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sherpa/sherpa: Sherpa 4.13.1

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


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    <dct:description>Sherpa 4.13.1 &lt;p&gt;This release of Sherpa includes various documentation updates, bug fixes, and infrastructure changes. The default branch in github has been migrated from master to main.&lt;/p&gt; &lt;ul&gt; &lt;li&gt;documentation changes:&lt;ul&gt; &lt;li&gt;updates to documentation for TableModel, Notice2D, cache support for evaluating models, and low level optimization code&lt;/li&gt; &lt;li&gt;jupyter notebook uopdates &lt;/li&gt; &lt;/ul&gt; &lt;/li&gt; &lt;li&gt;Infrastructure Changes:&lt;ul&gt; &lt;li&gt;the master branch has been migrated from master to main&lt;/li&gt; &lt;li&gt;updates to support numpy 1.20&lt;/li&gt; &lt;li&gt;updates to support astropy 4.2.1&lt;/li&gt; &lt;li&gt;updates to support matplotlib 3.4&lt;/li&gt; &lt;li&gt;test infrastructure clean up and updates&lt;/li&gt; &lt;/ul&gt; &lt;/li&gt; &lt;li&gt;bug fixes:&lt;ul&gt; &lt;li&gt;fix an issue with cache evaluation on 1D models using integrated bins&lt;/li&gt; &lt;li&gt;fix for aarch64 build issue&lt;/li&gt; &lt;li&gt;fix to sherpa citation command&lt;/li&gt; &lt;li&gt;fix to honor clearwindow setting for plot_source&lt;/li&gt; &lt;li&gt;fix errors from save_data when the output file exists&lt;/li&gt; &lt;li&gt;fix build issues using gcc 7.3 with -Werror=format-security compilation flag&lt;/li&gt; &lt;li&gt;fix for reg_proj and reg_unc erroring out when the min or max arguments are tuples rather than lists&lt;/li&gt; &lt;/ul&gt; &lt;/li&gt; &lt;/ul&gt; Details 754 - sample_flux now returns statistic values for each row &lt;pre&gt;&lt;code&gt;The sample_flux command now returns a statistic value for each iteration, even if those rows are not used in the reported flux distribution. Fixes #751. &lt;/code&gt;&lt;/pre&gt; 769 - add basic cache tracking &lt;pre&gt;&lt;code&gt;Adds the cache_status and cache_clear methods to models for verifying the cache behavior (this is only expected to be used in rare cases). The cache code has seen documentation improvements. &lt;/code&gt;&lt;/pre&gt; 946 - rework stats tests &lt;pre&gt;&lt;code&gt;Update the stats tests to use pytest. &lt;/code&gt;&lt;/pre&gt; 960 - Fix model evaluation when changing the integrate setting (fix #958) &lt;pre&gt;&lt;code&gt;Fixes an issue with cache evaluation on 1D models using integrated bins and the user has changed the integrate setting of the model. &lt;/code&gt;&lt;/pre&gt; 978 - Use C99 def for INFINITY, NAN, isfinite and isnan to build on aarch64 (fix issue #970) &lt;pre&gt;&lt;code&gt;Use the math constants (IFINITIY, NAN) and funcs (isfinite, isnan, signbit) from a C99 compliant compiler if the compiler option -std=c99 or greater is used, otherwise use the quantities as defined by the library. &lt;/code&gt;&lt;/pre&gt; 991 - lint changes &lt;pre&gt;&lt;code&gt;Applies a number of flake8-reported warnings to the code base (e.g. excessive or missing spaces and new lines). &lt;/code&gt;&lt;/pre&gt; 1000 - Improve sherpa.citation (fix #994 #987) &lt;pre&gt;&lt;code&gt;Fixes the sherpa.citation() command with its default argument (issue #994) and adds release 4.12.2 to the hard-coded list of releases. A typo in a warning message was fixed (#987). &lt;/code&gt;&lt;/pre&gt; 1001 - Allow command-line arguments for sherpa_test &lt;pre&gt;&lt;code&gt;Allow command-line arguments to be passed to the sherpa_test script. This allows running optional