1279 - rm the platform cause no longer need it
rm the platform module since it is not needed for ARM support
1281 - RTD: include parse_xspec_model_description
Fix a link on the Read The Docs pages from PR #1260
1282 - Add Zenodo details for 4.13.1
Include the Zenodo details for the 4.13.1 release into the hard-coded list of 
releases.
1285 - Added an option to reflect minim about the boundary
This PR adds the option on how the optimization minim will behave if the free 
parameter is beyond the limit. The default parameter reflect is True (will 
reflect by an equal amount about the limit). If reflect is set to False then 
model function will return DBL_MAX (~1e308) and therefore it will not be 
included in the simplex.
1287 - Remove C++ warning when compiling the pileup code
Use unique_ptr rather than auto_ptr in the pileup code to avoid C++ warnings. 
Fix #505
1288 - Improve the PHA simulation documentation
Fix up some links in the RTD documentation for simulating PHA data.
1290 - Fix the string output of CDFPlot
Corrected the order of the points, x, and y values when displaying a CDFPlot 
object, improve support for a list argument, and made minor additions to the 
documentation in the sherpa.plot module.
1291 - Comment: add link to the OSTI.GOV URL for the optimizing document
Add a reference to the OSTI.GOV technical report in the comments in the C++ 
code used for testing the optimization functions.
1292 - Update tests that were changed by #1246
Fix tests that started to fail once #1246 was merged.
1293 -RTD: add a "how to optimize a function" example
Add a section to the ReadTheDocs site explaining how to "optimize a function" 
as this is something we can do but only really with the low-level code.
1294 - RTD: Fix some sphinx warnings (sherpa.models.regrid)
Fix a minor warning when generating the Read The Docs pages.
1295 - Update XSkerrconv model for #1275
Rename the first two parameters of the XSPEC XSkerrconv convolution model from 
Index/Index1 to Index1/Index2. Fixes #1275
1296 - Document the neldermead reflect flag from #1285
Add documentation for the reflect keyword added in #1285 for the neldermead 
optimizer
1303 - Updated Introductory Section of the MCMC page
Added additional details regarding sherpa's MCMC inplementation to the 
documentation 
1308 - Docs: fix get_filter examples
Fix the examples in the get_filter documentation.
1310 -Update the python check for python setup.py installs to 3.7
Updates the minimum supported version of python supported in setup.py to use 
python 3.7
Caveats
  • Crates behavior change - PR #1273 fixes an issue with the crates backend where supplying a column filter "opt colnames=none" for an ascii file would utilize default column names 'col1..coln' instead of the column names specified in the file. Code which relied on the old behavior may now produce an IO error such as "IOErr: Required column 'col1' not found in [ <list of valid column names>]"
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