sherpa - Sherpa 4.17.1

Release Highlights

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

• enhancements:
  • improved handling for OGIP products that do not follow the standards (#2235)
  • Models can now be combined using arbitrary ufuncs (#2248)
  • various updates to XSpec interface (#2281) and support for XSpec 12.15.0 including the additional of 17 new models (#2252)
  • added interface to support ArviZ for analysis of Bayesian models (#2286)
• documentation changes:
  • provided option to install python packages needed to build sherpa documentation

• infrastructure and testing:

  • updated tests to work with python 3.13 (#2174)

• bug fixes:

  • fixed a bug in the caching code that limited the cache size to 1 (#2166)
  • update to use fake_pha for missions which don't use 1 as the first channel (#2214)

Details

#2039 - Add a security reporting policy Added a statement defining plans to deal with security issues and where users should report them

#2047 - Opt Clean up Improve the typing coverage of the sherpa.optmethods code and internal code clean up.

#2116- Add explicit support for XSPEC 12.14.1 Add models from XSPEC 12.14.1 and change the parameter settings to match those from 12.14.1, where necessary.

#2143 - Improve pre-commit script for ranges of years Improve pre-commit script for ranges of years

#2156 - Add macOS ARM Conda Package Builds Add macOS ARM Conda builds

#2164 - XSPEC: fix up error message Correct the information provided in the unlikely case that an XSPEC model fails.

#2166 -Fix bug in cache code that limited cache size to 1. Fix bug that limited cache size to 1.

#2170 - DOC: Example changes to Examples Change the docstring for calcsource and calcmodel to use Examples rather than Example.

#2171 - specify DS9 region format used in pytest Explicitly set region format to use ds9 format for ds9 region pytests

#2174: Allow tests to pass with Python 3.13.0 Allow the tests to pass with Python 3.13.0.

#2178 - Post 4.17.0 update to add DOI info to the README.md Adding the DOI for the 4.17.0 Release.

#2179 - add build doc option Provide the doc installation option which will install the python packages needed to build the documentation along with Sherpa.

#2181 - Fix typo in return value Correctly identify the return value of getsourcecomponents_plot. This does not change the behaviour of the code.

#2182 - DOC: Use "Examples" rather than "Example" Consistent use of "Examples" to indicate one or more examples in the documentation.

#2188 - TEST: address numpy 2 changes to output for docstring tests Allow the documentation tests to pass when using NumPy 2.0. There is no change to the actual code.

#2191: TEST: fix test related to issue #800 Clean up a test. There is no functional change to the code.

#2195 - Update ci-conda-workflow to use Miniforge Install Miniforge for use with ci-conda workflow.

#2198 - Allow both Intel and ARM macOS GitHub runners for the conda builds Add a macOS ARM build, and update the macOS Intel build to use the macOS-13 runner.

#2201: Change how invalid limits are checked for within the MCMC code Simplify a safety check within the MCMC proposed-parameter code.

#2203 - Allow pytest 8.3.4 to be used Allow the tests to pass with pytest version 8.3.4 by changing the test code. The GitHub macOS conda action is updated to macos-13 (for the Intel build). There is no functional change here.

#2204 - Update the GitHub Actions badge for Conda and Pip workflows Update the GitHub Actions badge in the README.md for the Conda and Pip workflows.

#2207- TESTS: avoid matplotlib version differences (fix #2206) Allow tests to pass when using matplotlib 3.10.0. This only changes the tests. Fix #2206.

#2208: BUILD: update ds9 from 8.5 to 8.6 Bump to DS9 version 8.6 for testing on GitHub actions (Linux). There is no functional change.

#2209: update to change .bz2 references to .conda to account for changes Modify workflows to use .conda instead of .bz2

#2213 - Better handle dataspace1d for DataPHA use cases when offset is not 1 The sherpa.astro.ui.utils.dataspace1d call can now be used to generate a channel grid that does not start at 1 for DataPHA data. The arguments are now checked to ensure they are sensible in this case (consecutive integer values).

#2214: Better handle fakepha when offset is not 1 Allow fakepha to work with missions where the first channel is not 1. Fix #2212.

#2215 - Minor xspec additions Minor changes to the XSPEC module, including added documentation to the setxsabund routine to note the availability of the "felc" table, and setxsstate no longer requires all fields to be present.

#2226 - Allow user-statistics to be referenced by name to match the documentation. Allow user-statistics to be set by name. The getstatname routine now returns the actual name of the user statistic, rather than the generic value "userstat". Fix #2225.

#2227 - Tests: compare Response1D and MultipleResponse1D behavior Improve testing of the multi-response code. There is no change in behaviour here.

#2229 - Error out if model names are not strings Raise an error if a model name is not a string

#2230 - Note that we need the file program to build Sherpa Note that the file command is needed to build Sherpa (it is used by extern/configure).

#2231 - Two small astropy-related doc changes Update links to astropy dev docs (that we link to in lieu of writing our own dev docs); Recommend installing astropy via pip, not conda

#2232 - TESTS: mark more that require the group module Mark several recently added tests with the requires_group decorator. There is no functional change.

#2233 - BUILD: pin conda-build (and therefore liblief) to last known working version There's a bug between conda-build and lief that's causing a package build failure. This pins to "conda- build==25.1.2=*_0", which we've also pinned to in CIAO for this same issue. related Conda-build issue: conda/conda-build#5626

#2235 - Deal with OGIP products that do not follow the standards Some OGIP products from missions occasionally do not follow the OGIP and FITS standards. Provide workarounds for two recent cases from NuSTAR and NICER (TLMIN/MAX values were recorded as a string, and a QUALITY array was stored as a boolean array). Fix #2185.

#2239 - REGION: test CXCDM region parser, when available Allow the region module to know how it was built (whether reading FITS binary region files is supported). This allows for improvements to the tests.

#2240 - Minor typing updates Minor internal changes to tests and code to improve typing statements and improve test coverage.

#2241 - drop "iterative fit method" in error-estimation screen output when not set The screen output when calling an error-estimation routine like conf will no longer return the iterative-fit method name when it is set to None.

#2243 - Internal improvements to stats, fit, optimization, and error estimation Add typing statements and apply minor code cleanup for the statistics, fit, optimization, and error estimation code. There is not expected to be any functional change unless code interacts with low-level details of the Sherpa code base.

#2248 - Allow combinations of models with arbitrary ufuncs Models can now be combined using arbitrary ufuncs. Before, it was possible to say model1 + model2 to create a combined model, now any numpy ufunc will work, e.g. np.greater(model1, model2).

#2249 - Update project.toml for PEP 639 Address setuptools deprecation of lower-kebab-case for names of options

#2252- Allow Sherpa to build against XSPEC 12.15.0 Allow building against XSPEC 12.15.0. Adds the following 17 models:

    additive: XSfeklor, XSvlorentz, XSvvoigt, XSzfeklor, XSzlorentz, XSzvlorentz, XSzvoigt, XSzvvoigt
    convolution: XSrgsext
    multiplicative: XSlorabs, XSvlorabs, XSvoigtabs, XSvvoigtabs, XSzlorabs, XSzvorlabs, XSzvoigtabs, XSzvvoigtabs

The XSPEC initialization file (~/.xspec/Xspec.init) may need to be removed or the AtomDB version in it updated before using XSPEC models.

#2255 - Add missed pep 639 config update

#2249 had a few stragglers in the update I missed when reviewing. This should get all the needed renames.

#2256 - Faster hash for modelCacher1D Select a faster hashing algorithm for the model cache by default

#2261 - Add tests related to analysis setting Add or enhance tests for several cases.

#2265 - Add new public methods to access the components of a model Add new methods to select the components of a model.

#2268 - Treat norm special in XSPEC additive models These code changes increase the speed of fitting data with XSPEC additive models by making the cache more effective.

#2273 - Make sure all datastack-wrapped functions are added to namespace Complete the datastack namespace for functions wrapped to operate on datastacks

#2274 - Set cache=0 by default for models that are fast to calculate Based on benchmarking for typical Sherpa use cases, some models are faster to recalculate than to cache. For those models, the default cache size is now set to 0 to save runtime and memory.

#2279 - Note support for Python 3.13 Note that Sherpa can be used with Python 3.13.

#2280 - Add option record_steps to Fit.fit() calls Add option recordsteps to Fit.fit() calls, which will add a field recordsteps to the FitResults object that the fitter returns. This can help to understand why a fit does not converge.

#2281 - Provide access to XSPEC abundances Minor improvements to the XSPEC interface: getxsabundances now takes an optional table name, getxsxset can be called with no argument, and clear_xsxset will clear the XSET database. Fix #2282.

#2286 - Add an interface to ArviZ Add an interface to ArviZ

#2287 - Use python 3.10 syntax for typing for the ui modules Use Python 3.10 syntax for typing statements in the ui modules. There are no functional changes in these commits.

#2288 - ui: add more examples of using SherpaVerbosity Point out the use of the sherpa.utils.logging.SherpaVerbosity context manager in the documentation of the fit and error-analysis UI routines.

#2289 - Update http -> https Update links in docs and source code from http -> https where possible

#2290 - Minor clean up of utility code Ensure a deprecated routine can still be used and remove a routine that has never worked.

- Python
Published by harlantc about 1 year ago

sherpa - Sherpa 4.17.0

Sherpa 4.17.0

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

• enhancements:
  • add calcmodel and calcsource 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 STATERR and SYSERR 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 setx/ylabel
• 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 plotxxxcomponents 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 sphinxrtdtheme deprecation warning

Specify sphinx < 8 for the read the doc environment and remove the call
to get_html_theme_path no longer needed.

- Python
Published by Marie-Terrell over 1 year ago

sherpa - Sherpa 4.16.1

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 loadxstablemodel not loadtablemodel

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

- Python
Published by Marie-Terrell about 2 years ago

sherpa - Sherpa 4.16.0

Sherpa 4.16.0

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

• enhancements:
  • the grouping commands like groupcounts and groupsnr 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 fakepha, saveall, allowing to write out RMF/ARF files
  • getplotprefs and getcontourprefs call to simplify access to the plot and contour preferences
  • implementation of RMFPlot and DataIMGPlot classes and associated UI functions (plotrmf, getrmf_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 getplotprefs/getcontourprefs 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 groupcounts, groupwidth, ..., 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, groupcounts(20, tabStops=[0] * 1024) or groupcounts(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 - saveall improvements for setpsf and loadxstablemodel

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 calcbkgstat - 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 reprhtml_ 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 setplotbackend

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.

- Python
Published by Marie-Terrell over 2 years ago

sherpa - Sherpa 4.15.1

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 savetype routine

Minor internal change to a routine in the utils code. There is no change in
behavior.

1720 - Fix getstatinfo 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

- Python
Published by Marie-Terrell about 3 years ago

sherpa - Sherpa 4.15.0

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 fakepha, calcftest, 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 testfakepha.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 getorderplot/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.

- Python
Published by Marie-Terrell over 3 years ago

sherpa - Sherpa 4.14.1

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 deletemodelcomponent 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 deletemodelcomponent

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 colummn 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
corner cases of the DataPHA class.

1374 - Address aarch/ppc64le test failures

Update tests to that they pass on aarch64. Fixes #1372

1376 - Very-minor tweaks to docs/tests

Fix a minor test issue and an unused reference in the documentation.

1387 - minimize C++ code duplications (rebase)

Remove code duplication in the XSPEC module.

1399 - Allow conf/covar/proj to be used with XSPEC model parameters (regression)

Ensure that conf, covar, and proj can be called with an XSPEC model parameter.
Fixes #1397.

1401 - Modified region code to remove implicit prototype error

This change updates the extern region code in sherpa to resolve a missing prototype
which causes build issues with clang 12.0.

1403 - Updates to fix typos in the plot documentation

Update to fix a few typos in the plot documentation

1410 - Add script and docs for pre-commit hook to update copyright

Add example script for a git pre-commit hook that checks the copyright is up to date.

1411 - Add sphinxrtdtheme to sphinx extensions and set min version

Our readthedocs pages have had some visual issues (in particular, bullets point
where missing from output) for a while. This fixes that by ensuring we are using
a recent version of the sphinx theme.

