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RELEASE_NOTES
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Release Notes
Sherpa 4.16.1
=============
This release of Sherpa includes various enhancements, documentation updates, bug fixes, and infrastructure changes.
* enhancements:
* minor plotting changes; add support for splitting model expression into
additive components and plot the results; support of log scale axes for
confidence plots; improved error messages for unavailable plot backends
* improved RMF plot display to allow choice of energy units
* documentation changes:
* updates to fake_pha documentation
* updates to install.rst to fix incorrect links and outdated version references
* updated read the docs documentation to match current code
* bug fixes:
* fixed multi-panel plot issue with Bokeh backend
Details
-------
#1608 - Remove the test setup.py option
Add the test configuration so that we can ensure the necessary testing
packages can be installed when the code is built. Support for running the
tests with 'python setup.py test' has been removed to match changes in the
Python packaging ecosystem.
#1679 - Automatically split a model expression into additive components and plot the results
Add plot_source_components and plot_model_components calls that will split
up a model like gal * (pl + line) into two lines: one for gal * pl and one
for gal * line. There are also corresponding get_source_components_plot and
get_model_components_plot calls, and the "source_components" and
"model_components" arguments can be used with the plot call.
#1684 -Fix fake_pha docs
Fix the documentation and some corner cases of sherpa.astro.fake.fake_pha.
There are several times when the simulated PHA output would not be correct
if the PHA contains at least one background component or a pileup model
was used.
#1926 - Let users know they should use load_xstable_model not load_table_model
Support for XSPEC table models in load_table_model was deprecated in the
4.9 release. Ensure users know that they should be using load_xstable_model
instead by adding a warning message whenever it is used.
#1934 - Zenodo broke the API we were using to request citation details.
Ensure that the sherpa.citation() command can query Zenodo for the release
information. Fix #1933.
#1938 - CI: temporarily remove ds9 tests on macOS
Avoid the DS9 tests on the macOS build to avoid the failure case we
currently often, but not always, trigger.
#1941 - Fix various typos
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.
#1946 - versioneer: update to version 0.29
Update the vendored copy of versioneer from 0.28 to 0.29.
#1947 - Ensure tests can be run when the group library does not exist
Annotate several tests with the requires_group decorator.
#1952 - Tests: better support of optional region/wcs dependencies
Ensure that the tests can pass if the region or WCS code is not available.
#1954 - CI: avoid failures due to missing pyarrow installation
Allow the CI runs to pass with new changes to pandas warning messages
(completely unrelated to Sherpa but caused the tests to fail).
#1957 - CI: support pytest 8.0.0
Allow the tests to pass when run with pytest 8.0.0.
#1959 - Support logarithmic axes for 1D and 2D confidence plots
The projection and uncertainty plots, for both interval (1D) and region (2D),
now correctly create a logarithmic scale when requested. Fix #1561.
#1962 - Pick up latest Python micro version in conda workflow
This resolves the missing crypt.h issue being seen in the conda test workflow
by picking up the latest micro version of the python packages for the conda
test build workflows.
#1965 - Improve the error message when a plot backend is not available.
Improve the error message when a plot backend is not available. Fix #1964
#1968 - Remove Conda build 3.25 pin from deployments
Removes the conda version specification (3.25) to avoid compatibility issues
#1969 - Tests: group the DS9 tests so they can be run with one worker process
Ensure those tests that use the requires_ds9 decorator all have the same
group marker, so that they will be run within a single worker process when
using pytest-xdist to run tests in parallel. There is no change if
pytest-xdist is not installed.
#1970 - Bump the minimum pytest version
Pytest occasionally changes behavior and it does not seem worth our time to
maintain backwards compatibility with old versions of pytest - see #1960
#1972 - Remove excess brackets in model names
Remove excess brackets from model and parameter expressions. This is purely
a cosmetic change, but hopefully makes complicated model expressions easier
to read. Fix #780.
#1973 - Fix the requires_pylab decorator
Change the testing code to better-handle those tests that want to check
plotting when using the pylab backend. Fix #1971.
#1974 - Allow linked parameters to be fit without including them in the model expression
Treat linked parameters as part of the model expression (via the new lpars
attribute and get_thawed_pars routine) so that they can be included in a
fit without including the linked model as part of the model expression.
Fix #777
#1976 - Fix bug in multi-panel plotting in bokeh
Fix bug in multi-panel plotting in bokeh
#1977 - model: improve examples in docstrings
Allow model.py, parameter.py, and regrid.py to be included in the
docstring pytest run.
