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@Marie-Terrell Marie-Terrell released this 18 May 16:05
· 729 commits to main since this release
4.15.1
bf275fc

Sherpa 4.15.1

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

  • enhancements:
    • further improvements to filtering/grouping including reporting a filter change in the UI
    • fake_pha can be called with a list of ARF/RMF names
    • added linewidth option for line and histogram plots
  • documentation changes:
    • fixed broken URLs
    • improved documentation for templates, plot_pvalue
    • added documentation testing with doctestplus
  • Infrastructure changes:
    • dropped support for Python 3.8
    • experimental support of Python 3.11
    • supported versions of Xspec are 12.12.0 - 12.13.0
  • bug fixes:
    • various updates to notice/ignore and group/ungroup code
    • fixed issue with show_bkg
    • fixed issue when binning values into a 1D histogram
    • fixed cache errors with the TableModel class

Details

#1396 - XSPEC minimum version is now 12.10.1
Bump the minimum-supported version of XSPEC from 12.9.0 to 12.10.1.
(superseded by #1609)

#1472 - tests: remove work-around for #1334 from #1336
Remove a test work around for our CI tests failing (issue #1334)

#1486 - Improve filtering/grouping behavior
Changing the grouping array of a PHA dataset (with set_grouping from the UI layer
or by setting the grouping attribute of a DataPHA object) will now re-create the
filter, to fix #1160.
It is suggested that the filter expression (e.g. as returned by the get_filter
routine for uses of the UI layer) is checked to ensure the result is still sensible.

#1502 - Cleanup template code
Improve the documentation and testing of the template-model code. There is no
significant change in behavior, but some use cases will generate more-appropriate
errors than they used to.

#1591 - Document params and return values for root finding functions
Add docstrings for root finding functions

#1607 - Fix an issue when binning values into a 1D histogram
Fix a problem when binning data into a histogram (issue #1605).

#1609 - XSPEC minimum version is now 12.12.0
Bump the minimum supported XSPEC version to version 12.12.0.

#1611 - Post 4.15.0 updates
Add the 4.15.0 DOI to the README.md.

#1613 - Allow testing of the documentation
Adds the ability to run doctests in py and rst files. Those tests will run
automatically, if doctestplus is installed (not on CI in the current setup) and
the file is not explicitly blacklisted for doctestplus.

#1621 - Fix a cache error with TableModel
Fix cache errors with the TableModel class (#1622), add validation of input
values, and minor additions to the documentation.

#1630 - Add support for XSPEC 12.13.0
Add explicit support for XSPEC 12.13.0. Sherpa can be built against XSPEC
12.13.0 without this PR, but this adds in support for the new cglumin
convolution model added in this release.

#1637 - report the filter changes when grouping is changed for the ui
Report the filter when data is grouped with UI commands - such as group,
group_counts, and set_grouping - to match the notice/ignore behavior added in
#1562. The logic for setting the background group flag has been moved from the
UI layer to the DataPHA class. Addresses #1632.

#1644 - Deployments via GH Actions
Dropped support for RH7 and macOS 10.15

#1656 - CIAOX deployments require force. As they deployed for main already.
Based on the current scheme used for the build number, we need to force uploads
for CIAOX as they have already been deployed for main. This was already done for
the previous GitLab builds.

#1660 - Associated group fixes
Clean up of the notice/ignore and group/ungroup code to avoid unnecessary work,
move logic from the UI layer into the DataPHA class, and ensure that if the
grouping field is set to None that the data is not grouped. Fix #1641, #1657,
and #1659

#1662 - Add grouping tests
Add a number of tests to check out corner case behavior, primarily for grouping
PHA data but there's also a number of routines from the UI code that have missed
some tests.