1413 - Add more editor/OS exclusions to .gitignore

Add a VSCode workspace summary files and MacOS directory preview files to .gitignore

1414 - Improve the handling of image coordinates

Address an error when converting between different coordinate systems for images.
Fixes #1380.

1415 - RTD fix missing and changed symbols

Update the ReadTheDocs build to cope with changes in #1191

1418 - Fix minor test issues

Address several minor test issues.

1419 - Keep .rc file backwards compatible

Default rc files will work in older version of sherpa as well.

1421 - Address usability issues with Data2DInt and DataIMGInt classes

Fix issues using the Data2DInt and DataIMGInt classes (#1379).

1423 - fix a compiler bug on macOS

update to address compiler issue when compiling on macOS

1424 - rm primini stat method

This PR removes the primini iterative statistical method. Please see issue #1392
for details

1425 - Allow users to freeze models

Models can now be frozen or thawed, which just calls the requested on all the 
parameters of the model (except for "alwaysfrozen" parameters which are skipped).
This is only relevant for users who are accessing the objects directly since the ui
versions of freeze and thaw already implemented this behavior. Fixes #1080.

1429 - Tests: fix up test problems shown by pytest 7.0.0

Fix up several tests so they can be run with pytest 7.0.0. Fixes #1428

1434 - Fix aarch64 test failures

Allow the tests to pass on aarch64 (numerical precision checks).

1435 - Minor clean up of the data code

Improves the docstrings for DataPHA, adds tests for several corner-cases, and makes
some minor code improvements to the code.

1440 - Minor clean up of the data routines

Address several minor code-style changes in the data handling (code and tests).

1441 - Clean up the data tests

Clean up of the data tests which were added as part of the data-class rework in #614.

1442 - Ensure channel and count fields for PHA are aliases of independent and dependent axes

Ensure that channel and the independent axis and counts and the dependent axis are 
synonymous for the DataPHA class.#1451 - Tests: ensure sherpa smoke tests are done
in a clean environment

1453 - Tests: mark those that require the group module

Note a number of tests that require the group module.

1454 - RTD: update copyright year and fix WCS library

Update the sphinx build instructions so that changes from PR #1414 will be documented
correctly on systems where the documentation is being built without first compiling
the code (such as read-the-docs).

1455 - RTD: update the build-from-CIAO documentation

Update the "build with CIAO" documentation to match the CIAO 4.14 conda instructions
and automate the process.

1458 - Improve several issues when building and testing Sherpa

Minor improvements to the build and test installation. The use of setuptools has
been restricted to match the current advice from NumPy (< 60, from 
https://numpy.org/devdocs/reference/distutils_status_migration.html).

1461 - Minor grouping cleanup

Minor internal change to how the group routines work for PHA objects.

1462 - Docs: fix up documentation of ui.set_grouping

Fix the documentation for set_grouping to match the code.

1463 - rm a redundant call to calc_h

Removed a redundant call the the calc_h method in the class fdJac

1464 - RTD: include the DataOgipResponse class in the documentation

Add a missing class (DataOgipResponse) to the documentation.

1473 - Data test minor cleanup

Minor test clean-ups.

1474 - Add basic tests of data validation

Ensure we test a number of corner cases related to data validation.

1484 - Include ciao region patch

Allow the CXC Data Model library to be used to parse region files, if available. 
This is primarily intended for building Sherpa as part of CIAO.

1485 - getheaderdata is an official method of the astro.io backend

An internal change to make sure that the get_header_data routine is part of the 
astro I/O backend API.

1490 - Basic support for XSPEC 12.12.1

Allow Sherpa to be built with XSPEC 12.12.1. It does not provide access to the three
new models - polconst, pollin, and polpow - added in this release of XSPEC.

1492 - Make tests pass on 3.10

One of the tests fails in Python 3.10 because the error message has been changed.

1493 - Remove deprecated distutils.version.LooseVersion

The distutils.version.LooseVersion class is now marked as deprecated so remove its
use when building Sherpa and when importing the Sherpa XSPEC module.

1494 - Update AXPYTHONDEVEL.m4 from serial 17 to 25

This update covers the cleanup of distutils in the configure files for grplib (and 
stklib in the case of standalone sherpa).

1495 - Note that we support Python 3.10

Note that Sherpa can be built using Python 3.10 and add two Python 3.10 CI test runs.

1496 - DS9 update from 8.2.1 to 8.3

Update to use ds9 v8.3 since v8.2.1 is no longer available

1497 - Tests: ensure matplotlib windows are closed after all tests are run

Ensure that our tests can run on CI cleanly.

- Python
Published by Marie-Terrell about 4 years ago

sherpa - Sherpa 4.14.0

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 loadmultiXXX

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 showstack 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 parsexspecmodel_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 [ ]"

- Python
Published by Marie-Terrell over 4 years ago

sherpa - Sherpa 4.13.1

Sherpa 4.13.1

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.

• documentation changes:
  • updates to documentation for TableModel, Notice2D, cache support for evaluating models, and low level optimization code
  • jupyter notebook uopdates
• Infrastructure Changes:
  • the master branch has been migrated from master to main
  • updates to support numpy 1.20
  • updates to support astropy 4.2.1
  • updates to support matplotlib 3.4
  • test infrastructure clean up and updates
• bug fixes:
  • fix an issue with cache evaluation on 1D models using integrated bins
  • fix for aarch64 build issue
  • fix to sherpa citation command
  • fix to honor clearwindow setting for plot_source
  • fix errors from save_data when the output file exists
  • fix build issues using gcc 7.3 with -Werror=format-security compilation flag
  • fix for regproj and regunc erroring out when the min or max arguments are tuples rather than lists

Details

754 - sample_flux now returns statistic values for each row

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.

769 - add basic cache tracking

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.

946 - rework stats tests

Update the stats tests to use pytest.

960 - Fix model evaluation when changing the integrate setting (fix #958)

Fixes an issue with cache evaluation on 1D models using integrated bins and 
the user has changed the integrate setting of the model.

978 - Use C99 def for INFINITY, NAN, isfinite and isnan to build on aarch64 (fix issue #970)

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.

991 - lint changes

Applies a number of flake8-reported warnings to the code base (e.g. excessive 
or missing spaces and new lines).

1000 - Improve sherpa.citation (fix #994 #987)

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).

1001 - Allow command-line arguments for sherpa_test

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).

1002 - Fix error with clobber=False for paging - issue #996

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.

1003 - Fix serialization of iter method data - issue #997

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.

1004- flake8 F811 - fix repeated test names

Clean up of several test files to fix repeated test names.

1005 - Add explicit get/set_datadir routines to sherpa.utils.testing

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.

1008 - rm warning msgs, fix issue #980

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

1012 - Tests: allow test_ui tests to be run with pytest-xdist

Allow the tests to be run with pytest-xdist.

1016 - Jupyter notebook representation not ideal if model components don't have unique names - issue: #1013

Fix an error in the HTML display of a model (used in the notebook) when two 
model components have the same name.

1017 - reword remark on normalization of Lorentz function

Updated the comments pertaining to Lorentz function for clarity

1018 - Fix ShekelModifiedInit missing init par vals

This PR fixes the missing initial fitted parameter values for the 
ShekelModifiedInit function. A fix for issue #1011

1028 - Update region lib code to correct build issues with gcc 7.3.0 compile

Corrects issue building with gcc 7.3.0+ compilers with the 
-Werror=format-security compilation flag

1034 - Add contextmanager and docs on how to control the output level of sherpa

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.

1039 - Add docs for basic.TableModel

Added missing documentation for TableModel class 

1049 - CI: pip submodule test to report coverage

Report the coverage data from the pip CI run. This only changes the GitHub 
Actions runs.

1053 - Release 4.13.0

Updates to support the 4.13.0 release

1054 - Post 4.13.0 updates

Updates the Zenodo DOI reference in the README.md to include 4.13.0.

1057 - Fix plot_source clearwindow setting

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).

1058 - Store the opstr of model combinations (unary and binary)

Store the operator string as well as the operator when creating the unary and 
binary operator expressions for models.

1062 - Minor code cleanup of sherpa.astro.ui.utils

The sherpa.astro.ui.utils module has seen a number of minor clean-ups, addressing 
pylint-reported issues.

1067 - Improve testing of sherpa.astro.ui.utils

Improve coverage of the sherpa.astro.ui.utils and require pytest 3.9.0 or later 
for testing Sherpa.

1068 - clean up typos in sherpa/plot code

Fixed several typos noticed while reviewing plot related fix for #1057

1072 - Update loaddata to match loadpha for PHA2 data

Ensure that load_data behaves like load_pha when given a PHA2 dataset.

1076 - sample_flux now uses the id argument

The sample_flux routine now uses the id argument rather than always using the 
data from the default dataset. Fixes #752

1078 - Add error checking for exceptional cases for sample_flux

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.

1082 - Improve documentation for notice2d

Minor improvements to the documentation of notice2d and ignore2d set of commands. 
Fixes #1059

1086 - Use the logging infrastructure for sample_flux output

The screen output from sample_flux is now generated by the Sherpa logger and 
so can be hidden by the user if required.

1088 - Allow two optimization test to pass

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.

1092- Numpy 1.20 warnings

Avoid test failures due to new warnings added by NumPy 1.20

1094 - Cleanup multi-plot code

Rework the code that handles the plot_fit_xxx and plot_bkg_fit_xxx calls. 
There should be no user-visible changes.

1096 - Reduce direct access to plot objects

Changes to the internals of the plot code, to access information via methods 
rather than direct access, which improves encapsulation and reduces code 
repetition.

1098 - Bump DS9 version to 8.2 for CI

Bump DS9 version used in CI tests from 8.1 to 8.2.

1100 - Address regproj and regunc failures (fix #1093)

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

1101 - Address upper limit issues with sample_flux (fix #457)

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).

1104 - Add basic documentation for the low-level optimization code

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.

1105 - Consolidate and harmonize the validation of dataset identifiers

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').

1108 - Read RMFs where N_CHAN is an array

Allow the pyfits backend to read a wider range of RMF files

1111 - Minor test updates

Minor updates to the test code, including a small enhancement to the tests run by 
the smoke_test command.

1112: XSPEC: require model evaluation to be sent low and high grid values

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.

1116: Add parameter-based tests for the PSF model

Adds several tests of edge-case handling of parameters for PSF convolution models.

1117 - Docs: improve cache discussion and documentation

Improve the discussion of the cache support when evaluating models.

1120 - Switch default branch to main

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).

1121- Hide AstroPy 4.2.1 FITS-related warnings

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. 

1122 - Update ds9 download

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.

1125: Support Matplotlib 3.4

Matplotlib 3.4 changes how the drawstyle argument is handled in some functions. 
This change removes the use of this argument for those functions.

1126 - Tweak plot docs

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.

1130: Fix save_data when the output file exists

Fix problems when save_data is used with clobber=False but the output file already 
exists. Fixes #1071

1132 - Update XQuartz for GH Actions workflow

Updates the xQuartz download location and version for the GitHub Actions Conda tests

1139 - Fix typo in Zenodo test that made it fail

Fixed a typo in the zenodo test which gets only run via the --runzenodo flag 

1142 - Add instruction for source build on Mac

Add instruction for source building on Mac that were previously only part of the 
internal release notes.

- Python
Published by Marie-Terrell about 5 years ago

sherpa - Sherpa 4.13.0

Sherpa 4.13.0

This release of Sherpa coincides with the CIAO 4.13 release. The release contains a few minor documentation updates, a version number update to coincide with CIAO version 4.13.0, and infrastructure changes to migrate from Travis-CI to GitHub Actions for testing. No additional functionality has been introduced.

Details

1043 - RTD: install more packages via pip

Install sphinx-astropy and ipykernel via pip instead of Conda for the Read the Docs
builds to avoid current indirect requirement conflicts.

1035 - Travis to GitHub Actions

Replaces the Travis test infrastructure with two GitHub Actions workflows.