#1984 - Rework x errorbar support to better-match community expectations
Improve the "x errorbar" handling for histogram-style data (including PHA),
including support for the wavelength setting (fix #1985), to better match
community expectations (e.g. #1817).
#1994 - Tests: improve coverage of parameter module
Improve the test coverage of the parameter module.
#1996 - docs: update examples to match current behavior
Update the ReadTheDocs documentation to match the current code.
#1998 - Cleanup XSPEC interface
A small number of XSPEC model parameter values have been changed to match
the default frozen state of XSPEC version 12.13.1.
#2000 - CM-481: update codecov action to v4, add upload token
Updates version of codecov being used
#2003 - Minor plot work
Internal clean up of the plotting code in preparation for future changes.
The ARFPlot class will now generate an IOErr rather than PlotErr if sent
a non-PHA dataset (to better match other calls). The DataHistogramPlot
class now treats xerr as a property that can not be changed, and is fixed
to be the half-width of the X bins, although note that this field is not
really used and may be removed at some point in the future.
#2004 - Minor improvements to the RMF plot capability
Improve the RMF plot display so that it recognizes the current units
setting and allows the choice of energies to be over-ridden by the user.
#2006 - Use a separate context when handling multiprocessing calls
Ensure that Sherpa does not change the global multiprocessing state but
instead uses the (new) sherpa.utils.parallel.context attribute. Fix #1015.
#2011 - Specialize the residual-style plots for histogram data
Improve the display of residual-style plots for integrated datasets.
Fix #1817.
#2012 - [CI] Update ci-conda-workflow.yml to pin back to macos-12
Pin back to macos-12. This version is specific to macOS-intel. 13 doesn't
work as conda is removed from it.
#2019 - update clone link and versions and DOI
This is a documentation update to fix the incorrect link in the source
install example. I also updated the version and DOI link in the description
of the source installation.
#2020 - CI: bump the checkout actions versions
Internal change to how the GitHub actions are run for CI.
#2021 - Update Conda Deployment Workflow Action Versions
Updates internal actions in the deployment workflow
#2025 - Improve support for NumPy 2.0
Improvements for running Sherpa with NumPy 2.0.
#2029 - Swap oldest-supported-numpy with numpy in requirements
Sherpa 4.16.0
=============
This release of Sherpa includes various enhancements, documentation updates, bug fixes, and infrastructure changes.
* enhancements:
* the grouping commands like group_counts and group_snr now default to only grouping within the noticed range of channels, which is a change in behaviour
* new plotting backend: Users can now choose between matplotlib and bokeh (experimental) support use of arbitrary python functions when linking model parameters
* updates to fake_pha, save_all, allowing to write out RMF/ARF files
* get_plot_prefs and get_contour_prefs call to simplify access to the plot and contour preferences
* implementation of RMFPlot and DataIMGPlot classes and associated UI functions (plot_rmf, get_rmf_plot)
* update support for XSPEC to include version 12.13.1, allow XSPEC table models which include the ESCALE parameter, and provide experimental support for writing out XSPEC table models.
* documentation changes:
* added doc strings for sherpa data classes
* several updates to in code and RTD documentation
* Infrastructure changes:
* revamp of plotting backends from modules to classes and adding support for multiple backends
* changes to use the NumPy random generator API
* bug fixes:
* PHA source plot Y axis scaling (#1825)
* fix model display for grouped data (#1779, #1784)
* Change in the ordering of operations when grouping background PHA datasets. (#1881)
Details
-------
#1382 - Plot changes: Step 1 A- Draft API for backend classes
Plotting infrastructure changes that make the plotting backends classes
instead of modules.
#1617 - Pass keyword arguments to models
Allow keyword arguments to be passed to models and ensure these arguments
are respected by the model cache.
#1629 - Note when a XSPEC model is changed to F77 form (double precision)
Update a script used when updating the XSPEC support to point out models
that use the double-precision FORTRAN support. There is no functional
change to the code.
#1653 - Allow arbitrary functions for linking parameters
Provide a way to use any Python function to be used for linking
parameters. Fix #1652
#1730 - Update xspec model creation
Update the code created by the sherpa.astro.utils.xspec routines to
account for changes in the XSPEC interface in Sherpa. This only affects
users who call these routines directly.