tests (e.g. the --runzenodo argument) and to configure the pytest configuration (e.g. to run coverage checks with --cov sherpa). &lt;/code&gt;&lt;/pre&gt; 1002 - Fix error with clobber=False for paging - issue #996 &lt;pre&gt;&lt;code&gt;Fix an error with clobber=False when the output file exists for several paging commands (e.g. show_data and sherpa.citation). Instead of getting a Sherpa IOErr being raised a NameError was being raised. &lt;/code&gt;&lt;/pre&gt; 1003 - Fix serialization of iter method data - issue #997 &lt;pre&gt;&lt;code&gt;If set_iter_fit_method has been called with a value other than 'none' then the output of save_all would be incorrect for the options for the iter-fit method. &lt;/code&gt;&lt;/pre&gt; 1004- flake8 F811 - fix repeated test names &lt;pre&gt;&lt;code&gt;Clean up of several test files to fix repeated test names. &lt;/code&gt;&lt;/pre&gt; 1005 - Add explicit get/set_datadir routines to sherpa.utils.testing &lt;pre&gt;&lt;code&gt;Internal changes to how the test data directory location is set and queried, including removing direct support from SherpaTestCase. Added tests for some of this functionality, and updated several test files to remove SherpaTestCase or use the new datadir functionality. &lt;/code&gt;&lt;/pre&gt; 1008 - rm warning msgs, fix issue #980 &lt;pre&gt;&lt;code&gt;Fix the compiler warning messages, by defining kwlist to be static const then use the C++ const_cast to remove the const to conform to PyArg_ParseTupleAnd Keywords prototype &lt;/code&gt;&lt;/pre&gt; 1012 - Tests: allow test_ui tests to be run with pytest-xdist &lt;pre&gt;&lt;code&gt;Allow the tests to be run with pytest-xdist. &lt;/code&gt;&lt;/pre&gt; 1016 - Jupyter notebook representation not ideal if model components don't have unique names - issue: #1013 &lt;pre&gt;&lt;code&gt;Fix an error in the HTML display of a model (used in the notebook) when two model components have the same name. &lt;/code&gt;&lt;/pre&gt; 1017 - reword remark on normalization of Lorentz function &lt;pre&gt;&lt;code&gt;Updated the comments pertaining to Lorentz function for clarity &lt;/code&gt;&lt;/pre&gt; 1018 - Fix ShekelModifiedInit missing init par vals &lt;pre&gt;&lt;code&gt;This PR fixes the missing initial fitted parameter values for the ShekelModifiedInit function. A fix for issue #1011 &lt;/code&gt;&lt;/pre&gt; 1028 - Update region lib code to correct build issues with gcc 7.3.0 compile &lt;pre&gt;&lt;code&gt;Corrects issue building with gcc 7.3.0+ compilers with the -Werror=format-security compilation flag &lt;/code&gt;&lt;/pre&gt; 1034 - Add contextmanager and docs on how to control the output level of sherpa &lt;pre&gt;&lt;code&gt;Sherpa uses logging for much of its output, this adds a docs and a context manager for controlling the output level for a particular piece of code. &lt;/code&gt;&lt;/pre&gt; 1039 - Add docs for basic.TableModel &lt;pre&gt;&lt;code&gt;Added missing documentation for TableModel class &lt;/code&gt;&lt;/pre&gt; 1049 - CI: pip submodule test to report coverage &lt;pre&gt;&lt;code&gt;Report the coverage data from the pip CI run. This only changes the GitHub Actions runs. &lt;/code&gt;&lt;/pre&gt; 1053 - Release 4.13.0 &lt;pre&gt;&lt;code&gt;Updates to support the 4.13.0 release &lt;/code&gt;&lt;/pre&gt; 1054 - Post 4.13.0 updates &lt;pre&gt;&lt;code&gt;Updates the Zenodo DOI reference in the README.md to include 4.13.0. &lt;/code&gt;&lt;/pre&gt; 1057 - Fix plot_source clearwindow setting &lt;pre&gt;&lt;code&gt;The plot_source function was ignoring the clearwindow parameter (always using