1036 - Cleaned up several typos in the RELEASE_NOTES file

Updates the RELEASE_NOTES file to correct several typos.

1038 - Docs: note Python version and new build status

Updates the build status badge to track GitHub Actions rather than Travis-CI and
report the python versions as 3.6, 3.7, and 3.8.

- Python
Published by Marie-Terrell over 5 years ago

sherpa - Sherpa 4.12.2

Sherpa 4.12.2

This release of Sherpa serves as the baseline release of Sherpa for CIAO 4.13. It contains numerous enhancements and fixes including items which are stand alone sherpa specific. Notable highlights include:

• plotting improvements
  • improved support for matplotlib (linestyle changes in matplotlib 3.3, support of alpha channels)
  • overplot support for plotfit* pltbkgfit_*
  • updates to histograms, residual plots
• data I/O and data handling
  • several bug fixes to handling of the PHA, ARF, RMF files
• modeling
  • support for regrid models in the binary expressions
  • improvements and bug fixes to background treatment in spectral models
  • improvements in the flux calculations and resampling
  • added the Voigt model
• documentation changes
  • improvements to Sherpa display in IPython/Jupyter notebooks
  • updates to the content of the docstrings for generation of ahelp files

Details

Testing and infrastructure fixes are not shown.

483 - An initial release of simultaneous fit on multicores (slower for most…

Distributes the evaluations of the multiple independent data sets using the 
multi-cores built-in the user's workstation. The current default setting for this 
PR is to evaluate the multiple independent data sets sequentially since the 
overhead for distributing the workload across multi-cores is high if the evaluation 
of the data sets is not time consuming.

631 - Add HTML representations of common classes for IPython display (fix #345)

An initial version of HTML display support for Sherpa objects for users of 
IPython/Jupyter notebooks. 

634 - Added invitation for native software citation

Adds a citation method to the sherpa module and updates CITATION to refer to this 
new functionality

693 - Address matplotlib linestyle removal in Matplotlib version 3.3

Matplotlib version 3.3 now requires you to split out the drawstyle and linestyle 
arguments. This set of PRs changes the code so that the two arguments are now set: 
linestyle defaults to solid and drawstyle to default for plots and step-mid for 
histograms. This appears to replicate the old version, and should be backwards 
compatible (drawstyle is supported in Matplotlib 2.2.5 and 1.5.3)

709 - Residual-style plots ignore the ylog setting (fi#586)

Residual, ratio, and delchi plots always use a linear scale for the y axis, no 
matter what the ylog setting is.

740 - resample_data: when the error range on a bin includes -1 and no-longer restrict

   sampling to +/-1 sigma
Fixes resample_data/ReSampleData so that it correctly handles bins where the range 
of data values (i.e. low to high limit) includes the value -1.

741 - Fix issue 638, guess needs to update fwhm/sigma bounds

Adds support for guessing the fwhm or sigma parameters of the Gauss2D, 
NormGauss2D, and SigmaGauss2D models

750 - Add xspec convolution api

Adds support for XSPEC convolution-style models - this link is valid for XSPEC 
12.10.1 documentation

765 - Add docs for setting up all dependencies of the source build with conda

Adds documentation on how to use conda to install source build dependencies

766 - No error for no-ops in ungroup and friends

Removes DataErrs when ungrouping a dataset that is not grouped or unsubtracting 
a dataset that was not subtracted

770 - Replace EmissionVoigt/AbsorptionVoigt models by Voigt model (fix #597)

Replaces the EmissionVoigt and AbsorptionVoigt models with a single model, 
Voigt1D. The EmissionVoigt and AbsorptionVoigt models will error out when an 
instance is created, pointing users to Voigt1D (as the parameter definitions 
have changed).

772 - Add XSPEC 12.11.0 support (HEAsoft 6.27)

Adds support for XSPEC 12.11.0 (released March 31 2020)

782 - Add a pyproject.toml file

Adds a pyproject.toml file to the top level (PEP 518) to document build 
requirements

789 - fix issue #788, fit using moncar with verbose=1 and/or numcores!=1

Fixes NameError in moncar when verbose setting >0

791 - Fix ignore/notice error-ing out when all bins have been set bad #790

Allow notice and ignore to be called on a dataset which has no "good" bins 
after ignore_bad has been called

793 - Accept masked arrays for Data XXX creation

Allows use the mask of numpy arrays when initializing DataXXX

803 - Updates to sampling of energy and photon fluxes: bug fixes and calculate

   unabsorbed components
Fixes and improvements to the energy_flux and photon_flux set of commands: 
sample_energy_flux, sample_photon_flux, plot_energy_flux, plot_photon_flux, 
get_energy_flux_hist, and get_photon_flux_hist

811 - Remove all future imports

Removes __future__ imports that were in place when sherpa supported python 2

812 - Add unsubtract and ungroup to datastack

Adds  corresponding unsubtract and ungroup methods to match subtract and group

815 - fix typo in rst docs

Fixes a typo in the rst docs

821 - Add hyperlink to similarly named SHERPA package

Documentation update to include a link to thethe similarly named package "SHERPA" 
for hyperparameter tuning of machine learning models

842 - Fix scaling of staterror when reading PHA file with rate instead of counts

Fixes scaling of STAT_ERR when reading a PHA spectra with a RATES column instead of 
COUNTS

845 - xspec table models: add out-of-bound check to avoid segfault

Adds explicit out of bounds checks to avoid segv when calling an Xspec table model

851 - Updates to the Read-The-Docs build environment

Update the Read-The-Docs configuration to the latest version (2), and switch to a 
cleaner build (using conda) for the documentation. The minimum Sphinx requirement is 
now 1.8 (updated from 1.3).

856 - Support setting the id value in load_pha with pha2 files (fix #666)

Updates load_pha to set the data ids of PHA2 datasets  to: id to id + nfiles - 1 
(when id is an integer), or "{}1".format(id) to "{}{}".format(id, nfiles) when id 
is a string.

858 - Minor documentation improvements to ReadTheDocs

Adds minor updates to the convolution, regrid, and model evaluation sections of 
the ReadTheDocs documentation

859 - Clean up of the XSPEC interface code

Internal changes to the XSPEC interface code, which reduces the amount of similar 
(sometimes identical) code. There is no change to the behavior of the XSPEC models.

865 - Minor documentation fixes

Several documentation fixes: XSPEC parameter names, avoiding confusion over links on 
references (Sphinx pages), and adding some basic documentation to the 
sherpa.astro.background module

866 - Add parameter-clipping strategy to routines that generate samples (fix #846)

The addition of the clip parameter lets users control how parameter values are 
clipped before use in sample_energy_flux, sample_photon_flux, plot_energy_flux, 
plot_photon_flux, get_energy_flux_hist, and get_photon_flux_hist.

868 - Add deletepileupmodel (fix #441), listpileupmodelids, listpsf_ids functions,

   fix list_models (fix #749)
Add the delete_pileup_model() function to allow a pileup model to be removed from 
a fit (issue #441), and list_psf_ids() and list_pileup_model_ids() routines to list 
those datasets with an associated PSF or pileup model. The list_models() routine 
no-longer returns an iterator but a list when given an option (issue #749).

871 - Add MacOS LDFLAGS warning to devdocs

Copies the warning about setting PYTHON_LDFLAGS from the install page to the 
developer docs

884 - Move logic from ui layer to DataPHA class: background responses (fix #879, #880)

Moves the logic for adding a background response, if one doesn't exist, from the UI 
layer to the DataPHA class to clear up several edge cases

888 - Support vector backscales and bugfix for background modeling

Supports fitting backgrounds to PHA datasets which have a variable BACKSCAL array 
(rather than a scalar), which can come from combining spectra (e.g. the CIAO contrib 
script combine_spectra) or from the data extraction process. In doing so a number of 
routines related to the scaling of background-to-source aperture data have seen 
adjustments to behavior and some enhanced functionality (such as 
sherpa.astro.ui.get_bkg_scale and the sherpa.astro.data.DataPHA.get_background_scale 
method).

897 - Add support for XSPEC 12.11.1

Allows Sherpa to be built against XSPEC 12.11.1. There are no new or changed models 
in this release compared to XSPEC 12.11.0.

899 - Update likelihood descriptions

Updates likelihood description in several doc-strings and clarifies descriptions 
of statistics.

900 - Ensure that 1D and 2D models are not combined in an expression.

Checks that models have the correct dimensionality when combining them, so 
expressions like gauss2d.src + const1d.bgnd will now raise a ModelErr.

906 - Improve and add support for histogram plots

Updates to the display of histogram-style plots, in particular for 1D integrated 
datasets and some model display for PHA data. The histograms now cover the full 
length of each bin (previously they only showed half the bin for the first and 
last bins), and gaps in the histogram (where the high edge of a bin is less than 
the lower edge of the next bin) are now correctly displayed.

907 - FEATURE: support alpha transparency for matplotlib plots

Supports the 'alpha' preference setting for most plots and contours generated 
by Matplotlib

909 - Refactor: remove getmodel/source methods

Removes the _get_source and _get_model methods as they are the same as 
get_source and get_model

910 - Docs: fix several minor issues

Documentation clean up - the load_template_interpolator function was named 
incorrectly in the example, and the examples for 
get_source_component_plot/get_model_component_plot were missing the trailing 
_plot for the function names

911 - Docstring: changes for ahelp

Formatting changes to the docstrings for several routines that are useful for 
SDS in generating ahelp files

918 - fix an issue with PHA filtering that affects plot_model

Fixes an issue when applying filters to generate the plot_model and 
plot_model_component plots for PHA datasets

919 - enable regrid for the BinaryOpModel class (rebased #798)

Enables composite models (created by a binary operation between two models) to 
be regridded. The composite model is evaluated at the new grid, and it is only 
the combined model expression that is rebinned to the data grid.

922 - channel settings with grouped PHA data and model plotting

Fixes a bug when filtering a grouped PHA dataset using analysis=channel. The 
selected bin ranges did not always match the versions you would have received 
when doing the same operation with energy or wavelength analysis (the first or 
last bin may have been different).

924 - Updated to ignore the .vscode directory

updates system .gitignore to skip over vscode directories

929 - Support overplot option in plotfitxxx (issue #700)

The overplot argument can now be used with the plot_fit_xxx and plot_bkg_fit_xxx 
routines (e.g. plot_fit_ratio).

931 - Update Data1DInt / DataPHA data plots to use the histogram plot style

Switch the plot_data/plot_bkg plots to draw the data as histograms for Data1DInt 
and DataPHA plots.  This will change the behavior of code that accesses the plot 
data - e.g. get_data_plot() or the dataplot element of get_fit_plot() - since for 
DataPHA and Data1DInt datasets the data will no-longer have an x attribute but 
xlo and xhi. To reduce the need for code changes for existing scripts - as many 
people use get_model_plot and get_data_plot to get the data - the histogram 
plots will return (xlo+xhi)/2 when asked for the x attribute.

939 - Docs: note XSPEC convolution models are new in 4.12.2

Documentation only change noting  that the support for XSPEC convolution models 
is new to 4.12.2.

940 - Minor documentation improvements

Fixed several minor issues in the existing documentation

944 - Improve handling of the default id with PHA background datasets (fix issue #943)

The sherpa.astro.ui.set_default_id call no-longer sets the default identifier for 
background ids, which are now kept as the value 1. This avoids several issues when 
using set_default_id with the background components of PHA datasets

950 - Documentation fixes

Minor documentation updates and adding ReSampleData to the RTD documentation

953 - docstring fixes

Cleans up typos in documentation

957 - Docs: include the example notebook in the RTD pages

Adds the example notebook (SherpaQuickStart.ipynb) to the Sphinx documentation 
under the "Notebooks" heading

961 - Update notebook support for Data1DInt/PHA data

Improves the display of Data1DInt and DataPHA objects when displayed directly 
by Jupyter notebook and add a new notebook showing off the notebook support

963 -Docs: note plotfitxxx overplot change and add info on notebook support

Adds documentation updates including notes on overplot support in plot_fit_xxx 
and plot_bkg_fit_xxx functions and RTD notes on adding notebooks 

964 - Docs: avoid invalid escape sequence warning

Very-minor tweak to the Chi2 docstring

968 - Fix 2d image filtering (fix #965)

Fix problems with ignore2d and notice2d when multiple regions are used.