#1734 - Unify the fake and fake_pha calls
The fake_pha call now accepts a method argument to match the fake call.
#1735 - Allow use of the NumPy random generator API
Take advantage of the NumPy random-number generator classes to provide
random numbers, and move away from using the global state provided by
numpy.random.seed and random.seed routines.
#1738 - Return more-useful information when an XSPEC model fails
Include the model name and parameter values in the error message of a failed XSPEC model.
#1750 - Replace pkg_resources as it is deprecated
Remove the use of the deprecated pkg_resources module and replace with use
of importlib.resources. Fix #1723
#1763 - Allow load_image to change the coordinate system
Ensure that the coordinate setting used in load_image calls is properly
handled (when not set to the default value of "logical"). Fix #1762
#1770 - Drop python2 ism in the fit code
Internal clean up of the fit code to replace a Python 2 method with a
Python 3 version and to use f-strings.
#1771 - utils: make sure OutOfBoundErr is an actual exception
Ensure that OutOfBoundErr is an exception (this is an internal feature).
#1772 - Tweak resample data code
Internal changes to the ReSampleData class to better handle invalid input.
#1773 - Internal clean up of estmethods
Code clean up of sherpa.estmethods.
#1775 - Change a single test to use explicit rather than implicit random state
from NumPy
Simplify a single test. There is no functional change.
#1776 - Move the parallel code into a separate module
Move the parallal_map code from sherpa.utils to the new sherpa.utils.
parallel module (the symbols are still accessible from the original
location but code should be updated to use the new location, including the
renames of _ncpus and _multi to ncpus and multi).#1777 - Change get_sample
to require named arguments
#1778 - Optmethods cleanup
Move testing code out of the optmethods modules and into a separate test,
along with a number of code clean ups. There is no functional change.
#1780 - Fix model plot display when factor is set for grouped PHA data (issue
#1779)
Ensure that model plots can be created for PHA data when set_analysis
routine is used to set factor > 0 and the data is grouped. Fixes #1779 and
#1784
#1781 - utils: remove the numpy_convolve routine
Remove the sherpa.utils.numpy_convolve routine.
#1785 - Add docs to Sherpa data classes
Add docstring to most Sherpa dataclasses.
#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.
#1794 - docs: note requirement on ar for building Sherpa
Add ar to the list of requirements for building Sherpa. Fix #1792
#1795 - Add docs to describe the inputs for the ``calc`` function of a user
model
Add docs that describe the arguments of the calc function for user models.
#1797 - model: explicitly send parameter argument to calc
Ensure that the calc method for models begins with the parameter array
(explicitly given) rather than extracting it from the named arguments sent
to the routine. This should not change any user code.
#1800 - utils: minor code clean up
Internal clean up of the sherpa.ui.utils module.
#1805 - Clean up display of dataset ids during fits
Ensure dataset ids are listed without leading brackets in the fit and
staterror string outputs (remove an accidental change made in #1770). Fix
#1804
#1806 - Activate sphinx directive to make plots
Use the Sphinx plot directive to generate (some of) the plots in the docs.
#1807 - NumPy 1.25 support
Remove deprecation warnings seen when using NumPy 1.25.0.
#1808 - Use Sherpa install instead of code only to build docs
Switches from building the documentations from the source directory, to
building it from an installed version of Sherpa.
#1809 - Update the hardcoded Zenodo releases to include the 4.14/4.15 releases
Update the stored Zenodo releases to include the 4.14.* and 4.15.* Sherpa
releases. Users should see no difference (other than avoiding the need for
an http call to retrieve this information) when calling sherpa.citation().
#1810 - RTD: fix script name for XSPEC updates
Improve the documentation on how to update to a new XSPEC version by
ensuring the correct helper script is run in an example.
#1811 - ui: use the default pickle version when dumping the state
Use the default version when pickling data (used by the UI save call)
rather than an old version. Fix #1243
#1812 - Autoupdate copyright year in sphinx docs
Autoupdate copyright year in sphinx docs.
#1813 - Fix ReadTheDocs warnings and then make RTD fail on warnings in CI
Fix ReadTheDocs warnings and then make RTD fail on warnings in CI.
#1819 - CI: hide NumPy 1.25 array ndim>0 deprecation warnings
Allow the tests to run with NumPy 1.25 and with Crates (from CIAO 4.15) as
the I/O backend. There are no functional changes.
#1821 - parallel: tweak ordering of checks for parallelization
Internal change to the decision of whether to use the multiprocessing
module to run code or not.