True) in calls to plot_source for non-PHA data. This was only for sherpa.astro.ui.plot_source (so sherpa.ui.plot_source did not have this problem). &lt;/code&gt;&lt;/pre&gt; 1058 - Store the opstr of model combinations (unary and binary) &lt;pre&gt;&lt;code&gt;Store the operator string as well as the operator when creating the unary and binary operator expressions for models. &lt;/code&gt;&lt;/pre&gt; 1062 - Minor code cleanup of sherpa.astro.ui.utils &lt;pre&gt;&lt;code&gt;The sherpa.astro.ui.utils module has seen a number of minor clean-ups, addressing pylint-reported issues. &lt;/code&gt;&lt;/pre&gt; 1067 - Improve testing of sherpa.astro.ui.utils &lt;pre&gt;&lt;code&gt;Improve coverage of the sherpa.astro.ui.utils and require pytest 3.9.0 or later for testing Sherpa. &lt;/code&gt;&lt;/pre&gt; 1068 - clean up typos in sherpa/plot code &lt;pre&gt;&lt;code&gt;Fixed several typos noticed while reviewing plot related fix for #1057 &lt;/code&gt;&lt;/pre&gt; 1072 - Update load_data to match load_pha for PHA2 data &lt;pre&gt;&lt;code&gt;Ensure that load_data behaves like load_pha when given a PHA2 dataset. &lt;/code&gt;&lt;/pre&gt; 1076 - sample_flux now uses the id argument &lt;pre&gt;&lt;code&gt;The sample_flux routine now uses the id argument rather than always using the data from the default dataset. Fixes #752 &lt;/code&gt;&lt;/pre&gt; 1078 - Add error checking for exceptional cases for sample_flux &lt;pre&gt;&lt;code&gt;Ensure that sample_flux errors out if the Xrays argument is False (as this code path is currently broken) or if the confidence argument is invalid. &lt;/code&gt;&lt;/pre&gt; 1082 - Improve documentation for notice2d &lt;pre&gt;&lt;code&gt;Minor improvements to the documentation of notice2d and ignore2d set of commands. Fixes #1059 &lt;/code&gt;&lt;/pre&gt; 1086 - Use the logging infrastructure for sample_flux output &lt;pre&gt;&lt;code&gt;The screen output from sample_flux is now generated by the Sherpa logger and so can be hidden by the user if required. &lt;/code&gt;&lt;/pre&gt; 1088 - Allow two optimization test to pass &lt;pre&gt;&lt;code&gt;Address an issue in the optimization tests that meant two tests were failing. This only changes the test code and makes no change to the behavior of the optimizers. &lt;/code&gt;&lt;/pre&gt; 1092- Numpy 1.20 warnings &lt;pre&gt;&lt;code&gt;Avoid test failures due to new warnings added by NumPy 1.20 &lt;/code&gt;&lt;/pre&gt; 1094 - Cleanup multi-plot code &lt;pre&gt;&lt;code&gt;Rework the code that handles the plot_fit_xxx and plot_bkg_fit_xxx calls. There should be no user-visible changes. &lt;/code&gt;&lt;/pre&gt; 1096 - Reduce direct access to plot objects &lt;pre&gt;&lt;code&gt;Changes to the internals of the plot code, to access information via methods rather than direct access, which improves encapsulation and reduces code repetition. &lt;/code&gt;&lt;/pre&gt; 1098 - Bump DS9 version to 8.2 for CI &lt;pre&gt;&lt;code&gt;Bump DS9 version used in CI tests from 8.1 to 8.2. &lt;/code&gt;&lt;/pre&gt; 1100 - Address reg_proj and reg_unc failures (fix #1093) &lt;pre&gt;&lt;code&gt;Calls to reg_proj and reg_unc could error out when the min or max arguments were set to tuples rather than lists. The code now converts these attributes to lists, which can result in changes to the string output of the objects (use of '[]' brackets rather than '()'). Fixes #1093 &lt;/code&gt;&lt;/pre&gt; 1101 - Address upper limit issues with sample_flux (fix #457) &lt;pre&gt;&lt;code&gt;sample_flux no-longer excludes samples at the parameter bounds (soft) when calculating the