969 - Support Python 3.8 for MacOSX

Add a new multiprocessing_start_method option to sherpa.rc and 
sherpa-standalone.rc and init code to set start multiprocessing method 
to fork by default.

971 - Docs: fix sphinx warnings

Fix documentation in sherpa.sim.sample on the ReadTheDocs site.

979 - Improve plots of PHA data sets and models when the response grid is not ideal

Improve the display (plots) of PHA data and models when the response grid contains minor numerical differences. 
(fixes #977)

984 - Address set_xlog/ylog problems with DataPHA/Data1DInt classes (#981)

Fix the set_xlog/ylog routines for PHA and 1D integrated datasets.

- Python
Published by Marie-Terrell over 5 years ago

sherpa - Sherpa 4.12.1

Sherpa 4.12.1

This release of Sherpa supports a patch for CIAO 4.12. This release is driven by fixes that were deemed necessary to warrant a patch to sherpa in the CIAO 4.12 release. The changes include issues which had the potential of impacting users by either stopping an analysis session or providing incorrect or potentially confusing results, particularly in the area of grating analysis and multiple datasets. Additionally, this patch includes several fixes and improvements such as initial support for Python 3.8.

This version of Sherpa has been tested with Python 3.5, 3.6, and 3.7. There has been limited python 3.8 testing as well.

Details

Testing and infrastructure fixes have been omitted

832 - Support building with NumPy 1.19

Compatibility updates for numpy v1.19 with regards to numpy.distutils and tostring deprecation

781 - Docs: fix typo in docstring for calc_kcorr

Fixed a typo in docstring for calc_kcorrFix a typo in the documentation 
for calc_kcorr: change "0." to "0.5" in one of the examples.

759 - revert PR #444 (caching)

Revert the ARF cache added in #444, as well as some of the related code 
changes, as they caused problems with Analysis in wavelength space 
(e.g. #746)

756 - calculatephotonflux/calculateenergyflux fix and improvement

Bug fixes and improvements for calculate_photon_flux and calculate_energy_flux:
    - address flux and flux-density calculation issues discussed (fix #619)
    - fix documentation of the lo and hi arguments (fix #308)
    - add model parameter to calc_photon/energy_flux which allows users to
      easily calculate "unabsorbed" fluxes

747 - reworked regrid to eval usr grid, but 0 every where else

Modifies the 1D grid implementation to evaluate over the user-supplied 
range, anything outside that is set to 0

745 - ensure that min/max limits are applied to linked parameters before use

Enforce parameter restrictions (they must lie within their min/max range) 
even when the parameter is linked to another (which has a different range).

739 - Post 4.12.0 Updates

Update readme to include DOI for 4.12.0

738 - Release 4.12.0

Merge the 4.12 Release into master

737 - Update copyright year for the documentation

Read-The-Docs: update copyright year

735 - Remove ChIPS support

Remove the ChIPS plotting code and configuration options from the code base

734 - Change datastack querybyheader_keyword to not error if keyword is missing

Change the sherpa.astro.datastack query_by_header_keyword routine so that 
it skips data sets which do not have the keyword, rather than raising a 
KeyError. This also affects query_by_obsid.

733 - fix a bug with fit(cache=False) passing the runtime option while fitting

732 - Remove unused Python 2.7 compatibility code

Remove unused code from the removal of Python 2.7 support.

696 - Support python 3.8

Updates to the support python 3.8 including
    - remove syntax warnings from use of is with a literal
    - remove deprecation warnings about PY_SSIZE_T_CLEAN
    - fix index error (use scalar indexes)
    - update the documentation to highlight initial python 3.8 support

- Python
Published by Marie-Terrell almost 6 years ago

sherpa - Sherpa 4.12.0

Sherpa 4.12.0

This release of Sherpa is based on the CIAO 4.12 release and includes additional bug fixes and improvements.

This version of Sherpa has been tested with Python 3.5, 3.6, and 3.7.

This release also provides support for XSPEC 12.10.1 (patch 'a' or later) in addition to versions 12.10.0 (included in CIAO) and version 12.9.1.

Details

Documentation and infrastructure fixes are not shown.

388 - Address indexing DeprecationWarning/IndexError from NumPy for PHA data with filter + ignore_bad (fix #361)

602 - Reduce integration tol

Changed integration routine tolerance from double epsilon to float epsilon
since opt routines hove tolerance of ~ 1.0e-7

606 - stop using numpy.typeNA which is now deprecated

A numpy deprecation warning was fixed by removing the usage of typeNA, which
was not documented and will be removed in a future release of numpy. The
print_fields function has been changed to include a default mapping using
the current typeNA implementation.

608 - update ciao default plotter to matplotlib

The default Sherpa plotting package has been changed to matplotlib for 
CIAO users as well (it had been the default for standalone users for
several years). The update will be applied to new users when the 
`sherpa` command is run. Users of previous versions would need to 
edit/regenerate the file.

616 - enable run-time-option to test cache (default=True)

Capability to allow the user to turn off caching at runtime for testing 
purpose.

622 - Do not create warnings about error bars in plots if no error bars are to be shown (fix #621)

Remove the The displayed errorbars have been supplied with the data or 
calculated using chi2xspecvar... warnings that appear for data, 
residual/ratio, and fit plots when the user has explicitly turned off 
the display of errorbars (by setting the yerrorbars plot-preference 
setting to False).

626 - add plotfitratio and plotbkgfit_ratio functions

Add the plot_fit_ratio function to the sherpa.ui layer (to match 
plot_fit_resid and plot_fit_delchi) and plot_bkg_fit_ratio to the
sherpa.astro.ui layer. Added tests for a number of plot types. 

640 - fix 'tuple index out of range' error in the fit.est_errors method

Sherpa's Confidence class is confused if a parameter is frozen then 
thawed after a fit resulting with an exception of the form: IndexError:
tuple index out of range. The error does not show up if conf is called
from the ui level

647 - fix numpy hist warnings

When plotting a PDF Sherpa now calls numpy.histogram with density=True |
False rather than normed=True|False. There is no change visible to the
user other than a warning that will not be issued anymore. normed=True 
was broken for non uniform bins, but our code always produces uniform
bins, so we should never hit the problematic case.

658 - Handle files with MJD_OBS or MJD-OBS keywords (datastack module)

The sherpa.astro.datastack module has been updated to deal with files 
that use the MJD-OBS keyword instead of MJD_OBS. This is only used by 
the show_stack routine, which prints out several keywords from each 
file in the stack.

665 - Remove python 2.7 support (fix #498)

Remove support for Python 2.7 from Sherpa. The metadata used by pip now
requires python 3.5 or higher (but not version 4),

667 - improve matplotlib plot_fit plots (order of data and model)

Changes to Zorder of plot objects drawn by matplotlib to be more readible

674 - Add link/unlink parameter tests

This PR adds three tests for sherpa's un/link commands.

677 - XSPEC: build against 12.10.1m by removing support for models

Remove support for XSrelline, XSrelline_lp, and XSrelline_lp_ext models.
These were added in 12.10.1 but removed in 12.10.1m. It does not seem
worth supporting just those versions where they were available.

680 - Remove the unused parameter in sherpa.astro.optical.LogEmission model (fix #219)

Remove the unused parameter in the sherpa.astro.optical.LogEmission 
model. The LogEmission model only has four parameters (fwhm, pos, flux
and skew) consistent within the calc method. The hidden parameter limit
and it doc were removed.

682 - jointplot now respects the ratio argument (top plot is larger) with matplotlib backend

The matplotlib back end now makes the main (top) plot taller than the 
secondary (bottom) plot when using the sherpa.ui.plot_fit_resid and 
sherpa.ui.plot_fit_delchi routines (this also holds for the 
sherpa.astro.ui variants).

683 - Remove chips from the documentation

Remove mention of ChIPS from the documentation (both on read the docs 
and in the sherpa.astro.ui and sherpa.ui modules), replacing with 
matplotlib where appropriate.

684 - Add default config options

Whenever an option is read from the configuration file (~/.sherpa.rc)
provide a default option in case the configuration file is missing
(or is missing this option).

685 - raise ModelErr when model using Data1DInt have overlapping bins

Adds a check to regrid make sure the integrated bins do not overlap. 
The PR is a fix for issue #569

688 - Improve documentation and testing for getsourceplot when sent lo/hi arguments

Improve the documentation for the sherpa.astro.ui.get_source_plot routine,
describing how touse the result when the lo or hi arguments are sent.

691 - add warning when chips is selected but cannot be imported (rebase of #648)

Sherpa now warns the user if Chips is selected as a backend but it is
not available in the installation

692 - Allow users to override plot preferences when creating a plot

Change to allow kwargs to be specified to change plot preferences at 
creation time

698 - Add warnings in documentation about masked arrays

Updates docstring to indicate that sherpa doesn't support numpy masked
arrays

701 - a fix for /data/lenin2/Test/CIAO4.11/SherpaRegressionBeta1/45

Enables the testers to turn on (or off) caching at runtime to test #444

704 - change calc_ftest from delta dof to dof (similar to XSPEC) - fix for #641

Update to make sherpa's calc_ftest provide same results as XSPEC's 
ftest (fix to #641)

705 - modelCacher1d needs to have a couple of deep instead of shallow copy()

Update to make deep copy of cached function values (fix to #673)

710 - Add warning about masked array to sherpa.astro.ui.load_arrays

Updates docstring to contain warning consistent with #698

712 Minor typo in docs

Corrects a typo "is is" in the documentation.

716 Fix for plot_cdf: plot() got an unexpected keyword argument 'clearwindpw'

Recent changes broke plot_cdf()due to a typo 'clearwindpw'. This update
corrects the typo.

721 Docs: update installation notes for conda environment

Add a warning about the need to set PYTHON_LDFLAGS to ' ' on macOS when
building within an anaconda environment. This is a documentation-only 
change.

725 convert a list to np.array to avoid warning messages

Fixes issue #723 (a lot of warnings while running 'resample_data()' in 
CIAO4.12 Sherpa)

728 a fix cause using loadmultiarfs causes caching error

Fixes issue #717 (unable to fit if script uses loadmultiarfs/rmfs)

- Python
Published by Marie-Terrell over 6 years ago

sherpa - Sherpa 4.11.1

Sherpa 4.11.1

This release of Sherpa introduces several functional improvements and bug fixes, in particular Sherpa now has support for: * asymmetric error bars * PSFs with better pixel resolution than the data * running optimization in parallel

Details

630 Fix "getintproj does not work when recalc=True" (#543)

get_int_proj did not work when recalc=True on Python 3. This has now been fixed.

615 Asymmetric Errors

Sherpa now supports asymmetric error bars. Errors can be read through a new

load_ascii_with_errors high level function, or through the new Data1DAsymmetricErrs class. Sherpa uses bootstrap for estimating the uncertainties.

585 plot pvalue

Updates to utilize the appropriate response files (ARF and RMF) for X-ray spectra
and changes to the p_value output to 1/(number of simulations) when p_value is 0
and the number of simulations in not large enough.

596 Run optimization algorithms over multiple cores

This PR enables the user to run the optimization algorithms (DifEvo, LevMar,

and NelderMead) on multi-cores.

607 PSF rebinning (fix #43)

Sherpa now supports using a PSF with a finer resolution than 2D images. If Sherpa

detects that the PSF has a smaller pixel size than the data, it will evaluate the model on a "PSF Space" that has the same resolution as the PSF and the same footprint as the data, then rebin the evaluated model back to the data space for calculating the statistic.

614 Refactor data classes (fix #563, #627, #628)

Sherpa's basic data classes have been refactored and cleaned up to help

facilitating fixing bugs and implementing new features. New tests were added to reduce the chances of introducing regressions in the future.