#1823 - sherpa_test: tweak how pytest/plugins are installed
Internal changes to how we check for test requirements used by the
sherpa_test script.
#1824 - remove non-existent datastack plotting backend initialization attribute
Clean up error condition by removing the sherpa.plot.backend.
initialize_backend attribute as no longer exists.
#1828 - Improve PHA source plots: support type=counts and factor above 1
Source plots for PHA data now follow the rate and factor analysis
settings. Prior to this the rate setting was ignored and the factor
setting produced incorrect values for factor=1 and factor=2). Fix #1825
#1829 - Limit precision in the comparison of string outputs
Update the tests to support running on ARM/AARCH64 platforms where numeric
differences can complicate string comparisons. Fix #1815.
#1832 - astropy: rework RMF input (fix #1344)
Allow the AstroPy backend to read in HRC-I RMF data. Fixes #1344.
#1835 - Note compatibility with XSPEC 12.13.1
Note that Sherpa can be built against XSPEC 12.13.1 and update some
parameter ranges or defaults to match the new values from this release.
#1836 - Allow ARF and RMF to be written out
Support writing out ARF and RMF data to FITS files (and, for ARF, ASCII
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
the plot and contour preferences.
#1840 - Fix #1828 - histogram plot issue
Fix up the histogram display for the unlikely case when the bin edges have
at least one gap, the low edges are integer values, and the high edges are
floating-point values.
#1841 - Minor refresh of AstroPy I/O code for better FITS and ASCII output
Minor rework of the sherpa.astro.io.pyfits_backend module to improve on
the output (both FITS and ASCII), such as a closer mapping of the data
type used on disk and written out to file, and some changes to the header
lines of ASCII files.
#1844 - XSPEC: allow table model redshift parameter range to change (fix #1814)
Allow the redshift range of XSPEC table models to be changed outside the
default 0 to 5 range. This restores a feature that was lost in the 4.15
release. Fix #1814
#1848 - Tests: add regrid corner case tests
Add tests for corner-cases for the regrid method. Many of these tests are
currently regression tests, and check that the code behavior has not
changed, rather than that it works correctly. There is no functional
change to the code.
#1851 - XSPEC: table model improvements
Address issues with the XSPEC table model support: models that set an
Escale parameter (feature added December 2020) are now supported
(previously they could cause a segmentation fault) and ensure that
parameters with a negative delta value are marked as frozen. Fix #1850 and
#1852.
#1853 - XSPEC: update model parameters to match XSPEC 12.13.1 / HEASOFT 6.32
Update the XSPEC parameter names and ranges to match those from XSPEC
12.13.1 / HEASOFT 6.32.
#1854 - models: change defaults for Box1D parameters
The xlow parameter of Box1D now defaults to 1 and the ampl parameter has a
greatly-increased range (from the previous version of -1 to 1).
#1855 - group_counts et al now default to using the existing mask as the
tabstops, unless explicitly given
When calling group_counts, group_width, ..., use the current mask as the
tabStops argument by default (actually, the inverse of the mask), that is,
when the tabStops argument is set to None (the default). This means that
the grouping is only applied to the selected channels, and means that the
filter range is less likely to change when filtered data is grouped.
This is a change in behaviour. To get the previous behaviour users need to
set tabStops to an array of zeros (length being the number of channels):
e.g. for Chandra ACIS imaging-mode data, group_counts(20, tabStops=[0] *
1024) or group_counts(20, tabStops=np.zeros(1024)). Fix #417 #956 #1081
#1856 - XSPEC: fix link for XSPEC gauss/zgauss models
Fix the link to the XSPEC documentation for the gauss and zgauss models.
#1858 - Correctly handle XSPEC table models with both ESCALE and Z parameters
Update XSPEC table model support for models with both ESCALE and REDSHIFT
keywords set to work correctly. Fix #1857
#1861 - Allow XSPEC table models to be created and written out
Provide experimental support for creating XSPEC table models (additive or
multiplicative). The output routines can be found in the sherpa.astro.ui.
xstable module. Note that XSPEC support is not required to write out an
XSPEC table (but it is to be able to read it back in and use it). Fix #1859
#1866 - Switch to conda-forge and use new Conda channel
Removes use of defaults channel and replaces it with conda-forge; removes
references to anaconda
#1867 - First fixes for NumPy 2.0
Internal code changes to improve support for NumPy 2.0.