flux distribution. This could lead to an over-estimation of the flux for upper limits (Fix #457). &lt;/code&gt;&lt;/pre&gt; 1104 - Add basic documentation for the low-level optimization code &lt;pre&gt;&lt;code&gt;Add and update documentation on the interfaces used by the low-level optimization code. Ensure that the plot classes are fully included in the documentation. &lt;/code&gt;&lt;/pre&gt; 1105 - Consolidate and harmonize the validation of dataset identifiers &lt;pre&gt;&lt;code&gt;Simplify the code used to validate dataset identifiers. Several names can no-longer be used as an identifier ('astrocompmodel', 'astrocompsource', 'astrodata', 'astromodel', 'astrosource', 'model_component', and 'source_component') and two can now be used ('energy' and 'photon'). &lt;/code&gt;&lt;/pre&gt; 1108 - Read RMFs where N_CHAN is an array &lt;pre&gt;&lt;code&gt;Allow the pyfits backend to read a wider range of RMF files &lt;/code&gt;&lt;/pre&gt; 1111 - Minor test updates &lt;pre&gt;&lt;code&gt;Minor updates to the test code, including a small enhancement to the tests run by the smoke_test command. &lt;/code&gt;&lt;/pre&gt; 1112: XSPEC: require model evaluation to be sent low and high grid values &lt;pre&gt;&lt;code&gt;XSPEC model classes must now be evaluated with bin edges - that is with low,high bins. The support for sending in a single grid and treating it a consecutive set of bins has been marked as deprecated from the model class interface. This feature is still supported for anyone evaluating the models directly from the sherpa.astro.xspec._xspec module or via the _calc method. &lt;/code&gt;&lt;/pre&gt; 1116: Add parameter-based tests for the PSF model &lt;pre&gt;&lt;code&gt;Adds several tests of edge-case handling of parameters for PSF convolution models. &lt;/code&gt;&lt;/pre&gt; 1117 - Docs: improve cache discussion and documentation &lt;pre&gt;&lt;code&gt;Improve the discussion of the cache support when evaluating models. &lt;/code&gt;&lt;/pre&gt; 1120 - Switch default branch to main &lt;pre&gt;&lt;code&gt;Change the default branch from master to main. Also includes minor documentation updates (CONTRIBUTING.md updates to switch to main, to reference GitHub Actions instead of Travis, and to remove a note about Python 3.5 support). &lt;/code&gt;&lt;/pre&gt; 1121- Hide AstroPy 4.2.1 FITS-related warnings &lt;pre&gt;&lt;code&gt;astropy.io.fits.open now creates warning messages about invalid FITS structures when given a non-FITS file. This updated hides those warning messages since routines such as sherpa.astro.io.load_data attempts to open files (including ascii files) as FITS. &lt;/code&gt;&lt;/pre&gt; 1122 - Update ds9 download &lt;pre&gt;&lt;code&gt;Update DS9 tests to use ubuntu18 and darwinhighsierra as ubuntu14 and darwinsierra are no longer supported. The DS9 version has been bumped from 8.2 to 8.2.1 as this is the latest version. &lt;/code&gt;&lt;/pre&gt; 1125: Support Matplotlib 3.4 &lt;pre&gt;&lt;code&gt;Matplotlib 3.4 changes how the drawstyle argument is handled in some functions. This change removes the use of this argument for those functions. &lt;/code&gt;&lt;/pre&gt; 1126 - Tweak plot docs &lt;p&gt;Adds a new notebook that shows off a number of plots created with matplotlib and exports the ScatterPlot, TracePlot, CDFPlot, PDFPlot, and LRHistogram classes from sherpa.plot.&lt;/p&gt; 1130: Fix save_data when the output file exists &lt;pre&gt;&lt;code&gt;Fix problems when save_data is used with clobber=False but the output file already exists. 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