612 Fix #609 User Model: unable to change parameter values

A regression introduced in Sherpa 4.10.0 presented users from change

user-model parameter values through direct access. This issue has been fixed. Several tests were added to reduce the chance of regressions in the future.

Fix #514 - the command line tool sherpa_smoke in the conda package now correctly honors command line arguments.

- Python
Published by olaurino almost 7 years ago

sherpa - Sherpa 4.10.1

Sherpa 4.10.1

This release fixes several bugs and introduces a few new features, notably the ability to evaluate model components on arbitrary grids and generate user-defined ARFs and RMFs. Also, as of this release Sherpa will no longer rely on any Fortran code. See the following section for details.

It is now possible to build the Sherpa documentation using Sphinx. Additionally, the Sphinx documentation is automatically built and hosted on ReadTheDocs: https://sherpa.readthedocs.io/

Details

407 Ensure 0-length array is an error in filter_resp (fix #405)

Add an explicit check in the C++ filter_resp code to error out if the noticed channels array
is empty.

422 Improve error message with wrong xspec version

Improve the handling of XSPEC versions mismatch.

466 Fix bounding box out-of-bounds memory read

Avoid an out-of-bounds memory read when calling pad_bounding_box (when the data is not 
matching the expected conditions for this call).

469 Evaluate model on finer grid

Sherpa users can now define arbitrary grids, called evaluation spaces, on which to 
evaluate individual model components, both in 1D and 2D. This can be useful in a number
of cases, for instance when it is desirable to evaluate models on a finer grid than the one
defined by the data, or in convolution models where information outside of the data range
can be used to reduce boundary effects or to inform the evaluation inside the data space. 
Also, when plotting individual 1D model components (plot_source_component), if a specific
evaluation space was attached to the model then the plot will be of the model evaluated
over that evaluation space, not the data space. Other plotting commands should be
unaffected by this change.

470 Order for np.ones() should be a one length string not a bool

Fixed a `DeprecationWarning` in the optimization module.

471 Using overwrite rather than clobber of astropy.io.fits

`clobber` in astropy has been deprecated for a while now in favour of overwrite and thus
issues a `DeprecationWarning`. Sherpa now uses `overwrite` instead.

475 Fix unecessary runtime warning (fix #402)

A condition check in the optimization code was modified so as not to produce a warning
when the value is a NaN.

481 Remove Fortran code

Sherpa does not rely on any Fortran routines anymore, except those compiled in XSPEC.
The existing Fortran code, which was used mainly in some of the optimization routines, has 
been replaced by equivalent C++ code. This means that gfortran is no longer required for
building Sherpa, although a version of libgfortran compatible with the one used to link the
XSPEC libraries would still be needed at runtime if the XSPEC extension is
built.

482 ARF/RMF creation functions

The `create_rmf` and `create_arf` functions now allow users to easily generate user
defined response objects.

486 ZeroDivisionError in calc_stat_info (fix #476)

Sherpa did not catch divisions by zero in the calc_stat_info command. That has been fixed.

484 Equivalent Width errors

Several optional arguments `(params=None, error=False, otherids=(), niter=1000)`, were
added to `eqwidth`. If `error = True`, then get_draws shall be run if the fit stat is one of the
following: (Cash,  CStat, WStat) otherwise a multivariate normal distribution shall be run to
generate the samples. The optional niter parameter is used to generate the number of 
samples. The optional parameter otherids is only used if get_draws is used internally when
multiple data sets were used to fit. Alternatively, the user can enter the samples via the
`params` option where the samples must be a `numpy.ndarray` of dimension `(num, npar)`.

487 PSF bin size warning

Sherpa assumes that the PSF image and the data have the same pixel size. When this is
not true Sherpa ignores the difference, which results in a larger PSF being applied. From
now on Sherpa will issue a warning when the PSF image
pixel size and the data image pixel size are different.

- Python
Published by olaurino about 7 years ago

sherpa - Sherpa 4.11.0

Sherpa 4.11.0

Optimization routines and statistic methods were made more robust with several bug fixes and improvements.

This version of Sherpa has been tested with Python 2.7, 3.5, 3.6, and 3.7. Support for Python 2.7 is being deprecated and may be dropped in future releases.

This release also provides support for XSPEC 12.10.1 (patch 'a' or later) in addition to versions 12.10.0 (included in CIAO) and version 12.9.1.

Details

Documentation and infrastructure fixes are not shown.

444 Improve caching

When fitting multiple datasets simultaneously Sherpa now tries to cache

model evaluations to improve performance.

465 Support XSPEC 12.10.0 (fix #436)

XSPEC 12.10.0e is now supported

508 Ensure fields are initialized before use (pileup code)

Resolved an issue where some fields in the C++ extension could have been

uninitialized in a corner case.

523 Ensure the ui modules have a unique list of exported symbols (fix #502)

Remove the `sherpa.utils.erf` symbol from the two `ui` modules as it is

"over-written" by the ModelWrapper-created symbol when applied to sherpa.models.basic.Erf.

524 Be explicit about 'invalid escape characters' in strings

Convert strings that contain "invalid" escape characters, which newer

versions of Python complain about, to raw strings by preceding them with a 'r' character.

525 Fixed based line radpro_dm test and changed double --> real (template)

530 Ensure XSPEC 12.10.0 uses ATOMDB 3.0.9 by default

Ensure that the default AtomDB version is 3.0.9 when using XSPEC 12.10.0.

This is to fix an issue with the models-only XSPEC installation in XSPEC 12.10.0 which uses a default version of 3.0.7 but only provides data files for 3.0.9. Without this change models such as XSapec would return all 0's (unless the AtomDB version was set manually by the user).

534 XSPEC 12.10.1 support and mtable fix

Sherpa now supports XSPEC 12.10.1. Several issues were fixed to ensure

compatibility with this release. Note that there are known issues with version 12.10.1 (no patches), so at least v12.10.1a must be used.

537 / #552 sherpa.rc changes

Sherpa does not read the verbosity.level setting from sherpa.rc anymore but

the option is still in the file for backward compatibility

539 Fix XSPEC models: mtable table models and ismabs (fix #535, #538, #540)

Fix to address issues with XSpec- #535 XSPEC multiplicative table models

(mtable models loaded with loadxstablemodel); #538 incorrect evaluation of the ismabs model; #540 the kerrd model evaluated to 0 for XSPEC 12.10.0 and later.

546 Small code cleanup in LevMar

small code cleanup in the LevMar class to match the other classes in that

file.

564 / #567 Harmonise the handling of dof is zero or negative in fit and calcstatinfo (fix #565)

The `fit` and `calc_stat_info` methods now use the same code to calculate

the reduced statistic (rstat) and "quality of fit" (qval) values. This avoids a TypeError when the number of degrees of freedom is negative in calc_stat_info and ensures that NaN is returned for both values when the goodness-of-fit calculation has failed (e.g. the reduced statistic is zero or less or the statistic is negative), whereas in previous versions the qval value could be None or 1 depending on the code path.

576 Fix regression with responses get_x method

Version 4.10.1 introduced a regression which made the `get_x()` method fail

when called on RMF and ARF objects. This has been resolved.

583 Update pager code (fix #445 #561)

Replace the use of an external pager (such as `more` or `less`) with a

Python one. This means that Sherpa no-longer uses the PAGER environment variable, and that the screen output from the show_* series of commands should now appear in the correct location when using a Jupyter notebook or the spyder application.

- Python
Published by olaurino over 7 years ago

sherpa - Sherpa 4.10.2

Sherpa 4.10.2

This release fixes a regression introduced in Sherpa 4.10.1 related to PSF convolution. As part of the long term PSF rebinning improvements, Sherpa 4.10.1 introduced a check to validate that the data pixel size and the PSF pixel size match. If they don't match, then a warning is issued. The change did not account for an edge error case. Sherpa 4.10.2 solves this problem. The regression introduced a downstream regression in the gammapy project.

Details

551 Fix gammapy/gammapy#1905, catch errors with psf pixel size.

Sherpa did not properly catch errors when checking the PSF pixel size matches the image pixel size. This has now been fixed.

Caveats

There is a potential issue for macOS conda users with python > 3.6 and matplotlib v3.0.1, when pyqt5 is not installed and selected as a matplotlib backend. With this specific combination of platform and dependencies matplotlib can fail to work properly. The issue can be replicated without importing Sherpa, so this is not a Sherpa bug.

Several workarounds exist, the simplest of which are: * install pyqt5 (conda install pyqt). * downgrade matplotlib to v2 or v3.0.0 (conda install matplotlib=3.0.0)

- Python
Published by olaurino over 7 years ago

sherpa - Sherpa 4.10.0

Sherpa 4.10.0

This release of Standalone Sherpa corresponds to the Sherpa code released as part of CIAO 4.10.

Sherpa 4.10.0 fixes several bugs related to the support of instrumental responses, including improved support of XMM and Swift responses.

Also, this release fixes a significant bug in the support of user statistics, improvements to the Python 3 compatibility, more robust usage of the numpy API, as well as several other minor bug fixes and new tests.

Additionally, this release introduces support for XSPEC 12.9.1n models, as well as the ability to use aliases for parameter names. Some parameter names have been deprecated and may be removed in a future release. We reviewed the parameter limits for many models and updated them to reflect the latest XSPEC specification. Also, multiple versions of XSPEC are now supported, through optional models and version-dependent low-level function calls. This feature is for advanced users building Sherpa from source. Note that Sherpa has been tested against XSPEC 12.9.0i, 12.9.0o, and 12.9.1n. Note that XSPEC is not directly supported by the standalone binary builds, and users are expected to build Sherpa from sources if they want to link it against their version of XSPEC. These changes make it easier for user to link different versions of XSPEC with the same Sherpa code base. Also note, however, that XSPEC 12.10 is not currently supported.

Sherpa now requires pytest-3.3 or later for running the tests.

Details

451 Release/4.10.0

Testing code now works with pip 10 as well, despite a change in the pip 10 API. Also, the README is now properly rendered as markdown in PyPI.

438 Change from error to warning for OGIP violations

Given that users can not easily change a response file, and previous versions of Sherpa would allow the responses to be used, this commit changes some of the errors recently introduced (in PR #383) into warnings. The errors for the first bin edge being <= 0 are still left in because users of the sherpa.astro.ui module will find that these files are auto-corrected for them (by PR #383).

430 Update XSPEC parameters

XSPEC model parameter default values, limits, and properties were reviewed and updated to reflect changes in or mismatches with the model.dat file shipped with XSPEC 12.9.1n.

428 handle function name changes in XSPEC 12.9.1

Sherpa now supports multiple versions of the XSPEC models from the 12.9.0 and 12.9.1 series. Some models recommend using the C-style interface over the older FORTRAN one, which may also resolve some memory access issues. For CIAO 4.10 users this means the interfaces to XSPEC models have been updated to the 12.9.1n versions. For Standalone Sherpa users this means they can build and run Sherpa against a larger range of XSPEC versions, and Sherpa will pick the XSPEC low level model function accordingly. Note that Sherpa has been tested against XSPEC 12.9.0i, 12.9.0o, and 12.9.1n. The 14 models that have been changed are: apec, bapec, bvapec, bvvapec, gaussian, lorentz, meka, mekal, raymond, vapec, vmeka, vmekal, vraymond, and vvapec.

427 Add support for XSPEC models added in 12.9.1 (fix #331)

Add support for models added in XSPEC 12.9.1: bvtapec, bvvtapec, tapec, vtapec, vvtapec, carbatm, hatm, ismabs, slimbh, snapec, TBfeo, TBgas, TBpcf, TBrel, voigt, xscat. Version 12.9.0 of XSPEC can still be used, in which case the models can be generated - e.g. a user can say xstapec.mdl to create a Python object - but it will error out when evaluated. The Si and S elemental parameters for the ismabs model have been renamed from the XSPEC versions since they are not unique using the caseinsensitive matching used by Sherpa: so SI, SII, SIII and SiI, SiII, SiIII have been renamed SI, SII, SIII and SiI, SiII, and SiIII respectively. Low level support for the following convolution models from XSPEC 12.9.1 has also been added, but there is no Python model support for these: clumin, rfxconv, vashift, vmshift, xilconv.