#1874 - save_all improvements for set_psf and load_xstable_model
Ensure that save_all includes set_psf calls, supports XSPEC table models,
and improve the support for data sets created with load_arrays or
dataspace1d/dataspace2d. Fixes #1873.
#1877 - un-whitelist deprecation warnings
Cleaned up deprecation warning exceptions from test white list
#1878 - Tests: better handle case where both astropy and crates are available
Fix up tests that would fail when both astropy and crates packages were
installed and the pyfits backend was chosen (the tested functionality was
not wrong, just they were testing the wrong things).
#1883 - Update setup_ds9.sh for DS9 8.5
Update to use newer ds9 version
#1888 - UI: set_analysis reports the filter change - fix #1590
The sherpa.astro.ui.set_analysis call now reports the new filter. It will
also now error out if no data has been loaded. Fix #1590 and #1368.
#1890 - Convert a RMF to an image
Add the sherpa.astro.instrument.rmf_to_image and sherpa.astro.instrument.
rmf_to_matrix routines for converting a RMF to DataIMG or a 2D matrix
respectively. Fix #1619. The create_non_delta_rmf routine in the same
module no-longer assumes the matrix is square. Fix #1889.
#1891 - ui: add calc_bkg_stat - fix #333
Adds the calc_bkg_stat, calc_bkg_stat_info, and get_bkg_stat_info
routines. Fix #333.
#1892 - data: group backgrounds before source - fix #1881
Change the ordering of operations when grouping background PHA datasets.
Fix #1881
#1899 - Bokeh class
Provides a new backend plotting class which utilizes the Bokeh
visualization package.
#1906 - Remove hardcoded matplotlib for _repr_html_ of RMF and DataImage2D
Implement RMFPlot and DataIMGPlot classes and associated UI functions
(plot_rmf, get_rmf_plot). Fix #1385
#1908 - Add versionadded note to set_plot_backend
Added note that the set_plot_backend command is new in 4.16
#1909 - Add security warnings to restore functions
Added documentation warning of inherent risks of importing binary files
when using restore functions.
#1911 - IO: add missing import for pyfits backend
Ensure a corner-case error condition when writing out responses fails with
the correct error.
#1912 - Warn when reading in a multi-matrix rmf
Ensure that attempts to read in a multi-matrix RMF will warn the user that
they are not yet supported.
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
Sherpa 4.15.0
=============
This release of Sherpa includes various enhancements, documentation updates, bug fixes, and infrastructure changes.
* enhancements:
* Improved validation of arguments when creating Data objects:
* 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.
* Increased test coverage for plotting
* documentation changes:
* updated readthedocs to use pip and pytest instead of setup.py
* several updates to documentation, including updates to fake_pha, calc_ftest, calc_mlr
* Infrastructure changes:
* Drop support for Python 3.7
* Updates to start creating Python 3.10 Conda packages.
* Use Numpy 1.20 for Python 3.8/3.9 and Numpy 1.21 for Python 3.10.
* Moves toward PEP-517 with some distutils cleanup and more configuration moved from setup.py to setup.cfg
* Various improvements to the GitHub Actions and GitLab workflows
* bug fixes:
* Ensure chi2xspecvar errors match XSPEC when 0 counts are present during background subtraction
* Remove model instances from the global symbol table when clean is called
* Addresses new warnings in the tests for Matplotlib 3.6.0 and AstroPy 5.1
* Minor copy and paste error in fake_pha docstring
* Test issues in test_fake_pha.py due to randomness
Details
-------
#1329 - Build updates (move towards PEP-517 support)
Move the Sherpa build system towards a more static configuration (PEP 517)
#1412 - XSPEC: initialize XSPEC library at load time
Simplify how and when the XSPEC model library is initialized. Fixes #1388
#1477 - Add data validation
Improve the validation of arguments when creating Data objects- 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.
#1504 - CI: rework setup
Update the GitHub workflows for Continuous Integration to better take advantage
of the workflow language.
#1505 - RTD use pip/pytest rather than setup.py for install/develop/test
Change the RTD documentation to use pip and pytest rather than setup.py when
building and testing Sherpa
#1507 - tests: ensure DS9 window is closed after the tests
Ensure that any DS9 process started by the Sherpa tests is closed when the tests
are finished.
#1510 - Tests: improve test coverage of plot code
Improve the testing coverage for several plot routines.