#1664 - Allow save_model/source/resid to work with 2D data (fix #1642)
Fix save_model/source/resid calls when used with 2D data sets. Fix #1642

#1665 - Fix an issue with show_bkg (fix #1645)
The show_bkg routine could fail when the set of backgrounds is not the same for
all datasets (e.g. one has a background and another does not). Fix #1645

#1666 - model-wrapped symbols now reference the actual model (fix #215)
Wrapped models, accessible from the UI layer, now reference the wrapped model
rather than being devoid of any useful information. Fix #215

#1672 - models: f-string changes
Change the models code to use f-strings where appropriate rather than other methods
of string interpolation. There is no change in behavior.

#1675 - Bump ds9 to 8.4.1 - Ubuntu 20 and macOS BigSur
Bump to the latest DS9 version and update to ubuntu20 version. This resolves #1674

#1676 - update model macro definitions for compiled code
Re-work the macro definitions used to build the compiled models and use this to
clean up the handling of the XSPEC models, in particular table models. There is
no functional change.

#1681 - XSPEC test cleanup
Minor clean up to some XSPEC tests to make better use of pytest.

#1689 - Address regression created by #1672
Internal change to the Sherpa-specific logging code, to ensure that logged
message includes all components. This fixes #1688 which was a regression created
when #1672 was recently merged.

#1693 - Test cleanup related to #1334
Complete the cleanup related to removing the #1334 workaround which was added in
#1336. These two tests were missed from #1472 (which was meant to remove these
changes). The two test files have also seen some minor style changes (no change
in behavior).

#1696 - Docs: fix #1694
Correct a link in the RTD documentation.

#1697 - Ds9 test tweaks
Minor cleanup of the DS9 tests (no functional change)

#1698 - Update versioneer to 0.28
Update the version of versioneer included in Sherpa from 0.21 to 0.28. Fix #1677.

#1708 -Ensure string id can be used for the background id in the DataPHA notice/ignore call
Allow a string identifier to be used for the bkg_id argument to the
DataPHA.notice (and ignore) method, fixing #1709 (it does not affect users
using the ui layer).

#1711 - plot: add linewidth option
Add the linewidth option for line and histogram plots (e.g. plot_data,
plot_model, plot_fit) with the matplotlib backend.

#1715 - utils: rework the error-column saving code
Internal clean up of the save_*error routines. There is no change in behavior.

#1716 - utils: tweak internal _save_type routine
Minor internal change to a routine in the utils code. There is no change in
behavior.

#1720 - Fix get_stat_info output for individual components
Fix the get_stat_info output for multiple PHA data when the data has a different
number of background components (fix #1721). The get_bkg_model routine will now
use the source PHA for a response if the background has no response (to match
what fit and fit_bkg do, fix #1724).

#1733 - Allow fake_pha to be called with a list of ARF/RMF names of length 1
Allow fake_pha to be called with a list of ARF and RMF names that only contains
one element. Fix #1722

#1739 - pyfits: be more lenient with FITS files with messed-up headers
Allow some FITS files with an invalid header to be used with the AstroPy I/O
backend.

#1747 - reduce chance of plot_pvalue getting stuck in a bad parameter space
Ensure that each simulation step for the likelihood ratios code, as used by
plot_pvalue, starts with the same parameter values to reduce the chance that the
results can get stuck in certain areas of parameter space. The ratios field of
the LikelihoodRatioResults structure - e.g. the return value of
get_pvalue_results() - can be plotted to see if this has happened (e.g. large
ranges where the ratio is close to zero.

#1751 - Explicitly require attrs module when testing Sherpa
Ensure that the attrs module is available for testing Sherpa.

#1752 - Drop Python 3.8 and Pick up Python 3.11 as a beta
move to be NEP-29 compliant with python version

#1753 - Initial support for Python 3.11
Basic support of Python 3.11.

#1755 - Tests: replace use of attrs package by dataclass
Change a test file to use data classes rather than use the attrs module, which
means that attrs is no-longer needed to test Sherpa. There is no functional
change in this PR.

#1756 - Fix broken URL in docs
Updated URLS which are no longer valid

#1759 - updated plot_pvalue docs
Updated docstring for plot_pvalue to include reference to the algorithm

#1760 - Tweak test tolerances mac arm
Improve test reliance when running on the macOS ARM platform

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