412 support ROSAT PSPC (and similar) RMF files with AstroPy

Add explicit tests for reading in, and using, ROSAT PSPC PHA and RMF files. Fix a bug in the AstroPy back-end handling of the ROSAT RMF file.

409 EmissionGaussian model when skew parameter is not unity (fix #403)

The sherpa.astro.optical.EmissionGaussian code has been fixed for the case when the skew parameter is not unity. The documentation has also been updated.

399 Python 3 fixes and new tests for pha2 datasets

Fixed several problems when using Sherpa with Python 3: failures when calling list_bkg_ids and list_response_ids and the parameter querying after paramprompt(True) has been called. There is also a change to avoid a FutureWarning being raised in the astropy backend when reading in PHA2 data files. Tests have been added to test the reading of a PHA2 format dataset, and new files added to the sherpa-test-data repository for this purpose.

398 Check that list_samplers returns a list (fix #397)

The list_samplers function now returns a list in Python 3 as well.

396 Fix set_xlog and related commands using Python 3 (fix #393)

Fix use of commands that set the plot state using the sherpa.astro.ui module, such as set_xlog and set_xlinear, when using Python 3.

395 Add xspec optional models

Sherpa has new infrastructure for supporting multiple versions of XSPEC at the same time, with models that are built and enabled conditionally depending on the version of XSPEC being linked. Models are assumed to have the same parameters and low level functions across supported versions.

394 XSPEC build and functionality improvements

Add support for reading and changing the path to the XSPEC "manager" directory, and reading the current XSPEC "model" directory (get_xspath_manager, set_xspath_manager, and get_xspath_model). These are intended for the power user and so require an explicit import from sherpa.astro.xspec. There are several improvements to the build and interface to the XSPEC model library: these have no user-visible changes.

390 Add nlapec model

The nlapec XSpec model has been added. Note that XSPEC 12.9.0 is now required.

385 DS9 calls return string in Python 2 and 3 (fix #319)

Some low lever xpa calls were returning byte strings rather than strings in Python 3. This had particular impact on the image_getregion function. This has now been fixed.

383 Replace 0-energy bins in ARF and RMFs (fix #332)

Sherpa now performs some validation of the energy ranges of ARF and RMF files against the OGIP standard. If the ranges are inconsistent then the code will return with an error. If one energy bound is 0 the bound is replaced with a small number to avoid numerical issues like division by zero. A new configuration option minimum_energy, if present, allows users to override Sherpa's default behavior.

379 Use a line not span to draw horizontal line (fix #378)

Ensure that the line at y=0 (residual) or y=1 (ratio) is drawn for residual or ratio plots when using matplotlib 2.0.

373 Make sure ds9 properly works with Python 2.7 (fix #368)

For Python versions prior to 3.2 add in explicit code to make _Popen work as a context manager.

352 Add low-level support for the XSPEC rgsxsrc convolution model

Add low-level support for the rgsxsrc convolution model in XSPEC. This is intended for R&D into fully supporting XSPEC convolution models in Sherpa.

255 Add aliases for parameter names so to support new xspec names (fix #74)

The XSPEC models have been updated to use parameter names that match the new XSPEC naming scheme introduced in XSPEC 12.9.0. The old parameter names can still be used as aliases for the new name, but are deprecated and may be removed in a next major release. Note this allows any models to define aliases for their parameters.

- Python
Published by olaurino about 8 years ago

sherpa - Sherpa 4.9.1

Sherpa 4.9.1

This version introduces full support for Python 3.6. It also fixes issues with non-Chandra response files, correctly handles the AREASCAL column in PHA files, and fixes a significant regression that was preventing user statistics from working in v4.8.2. It also introduces a number of smaller improvements and fixes. In particular, quite a few improvements have been made to the documentation and to the testing framework, including several new tests to improve stability.

Details

Infrastructure and minor non-functional changes have been omitted.

335 Fix setup.py install command

The setup.py install command was not enforcing the installation of the dependencies listed in setup.py. This has been fixed.

368 Remove ds9 warnings when run under Python 3.6

Update the DS9 code so that external processes are cleaned up properly, so to remove the potential ResourceWarning warnings when running DS9 on Python 3.6.

351 fix handling of AREASCAL column in PHA files (fix #350)

Add support for handling the AREASCAL value (either scalar of vector) for PHA data sets. This array is used in XMM RGS data to handle missing chips.

358 Properly handle Swift RMF when using Astropy backend (fix #357)

A Swift RMF could not be read in when the AstroPy back end was in use. The problem was that the code did not support RMF matrices that were not stored as variable-length arrays. This has now been fixed, and new tests have been added for this kind of files.

343 Fix user statistics regression (fix #341)

A number of regressions were introduced in version 4.8.1 up to version 4.9.0, so user statistics that were properly working in version 4.7 have not been working any more. This has been fixed, and a number of regression tests have been added.

- Python
Published by olaurino almost 9 years ago

sherpa - Sherpa 4.9.0

Sherpa 4.9.0

This version fixes many bugs in the Python 3 support. Moreover, it includes a significant refactoring of the Fit and Stat classes that made it possible to fix several bugs related to the recent wstat implementation while making these classes more maintainable and extensible.

Note that this version deprecates the use of load_table_model for XSPEC models. Sherpa/XSPEC users should use the new load_xstable_model function instead.

Details

Infrastructure and minor non-functional changes have been omitted.

242 Avoid use of inspect.getargspec in Python3

Finish off the replacement of inspect.getargspec by inspect.signature.

263 Listdataids() fails on py3 with mixed id types (Fix #262).

Sherpa was sorting the list of dataset IDs in a non-python3 compliant fashion, which resulted in issues when using strings and integers together as dataset IDs. This has now been fixed.

267 add wstat tests

Add several regression tests for wstat.

282 Parallel_map not working on py3 with numcores=1 (Fix #277).

The utils function parallel_map failed on Python 3 when called with numcores=1, i.e. on systems with only one processor/core. This has been fixed.

283 Sample flux and numpy deprecations (Fix #273 and #276).

The sample_flux function was not working under Python 3 if the scales argument was provided. This has been fixed. Also, a DeprecationWarning was issued by numpy because during the sample_flux execution values were extracted from an array with non-integer indices. This has also been fixed.

284 String representation of data classes under py3 (Fix #275).

Data classes DataPHA, DataARF, DataRMF, DataIMG, and DataIMGInt in sherpa.astro.data would throw an exception if users tried to print them as strings, under Python 3. This has been fixed.

287 Rewrite sherpa.stats.Stat.calc_stat and simplify sherpa.fit.Fit (fix #227 #248 #289 #292).

In order to fix several issues related to the WStat support, and in order to make the code more maintainable, the sherpa.stats.Stat.calc_stat and sherpa.fit.Fit classes have gone through a round of refactoring. This fixes the following issues: #227 Issues using wstat when grouping/filtering data; #248 backscal column not treated properly for WStat; #289 calc_stat does not error out if background subtracted data is used with Likelihood statistics; #292 stat info does not include reduced stat/qval for wstat.

295 Fix display of pileup model in Python 3.5 (Fix #294).

Fix display of instances of sherpa.astro.models.JDPileup so that, in Python 3.5, they can be displayed after the model has been evaluated.

304 replace file -> open (Fix #297).

The save and restore functions used to use the file function which is not compatible with Python 3. This has now been fixed.

305 Fix python 3 issues with some session commands (Fix #303).

The set_xlog, set_ylog, and show_bkg_model functions were not compatible with Python 3. This has now been fixed (Issue #303).

307 Move XSPEC table support to loadxstablemodel and deprecate its support

in loadtablemodel (Fix #270). Add the load_xstable_model routine to the sherpa.astro.ui module, which supports loading XSPEC additive or multiplicative (atable and mtable) models. The support for these models is still available via load_table_model in this release, but it is deprecated. The read_xstable_model routine has been added to the sherpa.astro.xspec module.

312 Fix over-zealous code clean up in PR #287 affecting sigmarej.

Fits using the sigmarej iterated-fit method were broken if a filter had been applied to the data before the fit and there are any bins that get ignored at larger bin values than the filtered-out data. (This fixes a subtle regression introduced by #287).

313 Allow sequence=None when using gridsearch and Python 3.5 (Fix #309).

Allow the gridsearch optimiser to be used with the sequence option set to None for Python 3.5.

Caveats

The requirements for Sherpa are to build with Python 2.7 and 3.5. There has been limited testing with Python 3.6, for which we distribute conda binaries. If in doubt, please install Sherpa in 2.7 or 3.5 environments only. Support for Python versions 3.3 and 3.4 is possible but would require community support.

It has been reported during testing that some versions of the matplotlib conda package do not install properly because of a pyqt v5 dependency. If you encounter this issue, please pin down pyqt to version 4, e.g. conda install matplotlib pyqt=4.

The sherpatest package is not distributed as a conda package anymore. This will probably be true for the foreseeable future. The sherpatest package contains data and functional tests that relies on external datasets, so it allows users and developers to run the entire regression tests suite. If you want to install sherpatest, please use pip and github:

$ pip install https://github.com/sherpa/sherpa-test-data/archive/4.9.0.tar.gz

If you decide to run the full regression tests suite you should also have matplotlib installed. If matplotlib is not installed a test will run and fail rather than being skipped. This issue will be fixed in the next release.

- Python
Published by olaurino over 9 years ago

sherpa - CIAO 4.9

This is a CIAO release. Binaries will be provided with the next standalone release. Release notes are collected for all changes since CIAO 4.8, which may be included from multiple standalone releases.

Release Notes

Sherpa 4.9 now runs under both Python 2.7 and Python 3.5. The test infrastructure has been modified including simplification of the smoke test. Several bug fixes and enhancements are also included. Specific details are identified below.

14361: Sherpa and Chips wrapper need to replace execfile for python 3 compatibility This fix modifies the sherpa and chips wrapper scripts to replace the 'execfile' command with an 'exec' command sequence that allows the wrapper script to be utilized by python 2.7 or python 3.5. Without the change, the option to specify a command script at the sherpa or chips command prompt (ie. 'chips /pool1/runme.py') will not work on python 3.5 since the execfile does not exist in python 3.5.

107: Normalize plot labels.

Plots created with plot_source used a different format to other plots when analysis=wavelength, in that LaTeX symbols were used for Angstrom and lambda (in other plots the string 'Angstrom' is used instead). The source plots now match the other plots.

138: improve and fix issues in save_all function.

• added a new argument to save_all: if outfile is None then the outfh argument is used to define the output handle (the argument can be any file-like argument, such as a file handle like sys.stdout or the output of open, or a StringIO object)
• setting the clobber argument to save_all now means that the output file (the outfile argument, if not None) is deleted if it already exists; prior to this, the file would be appended to instead
• the source expression is now saved correctly for most cases (e.g. when not using set_full_model); this is bug #97 but also affects non-PHA data sets
• the background model expression was not always written out correctly when using PHA data sets
• quality and grouping arrays of PHA data sets are now stored as 16-byte integers rather than a floating-point value (this has no affect on the results, but matches the OGIP standard)
• fixed up saving the grouping and quality arrays of background PHA data sets (this would only be an issue if the background is being fit, rather than subtracted)
• basic data sets created with the load_arrays function are now written out by save_all as part of the script; this is intended for small datasets and may have problems with precision if used with floating-point arrays
• calls to load_psf are now correctly restored (they may not have been written out correctly if multiple data sets were loaded)
• user models are now written out to disk; this consists of two parts:
• writing out the function that defines the model, which may or may not be possible (if not, a place-holder function is added to the output and a warning displayed).
• the necessary calls to load_user_model and add_user_pars are now included in the output
• the Python code created by save all has undergone several minor changes:
• it now explicitly imports the sherpa.astro.ui module, so that it can be run from the IPython prompt using the %run <filename> command, or directly as python <filename>
• it uses the create_model_component function rather than eval to create model components (this is CXC bug 12146)
• many optional arguments to functions are now given as name=value rather than being a positional argument, to make it clearer what the script is doing.
• calls to load_data have been replaced by more-specific versions - e.g. load_pha and load_image - if appropriate
• there have been several minor syntactic clean ups to better follow the suggestions from PEP8

When writing out code that defines a user-model, there is no attempt to make sure that modules used by the function are available. These will need to be added, either directly or imported, manually to the output.