#1513 - Minor UI tweaks
Added validation to the set_xlog/ylog/xlinear/ylinear and updated save_model,
save_source, save_resid, and save_delchi commands from sherpa.ui to not error
out if not given an explicit identifier.
#1516 - Consolidate plot and set_xlog handling
Use the same labels for the plot and set_xlog/set_ylog/set_xlinear/set_ylinear
functions. As a result, a number of names can no-longer be used as an identifier
for a dataset (bkg_chisqr, bkg_delchi, bkg_fit, bkg_model, bkg_ratio, bkg_resid,
bkg_source).
#1519 - Use direct html links instead of using `[1]` and a reference section
This replaces the use of a "References" section with direct URL links in
particular in cases where the reference is just a plain old HTML website and
not a scholarly publication.
#1523 - Ensure the region-lib code is re-generated when needed
Fix a build issue with clang where the region-library code caused an error
message
#1529 - Add arguments to -i in sed calls in config script
Update sed command in config script for improved portability
#1532 - Add plot related tests
Add more tests to cover corner case scenarios (mostly plotting related).
#1534 - docs: fix calc_ftest/mlr documentation
Note that calc_ftest and calc_mlr can return an array or scalar value, depending
on the input.
#1536 - Tests: add more tests of get_order_plot/plot_order
Add a test for multiple orders and plot_order.
#1537 - Remove model instances from the global symbol table when clean is called
Ensure that models are removed when clean() is called.
#1538 - Ensure chi2xspecvar errors match XSPEC when 0 counts are present during background subtraction
When using the chi2xspecvar statistic for estimating PHA errors, ensure that the
errors match those calculated by XSPEC when the background is subtracted and the
source or background group contains 0 counts
#1540 - Tests: fix the random seed for a fake_pha test
Remove randomness from a test.
#1547 - Fix CI failures from AstroPy 5.1 warning changes
Allow the macOS tests to run on CI with AstroPy 5.1.
#1554 - Install New libxcb Dependencies for Qt
For Linux GitHub Actions, we now install libxcb dependencies required for
Conda's Qt package.
#1555 - Bump the ci-pip-arch workflow to ubuntu-20.04
Update to use ubuntu 20 as GutHub Actions is deprecating ubuntu 18.04
#1562 - report the change in the filter because of calls to notice and ignore
When a notice or ignore call - including the variants like notice_id and
ignore2d - then the change in the filter is reported to the screen (for users
of the ui layer).
#1563 - Add Python 3.10 Conda Builds, Drop Python 3.7 and Numpy <1.20, Switch to Pip for Conda Builds
Drop official support for Python 3.7 and start creating Python 3.10 Conda
packages. Our Conda builds now use Numpy 1.20 for Python 3.8/3.9 and
Numpy 1.21 for Python 3.10.
#1566 - GitLab: Add version info to deploy test, update test OS, and allow interrupt.
Updates to gitlab to support automated tests, save version info, set default to
interruptible to allow canceling pipelines, and switched to source conda instead
of adding it to the path
#1567 - Fix minor copy and paste error in fake_pha docstring
Make UI layer fake_pha work for XMM/RGS by accepting input of arf=None when an
RMF file is given.
#1569 - Minor changes to the fake_pha test added in #1567
Internal changes to the test added for fake_pha in #1567
#1572 - Tests: fix a logical test error
Fix a logical error in a plotting test.
#1574 - Avoid occasional test errors from Tcl_AsyncDelete
Switch the matplotlib tests to use the Agg backend to avoid possible
Tcl_AsyncDelete errors (issue #1509)
#1578 - Gitlab: Reduce artifact retention period
reduces artifact retention from 2 weeks to 3 days due to new gitlab 5gb
restrictions
#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
Update the documentation to note the change to fake_pha in #1567
#1585 - Tests: work around matplotlib 3.6.0 warning
Allow the tests to pass when run with matplotlib version 3.6.0.
#1589 - Set the language when building the documentation
Ensure the language setting is defined for recent versions of Sphinx
#1594 - gitlab-ci: Set build num to 0 if not set
Set the default Sherpa build number to 0 in our GitLab workflow to know which
package to run deploy tests on for official release builds.
#1600 - Change the histogram1d and 2d routines so that they do not sort the input arguments
Address some failures in histogram1d and histogram2d routines by making sure
they copy the input arguments before sorting them.