153: Minor bug with calcchi2datavarerrors (Fix #148).

Make comparison test in calc_chi2datavar_errors less stringent, so to include the case where sqrt(x)=0.

155: Add argument to get_draws for supplying a covariance matrix.

The get_draws function now accepts a user-provided covariance matrix. If no covariance matrix is provided, the covariance matrix computed by the default implementation is used. Note that covar() must be invoked before invoking get_draws if no covariance matrix is provided, otherwise get_draws will exit with an error.

165: Remove usage of deprecated numpy API.

185: Protect XPA command to avoid shell confusion.

Fix the problem where if the working directory contained a file called x or y then the sherpa.astro.ui.image_data() function would fail with the message

DS9Err: Could not display image

187: Issue a more meaningful message when

sherpa.astro.io is imported directly and no fits backends are available. (Fix #92).

190: Datastack can be used if no plotter available.

The datastack package can now be used even if there is no available plotting backend. In this case, plotting functions will not be available, but the rest of the datastack functionality will. (Fix #22).

195 Generalize calc_stat API + example of how to have several datasets with

 different fit statistics. Attempts to generalize the `calc_stat` API and
 enable simultaneous fits with different statistics for different data sets.

209: Fix docstrings for group_snr() and group_adapt_snr().

Updates to the docstrings for clarity.

210: New Smoke Test

The smoke test has been greatly simplified: rather than running all the unit and regression tests that do not require test data, the smoke test now simply ensures that the basic installation works, i.e. that basic commands can be run and that dependencies can be reached.

211: Cleanup of documentation and code in sherpa.astro.utils.

The calc_kcorr function is now exported by sherpa.astro.utils. Minor changes to the documentation in sherpa.astro.utils were also made to conform to Sphinx standards.

221 Add model documentation (Fix #217).

Integrate existing model documentation (from external sources and the CIAO ahelp documentation system) into the model classes.

229: Code is both Python 2.7 and 3.5 compliant. (Fix #76).

242: Avoid use of inspect.argspec in Python 3

This change replaces the deprecated 'inspect.argspec' call with 'inspect.signature'.

252: Fix plot_photon_flux function. (Fix #241).

A bug where plotting photon flux was fixed by adding a missing argument to the sample_photon_flux call.

253 Make sure background is taken into account in calcstatinfo (Fix #147).

calc_stat_info call failed when wstat was selected, as the background was not taken into account. This issue has now been fixed.

254 Fix the documentation for set_rmf (Fix #236).

The documentation for set_rmf incorrectly referred to ARF rather than RMF.

256 Fix docstring in set_quality (Fix #205).

The docstring in set_quality now correctly indicates the quality flags. The previous documentation didn't describe the values of such flags properly.

257 Fix docstring for levmar tolerance (Fix #257).

The documentation string for the Levenberg-Marquardt optimization function now correctly states that the parameter default values are equal to the single precision epsilon, rather than the square root of the double precision epsilon.

263 Listdataids() fails on py3 with mixed id types (Fix #262).

Sherpa was sorting the list of dataset IDs in a non-python3 compliant fashion, which resulted in issues when using strings and integers together as dataset IDs. This has now been fixed.

267 add wstat tests

Add several regression tests for wstat.

282 Parallel_map not working on py3 with numcores=1 (Fix #277).

The utils function parallel_map failed on Python 3 when called with numcores=1, i.e. on systems with only one processor/core. This has been fixed.

283 Sample flux and numpy deprecations (Fix #273 and #276).

The sample_flux function was not working under Python 3 if the scales argument was provided. This has been fixed. Also, a DeprecationWarning was issued by numpy because during the sample_flux execution values were extracted from an array with non-integer indices. This has also been fixed.

284 String representation of data classes under py3 (Fix #275).

Data classes DataPHA, DataARF, DataRMF, DataIMG, and DataIMGInt in sherpa.astro.data would throw an exception if users tried to print them as strings, under Python 3. This has been fixed.

287 Rewrite sherpa.stats.Stat.calc_stat and simplify sherpa.fit.Fit (fix #227 #248 #289 #292).

In order to fix several issues related to the WStat support, and in order to make the code more maintainable, the sherpa.stats.Stat.calc_stat and sherpa.fit.Fit classes have gone through a round of refactoring. This fixes the following issues: #227 Issues using wstat when grouping/filtering data; #248 backscal column not treated properly for WStat; #289 calc_stat does not error out if background subtracted data is used with Likelihood statistics; #292 stat info does not include reduced stat/qval for wstat.

295 Fix display of pileup model in Python 3.5 (Fix #294).

Fix display of instances of sherpa.astro.models.JDPileup so that, in Python 3.5, they can be displayed after the model has been evaluated.

304 replace file -> open (Fix #297).

The save and restore functions used to use the file function which is not compatible with Python 3. This has now been fixed.

305 Fix python 3 issues with some session commands (Fix #303).

The set_xlog, set_ylog, and show_bkg_model functions were not compatible with Python 3. This has now been fixed (Issue #303).

307 Move XSPEC table support to loadxstablemodel and deprecate its support

in loadtablemodel (Fix #270). Add the load_xstable_model routine to the sherpa.astro.ui module, which supports loading XSPEC additive or multiplicative (atable and mtable) models. The support for these models is still available via load_table_model in this release, but it is deprecated. The read_xstable_model routine has been added to the sherpa.astro.xspec module.

312 Fix over-zealous code clean up in PR #287 affecting sigmarej.

Fits using the sigmarej iterated-fit method were broken if a filter had been applied to the data before the fit and there are any bins that get ignored at larger bin values than the filtered-out data. (This fixes a subtle regression introduced by #287).

313 Allow sequence=None when using gridsearch and Python 3.5 (Fix #309).

Allow the gridsearch optimiser to be used with the sequence option set to None for Python 3.5.

Caveats

319: image_getregion returns byte string on Py3.

SH-2: The new test_save_restore test in the CIAO regression tests suite is failing on all platforms. We are investigating the reasons of the failure. The failure is triggered when the test is not run in isolation, and only when certain other tests are run before it. Also, this only applies to CIAO and not to standalone Sherpa.

SH-3: Some tests are skipped during the CIAO regression tests.

SH-4: Several OS X regression tests are failing.

Note: The SH-2/3/4 caveats are issues with the tests themselves, not with the code, and only appear when running the full CIAO regression tests suite. User will not be affected by the above issues unless they run the full CIAO regression tests suite.

- Python
Published by olaurino over 9 years ago

sherpa - Sherpa 4.8.2

Sherpa 4.8.2

This version of Sherpa is the first one to run under both Python 2.7 and Python 3.5. The python 3 conversion is considered a beta designed to maintain backwards compatibility with python 2.7. As such, we expect to have some iterations before the Python 3.5 support stabilizes.

The smoke test has been greatly simplified: rather that running all of the unit and regression tests that do not require test data, the smoke test now simply ensures that the basic installation works, i.e. that basic commands can be run and that dependencies can be reached. This allows the use of more advanced tools for actual unit and regression tests without having to ship such tools to users.

Several bugs were fixed, some enhancements implemented, and some deprecated calls to external API replaced. In particular: - more documentation was migrated and is not part of the code base as docstrings. - the calc_stat API has been generalized to make statistic functions more extensible. - calc_stat_info now properly takes background into account when wstat is selected.

Details

Infrastructure and minor non-functional changes have been omitted.

209: Fix docstrings for group_snr() and group_adapt_snr(). Docstrings

used to say "Combine the data so that each bin has a signal-to-noise ratio of at least minimum" but the end of the groups are marked only if the SNR exceeds the given SNR.

210: The smoke test has been greatly simplified and it now simply ensures

that the basic installation works, i.e. that basic commands can be run and that dependencies can be reached. Previously, the smoke test would run all unit tests. Units and regression tests can now take advantage of py.test and mock packages (the latter is part of the standard library in Python3).

211: Cleanup of documentation and code in sherpa.astro.utils. The

calc_kcorr function is now exported by sherpa.astro.utils. Minor changes to the documentation in sherpa.astro.utils to conform to Sphinx standards.

221: Integrate existing model documentation (from external sources and

the CIAO ahelp documentation system) into the model classes.

229: Code is both Python 2.7 and 3.5 compliant. This included updating

the CIAO dependencies: region, group, and stack libraries, which were ported to Python 3 as well.

242: Avoid use of inspect.argspec, which was deprecated in Python3.

252: plot_photon_flux function was calling an internal function with

the wrong number of arguments and thus raising an error. This has been fixed.

253: calc_stat_info call failed when wstat was selected, as the

background was not taken into account. This issue has now been fixed.

256: Fix docstring in set_quality, which were listing the wrong values

of the quality flag.

257: Fix docstring for levmar tolerance, which was listing the wrong

function defaults.

Caveats/Known Issues

The following are known issues with the standalone 4.8.2 release

show_all does not work on Python3 with PHA. E.g., the following code throws an exception:

python from sherpa.astro.ui.utils import Session from sherpa.astro.data import DataPHA session = Session() session.load_arrays(1, [1, 2, 3], [1, 2, 3], DataPHA) session.show_all()

the parallel_map function throws an exception on Python 3 when only one core is available on the system running Sherpa. This impacts a number of functions taking advantage of tasks parallelization on multi-core systems. This functions include calc_flux, sample_flux, a number of functions for plotting parameter projections, and the grid_search optimization algorithm.

string representation of some (but not all) dataset classes is broken on Python 3. For instance, the following code will result in an exception:

python from sherpa.astro.ui import * load_pha('3c273.pi') print(get_data())

sample_flux does not work on Python 3 when called with the scales argument, e.g.:

``` python from sherpa.astro import ui

ui.loadpha('sherpa-test-data/sherpatest/3c273.pi') ui.setmodel('polynom1d.p1') ui.fit() ui.covar() scal = ui.getcovarresults().parmaxes ui.sample_flux(p1, 0.5, 1, num=5, correlated=False, scales=scal) ```

- Python
Published by olaurino over 9 years ago

sherpa - Sherpa 4.8.1

Sherpa 4.8.1

Sherpa 4.8.1 is the standalone counterpart to the 4.8.0 release, which was focused on supporting CIAO 4.8. In particular, this version introduces support for newer versions of the dependencies, along with some feature enhancements, bug fixes and additional, more accurate tests.

The newly supported dependencies: - matplotlib v1.5 - numpy 1.10 and 1.11 (with and without mkl support) - xspec v12.9.0i (when building from source) - astropy v1.1.2 - region library v4.8 (from CIAO 4.8)

Please see the Caveats section for known issues regarding the XSpec support.

Mode details below (infrastructure changes are not shown):

102: fix issues when writing out FITS files using the save_pha and

save_table commands when using the astropy/pyfits backend (bug #46). Fix for when the notice2did, notice2dimage, and the ignore version functions are called with an invalid identifier (i.e. an identifier that i snot an integer or string value). The error is now an ArgumentTypeErr with the message "'ids' must be an identifier or list of identifiers". It was a NameError with the message "global name 'argumenttype_error' is not defined".

107: Normalize plot labels. There are two main changes for plots of PHA data

sets (and related quantities, such as the source, model, and ARF): - plots with matplotlib now use the LaTeX support - so that 'cm^2' is now displayed as a superscript; previously they were displayed directly. This does not change the display with the ChIPS backend. - plots created with plot_source used a different format to other plots when analysis=wavelength, in that LaTeX symbols were used for Angstrom and lambda (in other plots the string 'Angstrom' is used instead). The source plots now match the other plots.

109: fix #103 and #113 in order to support matplotlib v1.5.

116: fix bug #27. The astropy.io.fits/pyfits interface used deprecated

functionality. The code was updated to use the replacement classes/methods when available, falling back to the original code if not. The interfaces that were changed were, when the new symbols are available, to: - use astropy.io.fits.BinTableHDU.from_columns rather than astropy.io.fits.new_table - use astropy.io.fits.Header rather than astropy.io.CardList

137: upgrade CIAO region library to v4.8

138: improve and fix issues in save_all function.

• added a new argument to save_all: if outfile is None then the outfh argument is used to define the output handle (the argument can be any file-like argument, such as a file handle like sys.stdout or the output of open, or a StringIO object)
• setting the clobber argument to save_all now means that the output file (the outfile argument, if not None) is deleted if it already exists; prior to this, the file would be appended to instead
• the source expression is now saved correctly for most cases (e.g. when not using set_full_model); this is bug #97 but also affects non-PHA data sets
• the background model expression was not always written out correctly when using PHA data sets
• quality and grouping arrays of PHA data sets are now stored as 16-byte integers rather than a floating-point value (this has no affect on the results, but matches the OGIP standard)
• fixed up saving the grouping and quality arrays of background PHA data sets (this would only be an issue if the background is being fit, rather than subtracted)
• basic data sets created with the load_arrays function are now written out by save_all as part of the script; this is intended for small datasets and may have problems with precision if used with floating-point arrays
• calls to load_psf are now correctly restored (they may not have been written out correctly if multiple data sets were loaded)
• user models are now written out to disk; this consists of two parts:
• writing out the function that defines the model, which may or may not be possible (if not, a place-holder function is added to the output and a warning displayed).
• the necessary calls to load_user_model and add_user_pars are now included in the output
• the Python code created by save all has undergone several minor changes:
• it now explicitly imports the sherpa.astro.ui module, so that it can be run from the IPython prompt using the %run <filename> command, or directly as python <filename>
• it uses the create_model_component function rather than eval to create model components (this is CXC bug 12146)
• many optional arguments to functions are now given as name=value rather than being a positional argument, to make it clearer what the script is doing.
• calls to load_data have been replaced by more-specific versions - e.g. load_pha and load_image - if appropriate
• there have been several minor syntactic clean ups to better follow the suggestions from PEP8

When writing out code that defines a user-model, there is no attempt to make sure that modules used by the function are available. These will need to be added, either directly or imported, manually to the output.

151: Ensure AstroPy and Crates behave the same with gzipped files. Change the

behaviour of the AstroPy back end so that it matches that of Crates when given a file name which does not exist, but a compressed version, with the suffix .gz does. The Crates behavior is to read the file. This extends to PHA files whose ancillary files - e.g. those stored in the BACKFILE, ANCRFILE, and RESPFILE keywords - are given as unzipped names, but only the gzipped names exist on disk.

As an example: if pha.fits.gz exists but pha.fits does not, then

load_pha('pha.fits')

will now load the file with either back end. If the response files are set to arf.fits and rmf.fits (via the ANCRFILE and RESPFILE keywords), but only the .gz versions exist, then they will now also be loaded by the AstroPy back end.

153: Make comparison test in calc_chi2datavar_errors less stringent, so to

include the case where sqrt(x)=0.

155: The get_draws function now accepts a user-provided covariance matrix. If

no covariance matrix is provided, the covariance matrix computed by the default implementation is used. Note that covar() must be invoked before invoking get_draws if no covariance matrix is provided, otherwise get_draws will exit with an error.

158: Fix bug that prevented region ascii files to be read in standalone

Sherpa.

165: Remove usage of deprecated numpy API.

185: Fix the problem where if the working directory contained a file called

x or y then the sherpa.astro.ui.image_data() function would fail with the message

DS9Err: Could not display image

187: Fix #92: a more meaningful message is given to the user when

sherpa.astro.io is imported directly and no fits backends are available.

188: Fix #93. The sherpa_test script now tries to install the test

dependencies before running the tests (but not the sherpatest package, which should be installed by the user if necessary, due to its footprint). If this is not possible, and the necessary dependencies (pytest) are not found, then a meaningful message is given to the user with instructions on how to install the dependencies. Also, the dependency on pytest-cov has been removed. Users can enable coverage reports from the command line if necessary.

190: Fix #22 - The datastack package can now be used even if there is no

available plotting backend. In this case, plotting functions will not be available, but the rest of the datastack functionality will.

Caveats

The following are known issues with the standalone 4.8.1 release

XSpec support: Several issues have been encountered with the optional source building with XSpec models on OSX platforms (Linux support appears unaffected). The issues include a name clash between the libcfitsio library and the astropy.io.fits Python extensions that results in XSpec failing to load fits files possibly resulting in a crash.

SAO DS9 issue on Ubuntu 14.04: the ds9 binaries shipped with Ubuntu and installed through apt-get install do not seem to work as expected. Binaries downloaded directly from the SAO ds9 page seem to work instead. (Note: this issue was listed in the 4.8.0 release as well).

Wrong save_data header keywords: when using astropy as a FITS backend to save PHA data with save_data some header keywords are incorrectly set by Sherpa. In particular, range information for certain columns may be inaccurate (see issue #203 for details).

- Python
Published by olaurino about 10 years ago

sherpa - Sherpa 4.8.0

Release Notes

Sherpa 4.8.0

This version of Sherpa introduces 'wstat' statistics which is an extension of 'cstat' with Poisson background data. It also provides the ability to include background data with the 'user statistics'.

Many changes were aimed at improving the Xspec extension by making it more robust, intuitive, and by fixing several bugs. Sherpa 4.8.0 supports Xspec 12.9.0d and was also tested against versions 12.8.2e, 12.8.2l, and 12.8.2q.

Most of the codebase was reviewed and cleaned up, in particular to remove the use of deprecated functionality and to comply with Python's PEP8 standard. More tests were added to the test suite, and a new testing infrastructure was put in place in order to simplify writing and running tests, and to measure the test suite code coverage.

More details below (infrastructure changes are not shown):

32: Fix segfault from CRATES update in 4.8b1. Since v4.8b1 CRATES returns

variable length arrays by default, rather than the zero-padded fixed length ones it used to return. Sherpa manipulated the arrays so to remove the zero-padding and obtaining variable length arrays. The change in the CRATES API resulted in Sherpa segfaulting when trying to manipulate the data coming from CRATES. In the patch, we use a new API offered by CRATES to get the old-style fixed-length arrays instead of the new default ones. In the future, we may want to update the Sherpa code to deal with the new arrays directly.

44: save_quality now correctly outputs 'QUALITY' as the column name,

instead of 'GROUPS'.

48: Fix up several issues seen in plot labels - titles and Y-axis labels -

for commands such as sherpa.ui.plot_data, sherpa.ui.plot_fit_resid, and sherpa.ui.plot_chisqr.

59: Fix bug #38 (grouping twice gives an IndexError exception). An un-handled

corner case in one of the Sherpa internal methods (utils.create_expr) was triggering an IndexError when two group_counts operations were performed back to back. The fix handles the case so that applying group_counts twice does not result in an Exception.

77: Replace == and != comparisons to None with is and is not.

78: OutOfBoundErr exceptions in some sherpa.utils

functions are properly caught. There were several places where screen output used either print or sys.stderr.write.

81: Ensure that XSPEC models which fail - for instance, because a data file

it needs is missing - return 0's for all bins, rather than random values. This should make it more obvious that something has gone wrong (for instance if the XSPEC chatter level is low enough not to show any error messages, as is the case for the default setting used by Sherpa, namely 0).

82: The XSpec "spectrum number" value is now set to 1 rather than 0, as this

value is 1-based in Xspec.

83: Removed S-Lang scripts, files, and references in the code.

84: Clarified error messages in Xspec extension. Also, changed the class of

the exception from RuntimeError to more appropriate exception types, in particular LookupError, ValueError, KeyError. This is a backwards-incompatible change, in that code that caught the RuntimeError will not catch the new error.

87: Some methods in sherpa/fit.py assigned mutable objects to default

arguments. This has now been fixed. More instances of this issue have been identified (Bug #95) and will removed in the future.

90: Added background data to the UserStat class.

94: Implement wstat statistic as described at the following url:

https://heasarc.gsfc.nasa.gov/xanadu/xspec/manual/XSappendixStatistics.html

96: Remove the unused myoptfct module.

99: Correct the documentation for the set_exposure function.

100 Fix bug #97, whereby the save_all function would not create the necessary

set_source() line. This does not fix all cases, but it does the simple PHA case such as

load_pha('src.pi') set_source(xsphabs.gal * powlaw1d.pl) save_all('test.out).

It also ensures that files created by save_all can be run using IPython's %run directive, by explicitly importing the sherpa.astro.ui module.

101: Fix handling of non-contiguous bins in Xspec - i.e. when a model is

called with both xlo and xhi arguments but the bins do not fully cover the energy, or wavelenth, range. This fixes #62 (for XSPEC 12.8.2; switching to XSPEC 12.9.0 should also fix it) and #56. It also fixes an (un-reported) problem with handling of non-contiguous grids when using a table model, where a crash was likely. When an XSPEC model is called with both low and high values for the grid - i.e. with two arguments - then the two arrays are checked to have the same length, and a ValueError is raised if this condition does not hold. This is a breaking change, but the results are not guaranteed to be correct if the two arrays are not the same length. The experimental interface for XSPEC convolution models has changed, so that the function call takes pars, fluxes, xlo, with optional xhi whereas before it was pars, xlo, xhi, fluxes. This is a breaking change, but this is in the low-level API that is not documented to users, and adds useful functionality (the ability to have xhi be optional). The cpflux convolution model has been added. Note that these models do not have Python classes associated with them as they are still an experimental interface. The test suite has been updated to test the new and changed functionality in this PR. The choice of models is made so as to avoid known problematic models (with a version check where relevant). It is believed that the changes in this PR fixes #42, although this is hard to prove conclusively given the erratic nature of the bug.

110: Update the sherpa.astro.datastack module documentation to include information from the

CIAO ahelp documentation and to match the style used by the sherpa.astro.ui module.

111: Update the documentation to include more information about the pyBLoCXS code.

Caveats

These caveats are being fixed for the 4.8.1 release.

Incompatibility with matplotlib 1.5: Sherpa 4.8.0 is not compatible with matplotlib 1.5. Unfortunately, this version is currently the default package installed by conda. Users should install sherpa with matplotlib=1.4 numpy=1.9.

Test requirements are not installed automatically: sherpatest does not work out of the box. Users should issue "pip install pytest-cov" in order for sherpatest to run.

SAO DS9 issue on Ubuntu 14.04: the ds9 binaries shipped with Ubuntu and installed through apt-get install do not seem to work as expected. Binaries downloaded directly from the SAO ds9 page seem to work instead.

- Python
Published by olaurino over 10 years ago

sherpa - Sherpa Standalone 4.7

Release Notes

This standalone release is based on CIAO Sherpa v4.7.

Release notes for this baseline version can be found at the following link: http://cxc.harvard.edu/ciao/releasenotes/ciao4.7release.html#Sherpa

Additionally, the present release includes some changes listed below: - Standalone Sherpa and CIAO sherpa now look for different configuration files in the $HOME directory. For standalone this is $HOME/.sherpa-standalone.rc. If this file is not present, Sherpa falls back to the internal configuration file. This file has defaults better suited for the standalone mode: pyfits and pylab are set as backends, and the stack trace is not silenced. Users can still override the configuration file location by exporting the SHERPARC environment variable, as supported by previous versions of Sherpa and CIAO. - All source files now have copyright and licensing information. A summary is included upfront in the repository main directory. - Orphan code that was not actually used has been removed. - Fixed code triggering deprecation warnings from Numpy 1.9. - Fixed code triggering compiler warnings. - Added documentation (README, ipython notebook). - The version string (sherpa.__version__) depends on the git commit/tag, unlike in CIAO where it is fixed to 40701. - Some classes from the template module were not exposed by __all__, and template models were not imported in the sherpa session. Now they are.

Known issues

• the datastack module is not imported if no plotting packages are available. Installing matplotlib in the same environment as Sherpa fixes the issue.

- Python
Published by olaurino about 11 years ago