Caveats
-----------
* There are known issues (#1602, #1605, #1606) in the histogram1d/histogram2d functions
leading to failures which were not fully addressed in this release (see the failed
case in the second histogram1d example). This is not the Sherpa core functionality
and numpy.histogram can be used if needed.
Sherpa 4.14.1
=============
This release of Sherpa includes various enhancements, documentation updates, bug fixes, and infrastructure changes.
* enhancements:
* various plotting backend improvements
* various i/o backend improvements
* data object class improvements
* basic support for Xspec 12.12.1
* beta support for python 3.10
* documentation changes:
* updated build with CIAO documentation
* Add a missing class (DataOgipResponse) to the documentation
* Improves the docstrings for DataPHA
* fixed typos in plot docs
* clean up readthedocs issues such as missing bullets
* Infrastructure changes:
* updates for compatibility with Clang 12.0
* updates to the regression tests
* bug fixes:
* Improve the FITS headers created when writing out a PHA file (to better match OGIP standards)
* addresses delete_model_component call failing if a key does not exist
* fixed issue with writing a PHA dataset as a table rather than a PHA file
* ensure FITS column access is case insensitive
* image handling and image coordinates
Details
-------
#1030 - Update lev3fft test to use PHYSICAL not WCS
Update a 2D image test to use physical rather than WCS coordinates for the fit.
#1185 - Simplify switching the astro.io backend
Add dummy_module, docs, and test case for switching the sherpa.astro.io backend.
io backend are now tried in a default order (crates, pyfits, dummy)
#1191 - Make it easier to switch the plotting backend
Make is easier to switch the plotting backend (note that we currently only have on
backend implemented anyway)
#1207 - Improve OGIP headers in PHA files
Improve the FITS headers created when writing out a PHA file (to better match OGIP
standards). Fixes #488 and #1209
#1314 - test: add requires_data decorator
Add a needed decorator for a test. There's no functional change to the code.
#1317 - Add requires group test decorators
Ensure the tests that require the group library are marked with the requires_group
decorator.
#1318 - Adjust a test for python 3.10
Adjust a test so that it passes with Python 3.10
#1326 - Write-up that environment variable in setup.cfg need to be expanded
Add a detail to developer docs about compiling in a conda ciao environment
#1328 - Versioneer cleanup
Update the versioneer module we use from 0.14 to 0.21 (latest).
#1331 - optmethods: remove Deprecation warning about invalid escape string
Remove a deprecation warning from sherpa.optmethods.optfcts and update some fake_pha
tests to each use a fixed random seed.
#1332 - Add Instrument test
improved the psf tests, adding low-level tests of the tcdData class
#1337 - Fix import statements
Change from using __import__ to importlib.import_module.
#1338 - clean up some C/C++ code in the _psf.cc file
Minor clean up of C/C++ code
#1339 - Add codecov.yml to fix path issue and update codecov uploader
Fix path parsing issue on codecov as well as updated for the new codecov uploader
#1340 - Change how the sherpa config file is accessed
Support environments where the HOME environment variable is not set when accessing
the Sherpa configuration file.
#1347 - Refactored array classes cause std::vector has non-virtual destructor
std::vector has non-virtual destructor so in this PR the refactored Array (1D and 2D)
classes no longer inherit from std::vector
#1348 - Minor internal code cleanup tracking errors
Minor internal changes to how some errors are raised. There should be no
user-visible differences due to this changes.
#1351 - Update the sherpa-test-data repo to the latest from main
updates that reference to the latest copy
#1353 - Fix issue with delete_model_component
The delete_model_component call could fail in certain circumstances, so fix those
cases. Fixes #16
#1355 - Minor cleanup of the I/O code
Minor internal clean-up of the I/O code. There should be no user-visible changes.
#1359 - Improve writing out data objects as a table (fix #47)
Fix writing out of PHA datasets as a generic table (both ASCII and FITS formats).
Fixes #47
#1360 - Add missing export statement to clang 12 note
Update documentation to be clearer on how to build on clang 12 and avoid compiler
error on implicit function declarations
#1361 - Ensure FITS column access is case insensitive for the pyfits I/O backend (fix #143)
Allow FITS column access with the pyfits backend to be case insensitive. Fixes #143.
#1365 - Simplify a test (fix #541)
Remove duplicated code in a test (fix #541).
#1370 - Minor tweaks to handling of PHA settings
Improve the checking of the factor and rate settings of set_analysis and the
plot_fac attribute of the DataPHA class, and add a few tests that exercise some